Press report December 2014 -------------------------- -------------------------- Q: should we report articles in the current issues, OR articles published online???? Both means that they will be reported twice: 1. online publication 2. publication in issue Journals----------------------------------------------------------------------------------------------------------------------------------------- - Sciene - Nature - PLoS Biology - Cell - Current Biology - PNAS - Evolution - Development - Genetics Pubmed Keyword search------------------------------------------------------------------------------------------------------------------------------ - genitalia development - genitalia development insect - external genitalia - Drosophila genitalia - sexual selection insect - mapping insect relevant papers----------------------------------------------------------------------------------------------------------------------------------- Evolutionary cell biology: Two origins, one objective Michael Lyncha,1, Mark C. Fieldb,2, Holly V. Goodsonc,2, Harmit S. Malikd,e,2, Jose B. Pereira-Lealf,2, David S. Roosg,2, Aaron P. Turkewitzh,2, and Shelley Sazeri,1 PNAS, vol. 111 no. 48, 16990-16994, December 2 doi: 10.1073/pnas.1415861111 All aspects of biological diversification ultimately trace to evolutionary modifications at the cellular level. This central role of cells frames the basic questions as to how cells work and how cells come to be the way they are. Although these two lines of inquiry lie respectively within the traditional provenance of cell biology and evolutionary biology, a comprehensive synthesis of evolutionary and cell-biological thinking is lacking. We define evolutionary cell biology as the fusion of these two eponymous fields with the theoretical and quantitative branches of biochemistry, biophysics, and population genetics. The key goals are to develop a mechanistic understanding of general evolutionary processes, while specifically infusing cell biology with an evolutionary perspective. The full development of this interdisciplinary field has the potential to solve numerous problems in diverse areas of biology, including the degree to which selection, effectively neutral processes, historical contingencies, and/or constraints at the chemical and biophysical levels dictate patterns of variation for intracellular features. These problems can now be examined at both the within- and among-species levels, with single-cell methodologies even allowing quantification of variation within genotypes. Some results from this emerging field have already had a substantial impact on cell biology, and future findings will significantly influence applications in agriculture, medicine, environmental science, and synthetic biology. Correlated variation and population differentiation in satellite DNA abundance among lines of Drosophila melanogaster Kevin H.-C. Wei, Jennifer K. Grenier, Daniel A. Barbash, and Andrew G. Clark1 PNAS vol. 111 no. 52, 18793-18798, December 30 doi: 10.1073/pnas.1421951112 Tandemly repeating satellite DNA elements in heterochromatin occupy a substantial portion of many eukaryotic genomes. Although often characterized as genomic parasites deleterious to the host, they also can be crucial for essential processes such as chromosome segregation. Adding to their interest, satellite DNA elements evolve at high rates; among Drosophila, closely related species often differ drastically in both the types and abundances of satellite repeats. However, due to technical challenges, the evolutionary mechanisms driving this rapid turnover remain unclear. Here we characterize natural variation in simple-sequence repeats of 2-10 bp from inbred Drosophila melanogaster lines derived from multiple populations, using a method we developed called k-Seek that analyzes unassembled Illumina sequence reads. In addition to quantifying all previously described satellite repeats, we identified many novel repeats of low to medium abundance. Many of the repeats show population differentiation, including two that are present in only some populations. Interestingly, the population structure inferred from overall satellite quantities does not recapitulate the expected population relationships based on the demographic history of D. melanogaster. We also find that some satellites of similar sequence composition are correlated across lines, revealing concerted evolution. Moreover, correlated satellites tend to be interspersed with each other, further suggesting that concerted change is partially driven by higher order structure. Surprisingly, we identified negative correlations among some satellites, suggesting antagonistic interactions. Our study demonstrates that current genome assemblies vastly underestimate the complexity, abundance, and variation of highly repetitive satellite DNA and presents approaches to understand their rapid evolutionary divergence A highly pleiotropic amino acid polymorphism in the Drosophila insulin receptor contributes to life-history adaptation Annalise B. Paaby1,2, Alan O. Bergland3, Emily L. Behrman1 and Paul S. Schmidt1 Article first published online: 20 NOV 2014 DOI: 10.1111/evo.12546 Evolution Volume 68, Issue 12, pages 3395-3409, December 2014 Finding the specific nucleotides that underlie adaptive variation is a major goal in evolutionary biology, but polygenic traits pose a challenge because the complex genotype-phenotype relationship can obscure the effects of individual alleles. However, natural selection working in large wild populations can shift allele frequencies and indicate functional regions of the genome. Previously, we showed that the two most common alleles of a complex amino acid insertion-deletion polymorphism in the Drosophila insulin receptor show independent, parallel clines in frequency across the North American and Australian continents. Here, we report that the cline is stable over at least a five-year period and that the polymorphism also demonstrates temporal shifts in allele frequency concurrent with seasonal change. We tested the alleles for effects on levels of insulin signaling, fecundity, development time, body size, stress tolerance, and life span. We find that the alleles are associated with predictable differences in these traits, consistent with patterns of Drosophila life-history variation across geography that likely reflect adaptation to the heterogeneous climatic environment. These results implicate insulin signaling as a major mediator of life-history adaptation in Drosophila, and suggest that life-history trade-offs can be explained by extensive pleiotropy at a single locus. Cold adaptation shapes the robustness of metabolic networks in Drosophila melanogaster Caroline M. Williams1, Miki Watanabe2, Mario R. Guarracino3, Maria B. Ferraro4, Arthur S. Edison5, Theodore J. Morgan6, Arezue F. B. Boroujerdi7 and Daniel A. Hahn8 Article first published online: 20 NOV 2014 DOI: 10.1111/evo.12541 Evolution Volume 68, Issue 12, pages 3505-3523, December 2014 When ectotherms are exposed to low temperatures, they enter a cold-induced coma (chill coma) that prevents resource acquisition, mating, oviposition, and escape from predation. There is substantial variation in time taken to recover from chill coma both within and among species, and this variation is correlated with habitat temperatures such that insects from cold environments recover more quickly. This suggests an adaptive response, but the mechanisms underlying variation in recovery times are unknown, making it difficult to decisively test adaptive hypotheses. We use replicated lines of Drosophila melanogaster selected in the laboratory for fast (hardy) or slow (susceptible) chill-coma recovery times to investigate modifications to metabolic profiles associated with cold adaptation. We measured metabolite concentrations of flies before, during, and after cold exposure using nuclear magnetic resonance (NMR) spectroscopy to test the hypotheses that hardy flies maintain metabolic homeostasis better during cold exposure and recovery, and that their metabolic networks are more robust to cold-induced perturbations. The metabolites of cold-hardy flies were less cold responsive and their metabolic networks during cold exposure were more robust, supporting our hypotheses. Metabolites involved in membrane lipid synthesis, tryptophan metabolism, oxidative stress, energy balance, and proline metabolism were altered by selection on cold tolerance. We discuss the potential significance of these alterations. Neural precursor-specific expression of multiple Drosophila genes is driven by dual enhancer modules with overlapping function Steven W. Miller, Mark Rebeiz1, Jenny E. Atanasov, and James W. Posakony PNAS vol. 111 no. 48, 17194-17199, December 2 doi: 10.1073/pnas.1415308111 Transcriptional cis-regulatory modules (CRMs), or enhancers, are responsible for directing gene expression in specific territories and cell types during development. In some instances, the same gene may be served by two or more enhancers with similar specificities. Here we show that the utilization of dual, or \93shadow\94, enhancers is a common feature of genes that are active specifically in neural precursor (NP) cells in Drosophila. By genome-wide computational discovery of statistically significant clusters of binding motifs for both proneural activator (P) proteins and basic helix-loop-helix (bHLH) repressor (R) factors (a \93P+R\94 regulatory code), we have identified NP-specific enhancer modules associated with multiple genes expressed in this cell type. These CRMs are distinct from those previously identified for the corresponding gene, establishing the existence of a dual-enhancer arrangement in which both modules reside close to the gene they serve. Using wild-type and mutant reporter gene constructs in vivo, we show that P sites in these modules mediate activation by proneural factors in \93proneural cluster\94 territories, whereas R sites mediate repression by bHLH repressors, which serves to restrict expression specifically to NP cells. To our knowledge, our results identify the first direct targets of these bHLH repressors. Finally, using genomic rescue constructs for neuralized (neur), we demonstrate that each of the gene's two NP-specific enhancers is sufficient to rescue neur function in the lateral inhibition process by which adult sensory organ precursor (SOP) cells are specified, but that deletion of both enhancers results in failure of this event. The role of aedeagus size and shape in failed mating interactions among recently diverged taxa in the Drosophila mojavensis species cluster Maxi Polihronakis Richmond BMC Evolutionary Biology 2014, 14:255 doi:10.1186/s12862-014-0255-3 10 December 2014 Background Investigating the evolution of species-specific insect genitalia is central to understanding how morphological diversification contributes to reproductive isolation and lineage divergence. While many studies evoke some form of sexual selection to explain genitalia diversity, the basis of selection and the mechanism of heterospecific mate exclusion remains vague. I conducted reciprocal mate pair trials in the Drosophila mojavensis species cluster to quantify the frequency of failed insemination attempts, historically referred to as pseudocopulation, between lineages with discrete size and shape differences of the male aedeagus. Results In cross-taxon matings aedeagus size had a significant effect on pseudocopulation frequencies, while aedeagus shape and genetic distance did not. The direction of the size difference was an important factor for successful mating. When females were mated to a cross-taxon male with a larger aedeagus than males from her own species, the pair could not establish a successful mating interaction. Females mated to cross-taxon males with a smaller aedeagus than conspecific males were able to establish the mating interaction but had issues disengaging at the end of the interaction. Conclusions The results of this study support a role for aedeagus size in the male-female mating interaction, with a secondary role for aedeagus shape. In natural populations, mating failure based on aedeagus size could serve as an important reproductive isolating mechanism resulting in failed insemination attempts after both the male and female show a willingness to mate. Serotonergic neurons respond to nutrients and regulate the timing of steroid hormone biosy... Yuko Shimada-Niwa, Ryusuke Niwa Nature Communications 5, Article number: 5778 doi:10.1038/ncomms6778 15 December 2014 The temporal transition of development is flexibly coordinated in the context of the nutrient environment, and this coordination is essential for organisms to increase their survival fitness and reproductive success. Steroid hormone, a key player of the juvenile-to-adult transition, is biosynthesized in a nutrient-dependent manner; however, the underlying genetic mechanism remains unclear. Here we report that the biosynthesis of insect steroid hormone, ecdysteroid, is regulated by a subset of serotonergic neurons in Drosophila melanogaster. These neurons directly innervate the prothoracic gland (PG), an ecdysteroid-producing organ and share tracts with the stomatogastric nervous system. Interestingly, the projecting neurites morphologically respond to nutrient conditions. Moreover, reduced activity of the PG-innervating neurons or of ?serotonin signalling in the PG strongly correlates with a delayed developmental transition. Our results suggest that serotonergic neurons form a link between the external environment and the internal endocrine system by adaptively tuning the timing of steroid hormone biosynthesis. Evolved differences in larval social behavior mediated by novel pheromones. Mast JD1, De Moraes CM2, Alborn HT3, Lavis LD1, Stern DL1. Elife. 2014 Dec 12;3. doi: 10.7554/eLife.04205. Pheromones, chemical signals that convey social information, mediate many insect social behaviors, including navigation and aggregation. Several studies have suggested that behavior during the immature larval stages of Drosophila development is influenced by pheromones, but none of these compounds or the pheromone-receptor neurons that sense them have been identified. Here we report a larval pheromone-signaling pathway. We found that larvae produce two novel long-chain fatty acids that are attractive to other larvae. We identified a single larval chemosensory neuron that detects these molecules. Two members of the pickpocket family of DEG/ENaC channel subunits (ppk23 and ppk29) are required to respond to these pheromones. This pheromone system is evolving quickly, since the larval exudates of D. simulans, the sister species of D. melanogaster, are not attractive to other larvae. Our results define a new pheromone signaling system in Drosophila that shares characteristics with pheromone systems in a wide diversity of insects. Identification of loci that cause phenotypic variation in diverse species with the reciprocal hemizygosity test. Stern DL Trends Genet. 2014 Dec;30(12):547-554. doi: 10.1016/j.tig.2014.09.006. Epub 2014 Sep 30. The reciprocal hemizygosity test is a straightforward genetic test that can positively identify genes that have evolved to contribute to a phenotypic difference between strains or between species. The test involves a comparison between hybrids that are genetically identical throughout the genome except at the test locus, which is rendered hemizygous for alternative alleles from the two parental strains. If the two reciprocal hemizygotes display different phenotypes, then the two parental alleles must have evolved. New methods for targeted mutagenesis will allow application of the reciprocal hemizygosity test in many organisms. This review discusses the principles, advantages, and limitations of the test. Low Affinity Binding Site Clusters Confer Hox Specificity and Regulatory Robustness Justin Crocker, Namiko Abe, Lucrezia Rinaldi, Alistair P. McGregor, Nicol\E1s Frankel, Shu Wang, Ahmad Alsawadi, Philippe Valenti, Serge Plaza, Fran\E7ois Payre, Richard S. Mann, David L. Stern DOI: http://dx.doi.org/10.1016/j.cell.2014.11.041 Cell December 31 In animals, Hox transcription factors define regional identity in distinct anatomical domains. How Hox genes encode this specificity is a paradox, because different Hox proteins bind with high affinity in vitro to similar DNA sequences. Here, we demonstrate that the Hox protein Ultrabithorax (Ubx) in complex with its cofactor Extradenticle (Exd) bound specifically to clusters of very low affinity sites in enhancers of the shavenbaby gene of Drosophila. These low affinity sites conferred specificity for Ubx binding in vivo, but multiple clustered sites were required for robust expression when embryos developed in variable environments. Although most individual Ubx binding sites are not evolutionarily conserved, the overall enhancer architecture\97clusters of low affinity binding sites\97is maintained and required for enhancer function. Natural selection therefore works at the level of the enhancer, requiring a particular density of low affinity Ubx sites to confer both specific and robust expression. Archaeology----------------------------------------------------------------------------------------------------------------------------------------- Nature (2014), 03 December 2014 Rival species recast significance of ‘first bird’ Ewen Callaway Archaeopteryx’s status is changing, but the animal is still key to the dinosaur–bird transition. Archaeopteryx meeting Novemeber 2014 Carnivorous leaves from Baltic amber Eva-Maria Sadowskia, Leyla J. Seyfullaha, Friederike Sadowskib, Andreas Fleischmannc, Hermann Behlingd, and Alexander R. Schmidta,1 PNAS December 1 doi: 10.1073/pnas.1414777111 The fossil record of carnivorous plants is very scarce and macrofossil evidence has been restricted to seeds of the extant aquatic genus Aldrovanda of the Droseraceae family. No case of carnivorous plant traps has so far been reported from the fossil record. Here, we present two angiosperm leaves enclosed in a piece of Eocene Baltic amber that share relevant morphological features with extant Roridulaceae, a carnivorous plant family that is today endemic to the Cape flora of South Africa. Modern Roridula species are unique among carnivorous plants as they digest prey in a complex mutualistic association in which the prey-derived nutrient uptake depends on heteropteran insects. As in extant Roridula, the fossil leaves possess two types of plant trichomes, including unicellular hairs and five size classes of multicellular stalked glands (or tentacles) with an apical pore. The apices of the narrow and perfectly tapered fossil leaves end in a single tentacle, as in both modern Roridula species. The glandular hairs of the fossils are restricted to the leaf margins and to the abaxial lamina, as in extant Roridula gorgonias. Our discovery supports current molecular age estimates for Roridulaceae and suggests a wide Eocene distribution of roridulid plants. behavior - physiology------------------------------------------------------------------------------------------------------------------------------- Experimentally induced innovations lead to persistent culture via conformity in wild birds Lucy M. Aplin, Damien R. Farine, Julie Morand-Ferron, Andrew Cockburn, Alex Thornton & Ben C. Sheldon Nature (2014), 03 December 2014 doi:10.1038/nature13998 In human societies, cultural norms arise when behaviours are transmitted through social networks via high-fidelity social learning1. However, a paucity of experimental studies has meant that there is no comparable understanding of the process by which socially transmitted behaviours might spread and persist in animal populations2, 3. Here we show experimental evidence of the establishment of foraging traditions in a wild bird population. We introduced alternative novel foraging techniques into replicated wild sub-populations of great tits (Parus major) and used automated tracking to map the diffusion, establishment and long-term persistence of the seeded innovations. Furthermore, we used social network analysis to examine the social factors that influenced diffusion dynamics. From only two trained birds in each sub-population, the information spread rapidly through social network ties, to reach an average of 75% of individuals, with a total of 414 knowledgeable individuals performing 57,909 solutions over all replicates. The sub-populations were heavily biased towards using the technique that was originally introduced, resulting in established local traditions that were stable over two generations, despite a high population turnover. Finally, we demonstrate a strong effect of social conformity, with individuals disproportionately adopting the most frequent local variant when first acquiring an innovation, and continuing to favour social information over personal information. Cultural conformity is thought to be a key factor in the evolution of complex culture in humans4, 5, 6, 7. In providing the first experimental demonstration of conformity in a wild non-primate, and of cultural norms in foraging techniques in any wild animal, our results suggest a much broader taxonomic occurrence of such an apparently complex cultural behaviour. The shocking predatory strike of the electric eel Kenneth Catania Science 5 December 2014: Vol. 346 no. 6214 pp. 1231-1234 DOI: 10.1126/science.1260807 Electric eels can incapacitate prey with an electric discharge, but the mechanism of the eel\92s attack is unknown. Through a series of experiments, I show that eel high-voltage discharges can activate prey motor neurons, and hence muscles, allowing eels to remotely control their target. Eels prevent escape in free-swimming prey using high-frequency volleys to induce immobilizing whole-body muscle contraction (tetanus). Further, when prey are hidden, eels can emit periodic volleys of two or three discharges that cause massive involuntary twitch, revealing the prey\92s location and eliciting the full, tetanus-inducing volley. The temporal patterns of eel electrical discharges resemble motor neuron activity that induces fast muscle contraction, suggesting that eel high-voltage volleys have been selected to most efficiently induce involuntary muscle contraction in nearby animals. Control of metabolic adaptation to fasting by dILP6-induced insulin signaling in Drosophila oenocytes Debamita Chatterjeea, Subhash D. Katewab, Yanyan Qib, Susan A. Jacksonb, Pankaj Kapahib, and Heinrich Jaspera,b,1 PNAS vol. 111 no. 50, 17959-17964, December 16 doi: 10.1073/pnas.1409241111 Metabolic adaptation to changing dietary conditions is critical to maintain homeostasis of the internal milieu. In metazoans, this adaptation is achieved by a combination of tissue-autonomous metabolic adjustments and endocrine signals that coordinate the mobilization, turnover, and storage of nutrients across tissues. To understand metabolic adaptation comprehensively, detailed insight into these tissue interactions is necessary. Here we characterize the tissue-specific response to fasting in adult flies and identify an endocrine interaction between the fat body and liver-like oenocytes that regulates the mobilization of lipid stores. Using tissue-specific expression profiling, we confirm that oenocytes in adult flies play a central role in the metabolic adaptation to fasting. Furthermore, we find that fat body-derived Drosophila insulin-like peptide 6 (dILP6) induces lipid uptake in oenocytes, promoting lipid turnover during fasting and increasing starvation tolerance of the animal. Selective activation of insulin/IGF signaling in oenocytes by a fat body-derived peptide represents a previously unidentified regulatory principle in the control of metabolic adaptation and starvation tolerance. Hummingbirds control hovering flight by stabilizing visual motion Benjamin Goller and Douglas L. Altshuler1 PNAS vol. 111 no. 51, 18375-18380 December 23 doi: 10.1073/pnas.1415975111 Relatively little is known about how sensory information is used for controlling flight in birds. A powerful method is to immerse an animal in a dynamic virtual reality environment to examine behavioral responses. Here, we investigated the role of vision during free-flight hovering in hummingbirds to determine how optic flow\97image movement across the retina\97is used to control body position. We filmed hummingbirds hovering in front of a projection screen with the prediction that projecting moving patterns would disrupt hovering stability but stationary patterns would allow the hummingbird to stabilize position. When hovering in the presence of moving gratings and spirals, hummingbirds lost positional stability and responded to the specific orientation of the moving visual stimulus. There was no loss of stability with stationary versions of the same stimulus patterns. When exposed to a single stimulus many times or to a weakened stimulus that combined a moving spiral with a stationary checkerboard, the response to looming motion declined. However, even minimal visual motion was sufficient to cause a loss of positional stability despite prominent stationary features. Collectively, these experiments demonstrate that hummingbirds control hovering position by stabilizing motions in their visual field. The high sensitivity and persistence of this disruptive response is surprising, given that the hummingbird brain is highly specialized for sensory processing and spatial mapping, providing other potential mechanisms for controlling position. Genomes - domestication and related ... ------------------------------------------------------------------------------------------------------ Bird genome Statistical binning enables an accurate coalescent-based estimation of the avian tree Siavash Mirarab1, Md. Shamsuzzoha Bayzid1, Bastien Boussau2, Tandy Warnow1,3,* Science 12 December 2014: Vol. 346 no. 6215 DOI: 10.1126/science.1250463 Gene tree incongruence arising from incomplete lineage sorting (ILS) can reduce the accuracy of concatenation-based estimations of species trees. Although coalescent-based species tree estimation methods can have good accuracy in the presence of ILS, they are sensitive to gene tree estimation error. We propose a pipeline that uses bootstrapping to evaluate whether two genes are likely to have the same tree, then it groups genes into sets using a graph-theoretic optimization and estimates a tree on each subset using concatenation, and finally produces an estimated species tree from these trees using the preferred coalescent-based method. Statistical binning improves the accuracy of MP-EST, a popular coalescent-based method, and we use it to produce the first genome-scale coalescent-based avian tree of life. Evidence for a single loss of mineralized teeth in the common avian ancestor Robert W. Meredith1,*, Guojie Zhang2,3, M. Thomas P. Gilbert4,5, Erich D. Jarvis6, Mark S. Springer7,* Science 12 December 2014: Vol. 346 no. 6215 DOI: 10.1126/science.1254390 Edentulism, the absence of teeth, has evolved convergently among vertebrates, including birds, turtles, and several lineages of mammals. Instead of teeth, modern birds (Neornithes) use a horny beak (rhamphotheca) and a muscular gizzard to acquire and process food. We performed comparative genomic analyses representing lineages of nearly all extant bird orders and recovered shared, inactivating mutations within genes expressed in both the enamel and dentin of teeth of other vertebrate species, indicating that the common ancestor of modern birds lacked mineralized teeth. We estimate that tooth loss, or at least the loss of enamel caps that provide the outer layer of mineralized teeth, occurred about 116 million years ago. Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs Richard E. Green1,*, Edward L. Braun2, Joel Armstrong1,3, Dent Earl1,3, Ngan Nguyen1,3, Glenn Hickey1,3, Michael W. Vandewege4, John A. St. John1,\A7, Salvador Capella-Gutierrez5,6, Todd A. Castoe7,8, Colin Kern9, Matthew K. Fujita8, Juan C. Opazo10, Jerzy Jurka11,\86, Kenji K. Kojima11, Juan Caballero12, Robert M. Hubley12, Arian F. Smit12, Roy N. Platt4,13, Christine A. Lavoie4, Meganathan P. Ramakodi4,13,\87, John W. Finger Jr.14, Alexander Suh15,16, Sally R. Isberg17,18,19, Lee Miles18,#, Amanda Y. Chong18, Weerachai Jaratlerdsiri18, Jaime Gongora18, Christopher Moran18, Andres Iriarte20, John McCormack21, Shane C. Burgess22, Scott V. Edwards23, Eric Lyons24, Christina Williams25, Matthew Breen25, Jason T. Howard26, Cathy R. Gresham13, Daniel G. Peterson13,27, J\FCrgen Schmitz15, David D. Pollock7, David Haussler3,28, Eric W. Triplett29, Guojie Zhang30,31, Naoki Irie32, Erich D. Jarvis26, Christopher A. Brochu33, Carl J. Schmidt34, Fiona M. McCarthy35, Brant C. Faircloth36,37, Federico G. Hoffmann4,13, Travis C. Glenn14, Toni Gabald\F3n5,6,38, Benedict Paten3, David A. Ray4,13,39,* Science 12 December 2014: Vol. 346 no. 6215 DOI: 10.1126/science.1254449 To provide context for the diversification of archosaurs\97the group that includes crocodilians, dinosaurs, and birds\97we generated draft genomes of three crocodilians: Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater crocodile), and Gavialis gangeticus (the Indian gharial). We observed an exceptionally slow rate of genome evolution within crocodilians at all levels, including nucleotide substitutions, indels, transposable element content and movement, gene family evolution, and chromosomal synteny. When placed within the context of related taxa including birds and turtles, this suggests that the common ancestor of all of these taxa also exhibited slow genome evolution and that the comparatively rapid evolution is derived in birds. The data also provided the opportunity to analyze heterozygosity in crocodilians, which indicates a likely reduction in population size for all three taxa through the Pleistocene. Finally, these data combined with newly published bird genomes allowed us to reconstruct the partial genome of the common ancestor of archosaurs, thereby providing a tool to investigate the genetic starting material of crocodilians, birds, and dinosaurs. Core and region-enriched networks of behaviorally regulated genes and the singing genome Osceola Whitney1,*,\86, Andreas R. Pfenning1,2,*,\86, Jason T. Howard1, Charles A Blatti3, Fang Liu4, James M. Ward1, Rui Wang1, Jean-Nicolas Audet5, Manolis Kellis2, Sayan Mukherjee6, Saurabh Sinha3, Alexander J. Hartemink7, Anne E. West4,*, Erich D. Jarvis1,* Science 12 December 2014: Vol. 346 no. 6215 DOI: 10.1126/science.1256780 Songbirds represent an important model organism for elucidating molecular mechanisms that link genes with complex behaviors, in part because they have discrete vocal learning circuits that have parallels with those that mediate human speech. We found that ~10% of the genes in the avian genome were regulated by singing, and we found a striking regional diversity of both basal and singing-induced programs in the four key song nuclei of the zebra finch, a vocal learning songbird. The region-enriched patterns were a result of distinct combinations of region-enriched transcription factors (TFs), their binding motifs, and presinging acetylation of histone 3 at lysine 27 (H3K27ac) enhancer activity in the regulatory regions of the associated genes. RNA interference manipulations validated the role of the calcium-response transcription factor (CaRF) in regulating genes preferentially expressed in specific song nuclei in response to singing. Thus, differential combinatorial binding of a small group of activity-regulated TFs and predefined epigenetic enhancer activity influences the anatomical diversity of behaviorally regulated gene networks. Convergent transcriptional specializations in the brains of humans and song-learning birds Andreas R. Pfenning1,*, Erina Hara1, Osceola Whitney1, Miriam V. Rivas1, Rui Wang1, Petra L. Roulhac1, Jason T. Howard1, Morgan Wirthlin2, Peter V. Lovell2, Ganeshkumar Ganapathy1, Jacquelyn Mouncastle1, M. Arthur Moseley3, J. Will Thompson3, Erik J. Soderblom3, Atsushi Iriki4, Masaki Kato4, M. Thomas P. Gilbert5,6, Guojie Zhang7,8, Trygve Bakken9, Angie Bongaarts9, Amy Bernard9, Ed Lein9, Claudio V. Mello2, Alexander J. Hartemink10,*, Erich D. Jarvis1,* Science 12 December 2014: Vol. 346 no. 6215 DOI: 10.1126/science.1256846 Song-learning birds and humans share independently evolved similarities in brain pathways for vocal learning that are essential for song and speech and are not found in most other species. Comparisons of brain transcriptomes of song-learning birds and humans relative to vocal nonlearners identified convergent gene expression specializations in specific song and speech brain regions of avian vocal learners and humans. The strongest shared profiles relate bird motor and striatal song-learning nuclei, respectively, with human laryngeal motor cortex and parts of the striatum that control speech production and learning. Most of the associated genes function in motor control and brain connectivity. Thus, convergent behavior and neural connectivity for a complex trait are associated with convergent specialized expression of multiple genes. Complex evolutionary trajectories of sex chromosomes across bird taxa Qi Zhou1,*,\86, Jilin Zhang2,*, Doris Bachtrog1,*, Na An2, Quanfei Huang2, Erich D. Jarvis3, M. Thomas P. Gilbert4,5, Guojie Zhang2,6,\86 Science 12 December 2014: Vol. 346 no. 6215 DOI: 10.1126/science.1246338 Sex-specific chromosomes, like the W of most female birds and the Y of male mammals, usually have lost most genes owing to a lack of recombination. We analyze newly available genomes of 17 bird species representing the avian phylogenetic range, and find that more than half of them do not have as fully degenerated W chromosomes as that of chicken. We show that avian sex chromosomes harbor tremendous diversity among species in their composition of pseudoautosomal regions and degree of Z/W differentiation. Punctuated events of shared or lineage-specific recombination suppression have produced a gradient of \93evolutionary strata\94 along the Z chromosome, which initiates from the putative avian sex-determining gene DMRT1 and ends at the pseudoautosomal region. W-linked genes are subject to ongoing functional decay after recombination was suppressed, and the tempo of degeneration slows down in older strata. Overall, we unveil a complex history of avian sex chromosome evolution. Comparative genomics reveals insights into avian genome evolution and adaptation Guojie Zhang1,2,*,\86, Cai Li1,3,*, Qiye Li1,3, Bo Li1, Denis M. Larkin4, Chul Lee5,6, Jay F. Storz7, Agostinho Antunes8,9, Matthew J. Greenwold10, Robert W. Meredith11, Anders \D6deen12, Jie Cui13,14, Qi Zhou15, Luohao Xu1,16, Hailin Pan1, Zongji Wang1,17, Lijun Jin1, Pei Zhang1, Haofu Hu1, Wei Yang1, Jiang Hu1, Jin Xiao1, Zhikai Yang1, Yang Liu1, Qiaolin Xie1, Hao Yu1, Jinmin Lian1, Ping Wen1, Fang Zhang1, Hui Li1, Yongli Zeng1, Zijun Xiong1, Shiping Liu1,17, Long Zhou1, Zhiyong Huang1, Na An1, Jie Wang1,18, Qiumei Zheng1, Yingqi Xiong1, Guangbiao Wang1, Bo Wang1, Jingjing Wang1, Yu Fan19, Rute R. da Fonseca3, Alonzo Alfaro-N\FA\F1ez3, Mikkel Schubert3, Ludovic Orlando3, Tobias Mourier3, Jason T. Howard20, Ganeshkumar Ganapathy20, Andreas Pfenning20, Osceola Whitney20, Miriam V. Rivas20, Erina Hara20, Julia Smith20, Marta Farre4, Jitendra Narayan21, Gancho Slavov21, Michael N Romanov22, Rui Borges8,9, Jo\E3o Paulo Machado8,23, Imran Khan8,9, Mark S. Springer24, John Gatesy24, Federico G. Hoffmann25,26, Juan C. Opazo27, Olle H\E5stad28, Roger H. Sawyer10, Heebal Kim5,6,29, Kyu-Won Kim5, Hyeon Jeong Kim6, Seoae Cho6, Ning Li30, Yinhua Huang30,31, Michael W. Bruford32, Xiangjiang Zhan32,33, Andrew Dixon34, Mads F. Bertelsen35, Elizabeth Derryberry36,37, Wesley Warren38, Richard K Wilson38, Shengbin Li39, David A. Ray26,\87, Richard E. Green40, Stephen J. O\92Brien41,42, Darren Griffin22, Warren E. Johnson43, David Haussler40, Oliver A. Ryder44, Eske Willerslev3, Gary R. Graves45,46, Per Alstr\F6m47,48, Jon Fjelds\E546, David P. Mindell49, Scott V. Edwards50, Edward L. Braun51, Carsten Rahbek46,52, David W. Burt53, Peter Houde54, Yong Zhang1, Huanming Yang1,55, Jian Wang1, Avian Genome Consortium\A7, Erich D. Jarvis20,\86, M. Thomas P. Gilbert3,56,\86, Jun Wang1,55,57,58,59,\86 Science 12 December 2014: Vol. 346 no. 6215 pp. 1311-1320 DOI: 10.1126/science.1251385 Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits. Whole-genome analyses resolve early branches in the tree of life of modern birds Science 12 December 2014: Vol. 346 no. 6215 pp. 1320-1331 DOI: 10.1126/science.1253451 Erich D. Jarvis, Siavash Mirarab, Andre J. Aberer, Bo Li, Peter Houde, Cai Li, Simon Y. W. Ho, Brant C. Faircloth, Benoit Nabholz, Jason T. Howard, Alexander Suh, Claudia C. Weber, Rute R. da Fonseca, Jianwen Li, Fang Zhang, Hui Li, Long Zhou, Nitish Narula, Liang Liu, Ganesh Ganapathy, Bastien Boussau, Md. Shamsuzzoha Bayzid, Volodymyr Zavidovych, Sankar Subramanian, Toni Gabald\F3n, Salvador Capella-Gutierrez, Jaime Huerta-Cepas, Bhanu Rekepalli, Kasper Munch, Mikkel Schierup, Bent Lindow, Wesley C. Warren, David Ray, Richard E. Green, Michael W. Bruford, Xiangjiang Zhan, Andrew Dixon, Shengbin Li, Ning Li, Yinhua Huang, Elizabeth P. Derryberry, Mads Frost Bertelsen, Frederick H. Sheldon, Robb T. Brumfield, Claudio V. Mello, Peter V. Lovell, Morgan Wirthlin, Maria Paula Cruz Schneider, Francisco Prosdocimi, Jose Alfredo Samaniego, Amhed Missael Vargas Velazquez, Alonzo Alfaro-N\FA\F1ez, Paula F. Campos, Bent Petersen, Thomas Sicheritz-Ponten, An Pas, Tom Bailey, Paul Scofield, Michael Bunce, David M. Lambert, Qi Zhou, Polina Perelman, Amy C. Driskell, Beth Shapiro, Zijun Xiong, Yongli Zeng, Shiping Liu, Zhenyu Li, Binghang Liu, Kui Wu, Jin Xiao, Xiong Yinqi, Qiuemei Zheng, Yong Zhang, Huanming Yang, Jian Wang, Linnea Smeds, Frank E. Rheindt, Michael Braun, Jon Fjeldsa, Ludovic Orlando, F. Keith Barker, Knud Andreas J\F8nsson, Warren Johnson, Klaus-Peter Koepfli, Stephen O\92Brien, David Haussler, Oliver A. Ryder, Carsten Rahbek, Eske Willerslev, Gary R. Graves, Travis C. Glenn, John McCormack, Dave Burt, Hans Ellegren, Per Alstr\F6m, Scott V. Edwards, Alexandros Stamatakis, David P. Mindell, Joel Cracraft, Edward L. Braun, Tandy Warnow, Wang Jun, M. Thomas P. Gilbert, and Guojie Zhang To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago. An integrative approach to understanding bird origins Xing Xu1,*, Zhonghe Zhou1, Robert Dudley2, Susan Mackem3, Cheng-Ming Chuong4,7, Gregory M. Erickson5, David J. Varricchio6 Science 12 December 2014: Vol. 346 no. 6215 DOI: 10.1126/science.1253293 Recent discoveries of spectacular dinosaur fossils overwhelmingly support the hypothesis that birds are descended from maniraptoran theropod dinosaurs, and furthermore, demonstrate that distinctive bird characteristics such as feathers, flight, endothermic physiology, unique strategies for reproduction and growth, and a novel pulmonary system originated among Mesozoic terrestrial dinosaurs. The transition from ground-living to flight-capable theropod dinosaurs now probably represents one of the best-documented major evolutionary transitions in life history. Recent studies in developmental biology and other disciplines provide additional insights into how bird characteristics originated and evolved. The iconic features of extant birds for the most part evolved in a gradual and stepwise fashion throughout archosaur evolution. However, new data also highlight occasional bursts of morphological novelty at certain stages particularly close to the origin of birds and an unavoidable complex, mosaic evolutionary distribution of major bird characteristics on the theropod tree. Research into bird origins provides a premier example of how paleontological and neontological data can interact to reveal the complexity of major innovations, to answer key evolutionary questions, and to lead to new research directions. A better understanding of bird origins requires multifaceted and integrative approaches, yet fossils necessarily provide the final test of any evolutionary model. Cat genome Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication Michael J. Montaguea,1, Gang Lib,1, Barbara Gandolfic, Razib Khand, Bronwen L. Akene, Steven M. J. Searlee, Patrick Minxa, LaDeana W. Hilliera, Daniel C. Koboldta, Brian W. Davisb, Carlos A. Driscollf, Christina S. Barrf, Kevin Blackistonef, Javier Quilezg, Belen Lorente-Galdosg, Tomas Marques-Bonetg,h, Can Alkani, Gregg W. C. Thomasj, Matthew W. Hahnj, Marilyn Menotti-Raymondk, Stephen J. O\92Brienl,m, Richard K. Wilsona, Leslie A. Lyonsc,2, William J. Murphyb,2, and Wesley C. Warrena,2 PNAS vol. 111 no. 48, 17230-17235 December 2 doi: 10.1073/pnas.1410083111 Little is known about the genetic changes that distinguish domestic cat populations from their wild progenitors. Here we describe a high-quality domestic cat reference genome assembly and comparative inferences made with other cat breeds, wildcats, and other mammals. Based upon these comparisons, we identified positively selected genes enriched for genes involved in lipid metabolism that underpin adaptations to a hypercarnivorous diet. We also found positive selection signals within genes underlying sensory processes, especially those affecting vision and hearing in the carnivore lineage. We observed an evolutionary tradeoff between functional olfactory and vomeronasal receptor gene repertoires in the cat and dog genomes, with an expansion of the feline chemosensory system for detecting pheromones at the expense of odorant detection. Genomic regions harboring signatures of natural selection that distinguish domestic cats from their wild congeners are enriched in neural crest-related genes associated with behavior and reward in mouse models, as predicted by the domestication syndrome hypothesis. Our description of a previously unidentified allele for the gloving pigmentation pattern found in the Birman breed supports the hypothesis that cat breeds experienced strong selection on specific mutations drawn from random bred populations. Collectively, these findings provide insight into how the process of domestication altered the ancestral wildcat genome and build a resource for future disease mapping and phylogenomic studies across all members of the Felidae. horse genome Prehistoric genomes reveal the genetic foundation and cost of horse domestication Mikkel Schuberta,1, H\E1kon J\F3nssona,1, Dan Changb,1, Clio Der Sarkissiana, Luca Erminia, Aurelien Ginolhaca, Anders Albrechtsenc, Isabelle Dupanloupd,e, Adrien Foucald,e, Bent Petersenf, Matteo Fumagallig, Maanasa Raghavana, Andaine Seguin-Orlandoa,h, Thorfinn S. Korneliussena, Amhed M. V. Velazqueza, Jesper Stenderupa, Cindi A. Hooveri, Carl-Johan Rubinj, Ahmed H. Alfarhank, Saleh A. Alquraishik, Khaled A. S. Al-Rasheidk, David E. MacHughl,m, Ted Kalbfleischn, James N. MacLeodo, Edward M. Rubini, Thomas Sicheritz-Pontenf, Leif Anderssonj, Michael Hofreiterp, Tomas Marques-Bonetq,r, M. Thomas P. Gilberta, Rasmus Nielsens, Laurent Excoffierd,e, Eske Willersleva, Beth Shapirob, and Ludovic Orlandoa,2 PNAS vol. 111 no. 52, E5661-E5669, December 30 doi: 10.1073/pnas.1416991111 The domestication of the horse ~5.5 kya and the emergence of mounted riding, chariotry, and cavalry dramatically transformed human civilization. However, the genetics underlying horse domestication are difficult to reconstruct, given the near extinction of wild horses. We therefore sequenced two ancient horse genomes from Taymyr, Russia (at 7.4- and 24.3-fold coverage), both predating the earliest archeological evidence of domestication. We compared these genomes with genomes of domesticated horses and the wild Przewalski\92s horse and found genetic structure within Eurasia in the Late Pleistocene, with the ancient population contributing significantly to the genetic variation of domesticated breeds. We furthermore identified a conservative set of 125 potential domestication targets using four complementary scans for genes that have undergone positive selection. One group of genes is involved in muscular and limb development, articular junctions, and the cardiac system, and may represent physiological adaptations to human utilization. A second group consists of genes with cognitive functions, including social behavior, learning capabilities, fear response, and agreeableness, which may have been key for taming horses. We also found that domestication is associated with inbreeding and an excess of deleterious mutations. This genetic load is in line with the \93cost of domestication\94 hypothesis also reported for rice, tomatoes, and dogs, and it is generally attributed to the relaxation of purifying selection resulting from the strong demographic bottlenecks accompanying domestication. Our work demonstrates the power of ancient genomes to reconstruct the complex genetic changes that transformed wild animals into their domesticated forms, and the population context in which this process took place. Speciation with gene flow in equids despite extensive chromosomal plasticity H\E1kon J\F3nssona,1, Mikkel Schuberta,1, Andaine Seguin-Orlandoa,b,1, Aurelien Ginolhaca, Lillian Petersenb, Matteo Fumagallic,d, Anders Albrechtsene, Bent Petersenf, Thorfinn S. Korneliussena, Julia T. Vilstrupa, Teri Learg, Jennifer Leigh Mykag, Judith Lundquistg, Donald C. Millerh, Ahmed H. Alfarhani, Saleh A. Alquraishii, Khaled A. S. Al-Rasheidi, Julia Stagegaardj, G\FCnter Straussk, Mads Frost Bertelsenl, Thomas Sicheritz-Pontenf, Douglas F. Antczakh, Ernest Baileyg, Rasmus Nielsenc, Eske Willersleva, and Ludovic Orlandoa,2 PNAS vol. 111 no. 52, 18655-18660, December 30 doi: 10.1073/pnas.1412627111 Horses, asses, and zebras belong to a single genus, Equus, which emerged 4.0-4.5 Mya. Although the equine fossil record represents a textbook example of evolution, the succession of events that gave rise to the diversity of species existing today remains unclear. Here we present six genomes from each living species of asses and zebras. This completes the set of genomes available for all extant species in the genus, which was hitherto represented only by the horse and the domestic donkey. In addition, we used a museum specimen to characterize the genome of the quagga zebra, which was driven to extinction in the early 1900s. We scan the genomes for lineage-specific adaptations and identify 48 genes that have evolved under positive selection and are involved in olfaction, immune response, development, locomotion, and behavior. Our extensive genome dataset reveals a highly dynamic demographic history with synchronous expansions and collapses on different continents during the last 400 ky after major climatic events. We show that the earliest speciation occurred with gene flow in Northern America, and that the ancestor of present-day asses and zebras dispersed into the Old World 2.1-3.4 Mya. Strikingly, we also find evidence for gene flow involving three contemporary equine species despite chromosomal numbers varying from 16 pairs to 31 pairs. These findings challenge the claim that the accumulation of chromosomal rearrangements drive complete reproductive isolation, and promote equids as a fundamental model for understanding the interplay between chromosomal structure, gene flow, and, ultimately, speciation. domestication arly Holocene chicken domestication in northern China Hai Xianga, Jianqiang Gaob, Baoquan Yuc, Hui Zhoud, Dawei Caid, Youwen Zhanga, Xiaoyong Chena, Xi Wanga, Michael Hofreitere,1, and Xingbo Zhaoa,1 PNAS vol. 111 no. 49, 17564-17569, December 9 doi: 10.1073/pnas.1411882111 Chickens represent by far the most important poultry species, yet the number, locations, and timings of their domestication have remained controversial for more than a century. Here we report ancient mitochondrial DNA sequences from the earliest archaeological chicken bones from China, dating back to ~10,000 B.P. The results clearly show that all investigated bones, including the oldest from the Nanzhuangtou site, are derived from the genus Gallus, rather than any other related genus, such as Phasianus. Our analyses also suggest that northern China represents one region of the earliest chicken domestication, possibly dating as early as 10,000 y B.P. Similar to the evidence from pig domestication, our results suggest that these early domesticated chickens contributed to the gene pool of modern chicken populations. Moreover, our results support the idea that multiple members of the genus Gallus, specifically Gallus gallus and Gallus sonneratii contributed to the gene pool of the modern domestic chicken. Our results provide further support for the growing evidence of an early mixed agricultural complex in northern China. Ecology - Conservation------------------------------------------------------------------------------------------------------------------------------ Signatures of aestivation and migration in Sahelian malaria mosquito populations A. Dao, A. S. Yaro, M. Diallo, S. Timbin\E9, D. L. Huestis, Y. Kassogu\E9, A. I. Traor\E9, Z. L. Sanogo, D. Samak\E9 & T. Lehmann Nature 516, 387-390 (18 December 2014) doi:10.1038/nature13987 Published online 26 November 2014 During the long Sahelian dry season, mosquito vectors of malaria are expected to perish when no larval sites are available; yet, days after the first rains, mosquitoes reappear in large numbers. How these vectors persist over the 3-6-month long dry season has not been resolved, despite extensive research for over a century1, 2, 3. Hypotheses for vector persistence include dry-season diapause (aestivation) and long-distance migration (LDM); both are facets of vector biology that have been highly controversial owing to lack of concrete evidence. Here we show that certain species persist by a form of aestivation, while others engage in LDM. Using time-series analyses, the seasonal cycles of Anopheles coluzzii, Anopheles gambiae sensu stricto (s.s.), and Anopheles arabiensis were estimated, and their effects were found to be significant, stable and highly species-specific. Contrary to all expectations, the most complex dynamics occurred during the dry season, when the density of A. coluzzii fluctuated markedly, peaking when migration would seem highly unlikely, whereas A. gambiae s.s. was undetected. The population growth of A. coluzzii followed the first rains closely, consistent with aestivation, whereas the growth phase of both A. gambiae s.s. and A. arabiensis lagged by two months. Such a delay is incompatible with local persistence, but fits LDM. Surviving the long dry season in situ allows A. coluzzii to predominate and form the primary force of malaria transmission. Our results reveal profound ecological divergence between A. coluzzii and A. gambiae s.s., whose standing as distinct species has been challenged, and suggest that climate is one of the selective pressures that led to their speciation. Incorporating vector dormancy and LDM is key to predicting shifts in the range of malaria due to global climate change4, and to the elimination of malaria from Africa. Extinctions of aculeate pollinators in Britain and the role of large-scale agricultural changes Jeff Ollerton1,*, Hilary Erenler1, Mike Edwards2, Robin Crockett1 Science 12 December 2014: Vol. 346 no. 6215 pp. 1360-1362 DOI: 10.1126/science.1257259 Pollinators are fundamental to maintaining both biodiversity and agricultural productivity, but habitat destruction, loss of flower resources, and increased use of pesticides are causing declines in their abundance and diversity. Using historical records, we assessed the rate of extinction of bee and flower-visiting wasp species in Britain from the mid-19th century to the present. The most rapid phase of extinction appears to be related to changes in agricultural policy and practice beginning in the 1920s, before the agricultural intensification prompted by the Second World War, often cited as the most important driver of biodiversity loss in Britain. Slowing of the extinction rate from the 1960s onward may be due to prior loss of the most sensitive species and/or effective conservation programs. Recovery of large carnivores in Europe\92s modern human-dominated landscapes Guillaume Chapron1,*,\86, Petra Kaczensky2, John D. C. Linnell3, Manuela von Arx4, Djuro Huber5, Henrik Andren1, Jose Vicente L\F3pez-Bao1,6,\86, Michal Adamec7, Francisco \C1lvares8, Ole Anders9, Linas Balciauskas10, Vaidas Balys11, Peter Bedo12, Ferdinand Bego13, Juan Carlos Blanco14, Urs Breitenmoser4,15, Henrik Br\F8seth3, Ludek Bufka16, Raimonda Bunikyte17, Paolo Ciucci18, Alexander Dutsov19, Thomas Engleder20, Christian Fuxj\E4ger21, Claudio Groff22, Katja Holmala23, Bledi Hoxha24, Yorgos Iliopoulos25, Ovidiu Ionescu26,27, Jasna Jeremic28, Klemen Jerina29, Gesa Kluth30, Felix Knauer2, Ilpo Kojola31, Ivan Kos29, Miha Krofel29, Jakub Kubala32, Sa\9Aa Kunovac33, Josip Kusak5, Miroslav Kutal34,35, Olof Liberg1, Aleksandra Majic29, Peep M\E4nnil36, Ralph Manz4, Eric Marboutin37, Francesca Marucco38, Dime Melovski39,40, Kujtim Mersini41, Yorgos Mertzanis25, Robert W. Myslajek42, Sabina Nowak43, John Odden3, Janis Ozolins44, Guillermo Palomero45, Milan Paunovic46, Jens Persson1, Hubert Potocnik29, Pierre-Yves Quenette47, Georg Rauer2, Ilka Reinhardt30, Robin Rigg12, Andreas Ryser4, Valeria Salvatori48, Toma\9E Skrbin\9Aek29, Aleksandar Stojanov39, Jon E. Swenson3,49, L\E1szl\F3 Szemethy50, Aleksand\EBr Traj\E7e24, Elena Tsingarska-Sedefcheva19, Martin V\E1na35, Rauno Veeroja36, Petter Wabakken51, Manfred W\F6lfl52, Sybille W\F6lfl53, Fridolin Zimmermann4, Diana Zlatanova54, Luigi Boitani18 Science 19 December 2014: Vol. 346 no. 6216 pp. 1517-1519 DOI: 10.1126/science.1257553 The conservation of large carnivores is a formidable challenge for biodiversity conservation. Using a data set on the past and current status of brown bears (Ursus arctos), Eurasian lynx (Lynx lynx), gray wolves (Canis lupus), and wolverines (Gulo gulo) in European countries, we show that roughly one-third of mainland Europe hosts at least one large carnivore species, with stable or increasing abundance in most cases in 21st-century records. The reasons for this overall conservation success include protective legislation, supportive public opinion, and a variety of practices making coexistence between large carnivores and people possible. The European situation reveals that large carnivores and people can share the same landscape. Trophic coherence determines food-web stability Samuel Johnsona,1,2, Virginia Dom\EDnguez-Garc\EDab,1, Luca Donettic, and Miguel A. Mu\F1ozb PNAS vol. 111 no. 50, 17923-17928, December 16 doi: 10.1073/pnas.1409077111 Why are large, complex ecosystems stable? Both theory and simulations of current models predict the onset of instability with growing size and complexity, so for decades it has been conjectured that ecosystems must have some unidentified structural property exempting them from this outcome. We show that trophic coherence\97a hitherto ignored feature of food webs that current structural models fail to reproduce\97is a better statistical predictor of linear stability than size or complexity. Furthermore, we prove that a maximally coherent network with constant interaction strengths will always be linearly stable. We also propose a simple model that, by correctly capturing the trophic coherence of food webs, accurately reproduces their stability and other basic structural features. Most remarkably, our model shows that stability can increase with size and complexity. This suggests a key to May\92s paradox, and a range of opportunities and concerns for biodiversity conservation. Nonrandom, diversifying processes are disproportionately strong in the smallest size classes of a tropical forest Peter T. Greena,b,1, Kyle E. Harmsc, and Joseph H. Connelld PNAS vol. 111 no. 52, 18649-18654, December 30 doi: 10.1073/pnas.1321892112 A variety of ecological processes influence diversity and species composition in natural communities. Most of these processes, whether abiotic or biotic, differentially filter individuals from birth to death, thereby altering species\92 relative abundances. Nonrandom outcomes could accrue throughout ontogeny, or the processes that generate them could be particularly influential at certain stages. One long-standing paradigm in tropical forest ecology holds that patterns of relative abundance among mature trees are largely set by processes operating at the earliest life cycle stages. Several studies confirm filtering processes at some stages, but the longevity of large trees makes a rigorous comparison across size classes impossible without long-term demographic data. Here, we use one of the world\92s longest-running, plot-based forest dynamics projects to compare nonrandom outcomes across stage classes. We considered a cohort of 7,977 individuals in 186 species that were alive in 1971 and monitored in 13 mortality censuses over 42 y to 2013. Nonrandom mortality with respect to species identity occurred more often in the smaller rather than the larger size classes. Furthermore, observed nonrandom mortality in the smaller size classes had a diversifying influence; species richness of the survivors was up to 30% greater than expected in the two smallest size classes, but not greater than expected in the larger size classes. These results highlight the importance of early life cycle stages in tropical forest community dynamics. More generally, they add to an accumulating body of evidence for the importance of early-stage nonrandom outcomes to community structure in marine and terrestrial environments. Yellowstone Wolves and the Forces That Structure Natural Systems Andy P. Dobson mail PLoS Biology Published: December 23, 2014 DOI: 10.1371/journal.pbio.1002025 Since their introduction in 1995 and 1996, wolves have had effects on Yellowstone that ripple across the entire structure of the food web that defines biodiversity in the Northern Rockies ecosystem. Ecological interpretations of the wolves have generated a significant amount of debate about the relative strength of top-down versus bottom-up forces in determining herbivore and vegetation abundance in Yellowstone. Debates such as this are central to the resolution of broader debates about the role of natural enemies and climate as forces that structure food webs and modify ecosystem function. Ecologists need to significantly raise the profile of these discussions; understanding the forces that structure food webs and determine species abundance and the supply of ecosystem services is one of the central scientific questions for this century; its complexity will require new minds, new mathematics, and significant, consistent funding. EvoDevo------------------------------------------------------------------------------------------------------------------------------------------ Spatiotemporal transcriptomics reveals the evolutionary history of the endoderm germ layer Tamar Hashimshony, Martin Feder, Michal Levin, Brian K. Hall & Itai Yanai Nature doi:10.1038/nature13996 Published online, 10 December 2014 The concept of germ layers has been one of the foremost organizing principles in developmental biology, classification, systematics and evolution for 150 years (refs 1, 2, 3). Of the three germ layers, the mesoderm is found in bilaterian animals but is absent in species in the phyla Cnidaria and Ctenophora, which has been taken as evidence that the mesoderm was the final germ layer to evolve1, 4, 5. The origin of the ectoderm and endoderm germ layers, however, remains unclear, with models supporting the antecedence of each as well as a simultaneous origin4, 6, 7, 8, 9. Here we determine the temporal and spatial components of gene expression spanning embryonic development for all Caenorhabditis elegans genes and use it to determine the evolutionary ages of the germ layers. The gene expression program of the mesoderm is induced after those of the ectoderm and endoderm, thus making it the last germ layer both to evolve and to develop. Strikingly, the C. elegans endoderm and ectoderm expression programs do not co-induce; rather the endoderm activates earlier, and this is also observed in the expression of endoderm orthologues during the embryology of the frog Xenopus tropicalis, the sea anemone Nematostella vectensis and the sponge Amphimedon queenslandica. Querying the phylogenetic ages of specifically expressed genes reveals that the endoderm comprises older genes. Taken together, we propose that the endoderm program dates back to the origin of multicellularity, whereas the ectoderm originated as a secondary germ layer freed from ancestral feeding functions. Evolution of the new vertebrate head by co-option of an ancient chordate skeletal tissue David Jandzik, Aaron T. Garnett, Tyler A. Square, Maria V. Cattell, Jr-Kai Yu & Daniel M. Medeiros Nature doi:10.1038/nature14000 Pubished online, 08 December 2014 A defining feature of vertebrates (craniates) is a pronounced head that is supported and protected by a robust cellular endoskeleton. In the first vertebrates, this skeleton probably consisted of collagenous cellular cartilage, which forms the embryonic skeleton of all vertebrates and the adult skeleton of modern jawless and cartilaginous fish. In the head, most cellular cartilage is derived from a migratory cell population called the neural crest, which arises from the edges of the central nervous system. Because collagenous cellular cartilage and neural crest cells have not been described in invertebrates1, the appearance of cellular cartilage derived from neural crest cells is considered a turning point in vertebrate evolution2. Here we show that a tissue with many of the defining features of vertebrate cellular cartilage transiently forms in the larvae of the invertebrate chordate Branchiostoma floridae (Florida amphioxus). We also present evidence that during evolution, a key regulator of vertebrate cartilage development, SoxE, gained new cis-regulatory sequences that subsequently directed its novel expression in neural crest cells. Together, these results suggest that the origin of the vertebrate head skeleton did not depend on the evolution of a new skeletal tissue, as is commonly thought, but on the spread of this tissue throughout the head. We further propose that the evolution of cis-regulatory elements near an ancient regulator of cartilage differentiation was a major factor in the evolution of the vertebrate head skeleton. A relative shift in cloacal location repositions external genitalia in amniote evolution Patrick Tschopp, Emma Sherratt, Thomas J. Sanger, Anna C. Groner, Ariel C. Aspiras, Jimmy K. Hu, Olivier Pourqui\E9, J\E9r\F4me Gros & Clifford J. Tabin Nature 516,391-394 (18 December 2014) doi:10.1038/nature13819 Published online 05 November 2014 Corrected online 17 December 2014 The move of vertebrates to a terrestrial lifestyle required major adaptations in their locomotory apparatus and reproductive organs. While the fin-to-limb transition has received considerable attention1, 2, little is known about the developmental and evolutionary origins of external genitalia. Similarities in gene expression have been interpreted as a potential evolutionary link between the limb and genitals3, 4, 5, 6; however, no underlying developmental mechanism has been identified. We re-examined this question using micro-computed tomography, lineage tracing in three amniote clades, and RNA-sequencing-based transcriptional profiling. Here we show that the developmental origin of external genitalia has shifted through evolution, and in some taxa limbs and genitals share a common primordium. In squamates, the genitalia develop directly from the budding hindlimbs, or the remnants thereof, whereas in mice the genital tubercle originates from the ventral and tail bud mesenchyme. The recruitment of different cell populations for genital outgrowth follows a change in the relative position of the cloaca, the genitalia organizing centre. Ectopic grafting of the cloaca demonstrates the conserved ability of different mesenchymal cells to respond to these genitalia-inducing signals. Our results support a limb-like developmental origin of external genitalia as the ancestral condition. Moreover, they suggest that a change in the relative position of the cloacal signalling centre during evolution has led to an altered developmental route for external genitalia in mammals, while preserving parts of the ancestral limb molecular circuitry owing to a common evolutionary origin. Regulatory modulation of the T-box gene Tbx5 links development, evolution, and adaptation of the sternum Sorrel R. B. Bickleya and Malcolm P. O. Logana,b,1 PNAS vol. 111 no. 50, 17917-17922, December 16 doi: 10.1073/pnas.1409913111 The sternum bone lies at the ventral midline of the thorax where it provides a critical attachment for the pectoral muscles that allow the forelimbs to raise the body from the ground. Among tetrapods, sternum morphology is correlated with the mode of locomotion: Avians that fly have a ventral extension, or keel, on their sterna, which provides an increased area for flight muscle attachment. The sternum is fused with the ribs attaching on either side; however, unlike the ribs, the sternal precursors do not originate from the somites. Despite the crucial role of the sternum in tetrapod locomotion, little attention has been given to its acquisition, evolution, and embryological development. We demonstrate an essential role for the T-box transcription factor gene Tbx5 in sternum and forelimb formation and show that both structures share an embryological origin within the lateral plate mesoderm. Consistent with this shared origin and role of Tbx5, sternum defects are a characteristic feature of Holt-Oram Syndrome (OMIM 142900) caused by mutations in TBX5. We demonstrate a link between sternum size and forelimb use across avians and provide evidence that modulation of Tbx5 expression underlies the reduction in sternum and wing size in a flightless bird, the emu. We demonstrate that Tbx5 is a common node in the genetic pathways regulating forelimb and sternum development, enabling specific adaptations of these features without affecting other skeletal elements and can also explain the linked adaptation of sternum and forelimb morphology correlated with mode of locomotion. Neuromolecular responses to social challenge: Common mechanisms across mouse, stickleback fish, and honey bee Clare C. Rittschofa,b,c,d,1, Syed Abbas Bukharia,e,2, Laura G. Sloofmana,f,2, Joseph M. Troya,e,2, Derek Caetano-Anollesa,g, Amy Cash-Ahmeda,b, Molly Kenta,c, Xiaochen Lua,g, Yibayiri O. Sanogoa,h, Patricia A. Weisnera,c, Huimin Zhanga,g, Alison M. Bella,c,i,j, Jian Maa,k, Saurabh Sinhaa,b,l, Gene E. Robinsona,b,c,j,1, and Lisa Stubbsa,c,g,1 PNAS vol. 111 no. 50 17929-17934, December 16 doi: 10.1073/pnas.1420369111 Certain complex phenotypes appear repeatedly across diverse species due to processes of evolutionary conservation and convergence. In some contexts like developmental body patterning, there is increased appreciation that common molecular mechanisms underlie common phenotypes; these molecular mechanisms include highly conserved genes and networks that may be modified by lineage-specific mutations. However, the existence of deeply conserved mechanisms for social behaviors has not yet been demonstrated. We used a comparative genomics approach to determine whether shared neuromolecular mechanisms could underlie behavioral response to territory intrusion across species spanning a broad phylogenetic range: house mouse (Mus musculus), stickleback fish (Gasterosteus aculeatus), and honey bee (Apis mellifera). Territory intrusion modulated similar brain functional processes in each species, including those associated with hormone-mediated signal transduction and neurodevelopment. Changes in chromosome organization and energy metabolism appear to be core, conserved processes involved in the response to territory intrusion. We also found that several homologous transcription factors that are typically associated with neural development were modulated across all three species, suggesting that shared neuronal effects may involve transcriptional cascades of evolutionarily conserved genes. Furthermore, immunohistochemical analyses of a subset of these transcription factors in mouse again implicated modulation of energy metabolism in the behavioral response. These results provide support for conserved genetic \93toolkits\94 that are used in independent evolutions of the response to social challenge in diverse taxa. Phylogenomic Resolution of the Hemichordate and Echinoderm Clade Johanna T. Cannon, Kevin M. Kocot, Damien S. Waits, David A. Weese, Billie J. Swalla, Scott R. Santos, Kenneth M. Halanych Current Biology Volume 24, Issue 23, p2827-2832, 1 December 2014 DOI: http://dx.doi.org/10.1016/j.cub.2014.10.016 Ambulacraria, comprising Hemichordata and Echinodermata [ 1 ], is closely related to Chordata, making it integral to understanding chordate origins and polarizing chordate molecular and morphological characters [ 2-4 ]. Unfortunately, relationships within Hemichordata and Echinodermata have remained unresolved [ 1, 5-10 ], compromising our ability to extrapolate findings from the most closely related molecular and developmental models outside of Chordata (e.g., the acorn worms Saccoglossus kowalevskii and Ptychodera flava and the sea urchin Strongylocentrotus purpuratus). To resolve long-standing phylogenetic issues within Ambulacraria, we sequenced transcriptomes for 14 hemichordates as well as 8 echinoderms and complemented these with existing data for a total of 33 ambulacrarian operational taxonomic units (OTUs). Examination of leaf stability values revealed rhabdopleurid pterobranchs and the enteropneust Stereobalanus canadensis were unstable in placement; therefore, analyses were also run without these taxa. Analyses of 185 genes resulted in reciprocal monophyly of Enteropneusta and Pterobranchia, placed the deep-sea family Torquaratoridae within Ptychoderidae, and confirmed the position of ophiuroid brittle stars as sister to asteroid sea stars (the Asterozoa hypothesis). These results are consistent with earlier perspectives concerning plesiomorphies of Ambulacraria, including pharyngeal gill slits, a single axocoel, and paired hydrocoels and somatocoels [ 1, 4, 11 ]. The resolved ambulacrarian phylogeny will help clarify the early evolution of chordate characteristics and has implications for our understanding of major fossil groups, including graptolites and somasteroideans. Evolution of the new vertebrate head by co-option of an ancient chordate skeletal tissue David Jandzik, Aaron T. Garnett, Tyler A. Square, Maria V. Cattell, Jr-Kai Yu & Daniel M. Medeiros Nature doi:10.1038/nature14000 Pubished online, 08 December 2014 A defining feature of vertebrates (craniates) is a pronounced head that is supported and protected by a robust cellular endoskeleton. In the first vertebrates, this skeleton probably consisted of collagenous cellular cartilage, which forms the embryonic skeleton of all vertebrates and the adult skeleton of modern jawless and cartilaginous fish. In the head, most cellular cartilage is derived from a migratory cell population called the neural crest, which arises from the edges of the central nervous system. Because collagenous cellular cartilage and neural crest cells have not been described in invertebrates1, the appearance of cellular cartilage derived from neural crest cells is considered a turning point in vertebrate evolution2. Here we show that a tissue with many of the defining features of vertebrate cellular cartilage transiently forms in the larvae of the invertebrate chordate Branchiostoma floridae (Florida amphioxus). We also present evidence that during evolution, a key regulator of vertebrate cartilage development, SoxE, gained new cis-regulatory sequences that subsequently directed its novel expression in neural crest cells. Together, these results suggest that the origin of the vertebrate head skeleton did not depend on the evolution of a new skeletal tissue, as is commonly thought, but on the spread of this tissue throughout the head. We further propose that the evolution of cis-regulatory elements near an ancient regulator of cartilage differentiation was a major factor in the evolution of the vertebrate head skeleton. Innovation - adaptation - coevolution--------------------------------------------------------------------------------------------------------------- An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons Frank M. J. Jacobs, David Greenberg, Ngan Nguyen, Maximilian Haeussler, Adam D. Ewing, Sol Katzman, Benedict Paten, Sofie R. Salama & David Haussler Nature 516, 242–245 (11 December 2014) doi:10.1038/nature13760 Published online 28 September 2014 Throughout evolution primate genomes have been modified by waves of retrotransposon insertions1, 2, 3. For each wave, the host eventually finds a way to repress retrotransposon transcription and prevent further insertions. In mouse embryonic stem cells, transcriptional silencing of retrotransposons requires KAP1 (also known as TRIM28) and its repressive complex, which can be recruited to target sites by KRAB zinc-finger (KZNF) proteins such as murine-specific ZFP809 which binds to integrated murine leukaemia virus DNA elements and recruits KAP1 to repress them4, 5. KZNF genes are one of the fastest growing gene families in primates and this expansion is hypothesized to enable primates to respond to newly emerged retrotransposons6, 7. However, the identity of KZNF genes battling retrotransposons currently active in the human genome, such as SINE-VNTR-Alu (SVA)8 and long interspersed nuclear element 1 (L1)9, is unknown. Here we show that two primate-specific KZNF genes rapidly evolved to repress these two distinct retrotransposon families shortly after they began to spread in our ancestral genome. ZNF91 underwent a series of structural changes 8–12 million years ago that enabled it to repress SVA elements. ZNF93 evolved earlier to repress the primate L1 lineage until ~12.5 million years ago when the L1PA3-subfamily of retrotransposons escaped ZNF93’s restriction through the removal of the ZNF93-binding site. Our data support a model where KZNF gene expansion limits the activity of newly emerged retrotransposon classes, and this is followed by mutations in these retrotransposons to evade repression, a cycle of events that could explain the rapid expansion of lineage-specific KZNF genes. Hominids adapted to metabolize ethanol long before human-directed fermentation Matthew A. Carrigana,b,1, Oleg Uryasevb, Carole B. Fryeb, Blair L. Eckmanb, Candace R. Myersc, Thomas D. Hurleyc, and Steven A. Bennerb PNAS December 1, 2014 doi: 10.1073/pnas.1404167111 Paleogenetics is an emerging field that resurrects ancestral proteins from now-extinct organisms to test, in the laboratory, models of protein function based on natural history and Darwinian evolution. Here, we resurrect digestive alcohol dehydrogenases (ADH4) from our primate ancestors to explore the history of primate–ethanol interactions. The evolving catalytic properties of these resurrected enzymes show that our ape ancestors gained a digestive dehydrogenase enzyme capable of metabolizing ethanol near the time that they began using the forest floor, about 10 million y ago. The ADH4 enzyme in our more ancient and arboreal ancestors did not efficiently oxidize ethanol. This change suggests that exposure to dietary sources of ethanol increased in hominids during the early stages of our adaptation to a terrestrial lifestyle. Because fruit collected from the forest floor is expected to contain higher concentrations of fermenting yeast and ethanol than similar fruits hanging on trees, this transition may also be the first time our ancestors were exposed to (and adapted to) substantial amounts of dietary ethanol. New insight into the evolution of the vertebrate respiratory system and the discovery of unidirectional airflow in iguana lungs Robert L. Cieria, Brent A. Cravenb, Emma R. Schachnera, and C. G. Farmera,1 PNAS vol. 111 no. 48, 17218-17223, December 2 doi: 10.1073/pnas.1405088111 The generally accepted framework for the evolution of a key feature of the avian respiratory system, unidirectional airflow, is that it is an adaptation for efficiency of gas exchange and expanded aerobic capacities, and therefore it has historically been viewed as important to the ability of birds to fly and to maintain an endothermic metabolism. This pattern of flow has been presumed to arise from specific features of the respiratory system, such as an enclosed intrapulmonary bronchus and parabronchi. Here we show unidirectional airflow in the green iguana, a lizard with a strikingly different natural history from that of birds and lacking these anatomical features. This discovery indicates a paradigm shift is needed. The selective drivers of the trait, its date of origin, and the fundamental aerodynamic mechanisms by which unidirectional flow arises must be reassessed to be congruent with the natural history of this lineage. Unidirectional flow may serve functions other than expanded aerobic capacity; it may have been present in the ancestral diapsid; and it can occur in structurally simple lungs. Coevolution Drives the Emergence of Complex Traits and Promotes Evolvability Luis Zaman mail, Justin R. Meyer, Suhas Devangam, David M. Bryson, Richard E. Lenski, Charles Ofria mail PLoS Biology Published: December 16, 2014 DOI: 10.1371/journal.pbio.1002023 The evolution of complex organismal traits is obvious as a historical fact, but the underlying causes\97including the role of natural selection\97are contested. Gould argued that a random walk from a necessarily simple beginning would produce the appearance of increasing complexity over time. Others contend that selection, including coevolutionary arms races, can systematically push organisms toward more complex traits. Methodological challenges have largely precluded experimental tests of these hypotheses. Using the Avida platform for digital evolution, we show that coevolution of hosts and parasites greatly increases organismal complexity relative to that otherwise achieved. As parasites evolve to counter the rise of resistant hosts, parasite populations retain a genetic record of past coevolutionary states. As a consequence, hosts differentially escape by performing progressively more complex functions. We show that coevolution's unique feedback between host and parasite frequencies is a key process in the evolution of complexity. Strikingly, the hosts evolve genomes that are also more phenotypically evolvable, similar to the phenomenon of contingency loci observed in bacterial pathogens. Because coevolution is ubiquitous in nature, our results support a general model whereby antagonistic interactions and natural selection together favor both increased complexity and evolvability. Evolution of RNA-Protein Interactions: Non-Specific Binding Led to RNA Splicing Activity of Fungal Mitochondrial Tyrosyl-tRNA Synthetases Lilian T. Lamech, Anna L. Mallam, Alan M. Lambowitz mail PLoS Biology Published: December 23, 2014 DOI: 10.1371/journal.pbio.1002028 The Neurospora crassa mitochondrial tyrosyl-tRNA synthetase (mtTyrRS; CYT-18 protein) evolved a new function as a group I intron splicing factor by acquiring the ability to bind group I intron RNAs and stabilize their catalytically active RNA structure. Previous studies showed: (i) CYT-18 binds group I introns by using both its N-terminal catalytic domain and flexibly attached C-terminal anticodon-binding domain (CTD); and (ii) the catalytic domain binds group I introns specifically via multiple structural adaptations that occurred during or after the divergence of Peziomycotina and Saccharomycotina. However, the function of the CTD and how it contributed to the evolution of splicing activity have been unclear. Here, small angle X-ray scattering analysis of CYT-18 shows that both CTDs of the homodimeric protein extend outward from the catalytic domain, but move inward to bind opposite ends of a group I intron RNA. Biochemical assays show that the isolated CTD of CYT-18 binds RNAs non-specifically, possibly contributing to its interaction with the structurally different ends of the intron RNA. Finally, we find that the yeast mtTyrRS, which diverged from Pezizomycotina fungal mtTyrRSs prior to the evolution of splicing activity, binds group I intron and other RNAs non-specifically via its CTD, but lacks further adaptations needed for group I intron splicing. Our results suggest a scenario of constructive neutral (i.e., pre-adaptive) evolution in which an initial non-specific interaction between the CTD of an ancestral fungal mtTyrRS and a self-splicing group I intron was \93fixed\94 by an intron RNA mutation that resulted in protein-dependent splicing. Once fixed, this interaction could be elaborated by further adaptive mutations in both the catalytic domain and CTD that enabled specific binding of group I introns. Our results highlight a role for non-specific RNA binding in the evolution of RNA-binding proteins. Cryptic genetic variation can make \93irreducible complexity\94 a common mode of adaptation in sexual populations Meredith V. Trotter1,2, Daniel B. Weissman3,4, Grant I. Peterson2, Kayla M. Peck2,5 and Joanna Masel2 Article first published online: 29 SEP 2014 DOI: 10.1111/evo.12517 Evolution Volume 68, Issue 12, pages 3357-3367, December 2014 The existence of complex (multiple-step) genetic adaptations that are \93irreducible\94 (i.e., all partial combinations are less fit than the original genotype) is one of the longest standing problems in evolutionary biology. In standard genetics parlance, these adaptations require the crossing of a wide adaptive valley of deleterious intermediate stages. Here, we demonstrate, using a simple model, that evolution can cross wide valleys to produce \93irreducibly complex\94 adaptations by making use of previously cryptic mutations. When revealed by an evolutionary capacitor, previously cryptic mutants have higher initial frequencies than do new mutations, bringing them closer to a valley-crossing saddle in allele frequency space. Moreover, simple combinatorics implies an enormous number of candidate combinations exist within available cryptic genetic variation. We model the dynamics of crossing of a wide adaptive valley after a capacitance event using both numerical simulations and analytical approximations. Although individual valley crossing events become less likely as valleys widen, by taking the combinatorics of genotype space into account, we see that revealing cryptic variation can cause the frequent evolution of complex adaptations. The temporal distribution of directional gradients under selection for an optimum Luis-Miguel Chevin and Benjamin C. Haller Article first published online: 21 NOV 2014 DOI: 10.1111/evo.12532 Evolution, Volume 68, Issue 12, pages 3381-3394, December 2014 Temporal variation in phenotypic selection is often attributed to environmental change causing movements of the adaptive surface relating traits to fitness, but this connection is rarely established empirically. Fluctuating phenotypic selection can be measured by the variance and autocorrelation of directional selection gradients through time. However, the dynamics of these gradients depend not only on environmental changes altering the fitness surface, but also on evolution of the phenotypic distribution. Therefore, it is unclear to what extent variability in selection gradients can inform us about the underlying drivers of their fluctuations. To investigate this question, we derive the temporal distribution of directional gradients under selection for a phenotypic optimum that is either constant or fluctuates randomly in various ways in a finite population. Our analytical results, combined with population- and individual-based simulations, show that although some characteristic patterns can be distinguished, very different types of change in the optimum (including a constant optimum) can generate similar temporal distributions of selection gradients, making it difficult to infer the processes underlying apparent fluctuating selection. Analyzing changes in phenotype distributions together with changes in selection gradients should prove more useful for inferring the mechanisms underlying estimated fluctuating selection. Do age-specific survival patterns of wild boar fit current evolutionary theories of senescence? Marlene Gamelon1, Stefano Focardi2, Jean-Michel Gaillard3, Olivier Gimenez4, Christophe Bonenfant3, Barbara Franzetti5, Remi Choquet4, Francesca Ronchi5, Eric Baubet6 and Jean-Fran\E7ois Lema\EEtre3 Article first published online: 30 SEP 2014 DOI: 10.1111/evo.12519 Evolution Volume 68, Issue 12, pages 3636-3643, December 2014 Actuarial senescence is widespread in age-structured populations. In growing populations, the progressive decline of Hamiltonian forces of selection with age leads to decreasing survival. As actuarial senescence is overcompensated by a high fertility, actuarial senescence should be more intense in species with high reproductive effort, a theoretical prediction that has not been yet explicitly tested across species. Wild boar (Sus scrofa) females have an unusual life-history strategy among large mammals by associating both early and high reproductive effort with potentially long lifespan. Therefore, wild boar females should show stronger actuarial senescence than similar-sized related mammals. Moreover, being polygynous and much larger than females, males should display higher senescence rates than females. Using a long-term monitoring (18 years) of a wild boar population, we tested these predictions. We provided clear evidence of actuarial senescence in both sexes. Wild boar females had earlier but not stronger actuarial senescence than similar-sized ungulates. Both sexes displayed similar senescence rates. Our study indicates that the timing of senescence, not the rate, is associated with the magnitude of fertility in ungulates. This demonstrates the importance of including the timing of senescence in addition to its rate to understand variation in senescence patterns in wild populations. Mate choice Termite queens close the sperm gates of eggs to switch from sexual to asexual reproduction Toshihisa Yashiro and Kenji Matsuura1 PNAS vol. 111 no. 48, 17212-17217 December 2 doi: 10.1073/pnas.1412481111 Males and females are in conflict over genetic transmission in the evolution of parthenogenesis, because it enhances female reproductive output but deprives the males\92 genetic contribution. For males, any trait that coerces females into sexual reproduction should increase their fitness. However, in the termite Reticulitermes speratus, queens produce their replacements (neotenic queens) parthenogenetically while using normal sexual reproduction to produce other colony members. Here, we show that termite queens produce parthenogenetic offspring in the presence of kings by closing the micropyles (sperm gates; i.e., openings for sperm entry) of their eggs. Our field survey showed that termite eggs show large variation in numbers of micropyles, with some having none. Microsatellite analysis showed that embryos of micropyleless eggs develop parthenogenetically, whereas those of eggs with micropyles are fertilized and develop sexually. Surveys of eggs among queens of different age groups showed that queens begin to lay micropyleless eggs when they are older and thus, need to produce their replacements parthenogenetically. In addition, we found clear seasonality in new neotenic queen differentiation and micropyleless egg production. This micropyle-dependent parthenogenesis is the first identification, to our knowledge, of the mechanism through which females control egg fertilization over time in diploid animals, implying a novel route of the evolution of parthenogenesis in favor of female interests without interference from males. Sexual selection is influenced by both developmental and adult environments Stephanie R. Gillespie1,2, M. Scarlett Tudor3,4, Allen J. Moore5,6 and Christine W. Miller1 Article first published online: 23 OCT 2014 DOI: 10.1111/evo.12526 Evolution Volume 68, Issue 12, pages 3421-3432, December 2014 Sexual selection is often assumed to be strong and consistent, yet increasing research shows it can fluctuate over space and time. Few experimental studies have examined changes in sexual selection in response to natural environmental variation. Here, we use a difference in resource quality to test for the influence of past environmental conditions and current environmental conditions on male and female mate choice and resulting selection gradients for leaf-footed cactus bugs, Narnia femorata. We raised juveniles on natural high- and low-quality diets, cactus pads with and without ripe cactus fruits. New adults were again assigned a cactus pad with or without fruit, paired with a potential mate, and observed for mating behaviors. We found developmental and adult encounter environments affected mating decisions and the resulting patterns of sexual selection for both males and females. Males were not choosy in the low-quality encounter environment, cactus without fruit, but they avoided mating with small females in the high-quality encounter environment. Females were choosy in both encounter environments, avoiding mating with small males. However, they were the choosiest when they were in the low-quality encounter environment. Female mate choice was also context dependent by male developmental environment. Females were more likely to mate with males that had developed on cactus with fruit when they were currently in the cactus with fruit environment. This pattern disappeared when females were in the cactus without fruit environment. Altogether, these results experimentally demonstrate context-dependent mate choice by both males and females. Furthermore, we demonstrate that simple, seasonal changes in resources can lead to fluctuations in sexual selection. Female sperm use and storage between fertilization events drive sperm competition and male ejaculate allocation Gustavo S. Requena and Suzanne H. Alonzo Article first published online: 20 NOV 2014 DOI: 10.1111/evo.12540 Evolution Volume 68, Issue 12, pages 3433-3444, December 2014 Sperm competition theory has traditionally focused on how male allocation responds to female promiscuity, when males compete to fertilize a single clutch of eggs. Here, we develop a model to ask how female sperm use and storage across consecutive reproductive events affect male ejaculate allocation and patterns of mating and paternity. In our model, sperm use (a single parameter under female control) is the main determinant of sperm competition, which alters the effect of female promiscuity on male success and, ultimately, male reproductive allocation. Our theory reproduces the general pattern predicted by existing theory that increased sperm competition favors increased allocation to ejaculates. However, our model predicts a negative correlation between male ejaculate allocation and female promiscuity, challenging the generality of a prevailing expectation of sperm competition theory. Early models assumed that the energetic costs of precopulatory competition and the level of sperm competition are both determined by female promiscuity, which leads to an assumed covariation between these two processes. By modeling precopulatory costs and sperm competition independently, our theoretical framework allows us to examine how male allocation should respond independently to variation in sperm competition and energetic trade-offs in mating systems that have been overlooked in the past. The evolution of photosynthesis in chromist algae through serial endosymbioses John W. Stiller, John Schreiber, Jipei Yue, Hui Guo, Qin Ding & Jinling Huang Nature Communications 5, Article number: 5764 doi:10.1038/ncomms6764 Published 10 December 2014 Chromist algae include diverse photosynthetic organisms of great ecological and social importance. Despite vigorous research efforts, a clear understanding of how various chromists acquired photosynthetic organelles has been complicated by conflicting phylogenetic results, along with an undetermined number and pattern of endosymbioses, and the horizontal movement of genes that accompany them. We apply novel statistical approaches to assess impacts of endosymbiotic gene transfer on three principal chromist groups at the heart of long-standing controversies. Our results provide robust support for acquisitions of photosynthesis through serial endosymbioses, beginning with the adoption of a red alga by cryptophytes, then a cryptophyte by the ancestor of ochrophytes, and finally an ochrophyte by the ancestor of haptophytes. Resolution of how chromist algae are related through endosymbioses provides a framework for unravelling the further reticulate history of red algal-derived plastids, and for clarifying evolutionary processes that gave rise to eukaryotic photosynthetic diversity. Evolutionary innovation and conservation in the embryonic derivation of the vertebrate skull Nadine Piekarski, Joshua B. Gross & James Hanken Nature Communications 5, Article number: 5661 doi:10.1038/ncomms6661 Published 01 December 2014 Development of the vertebrate skull has been studied intensively for more than 150 years, yet many essential features remain unresolved. One such feature is the extent to which embryonic derivation of individual bones is evolutionarily conserved or labile. We perform long-term fate mapping using GFP-transgenic axolotl and Xenopus laevis to document the contribution of individual cranial neural crest streams to the osteocranium in these amphibians. Here we show that the axolotl pattern is strikingly similar to that in amniotes; it likely represents the ancestral condition for tetrapods. Unexpectedly, the pattern in Xenopus is much different; it may constitute a unique condition that evolved after anurans diverged from other amphibians. Such changes reveal an unappreciated relation between life history evolution and cranial development and exemplify \91developmental system drift\92, in which interspecific divergence in developmental processes that underlie homologous characters occurs with little or no concomitant change in the adult phenotype. Symbiotic adaptations in the fungal cultivar of leaf-cutting ants Henrik H. De Fine Licht, Jacobus J. Boomsma & Anders Tunlid Nature Communications 5, Article number: 5675 doi:10.1038/ncomms6675 Published 01 December 2014 Centuries of artificial selection have dramatically improved the yield of human agriculture; however, strong directional selection also occurs in natural symbiotic interactions. Fungus-growing attine ants cultivate basidiomycete fungi for food. One cultivar lineage has evolved inflated hyphal tips (gongylidia) that grow in bundles called staphylae, to specifically feed the ants. Here we show extensive regulation and molecular signals of adaptive evolution in gene trancripts associated with gongylidia biosynthesis, morphogenesis and enzymatic plant cell wall degradation in the leaf-cutting ant cultivar Leucoagaricus gongylophorus. Comparative analysis of staphylae growth morphology and transcriptome-wide expressional and nucleotide divergence indicate that gongylidia provide leaf-cutting ants with essential amino acids and plant-degrading enzymes, and that they may have done so for 20-25 million years without much evolutionary change. These molecular traits and signatures of selection imply that staphylae are highly advanced coevolutionary organs that play pivotal roles in the mutualism between leaf-cutting ants and their fungal cultivars. Directional selection can drive the evolution of modularity in complex traits Diogo Melo1 and Gabriel Marroig PNAS December 29 doi: 10.1073/pnas.1322632112 Modularity is a central concept in modern biology, providing a powerful framework for the study of living organisms on many organizational levels. Two central and related questions can be posed in regard to modularity: How does modularity appear in the first place, and what forces are responsible for keeping and/or changing modular patterns? We approached these questions using a quantitative genetics simulation framework, building on previous results obtained with bivariate systems and extending them to multivariate systems. We developed an individual-based model capable of simulating many traits controlled by many loci with variable pleiotropic relations between them, expressed in populations subject to mutation, recombination, drift, and selection. We used this model to study the problem of the emergence of modularity, and hereby show that drift and stabilizing selection are inefficient at creating modular variational structures. We also demonstrate that directional selection can have marked effects on the modular structure between traits, actively promoting a restructuring of genetic variation in the selected population and potentially facilitating the response to selection. Furthermore, we give examples of complex covariation created by simple regimes of combined directional and stabilizing selection and show that stabilizing selection is important in the maintenance of established covariation patterns. Our results are in full agreement with previous results for two-trait systems and further extend them to include scenarios of greater complexity. Finally, we discuss the evolutionary consequences of modular patterns being molded by directional selection. Development - Signaling pathways-------------------------------------------------------------------------------------------------------------------- An ancient defense system eliminates unfit cells from developing tissues during cell competition S. N. Meyer1,*, M. Amoyel2,*,\86, C. Berganti\F1os2,*, C. de la Cova2, C. Schertel1, K. Basler1,\87, L. A. Johnston2,\87 Science 5 December 2014: Vol. 346 no. 6214 DOI: 10.1126/science.1258236 Developing tissues that contain mutant or compromised cells present risks to animal health. Accordingly, the appearance of a population of suboptimal cells in a tissue elicits cellular interactions that prevent their contribution to the adult. Here we report that this quality control process, cell competition, uses specific components of the evolutionarily ancient and conserved innate immune system to eliminate Drosophila cells perceived as unfit. We find that Toll-related receptors (TRRs) and the cytokine Sp\E4tzle (Spz) lead to NF?B-dependent apoptosis. Diverse \93loser\94 cells require different TRRs and NF?B factors and activate distinct pro-death genes, implying that the particular response is stipulated by the competitive context. Our findings demonstrate a functional repurposing of components of TRRs and NF?B signaling modules in the surveillance of cell fitness during development. Wnts produced by Osterix-expressing osteolineage cells regulate their proliferation and differentiation Si Hui Tana,b, Kshemendra Senarath-Yapac, Michael T. Chungc,1, Michael T. Longakerc, Joy Y. Wud, andR oeland Nusseb,e,2 PNAS vol. 111 no. 49, E5262-E5271, December 9 doi: 10.1073/pnas.1420463111 Wnt signaling is a critical regulator of bone development, but the identity and role of the Wnt-producing cells are still unclear. We addressed these questions through in situ hybridization, lineage tracing, and genetic experiments. First, we surveyed the expression of all 19 Wnt genes and Wnt target gene Axin2 in the neonatal mouse bone by in situ hybridization, and demonstrated\97to our knowledge for the first time\97that Osterix-expressing cells coexpress Wnt and Axin2. To track the behavior and cell fate of Axin2-expressing osteolineage cells, we performed lineage tracing and showed that they sustain bone formation over the long term. Finally, to examine the role of Wnts produced by Osterix-expressing cells, we inhibited Wnt secretion in vivo, and observed inappropriate differentiation, impaired proliferation, and diminished Wnt signaling response. Therefore, Osterix-expressing cells produce their own Wnts that in turn induce Wnt signaling response, thereby regulating their proliferation and differentiation. The Toll/NF-?B signaling pathway is required for epidermal wound repair in Drosophila Lara Carvalhoa,b, Ant\F3nio Jacintoa,b, and Nina Matovaa,1 PNAS vol. 111 no. 50, E5373-E5382, December 16 doi: 10.1073/pnas.1408224111 The Toll/NF-?B pathway, first identified in studies of dorsal-ventral polarity in the early Drosophila embryo, is well known for its role in the innate immune response. Here, we reveal that the Toll/NF-?B pathway is essential for wound closure in late Drosophila embryos. Toll mutants and Dif dorsal (NF-?B) double mutants are unable to repair epidermal gaps. Dorsal is activated on wounding, and Dif and Dorsal are required for the sustained down-regulation of E-cadherin, an obligatory component of the adherens junctions (AJs), at the wound edge. This remodeling of the AJs promotes the assembly of an actin-myosin cable at the wound margin; contraction of the actin cable, in turn, closes the wound. In the absence of Toll or Dif and dorsal (dl), both E-cadherin down-regulation and actin-cable formation fail, thus resulting in open epidermal gaps. Given the conservation of the Toll/NF-?B pathway in mammals and the epithelial expression of many components of the pathway, this function in wound healing is likely to be conserved in vertebrates. Hedgehog-induced phosphorylation by CK1 sustains the activity of Ci/Gli activator Qing Shia, Shuang Lia, Shuangxi Lia,b, Alice Jianga, Yongbin Chenc,d, and Jin Jianga,e,1 PNAS vol. 111 no. 52, E5651-E5660, December 30 doi: 10.1073/pnas.1416652111 Hedgehog (Hh) signaling governs many developmental processes by regulating the balance between the repressor (CiR/GliR) and activator (CiA/GliA) forms of Cubitus interruptus (Ci)/glioma-associated oncogene homolog (Gli) transcription factors. Although much is known about how CiR/GliR is controlled, the regulation of CiA/GliA remains poorly understood. Here we demonstrate that Casein kinase 1 (CK1) sustains Hh signaling downstream of Costal2 and Suppressor of fused (Sufu) by protecting CiA from premature degradation. We show that Hh stimulates Ci phosphorylation by CK1 at multiple Ser/Thr-rich degrons to inhibit its recognition by the Hh-induced MATH and BTB domain containing protein (HIB), a substrate receptor for the Cullin 3 family of E3 ubiquitin ligases. In Hh-receiving cells, reduction of CK1 activity accelerated HIB-mediated degradation of CiA, leading to premature loss of pathway activity. We also provide evidence that GliA is regulated by CK1 in a similar fashion and that CK1 acts downstream of Sufu to promote Sonic hedgehog signaling. Taken together, our study not only reveals an unanticipated and conserved mechanism by which phosphorylation of Ci/Gli positively regulates Hh signaling but also provides the first evidence, to our knowledge, that substrate recognition by the Cullin 3 family of E3 ubiquitin ligases is negatively regulated by a kinase. PTEN signaling through RAF1 proto-oncogene serine/threonine kinase (RAF1)/ERK in the epididymis is essential for male fertility Bingfang Xu, Angela M. Washington, and Barry T. Hinton1 PNAS vol. 111 no. 52, 18643-18648, December 30 doi: 10.1073/pnas.1413186112 Without a fully developed initial segment, the most proximal region of the epididymis, male infertility results. Therefore, it is important to understand the development and regulation of this crucial region. In addition to distinctively high activity levels of the components of the ERK pathway, which are essential for initial-segment differentiation, the initial segment exhibits high protein and activity levels of phosphatase and tensin homolog (PTEN). To understand the role of PTEN in the regulation of the initial segment, we generated a mouse model with a conditional deletion of Pten from the epithelial cells of the proximal epididymis from postnatal day 17 (P17) onward. Shortly after Pten deletion, hypertrophy of the proximal epididymis became evident. Loss of Pten resulted in activation of the AKT (protein kinase B) pathway components from P28 onward, which in turn gradually suppressed RAF1 proto-oncogene serine/threonine kinase (RAF1)/ERK signaling through the interaction between AKT and RAF1. Consistent with progressive changes in RAF1/ERK signaling, loss of Pten progressively altered cell shape, size, organization, proliferation, and survival in the initial-segment epithelium and resulted in dedifferentiation and extensive epithelial folding. Most importantly, knockout males progressively lost fertility and became infertile from 6 to 12 mo. Spermatozoa from older knockout mice showed a lower percentage of motility and a higher percentage of flagellar angulation compared with controls, suggesting compromised sperm maturation. Therefore, under normal physiological conditions, PTEN suppresses AKT activity to maintain activation of the RAF1/ERK signaling pathway, which in turn maintains normal function of the initial segment and therefore, normal sperm maturation. TORC1 regulators Iml1/GATOR1 and GATOR2 control meiotic entry and oocyte development in Drosophila Youheng Wei, Brad Reveal, John Reich, Willem J. Laursen1, Stefania Senger2, Tanveer Akbar, Takako Iida-Jones3, Weili Cai, Michal Jarnik, and Mary A. Lilly4 PNAS vol. 111 no. 52, E5670-E5677, December 30 doi: 10.1073/pnas.1419156112 In single-cell eukaryotes the pathways that monitor nutrient availability are central to initiating the meiotic program and gametogenesis. In Saccharomyces cerevisiae an essential step in the transition to the meiotic cycle is the down-regulation of the nutrient-sensitive target of rapamycin complex 1 (TORC1) by the increased minichromosome loss 1/ GTPase-activating proteins toward Rags 1 (Iml1/GATOR1) complex in response to amino acid starvation. How metabolic inputs influence early meiotic progression and gametogenesis remains poorly understood in metazoans. Here we define opposing functions for the TORC1 regulatory complexes Iml1/GATOR1 and GATOR2 during Drosophila oogenesis. We demonstrate that, as is observed in yeast, the Iml1/GATOR1 complex inhibits TORC1 activity to slow cellular metabolism and drive the mitotic/meiotic transition in developing ovarian cysts. In iml1 germline depletions, ovarian cysts undergo an extra mitotic division before meiotic entry. The TORC1 inhibitor rapamycin can suppress this extra mitotic division. Thus, high TORC1 activity delays the mitotic/meiotic transition. Conversely, mutations in Tor, which encodes the catalytic subunit of the TORC1 complex, result in premature meiotic entry. Later in oogenesis, the GATOR2 components Mio and Seh1 are required to oppose Iml1/GATOR1 activity to prevent the constitutive inhibition of TORC1 and a block to oocyte growth and development. To our knowledge, these studies represent the first examination of the regulatory relationship between the Iml1/GATOR1 and GATOR2 complexes within the context of a multicellular organism. Our data imply that the central role of the Iml1/GATOR1 complex in the regulation of TORC1 activity in the early meiotic cycle has been conserved from single cell to multicellular organisms. Genetic modifiers of EGFR dependence in non-small cell lung cancer Tanaz Sharifniaa,b,c, Victor Rusua,d, Federica Piccionia, Mukta Bagula, Marcin Imielinskia,b,c, Andrew D. Cherniacka, Chandra Sekhar Pedamallua,c, Bang Wonga, Frederick H. Wilsona,c, Levi A. Garrawaya,c, David Altshulera,d,e, Todd R. Goluba, David E. Roota, Aravind Subramaniana, and Matthew Meyersona,b,c,1 PNAS vol. 111 no. 52, 18661-18666, December 30 doi: 10.1073/pnas.1412228112 Lung adenocarcinomas harboring activating mutations in the epidermal growth factor receptor (EGFR) represent a common molecular subset of non-small cell lung cancer (NSCLC) cases. EGFR mutations predict sensitivity to EGFR tyrosine kinase inhibitors (TKIs) and thus represent a dependency in NSCLCs harboring these alterations, but the genetic basis of EGFR dependence is not fully understood. Here, we applied an unbiased, ORF-based screen to identify genetic modifiers of EGFR dependence in EGFR-mutant NSCLC cells. This approach identified 18 kinase and kinase-related genes whose overexpression can substitute for EGFR in EGFR-dependent PC9 cells, and these genes include seven of nine Src family kinase genes, FGFR1, FGFR2, ITK, NTRK1, NTRK2, MOS, MST1R, and RAF1. A subset of these genes can complement loss of EGFR activity across multiple EGFR-dependent models. Unbiased gene-expression profiling of cells overexpressing EGFR bypass genes, together with targeted validation studies, reveals EGFR-independent activation of the MEK-ERK and phosphoinositide 3-kinase (PI3K)-AKT pathways. Combined inhibition of PI3K-mTOR and MEK restores EGFR dependence in cells expressing each of the 18 EGFR bypass genes. Together, these data uncover a broad spectrum of kinases capable of overcoming dependence on EGFR and underscore their convergence on the PI3K-AKT and MEK-ERK signaling axes in sustaining EGFR-independent survival. The majority of early primordial germ cells acquire pluripotency by AKT activation Yasuhisa Matsui1,2,*, Asuka Takehara1, Yuko Tokitake1,2, Makiko Ikeda1, Yuka Obara1, Yuiko Morita-Fujimura3, Tohru Kimura4 and Toru Nakano2,5 Posted online before print October 30, 2014, doi: 10.1242/dev.113779 December 2014 Development 141, 4457-4467. Primordial germ cells (PGCs) are undifferentiated germ cells in embryos, the fate of which is to become gametes; however, mouse PGCs can easily be reprogrammed into pluripotent embryonic germ cells (EGCs) in culture in the presence of particular extracellular factors, such as combinations of Steel factor (KITL), LIF and bFGF (FGF2). Early PGCs form EGCs more readily than do later PGCs, and PGCs lose the ability to form EGCs by embryonic day (E) 15.5. Here, we examined the effects of activation of the serine/threonine kinase AKT in PGCs during EGC formation; notably, AKT activation, in combination with LIF and bFGF, enhanced EGC formation and caused ~60% of E10.5 PGCs to become EGCs. The results indicate that the majority of PGCs at E10.5 could acquire pluripotency with an activated AKT signaling pathway. Importantly, AKT activation did not fully substitute for bFGF and LIF, and AKT activation without both LIF and bFGF did not result in EGC formation. These findings indicate that AKT signal enhances and/or collaborates with signaling pathways of bFGF and of LIF in PGCs for the acquisition of pluripotency. Myosin VIIA regulates microvillus morphogenesis and interacts with cadherin Cad99C in Drosophila oogenesis Cory Glowinski*, Ri-Hua Sandy Liu*, Xi Chen, Audrey Darabie and Dorothea Godt\87 Advance Online Article September 18, 2014 doi: 10.1242/?jcs.099242 November 15, 2014 J Cell Sci 127, 4821-4832. Microvilli and related actin-based protrusions permit multiple interactions between cells and their environment. How the shape, length and arrangement of microvilli are determined remains largely unclear. To address this issue and explore the cooperation of the two main components of a microvillus, the central F-actin bundle and the enveloping plasma membrane, we investigated the expression and function of Myosin VIIA (Myo7A), which is encoded by crinkled (ck), and its interaction with cadherin Cad99C in the microvilli of the Drosophila follicular epithelium. Myo7A is present in the microvilli and terminal web of follicle cells, and associates with several other F-actin-rich structures in the ovary. Loss of Myo7A caused brush border defects and a reduction in the amount of the microvillus regulator Cad99C. We show that Myo7A and Cad99C form a molecular complex and that the cytoplasmic tail of Cad99C recruits Myo7A to microvilli. Our data indicate that Myo7A regulates the structure and spacing of microvilli, and interacts with Cad99C in vivo. A comparison of the mutant phenotypes suggests that Myo7A and Cad99C have co-dependent and independent functions in microvilli. Inhibitors of endocytosis prevent Wnt/Wingless signalling by reducing the level of basal \DF-catenin/Armadillo Maria Gagliardi1,*, Ana Hernandez2, Ian J. McGough1 and Jean-Paul Vincent1,\87 Advance Online Article September 18, 2014 doi: 10.1242/?jcs.155424 November 15, 2014 J Cell Sci 127, 4918-4926. A key step in the canonical Wnt signalling pathway is the inhibition of GSK3\DF, which results in the accumulation of nuclear \DF-catenin (also known as CTNNB1), and hence regulation of target genes. Evidence suggests that endocytosis is required for signalling, yet its role and the molecular understanding remains unclear. A recent and controversial model suggests that endocytosis contributes to Wnt signalling by causing the sequestration of the ligand-receptor complex, including LRP6 and GSK3 to multivesicular bodies (MVBs), thus preventing GSK3\DF from accessing \DF-catenin. Here, we use specific inhibitors (Dynasore and Dyngo-4a) to confirm the essential role of endocytosis in Wnt/Wingless signalling in human and Drosophila cells. However, we find no evidence that, in Drosophila cells or wing imaginal discs, LRP6/Arrow traffics to MVBs or that MVBs are required for Wnt/Wingless signalling. Moreover, we show that activation of signalling through chemical blockade of GSK3\DF is prevented by endocytosis inhibitors, suggesting that endocytosis impacts on Wnt/Wingless signalling downstream of the ligand-receptor complex. We propose that, through an unknown mechanism, endocytosis boosts the resting pool of \DF-catenin upon which GSK3\DF normally acts. Evolutionary changes in TGFa distribution underlie morphological diversity in eggshells from Drosophila species Matthew G. Niepielko and Nir Yakoby* doi: 10.1242/dev.111898 December 15, 2014 Development 141, 4710-4715. Drosophila eggshells display remarkable morphological diversity among species; however, the molecular origin of this structural diversification is mostly unknown. Here, we analyzed the dorsal ridge (DR), a lumen-like structure along the dorsal side of eggshells, from numerous Drosophila species. This structure varies in length and width across species, and is absent from D. melanogaster eggshells. We associated DR formation with distinct spatiotemporal changes in epidermal growth factor receptor (EGFR) activation, which acts as a key receptor in eggshell patterning. We show that changes in the distribution of the TGFa-like ligand Gurken (GRK), a crucial ligand for axis formation, underlies EGFR activation and DR formation in D. willistoni. Furthermore, we demonstrate that GRK from D. willistoni rescues a grk-null D. melanogaster fly and, remarkably, it is also sufficient to generate a DR-like structure on its eggshell. Wnt/\DF-catenin signaling integrates patterning and metabolism of the insect growth zone Georg Oberhofer1, Daniela Grossmann1, Janna L. Siemanowski1, Tim Beissbarth2 and Gregor Bucher1,* Posted online before print November 13, 2014, doi: 10.1242/dev.112797 December 15, 2014 Development 141, 4740-4750. Wnt/\DF-catenin and hedgehog (Hh) signaling are essential for transmitting signals across cell membranes in animal embryos. Early patterning of the principal insect model, Drosophila melanogaster, occurs in the syncytial blastoderm, where diffusion of transcription factors obviates the need for signaling pathways. However, in the cellularized growth zone of typical short germ insect embryos, signaling pathways are predicted to play a more fundamental role. Indeed, the Wnt/\DF-catenin pathway is required for posterior elongation in most arthropods, although which target genes are activated in this context remains elusive. Here, we use the short germ beetle Tribolium castaneum to investigate two Wnt and Hh signaling centers located in the head anlagen and in the growth zone of early embryos. We find that Wnt/\DF-catenin signaling acts upstream of Hh in the growth zone, whereas the opposite interaction occurs in the head. We determine the target gene sets of the Wnt/\DF-catenin and Hh pathways and find that the growth zone signaling center activates a much greater number of genes and that the Wnt and Hh target gene sets are essentially non-overlapping. The Wnt pathway activates key genes of all three germ layers, including pair-rule genes, and Tc-caudal and Tc-twist. Furthermore, the Wnt pathway is required for hindgut development and we identify Tc-senseless as a novel hindgut patterning gene required in the early growth zone. At the same time, Wnt acts on growth zone metabolism and cell division, thereby integrating growth with patterning. Posterior Hh signaling activates several genes potentially involved in a proteinase cascade of unknown function. The ESCRT machinery regulates the secretion and long-range activity of Hedgehog Tam\E1s Matusek, Franz Wendler, Sophie Poles, Sandrine Pizette, Gisela D\92Angelo, Maximilian F\FCrthauer & Pascal P. Therond Nature 516, 99-103 (04 December 2014) doi:10.1038/nature13847 Published online 03 December 2014 The conserved family of Hedgehog (Hh) proteins acts as short- and long-range secreted morphogens, controlling tissue patterning and differentiation during embryonic development1. Mature Hh carries hydrophobic palmitic acid and cholesterol modifications essential for its extracellular spreading2. Various extracellular transportation mechanisms for Hh have been suggested, but the pathways actually used for Hh secretion and transport in vivo remain unclear. Here we show that Hh secretion in Drosophila wing imaginal discs is dependent on the endosomal sorting complex required for transport (ESCRT)3. In vivo the reduction of ESCRT activity in cells producing Hh leads to a retention of Hh at the external cell surface. Furthermore, we show that ESCRT activity in Hh-producing cells is required for long-range signalling. We also provide evidence that pools of Hh and ESCRT proteins are secreted together into the extracellular space in vivo and can subsequently be detected together at the surface of receiving cells. These findings uncover a new function for ESCRT proteins in controlling morphogen activity and reveal a new mechanism for the transport of secreted Hh across the tissue by extracellular vesicles, which is necessary for long-range target induction. Flight muscle Development !! Subcellular Trafficking of FGF Controls Tracheal Invasion of Drosophila Flight Muscle Soren J. Peterson, Mark A. Krasnow DOI: http://dx.doi.org/10.1016/j.cell.2014.11.043 Cell December 31 To meet the extreme oxygen demand of insect flight muscle, tracheal (respiratory) tubes ramify not only on its surface, as in other tissues, but also within T-tubules and ultimately surrounding every mitochondrion. Although this remarkable physiological specialization has long been recognized, its cellular and molecular basis is unknown. Here, we show that Drosophila tracheoles invade flight muscle T-tubules through transient surface openings. Like other tracheal branching events, invasion requires the Branchless FGF pathway. However, localization of the FGF chemoattractant changes from all muscle membranes to T-tubules as invasion begins. Core regulators of epithelial basolateral membrane identity localize to T-tubules, and knockdown of AP-1?, required for basolateral trafficking, redirects FGF from T-tubules to surface, increasing tracheal surface ramification and preventing invasion. We propose that tracheal invasion is controlled by an AP-1-dependent switch in FGF trafficking. Thus, subcellular targeting of a chemoattractant can direct outgrowth to specific domains, including inside the cell. The GTPase Regulatory Proteins Pix and Git Control Tissue Growth via the Hippo Pathway Lucas G. Dent, Carole L.C. Poon, Xiaomeng Zhang, Joffrey L. Degoutin, Marla Tipping, Alexey Veraksa, Kieran F. Harvey Current Biology December 4 DOI: http://dx.doi.org/10.1016/j.cub.2014.11.041 The Salvador-Warts-Hippo (Hippo) pathway is a conserved regulator of organ size and is deregulated in human cancers [ 1 ]. In epithelial tissues, the Hippo pathway is regulated by fundamental cell biological properties, such as polarity and adhesion, and coordinates these with tissue growth [ 2-4 ]. Despite its importance in disease, development, and regeneration, the complete set of proteins that regulate Hippo signaling remain undefined. To address this, we used proteomics to identify proteins that bind to the Hippo (Hpo) kinase. Prominent among these were PAK-interacting exchange factor (known as Pix or RtGEF) and G-protein-coupled receptor kinase-interacting protein (Git). Pix is a conserved Rho-type guanine nucleotide exchange factor (Rho-GEF) homologous to Beta-PIX and Alpha-PIX in mammals. Git is the single Drosophila melanogaster homolog of the mammalian GIT1 and GIT2 proteins, which were originally identified in the search for molecules that interact with G-protein-coupled receptor kinases [ 5 ]. Pix and Git form an oligomeric scaffold to facilitate sterile 20-like kinase activation and have also been linked to GTPase regulation [ 5-8 ]. We show that Pix and Git regulate Hippo-pathway-dependent tissue growth in D. melanogaster and that they do this in parallel to the known upstream regulator Fat cadherin. Pix and Git influence activity of the Hpo kinase by acting as a scaffold complex, rather than enzymes, and promote Hpo dimerization and autophosphorylation of Hpo\92s activation loop. Therefore, we provide important new insights into an ancient signaling network that controls the growth of metazoan tissues. gene regulation - transcriptional regulation--------------------------------------------------------------------------------------------------------- Protein-DNA binding in the absence of specific base-pair recognition Ariel Afeka, Joshua L. Schipperb, John Hortonb, Raluca Gord\E2nb,1, and David B. Lukatskya,1 PNAS vol. 111 no. 48, 17140-17145 December 2 doi: 10.1073/pnas.1410569111 Until now, it has been reasonably assumed that specific base-pair recognition is the only mechanism controlling the specificity of transcription factor (TF)-DNA binding. Contrary to this assumption, here we show that nonspecific DNA sequences possessing certain repeat symmetries, when present outside of specific TF binding sites (TFBSs), statistically control TF-DNA binding preferences. We used high-throughput protein-DNA binding assays to measure the binding levels and free energies of binding for several human TFs to tens of thousands of short DNA sequences with varying repeat symmetries. Based on statistical mechanics modeling, we identify a new protein-DNA binding mechanism induced by DNA sequence symmetry in the absence of specific base-pair recognition, and experimentally demonstrate that this mechanism indeed governs protein-DNA binding preferences Neural precursor-specific expression of multiple Drosophila genes is driven by dual enhancer modules with overlapping function Steven W. Miller, Mark Rebeiz1, Jenny E. Atanasov, and James W. Posakony PNAS vol. 111 no. 48, 17194-17199, December 2 doi: 10.1073/pnas.1415308111 Transcriptional cis-regulatory modules (CRMs), or enhancers, are responsible for directing gene expression in specific territories and cell types during development. In some instances, the same gene may be served by two or more enhancers with similar specificities. Here we show that the utilization of dual, or \93shadow\94, enhancers is a common feature of genes that are active specifically in neural precursor (NP) cells in Drosophila. By genome-wide computational discovery of statistically significant clusters of binding motifs for both proneural activator (P) proteins and basic helix-loop-helix (bHLH) repressor (R) factors (a \93P+R\94 regulatory code), we have identified NP-specific enhancer modules associated with multiple genes expressed in this cell type. These CRMs are distinct from those previously identified for the corresponding gene, establishing the existence of a dual-enhancer arrangement in which both modules reside close to the gene they serve. Using wild-type and mutant reporter gene constructs in vivo, we show that P sites in these modules mediate activation by proneural factors in \93proneural cluster\94 territories, whereas R sites mediate repression by bHLH repressors, which serves to restrict expression specifically to NP cells. To our knowledge, our results identify the first direct targets of these bHLH repressors. Finally, using genomic rescue constructs for neuralized (neur), we demonstrate that each of the gene's two NP-specific enhancers is sufficient to rescue neur function in the lateral inhibition process by which adult sensory organ precursor (SOP) cells are specified, but that deletion of both enhancers results in failure of this event. Tissue-Resident Macrophage Enhancer Landscapes Are Shaped by the Local Microenvironment Yonit Lavin3, Deborah Winter3, Ronnie Blecher-Gonen3, Eyal David, Hadas Keren-Shaul, Miriam Merad4, Steffen Jung4, Ido Amit4 Cell Volume 159, Issue 6, p1312-1326, 4 December 2014 DOI: http://dx.doi.org/10.1016/j.cell.2014.11.018 Macrophages are critical for innate immune defense and also control organ homeostasis in a tissue-specific manner. They provide a fitting model to study the impact of ontogeny and microenvironment on chromatin state and whether chromatin modifications contribute to macrophage identity. Here, we profile the dynamics of four histone modifications across seven tissue-resident macrophage populations. We identify 12,743 macrophage-specific enhancers and establish that tissue-resident macrophages have distinct enhancer landscapes beyond what can be explained by developmental origin. Combining our enhancer catalog with gene expression profiles and open chromatin regions, we show that a combination of tissue- and lineage-specific transcription factors form the regulatory networks controlling chromatin specification in tissue-resident macrophages. The environment is capable of shaping the chromatin landscape of transplanted bone marrow precursors, and even differentiated macrophages can be reprogramed when transferred into a new microenvironment. These results provide a comprehensive view of macrophage regulatory landscape and highlight the importance of the microenvironment, along with pioneer factors in orchestrating identity and plasticity. Epigenetics Paternal Diet Defines Offspring Chromatin State and Intergenerational Obesity Anita \D6st8, Adelheid Lempradl8, Eduard Casas, Melanie Weigert, Theodor Tiko, Merdin Deniz, Lorena Pantano, Ulrike Boenisch, Pavel M. Itskov, Marlon Stoeckius, Marius Ruf, Nikolaus Rajewsky, Gunter Reuter, Nicola Iovino, Carlos Ribeiro, Mattias Alenius, Steffen Heyne, Tanya Vavouri, J. Andrew Pospisilik Cell Volume 159, Issue 6, p1352-1364, 4 December 2014 DOI: http://dx.doi.org/10.1016/j.cell.2014.11.005 The global rise in obesity has revitalized a search for genetic and epigenetic factors underlying the disease. We present a Drosophila model of paternal-diet-induced intergenerational metabolic reprogramming (IGMR) and identify genes required for its encoding in offspring. Intriguingly, we find that as little as 2 days of dietary intervention in fathers elicits obesity in offspring. Paternal sugar acts as a physiological suppressor of variegation, desilencing chromatin-state-defined domains in both mature sperm and in offspring embryos. We identify requirements for H3K9/K27me3-dependent reprogramming of metabolic genes in two distinct germline and zygotic windows. Critically, we find evidence that a similar system may regulate obesity susceptibility and phenotype variation in mice and humans. The findings provide insight into the mechanisms underlying intergenerational metabolic reprogramming and carry profound implications for our understanding of phenotypic variation and evolution. An ecdysone-responsive nuclear receptor regulates circadian rhythms in Drosophila Shailesh Kumar, Dechun Chen, Christopher Jang, Alexandra Nall, Xiangzhong Zheng & Amita Sehgal Nature Communications 5, Article number: 5697 doi:10.1038/ncomms6697 Published 16 December 2014 Little is known about molecular links between circadian clocks and steroid hormone signalling, although both are important for normal physiology. Here we report a circadian function for a nuclear receptor, ?ecdysone-induced protein 75 (?Eip75/?E75), which we identified through a gain-of-function screen for circadian genes in Drosophila melanogaster. Overexpression or knockdown of ?E75 in clock neurons disrupts rest:activity rhythms and dampens molecular oscillations. ?E75 represses expression of the gene encoding the transcriptional activator, ?CLOCK (?CLK), and may also affect circadian output. ?PER inhibits the activity of ?E75 on the ?Clk promoter, thereby providing a mechanism for a previously proposed de-repressor effect of ?PER on ?Clk transcription. The ecdysone receptor is also expressed in central clock cells and manipulations of its expression produce effects similar to those of ?E75 on circadian rhythms. We find that ?E75 protects rhythms under stressful conditions, suggesting a function for steroid signalling in the maintenance of circadian rhythms in Drosophila. Enhancer--core-promoter specificity separates developmental and housekeeping gene regulation Muhammad A. Zabidi, Cosmas D. Arnold, Katharina Schernhuber, Michaela Pagani, Martina Rath, Olga Frank & Alexander Stark Nature (2014) doi:10.1038/nature13994 Published online 15 December 2014 Gene transcription in animals involves the assembly of RNA polymerase II at core promoters and its cell-type-specific activation by enhancers that can be located more distally1. However, how ubiquitous expression of housekeeping genes is achieved has been less clear. In particular, it is unknown whether ubiquitously active enhancers exist and how developmental and housekeeping gene regulation is separated. An attractive hypothesis is that different core promoters might exhibit an intrinsic specificity to certain enhancers2, 3, 4, 5, 6. This is conceivable, as various core promoter sequence elements are differentially distributed between genes of different functions7, including elements that are predominantly found at either developmentally regulated or at housekeeping genes8, 9, 10. Here we show that thousands of enhancers in Drosophila melanogaster S2 and ovarian somatic cells (OSCs) exhibit a marked specificity to one of two core promoters\97one derived from a ubiquitously expressed ribosomal protein gene and another from a developmentally regulated transcription factor\97and confirm the existence of these two classes for five additional core promoters from genes with diverse functions. Housekeeping enhancers are active across the two cell types, while developmental enhancers exhibit strong cell-type specificity. Both enhancer classes differ in their genomic distribution, the functions of neighbouring genes, and the core promoter elements of these neighbouring genes. In addition, we identify two transcription factors\97Dref and Trl\97that bind and activate housekeeping versus developmental enhancers, respectively. Our results provide evidence for a sequence-encoded enhancer-core-promoter specificity that separates developmental and housekeeping gene regulatory programs for thousands of enhancers and their target genes across the entire genome. Deep conservation of wrist and digit enhancers in fish Andrew R. Gehrkea, Igor Schneiderb, Elisa de la Calle-Mustienesc, Juan J. Tenac, Carlos Gomez-Marinc, Mayuri Chandrana, Tetsuya Nakamuraa, Ingo Braaschd, John H. Postlethwaitd, Jose Luis G\F3mez-Skarmetac, and Neil H. Shubina,1 PNAS December 22, doi: 10.1073/pnas.1420208112 There is no obvious morphological counterpart of the autopod (wrist/ankle and digits) in living fishes. Comparative molecular data may provide insight into understanding both the homology of elements and the evolutionary developmental mechanisms behind the fin to limb transition. In mouse limbs the autopod is built by a \93late\94 phase of Hoxd and Hoxa gene expression, orchestrated by a set of enhancers located at the 5' end of each cluster. Despite a detailed mechanistic understanding of mouse limb development, interpretation of Hox expression patterns and their regulation in fish has spawned multiple hypotheses as to the origin and function of \93autopod\94 enhancers throughout evolution. Using phylogenetic footprinting, epigenetic profiling, and transgenic reporters, we have identified and functionally characterized hoxD and hoxA enhancers in the genomes of zebrafish and the spotted gar, Lepisosteus oculatus, a fish lacking the whole genome duplication of teleosts. Gar and zebrafish \93autopod\94 enhancers drive expression in the distal portion of developing zebrafish pectoral fins, and respond to the same functional cues as their murine orthologs. Moreover, gar enhancers drive reporter gene expression in both the wrist and digits of mouse embryos in patterns that are nearly indistinguishable from their murine counterparts. These functional genomic data support the hypothesis that the distal radials of bony fish are homologous to the wrist and/or digits of tetrapods. MicroRNAs Influence Reproductive Responses by Females to Male Sex Peptide in Drosophila melanogaster Claudia Fricke*,\86, Darrell Green*,\87, Damian Smith*, Tamas Dalmay* and Tracey Chapman*,1 Early Online September 22, 2014, doi: 10.1534/genetics.114.167320 Genetics December 1, 2014 vol. 198 no. 4 1603-1619 Across taxa, female behavior and physiology change significantly following the receipt of ejaculate molecules during mating. For example, receipt of sex peptide (SP) in female Drosophila melanogaster significantly alters female receptivity, egg production, lifespan, hormone levels, immunity, sleep, and feeding patterns. These changes are underpinned by distinct tissue- and time-specific changes in diverse sets of mRNAs. However, little is yet known about the regulation of these gene expression changes, and hence the potential role of microRNAs (miRNAs), in female postmating responses. A preliminary screen of genomic responses in females to receipt of SP suggested that there were changes in the expression of several miRNAs. Here we tested directly whether females lacking four of the candidate miRNAs highlighted (miR-279, miR-317, miR-278, and miR-184) showed altered fecundity, receptivity, and lifespan responses to receipt of SP, when mated once or continually to SP null or control males. The results showed that miRNA-lacking females mated to SP null males exhibited altered receptivity, but not reproductive output, in comparison to controls. However, these effects interacted significantly with the genetic background of the miRNA-lacking females. No significant survival effects were observed in miRNA-lacking females housed continually with SP null or control males. However, continual exposure to control males that transferred SP resulted in significantly higher variation in miRNA-lacking female lifespan than did continual exposure to SP null males. The results provide the first insight into the effects and importance of miRNAs in regulating postmating responses in females. involving microbes ...--------------------------------------------------------------------------------------------------------------------------- Escape from bacterial iron piracy through rapid evolution of transferrin Matthew F. Barber, Nels C. Elde* Science 12 December 2014: Vol. 346 no. 6215 pp. 1362-1366 DOI: 10.1126/science.1259329 Iron sequestration provides an innate defense, termed nutritional immunity, leading pathogens to scavenge iron from hosts. Although the molecular basis of this battle for iron is established, its potential as a force for evolution at host-pathogen interfaces is unknown. We show that the iron transport protein transferrin is engaged in ancient and ongoing evolutionary conflicts with TbpA, a transferrin surface receptor from bacteria. Single substitutions in transferrin at rapidly evolving sites reverse TbpA binding, providing a mechanism to counteract bacterial iron piracy among great apes. Furthermore, the C2 transferrin polymorphism in humans evades TbpA variants from Haemophilus influenzae, revealing a functional basis for standing genetic variation. These findings identify a central role for nutritional immunity in the persistent evolutionary conflicts between primates and bacterial pathogens. Evolutionary limits to cooperation in microbial communities Nuno M. Oliveira, Rene Niehus, and Kevin R. Foster1 PNAS vol. 111 no. 50, 17941-17946, December 16 doi: 10.1073/pnas.1412673111 Microbes produce many compounds that are costly to a focal cell but promote the survival and reproduction of neighboring cells. This observation has led to the suggestion that microbial strains and species will commonly cooperate by exchanging compounds. Here, we examine this idea with an ecoevolutionary model where microbes make multiple secretions, which can be exchanged among genotypes. We show that cooperation between genotypes only evolves under specific demographic regimes characterized by intermediate genetic mixing. The key constraint on cooperative exchanges is a loss of autonomy: strains become reliant on complementary genotypes that may not be reliably encountered. Moreover, the form of cooperation that we observe arises through mutual exploitation that is related to cheating and \93Black Queen\94 evolution for a single secretion. A major corollary is that the evolution of cooperative exchanges reduces community productivity relative to an autonomous strain that makes everything it needs. This prediction finds support in recent work from synthetic communities. Overall, our work suggests that natural selection will often limit cooperative exchanges in microbial communities and that, when exchanges do occur, they can be an inefficient solution to group living. PNAS vol. 111 no. 51, 18273-18278, December 23 doi: 10.1073/pnas.1411617111 Anaerobic methane oxidation coupled to denitrification is the dominant methane sink in a deep lake Joerg S. Deutzmanna,b, Peter Stiefc,d, Josephin Brandesa, and Bernhard Schinka,1 Anaerobic methane oxidation coupled to denitrification, also known as \93nitrate/nitrite-dependent anaerobic methane oxidation\94 (n-damo), was discovered in 2006. Since then, only a few studies have identified this process and the associated microorganisms in natural environments. In aquatic sediments, the close proximity of oxygen- and nitrate-consumption zones can mask n-damo as aerobic methane oxidation. We therefore investigated the vertical distribution and the abundance of denitrifying methanotrophs related to Candidatus Methylomirabilis oxyfera with cultivation-independent molecular techniques in the sediments of Lake Constance. Additionally, the vertical distribution of methane oxidation and nitrate consumption zones was inferred from high-resolution microsensor profiles in undisturbed sediment cores. M. oxyfera-like bacteria were virtually absent at shallow-water sites (littoral sediment) and were very abundant at deep-water sites (profundal sediment). In profundal sediment, the vertical distribution of M. oxyfera-like bacteria showed a distinct peak in anoxic layers that coincided with the zone of methane oxidation and nitrate consumption, a strong indication for n-damo carried out by M. oxyfera-like bacteria. Both potential n-damo rates calculated from cell densities (660-4,890 \B5mol CH4\B7m-2\B7d-1) and actual rates calculated from microsensor profiles (31-437 \B5mol CH4\B7m-2\B7d-1) were sufficiently high to prevent methane release from profundal sediment solely by this process. Additionally, when nitrate was added to sediment cores exposed to anoxic conditions, the n-damo zone reestablished well below the sediment surface, completely preventing methane release from the sediment. We conclude that the previously overlooked n-damo process can be the major methane sink in stable freshwater environments if nitrate is available in anoxic zones. Silencing urease: A key evolutionary step that facilitated the adaptation of Yersinia pestis to the flea-borne transmission route Iman Chouikha1 and B. Joseph Hinnebusch PNAS vol. 111 no. 52, 18709-18714, December 30 doi: 10.1073/pnas.1413209111 The arthropod-borne transmission route of Yersinia pestis, the bacterial agent of plague, is a recent evolutionary adaptation. Yersinia pseudotuberculosis, the closely related food-and water-borne enteric species from which Y. pestis diverged less than 6,400 y ago, exhibits significant oral toxicity to the flea vectors of plague, whereas Y. pestis does not. In this study, we identify the Yersinia urease enzyme as the responsible oral toxin. All Y. pestis strains, including those phylogenetically closest to the Y. pseudotuberculosis progenitor, contain a mutated ureD allele that eliminated urease activity. Restoration of a functional ureD was sufficient to make Y. pestis orally toxic to fleas. Conversely, deletion of the urease operon in Y. pseudotuberculosis rendered it nontoxic. Enzymatic activity was required for toxicity. Because urease-related mortality eliminates 30-40% of infective flea vectors, ureD mutation early in the evolution of Y. pestis was likely subject to strong positive selection because it significantly increased transmission potential. Wolbachia small noncoding RNAs and their role in cross-kingdom communications Jaime G. Mayorala, Mazhar Hussaina, D. Albert Joubertb, I\F1aki Iturbe-Ormaetxeb, Scott L. O\92Neillb, and Sassan Asgaria,1 PNAS vol. 111 no. 52, 18721-18726, December 30 doi: 10.1073/pnas.1420131112 In prokaryotes, small noncoding RNAs (snRNAs) of 50-500 nt are produced that are important in bacterial virulence and response to environmental stimuli. Here, we identified and characterized snRNAs from the endosymbiotic bacteria, Wolbachia, which are widespread in invertebrates and cause reproductive manipulations. Most importantly, some strains of Wolbachia inhibit replication of several vector-borne pathogens in insects. We demonstrate that two abundant snRNAs, WsnRNA-46 and WsnRNA-49, are expressed in Wolbachia from noncoding RNA transcripts that contain precursors with stem-loop structures. WsnRNAs were detected in Aedes aegypti mosquitoes infected with the wMelPop-CLA strain of Wolbachia and in Drosophila melanogaster and Drosophila simulans infected with wMelPop and wAu strains, respectively, indicating that the WsnRNAs are conserved across species and strains. In addition, we show that the WsnRNAs may potentially regulate host genes and Wolbachia genes. Our findings provide evidence for the production of functional snRNAs by Wolbachia that play roles in cross-kingdom communication between the endosymbiont and the host. Host Adaptation of a Bacterial Toxin from the Human Pathogen Salmonella Typhi Lingquan Deng8, Jeongmin Song89, Xiang Gao8, Jiawei Wang, Hai Yu, Xi Chen, Nissi Varki, Yuko Naito-Matsui, Jorge E. Gal\E1n, Ajit Varki Cell Volume 159, Issue 6, p1290-1299, 4 December 2014 DOI: http://dx.doi.org/10.1016/j.cell.2014.10.057 Salmonella Typhi is an exclusive human pathogen that causes typhoid fever. Typhoid toxin is a S. Typhi virulence factor that can reproduce most of the typhoid fever symptoms in experimental animals. Toxicity depends on toxin binding to terminally sialylated glycans on surface glycoproteins. Human glycans are unusual because of the lack of CMAH, which in other mammals converts N-acetylneuraminic acid (Neu5Ac) to N-glycolylneuraminic acid (Neu5Gc). Here, we report that typhoid toxin binds to and is toxic toward cells expressing glycans terminated in Neu5Ac (expressed by humans) over glycans terminated in Neu5Gc (expressed by other mammals). Mice constitutively expressing CMAH thus displaying Neu5Gc in all tissues are resistant to typhoid toxin. The atomic structure of typhoid toxin bound to Neu5Ac reveals the structural bases for its binding specificity. These findings provide insight into the molecular bases for Salmonella Typhi\92s host specificity and may help the development of therapies for typhoid fever. Genetics------------------------------------------------------------------------------------------------------------------------------------------- Dominance hierarchy arising from the evolution of a complex small RNA regulatory network Eleonore Durand1,*, Rapha\EBl Meheust1,*, Marion Soucaze1, Pauline M. Goubet1, Sophie Gallina1, Celine Poux1, Isabelle Fobis-Loisy2, Eline Guillon2, Thierry Gaude2, Alexis Sarazin3, Martin Figeac4, Elisa Prat5, William Marande5, Helene Berges5, Xavier Vekemans1, Sylvain Billiard1, Vincent Castric1 Science 5 December 2014: Vol. 346 no. 6214 pp. 1200-1205 DOI: 10.1126/science.1259442 The prevention of fertilization through self-pollination (or pollination by a close relative) in the Brassicaceae plant family is determined by the genotype of the plant at the self-incompatibility locus (S locus). The many alleles at this locus exhibit a dominance hierarchy that determines which of the two allelic specificities of a heterozygous genotype is expressed at the phenotypic level. Here, we uncover the evolution of how at least 17 small RNA (sRNA)-producing loci and their multiple target sites collectively control the dominance hierarchy among alleles within the gene controlling the pollen S-locus phenotype in a self-incompatible Arabidopsis species. Selection has created a dynamic repertoire of sRNA-target interactions by jointly acting on sRNA genes and their target sites, which has resulted in a complex system of regulation among alleles. Reducing the genetic code induces massive rearrangement of the proteome Patrick O\92Donoghuea,b, Laure Pratc, Martin Kucklickd, Johannes G. Sch\E4ferc, Katharina Riedele, Jesse Rinehartf,g, Dieter S\F6llc,h,1, and Ilka U. Heinemanna,1 PNAS vol. 111 no. 48, 17206-17211 December 2 doi: 10.1073/pnas.1420193111 Expanding the genetic code is an important aim of synthetic biology, but some organisms developed naturally expanded genetic codes long ago over the course of evolution. Less than 1% of all sequenced genomes encode an operon that reassigns the stop codon UAG to pyrrolysine (Pyl), a genetic code variant that results from the biosynthesis of Pyl-tRNAPyl. To understand the selective advantage of genetically encoding more than 20 amino acids, we constructed a markerless tRNAPyl deletion strain of Methanosarcina acetivorans (?pylT) that cannot decode UAG as Pyl or grow on trimethylamine. Phenotypic defects in the ?pylT strain were evident in minimal medium containing methanol. Proteomic analyses of wild type (WT) M. acetivorans and ?pylT cells identified 841 proteins from >7,000 significant peptides detected by MS/MS. Protein production from UAG-containing mRNAs was verified for 19 proteins. Translation of UAG codons was verified by MS/MS for eight proteins, including identification of a Pyl residue in PylB, which catalyzes the first step of Pyl biosynthesis. Deletion of tRNAPyl globally altered the proteome, leading to >300 differentially abundant proteins. Reduction of the genetic code from 21 to 20 amino acids led to significant down-regulation in translation initiation factors, amino acid metabolism, and methanogenesis from methanol, which was offset by a compensatory (100-fold) up-regulation in dimethyl sulfide metabolic enzymes. The data show how a natural proteome adapts to genetic code reduction and indicate that the selective value of an expanded genetic code is related to carbon source range and metabolic efficiency. Evolution in changing environments: Modifiers of mutation, recombination, and migration Oana Carjaa,1, Uri Libermanb, and Marcus W. Feldmana,1 PNAS vol. 111 no. 50, 17935-17940, December 16 doi: 10.1073/pnas.1417664111 The production and maintenance of genetic and phenotypic diversity under temporally fluctuating selection and the signatures of environmental changes in the patterns of this variation have been important areas of focus in population genetics. On one hand, periods of constant selection pull the genetic makeup of populations toward local fitness optima. On the other, to cope with changes in the selection regime, populations may evolve mechanisms that create a diversity of genotypes. By tuning the rates at which variability is produced\97such as the rates of recombination, mutation, or migration\97populations may increase their long-term adaptability. Here we use theoretical models to gain insight into how the rates of these three evolutionary forces are shaped by fluctuating selection. We compare and contrast the evolution of recombination, mutation, and migration under similar patterns of environmental change and show that these three sources of phenotypic variation are surprisingly similar in their response to changing selection. We show that the shape, size, variance, and asymmetry of environmental fluctuation have different but predictable effects on evolutionary dynamics. A Novel Targeted Learning Method for Quantitative Trait Loci Mapping Hui Wang*,1,2, Zhongyang Zhang\86,1, Sherri Rose\87 and Mark van der Laan\A7 Early Online September 24, 2014, doi: 10.1534/genetics.114.168955 December 1, 2014 Genetics vol. 198 no. 4 1369-1376 We present a novel semiparametric method for quantitative trait loci (QTL) mapping in experimental crosses. Conventional genetic mapping methods typically assume parametric models with Gaussian errors and obtain parameter estimates through maximum-likelihood estimation. In contrast with univariate regression and interval-mapping methods, our model requires fewer assumptions and also accommodates various machine-learning algorithms. Estimation is performed with targeted maximum-likelihood learning methods. We demonstrate our semiparametric targeted learning approach in a simulation study and a well-studied barley data set. Mapping eQTL Networks with Mixed Graphical Markov Models Inma Tur*,\86, Alberto Roverato\87 and Robert Castelo*,\86,1 Early Online September 29, 2014, doi: 10.1534/genetics.114.169573 Genetics December 1, 2014 vol. 198 no. 4 1377-1393 Expression quantitative trait loci (eQTL) mapping constitutes a challenging problem due to, among other reasons, the high-dimensional multivariate nature of gene-expression traits. Next to the expression heterogeneity produced by confounding factors and other sources of unwanted variation, indirect effects spread throughout genes as a result of genetic, molecular, and environmental perturbations. From a multivariate perspective one would like to adjust for the effect of all of these factors to end up with a network of direct associations connecting the path from genotype to phenotype. In this article we approach this challenge with mixed graphical Markov models, higher-order conditional independences, and q-order correlation graphs. These models show that additive genetic effects propagate through the network as function of gene-gene correlations. Our estimation of the eQTL network underlying a well-studied yeast data set leads to a sparse structure with more direct genetic and regulatory associations that enable a straightforward comparison of the genetic control of gene expression across chromosomes. Interestingly, it also reveals that eQTLs explain most of the expression variability of network hub genes. A New Simple Method for Improving QTL Mapping Under Selective Genotyping Hsin-I Lee*, Hsiang-An Ho* and Chen-Hung Kao*,\86,1 Early Online September 22, 2014, doi: 10.1534/genetics.114.168385 Genetics December 1, 2014 vol. 198 no. 4 1685-1698 The selective genotyping approach, where only individuals from the high and low extremes of the trait distribution are selected for genotyping and the remaining individuals are not genotyped, has been known as a cost-saving strategy to reduce genotyping work and can still maintain nearly equivalent efficiency to complete genotyping in QTL mapping. We propose a novel and simple statistical method based on the normal mixture model for selective genotyping when both genotyped and ungenotyped individuals are fitted in the model for QTL analysis. Compared to the existing methods, the main feature of our model is that we first provide a simple way for obtaining the distribution of QTL genotypes for the ungenotyped individuals and then use it, rather than the population distribution of QTL genotypes as in the existing methods, to fit the ungenotyped individuals in model construction. Another feature is that the proposed method is developed on the basis of a multiple-QTL model and has a simple estimation procedure similar to that for complete genotyping. As a result, the proposed method has the ability to provide better QTL resolution, analyze QTL epistasis, and tackle multiple QTL problem under selective genotyping. In addition, a truncated normal mixture model based on a multiple-QTL model is developed when only the genotyped individuals are considered in the analysis, so that the two different types of models can be compared and investigated in selective genotyping. The issue in determining threshold values for selective genotyping in QTL mapping is also discussed. Simulation studies are performed to evaluate the proposed methods, compare the different models, and study the QTL mapping properties in selective genotyping. The results show that the proposed method can provide greater QTL detection power and facilitate QTL mapping for selective genotyping. Also, selective genotyping using larger genotyping proportions may provide roughly equivalent power to complete genotyping and that using smaller genotyping proportions has difficulties doing so. The R code of our proposed method is available on http://www.stat.sinica.edu.tw/chkao/. Purifying Selection, Drift, and Reversible Mutation with Arbitrarily High Mutation Rates Brian Charlesworth*,1 and Kavita Jain\86 Early Online September 16, 2014, doi: 10.1534/genetics.114.167973 Genetics December 1, 2014 vol. 198 no. 4 1587-1602 Some species exhibit very high levels of DNA sequence variability; there is also evidence for the existence of heritable epigenetic variants that experience state changes at a much higher rate than sequence variants. In both cases, the resulting high diversity levels within a population (hyperdiversity) mean that standard population genetics methods are not trustworthy. We analyze a population genetics model that incorporates purifying selection, reversible mutations, and genetic drift, assuming a stationary population size. We derive analytical results for both population parameters and sample statistics and discuss their implications for studies of natural genetic and epigenetic variation. In particular, we find that (1) many more intermediate-frequency variants are expected than under standard models, even with moderately strong purifying selection, and (2) rates of evolution under purifying selection may be close to, or even exceed, neutral rates. These findings are related to empirical studies of sequence and epigenetic variation. A Multivariate Analysis of Genetic Constraints to Life History Evolution in a Wild Population of Red Deer Craig A. Walling*,1, Michael B. Morrissey\86, Katharina Foerster\87, Tim H. Clutton-Brock\A7, Josephine M. Pemberton* and Loeske E. B. Kruuk*,* Early Online October 2, 2014, doi: 10.1534/genetics.114.164319 Genetics December 1, 2014 vol. 198 no. 4 1735-1749 Evolutionary theory predicts that genetic constraints should be widespread, but empirical support for their existence is surprisingly rare. Commonly applied univariate and bivariate approaches to detecting genetic constraints can underestimate their prevalence, with important aspects potentially tractable only within a multivariate framework. However, multivariate genetic analyses of data from natural populations are challenging because of modest sample sizes, incomplete pedigrees, and missing data. Here we present results from a study of a comprehensive set of life history traits (juvenile survival, age at first breeding, annual fecundity, and longevity) for both males and females in a wild, pedigreed, population of red deer (Cervus elaphus). We use factor analytic modeling of the genetic variance-covariance matrix (G) to reduce the dimensionality of the problem and take a multivariate approach to estimating genetic constraints. We consider a range of metrics designed to assess the effect of G on the deflection of a predicted response to selection away from the direction of fastest adaptation and on the evolvability of the traits. We found limited support for genetic constraint through genetic covariances between traits, both within sex and between sexes. We discuss these results with respect to other recent findings and to the problems of estimating these parameters for natural populations. Colonization Zaprionus Population genetics and recent colonization history of the invasive drosophilid Zaprionus indianus in Mexico and Central America Therese Ann Markow, Giovanni Hanna, Juan R. Riesgo-Escovar, Aldo A. Tellez-Garcia, Maxi Polihronakis Richmond, Nestor O. Nazario-Yepiz, Mariana Ram\EDrez Loustalot Laclette, Javier Carpinteyro-Ponce, Edward Pfeiler, Biological Invasions 11/2014; 16(11). November 2014 DOI: 10.1007/s10530-014-0674-5 Zaprionus indianus, also known as the African fig fly, is an invasive pest of a variety of commercial and native fruit. The species was first reported in Brazil in 1999, but has established itself in much of the New World within the last 10-15 years. We used nucleotide sequences from a segment of the mitochondrial cytochrome c oxidase subunit I (COI) gene to examine haplotype relationships, population structure, and infer the colonization history of Z. indianus in Mexico and Panama. Construction of a haplotype network showed that six COI haplotypes, obtained from flies collected at six localities in Mexico and one in Panama, clustered into three distinct clades. Clade composition was generally consistent in flies from Panama to northwestern Mexico, and analysis of molecular variance indicated no significant structure among populations. Three of the six haplotypes from Mexico and Panama were identical to previously reported haplotypes from Brazil. None of the six haplotypes, however, were shared with previously reported haplotypes from potential source populations in the Old World. The results of our genetic analysis suggest that the invasion of Z. indianus into Central America and Mexico most probably includes a northward migration of individuals from Brazil, with the possibility of at least one additional introduction of Z. indianus to the New World. Additional sequence data from potential source populations in the Old World will be required to confidently determine the number of introductions of Z. indianus into the New World, and to identify the geographic source. Species-wide Genetic Incompatibility Analysis Identifies Immune Genes as Hot Spots of Deleterious Epistasis Eunyoung Chae, Kirsten Bomblies3, Sang-Tae Kim4, Darya Karelina, Maricris Zaidem, Stephan Ossowski5, Carmen Mart\EDn-Pizarro, Roosa A.E. Laitinen6, Beth A. Rowan, Hezi Tenenboim6, Sarah Lechner7, Monika Demar, Anette Habring-M\FCller, Christa Lanz, Gunnar R\E4tsch8, Detlef Weigel Cell Volume 159, Issue 6, p1341-1351, 4 December 2014 DOI: http://dx.doi.org/10.1016/j.cell.2014.10.049 Intraspecific genetic incompatibilities prevent the assembly of specific alleles into single genotypes and influence genome- and species-wide patterns of sequence variation. A common incompatibility in plants is hybrid necrosis, characterized by autoimmune responses due to epistatic interactions between natural genetic variants. By systematically testing thousands of F1 hybrids of Arabidopsis thaliana strains, we identified a small number of incompatibility hot spots in the genome, often in regions densely populated by nucleotide-binding domain and leucine-rich repeat (NLR) immune receptor genes. In several cases, these immune receptor loci interact with each other, suggestive of conflict within the immune system. A particularly dangerous locus is a highly variable cluster of NLR genes, DM2, which causes multiple independent incompatibilities with genes that encode a range of biochemical functions, including NLRs. Our findings suggest that deleterious interactions of immune receptors limit the combinations of favorable disease resistance alleles accessible to plant genomes. Neuroscience---------------------------------------------------------------------------------------------------------------------------------------- Millisecond-Scale Motor Encoding in a Cortical Vocal Area Claire Tang, Diala Chehayeb, Kyle Srivastava, Ilya Nemenman, Samuel J. Sober PLoS Biology December 09, 2014 DOI: 10.1371/journal.pbio.1002018 Studies of motor control have almost universally examined firing rates to investigate how the brain shapes behavior. In principle, however, neurons could encode information through the precise temporal patterning of their spike trains as well as (or instead of) through their firing rates. Although the importance of spike timing has been demonstrated in sensory systems, it is largely unknown whether timing differences in motor areas could affect behavior. We tested the hypothesis that significant information about trial-by-trial variations in behavior is represented by spike timing in the songbird vocal motor system. We found that neurons in motor cortex convey information via spike timing far more often than via spike rate and that the amount of information conveyed at the millisecond timescale greatly exceeds the information available from spike counts. These results demonstrate that information can be represented by spike timing in motor circuits and suggest that timing variations evoke differences in behavior. Epigenetic Control of Learning and Memory in Drosophila by Tip60 HAT Action Songjun Xu, Rona Wilf, Trisha Menon, Priyalakshmi Panikker, Jessica Sarthi and Felice Elefant1 Early Online October 17, 2014, doi: 10.1534/genetics.114.171660 Genetics December 1, 2014 vol. 198 no. 4 1571-1586 Disruption of epigenetic gene control mechanisms in the brain causes significant cognitive impairment that is a debilitating hallmark of most neurodegenerative disorders, including Alzheimer\92s disease (AD). Histone acetylation is one of the best characterized of these epigenetic mechanisms that is critical for regulating learning- and memory- associated gene expression profiles, yet the specific histone acetyltransferases (HATs) that mediate these effects have yet to be fully characterized. Here, we investigate an epigenetic role for the HAT Tip60 in learning and memory formation using the Drosophila CNS mushroom body (MB) as a well-characterized cognition model. We show that Tip60 is endogenously expressed in the Kenyon cells, the intrinsic neurons of the MB, and in the MB axonal lobes. Targeted loss of Tip60 HAT activity in the MB causes thinner and shorter axonal lobes while increasing Tip60 HAT levels cause no morphological defects. Functional consequences of both loss and gain of Tip60 HAT levels in the MB are evidenced by defects in immediate-recall memory. Our ChIP-Seq analysis reveals that Tip60 target genes are enriched for functions in cognitive processes, and, accordingly, key genes representing these pathways are misregulated in the Tip60 HAT mutant fly brain. Remarkably, we find that both learning and immediate-recall memory deficits that occur under AD-associated, amyloid precursor protein (APP)-induced neurodegenerative conditions can be effectively rescued by increasing Tip60 HAT levels specifically in the MB. Together, our findings uncover an epigenetic transcriptional regulatory role for Tip60 in cognitive function and highlight the potential of HAT activators as a therapeutic option for neurodegenerative disorders. Asymmetric speech processing in dog brain Orienting Asymmetries in Dogs\92 Responses to Different Communicatory Components of Human Speech Victoria F. Ratcliffe, David Reby Current Biology Volume 24, Issue 24, p2908-2912, 15 December 2014 DOI: http://dx.doi.org/10.1016/j.cub.2014.10.030 It is well established that in human speech perception the left hemisphere (LH) of the brain is specialized for processing intelligible phonemic (segmental) content (e.g., [ 1-3 ]), whereas the right hemisphere (RH) is more sensitive to prosodic (suprasegmental) cues [ 4, 5 ]. Despite evidence that a range of mammal species show LH specialization when processing conspecific vocalizations [ 6 ], the presence of hemispheric biases in domesticated animals\92 responses to the communicative components of human speech has never been investigated. Human speech is familiar and relevant to domestic dogs (Canis familiaris), who are known to perceive both segmental phonemic cues [ 7-10 ] and suprasegmental speaker-related [ 11, 12 ] and emotional [ 13 ] prosodic cues. Using the head-orienting paradigm, we presented dogs with manipulated speech and tones differing in segmental or suprasegmental content and recorded their orienting responses. We found that dogs showed a significant LH bias when presented with a familiar spoken command in which the salience of meaningful phonemic (segmental) cues was artificially increased but a significant RH bias in response to commands in which the salience of intonational or speaker-related (suprasegmental) vocal cues was increased. Our results provide insights into mechanisms of interspecific vocal perception in a domesticated mammal and suggest that dogs may share ancestral or convergent hemispheric specializations for processing the different functional communicative components of speech with human listeners. Asymmetric Processing of Visual Motion for Simultaneous Object and Background Responses Lisa M. Fenk2, Andreas Poehlmann2, Andrew D. Straw Current Biology Volume 24, Issue 24, p2913-2919, 15 December 2014 DOI: http://dx.doi.org/10.1016/j.cub.2014.10.042 Visual object fixation and figure-ground discrimination in Drosophila are robust behaviors requiring sophisticated computation by the visual system, yet the neural substrates remain unknown. Recent experiments in walking flies revealed object fixation behavior mediated by circuitry independent from the motion-sensitive T4-T5 cells required for wide-field motion responses [ 1 ]. In tethered flight experiments under closed-loop conditions, we found similar results for one feedback gain, whereas intact T4-T5 cells were necessary for robust object fixation at a higher feedback gain and in figure-ground discrimination tasks. We implemented dynamical models (available at http://strawlab.org/asymmetric-motion/) based on neurons downstream of T4-T5 cells\97one a simple phenomenological model and another, physiologically more realistic model\97and found that both predict key features of stripe fixation and figure-ground discrimination and are consistent with a classical formulation [ 2 ]. Fundamental to both models is motion asymmetry in the responses of model neurons, whereby front-to-back motion elicits stronger responses than back-to-front motion. When a bilateral pair of such model neurons, based on well-understood horizontal system cells [ 3, 4 ], downstream of T4-T5 [ 5 ], is coupled to turning behavior, asymmetry leads to object fixation and figure-ground discrimination in the presence of noise. Furthermore, the models also predict fixation in front of a moving background, a behavior previously suggested to require an additional pathway [ 1 ]. Thus, the models predict several aspects of object responses on the basis of neurons that are also thought to serve a key role in background stabilization [ 6-12 ]. harmful stimuli response Drosophila larvae Balboa Binds to Pickpocket In Vivo and Is Required for Mechanical Nociception in Drosophila Larvae Stephanie E. Mauthner, Richard Y. Hwang, Amanda H. Lewis, Qi Xiao, Asako Tsubouchi4, Yu Wang, Ken Honjo5, J.H. Pate Skene, J\F6rg Grandl, W. Daniel Tracey Jr. Current Biology Volume 24, Issue 24, p2920-2925, 15 December 2014 DOI: http://dx.doi.org/10.1016/j.cub.2014.10.038 The Drosophila gene pickpocket (ppk) encodes an ion channel subunit of the degenerin/epithelial sodium channel (DEG/ENaC) family [ 1 ]. PPK is specifically expressed in nociceptive, class IV multidendritic (md) neurons and is functionally required for mechanical nociception responses [ 2, 3 ]. In this study, in a genome-wide genetic screen for other ion channel subunits required for mechanical nociception, we identify a gene that we name balboa (also known as CG8546, ppk26) [ 4 ]. Interestingly, the balboa locus encodes a DEG/ENaC ion channel subunit highly similar in amino acid sequence to PPK [ 5 ]. Moreover, laser-capture isolation of RNA from larval neurons and microarray analyses reveal that balboa is also highly enriched in nociceptive neurons. The requirement for Balboa and PPK in mechanical nociception behaviors and their specific expression in larval nociceptors led us to hypothesize that these DEG/ENaC subunits form an ion channel complex in vivo. In nociceptive neurons, Balboa::GFP proteins distribute uniformly throughout dendrites but remarkably localize to discrete foci when ectopically expressed in other neuron subtypes (where PPK is not expressed). Indeed, ectopically coexpressing ppk transforms this punctate Balboa::GFP expression pattern to the uniform distribution observed in its native cell type. Furthermore, ppk-RNAi in class IV neurons alters the broad Balboa::GFP pattern to a punctate distribution. Interestingly, this interaction is mutually codependent as balboa-RNAi eliminates Venus::PPK from the sensory dendrites of nociceptors. Finally, using a GFP-reconstitution approach in transgenic larvae, we directly detect in vivo physical interactions among PPK and Balboa subunits. Combined, our results indicate a critical mechanical nociception function for heteromeric PPK and Balboa channels in vivo Mechanosensory interactions drive collective behaviour in Drosophila Pavan Ramdya, Pawel Lichocki, Steeve Cruchet, Lukas Frisch, Winnie Tse, Dario Floreano & Richard Benton Nature (2014) doi:10.1038/nature14024 Published online 24 December 2014 Collective behaviour enhances environmental sensing and decision-making in groups of animals1, 2. Experimental and theoretical investigations of schooling fish, flocking birds and human crowds have demonstrated that simple interactions between individuals can explain emergent group dynamics3, 4. These findings indicate the existence of neural circuits that support distributed behaviours, but the molecular and cellular identities of relevant sensory pathways are unknown. Here we show that Drosophila melanogaster exhibits collective responses to an aversive odour: individual flies weakly avoid the stimulus, but groups show enhanced escape reactions. Using high-resolution behavioural tracking, computational simulations, genetic perturbations, neural silencing and optogenetic activation we demonstrate that this collective odour avoidance arises from cascades of appendage touch interactions between pairs of flies. Inter-fly touch sensing and collective behaviour require the activity of distal leg mechanosensory sensilla neurons and the mechanosensory channel NOMPC5, 6. Remarkably, through these inter-fly encounters, wild-type flies can elicit avoidance behaviour in mutant animals that cannot sense the odour\97a basic form of communication. Our data highlight the unexpected importance of social context in the sensory responses of a solitary species and open the door to a neural-circuit-level understanding of collective behaviour in animal groups. Sensory determinants of behavioral dynamics in Drosophila thermotaxis Mason Kleina, Bruno Afonsoa,b,1, Ashley J. Vonnera,1, Luis Hernandez-Nuneza,1, Matthew Bercka, Christopher J. Tabonea, Elizabeth A. Kanea, Vincent A. Pieribonec,d, Michael N. Nitabachc,e,f, Albert Cardonab, Marta Zlaticb,2, Simon G. Sprecherb,g,2, Marc Gershowa,2, Paul A. Garrityh,2, and Aravinthan D. T. Samuela,b,2,3 PNAS December 30 Complex animal behaviors are built from dynamical relationships between sensory inputs, neuronal activity, and motor outputs in patterns with strategic value. Connecting these patterns illuminates how nervous systems compute behavior. Here, we study Drosophila larva navigation up temperature gradients toward preferred temperatures (positive thermotaxis). By tracking the movements of animals responding to fixed spatial temperature gradients or random temperature fluctuations, we calculate the sensitivity and dynamics of the conversion of thermosensory inputs into motor responses. We discover three thermosensory neurons in each dorsal organ ganglion (DOG) that are required for positive thermotaxis. Random optogenetic stimulation of the DOG thermosensory neurons evokes behavioral patterns that mimic the response to temperature variations. In vivo calcium and voltage imaging reveals that the DOG thermosensory neurons exhibit activity patterns with sensitivity and dynamics matched to the behavioral response. Temporal processing of temperature variations carried out by the DOG thermosensory neurons emerges in distinct motor responses during thermotaxis. Neural Control of Wing Coordination in Flies Sufia Sadaf, O. Venkateswara Reddy, Sanjay P. Sane, Gaiti Hasan Current Biology December 11 DOI: http://dx.doi.org/10.1016/j.cub.2014.10.069 At the onset of each flight bout in flies, neural circuits in the CNS must rapidly integrate multimodal sensory stimuli and synchronously engage hinges of the left and right wings for coordinated wing movements. Whereas anatomical and physiological investigations of flight have been conducted on larger flies [ 1 ], molecular genetic studies in Drosophila have helped identify neurons that mediate various levels of flight control [ 2-7 ]. However, neurons that might mediate bilateral coordination of wing movements to precisely synchronize left and right wing engagement at flight onset and maintain their movement in perfect coordination at rapid frequencies during flight maneuvers remain largely unexplored. Wing coordination could be directly modulated via bilateral sensory inputs to motoneurons of steering muscles [ 6, 8 ] and/or through central interneurons. Using a Ca2+-activity-based GFP reporter, we identified three flight-activated central dopaminergic interneurons in the ventral ganglion, which connect to and activate motoneurons that innervate a pair of direct-steering flight muscles. The activation of these newly identified dopaminergic interneurons is context specific. Whereas bilateral wing engagement for flight requires these neurons, they do not control unilateral wing extension during courtship. Thus, independent central circuits function in the context of different natural behaviors to control the motor circuit for Drosophila wing movement. Egg-Laying Demand Induces Aversion of UV Light in Drosophila Females Edward Y. Zhu, Ananya R. Guntur, Ruo He, Ulrich Stern, Chung-Hui Yang Current Biology Volume 24, Issue 23, p2797-2804, 1 December 2014 DOI: http://dx.doi.org/10.1016/j.cub.2014.09.076 Drosophila melanogaster females are highly selective about the chemosensory quality of their egg-laying sites [ 1-6 ], an important trait that promotes the survival and fitness of their offspring. How egg-laying females respond to UV light is not known, however. UV is a well-documented phototactic cue for adult Drosophila [ 7-13 ], but it is an aversive cue for larvae [ 14-17 ]. Here, we show that female flies exhibit UV aversion in response to their egg-laying demand. First, females exhibit egg-laying aversion of UV: they prefer to lay eggs on dark sites when choosing between UV-illuminated and dark sites. Second, they also exhibit movement aversion of UV: positional tracking of single females suggests that egg-laying demand increases their tendency to turn away from UV. Genetic manipulations of the retina suggest that egg-laying and movement aversion of UV are both mediated by the inner (R7) and not the outer (R1-R6) photoreceptors. Finally, we show that the Dm8 amacrine neurons, a synaptic target of R7 photoreceptors and a mediator of UV spectral preference [ 12 ], are dispensable for egg-laying aversion but essential for movement aversion of UV. This study suggests that egg-laying demand can temporarily convert UV into an aversive cue for female Drosophila and that R7 photoreceptors recruit different downstream targets to control different egg-laying-induced behavioral modifications. Protein Evolution-------------------------------------------------------------------------------------------------------------------------------- Evolution of oligomeric state through allosteric pathways that mimic ligand binding Tina Perica1,2,*, Yasushi Kondo2, Sandhya P. Tiwari3,4, Stephen H. McLaughlin2, Katherine R. Kemplen5, Xiuwei Zhang1, Annette Steward5, Nathalie Reuter3,4, Jane Clarke5, Sarah A. Teichmann1,\86 Science 19 December 2014: Vol. 346 no. 6216 DOI: 10.1126/science.1254346 Evolution and design of protein complexes are almost always viewed through the lens of amino acid mutations at protein interfaces. We showed previously that residues not involved in the physical interaction between proteins make important contributions to oligomerization by acting indirectly or allosterically. In this work, we sought to investigate the mechanism by which allosteric mutations act, using the example of the PyrR family of pyrimidine operon attenuators. In this family, a perfectly sequence-conserved helix that forms a tetrameric interface is exposed as solvent-accessible surface in dimeric orthologs. This means that mutations must be acting from a distance to destabilize the interface. We identified 11 key mutations controlling oligomeric state, all distant from the interfaces and outside ligand-binding pockets. Finally, we show that the key mutations introduce conformational changes equivalent to the conformational shift between the free versus nucleotide-bound conformations of the proteins. vision----------------------------------------------------------------------------------------------------------------------------------------- Cockroach optomotor responses below single photon level Anna Honkanen1,2, Jouni Takalo1, Kyösti Heimonen1, Mikko Vähäsöyrinki1 and Matti Weckström1,* doi: 10.1242/​jeb.112425 December 1, 2014 J Exp Biol 217, 4262-4268. Reliable vision in dim light depends on the efficient capture of photons. Moreover, visually guided behaviour requires reliable signals from the photoreceptors to generate appropriate motor reactions. Here, we show that at behavioural low-light threshold, cockroach photoreceptors respond to moving gratings with single-photon absorption events known as ‘quantum bumps’ at or below the rate of 0.1 s−1. By performing behavioural experiments and intracellular recordings from photoreceptors under identical stimulus conditions, we demonstrate that continuous modulation of the photoreceptor membrane potential is not necessary to elicit visually guided behaviour. The results indicate that in cockroach motion detection, massive temporal and spatial pooling takes place throughout the eye under dim conditions, involving currently unknown neural processing algorithms. The extremely high night-vision capability of the cockroach visual system provides a roadmap for bio-mimetic imaging design. Rhodopsin optogenetics Synthetic ?retinal analogues modify the spectral and kinetic characteristics of microbial rhodopsin optogenetic tools N. AzimiHashemi, K. Erbguth, A. Vogt, T. Riemensperger, E. Rauch, D. Woodmansee, J. Nagpal, M. Brauner, M. Sheves, A. Fiala, L. Kattner, D. Trauner, P. Hegemann, A. Gottschalk & J. F. Liewald Nature Communications 5, Article number: 5810 doi:10.1038/ncomms6810 Published 15 December 2014 Optogenetic tools have become indispensable in neuroscience to stimulate or inhibit excitable cells by light. ?Channelrhodopsin-2 (?ChR2) variants have been established by mutating the opsin backbone or by mining related algal genomes. As an alternative strategy, we surveyed synthetic ?retinal analogues combined with microbial rhodopsins for functional and spectral properties, capitalizing on assays in C. elegans, HEK cells and larval Drosophila. Compared with ?all-trans retinal (?ATR), ?Dimethylamino-retinal (?DMAR) shifts the action spectra maxima of ?ChR2 variants H134R and H134R/T159C from 480 to 520?nm. Moreover, ?DMAR decelerates the photocycle of ?ChR2(H134R) and (H134R/T159C), thereby reducing the light intensity required for persistent channel activation. In hyperpolarizing ?archaerhodopsin-3 and ?Mac, ?naphthyl-retinal and thiophene-retinal support activity alike ?ATR, yet at altered peak wavelengths. Our experiments enable applications of ?retinal analogues in colour tuning and altering photocycle characteristics of optogenetic tools, thereby increasing the operational light sensitivity of existing cell lines or transgenic animals. Ancestral duplications and highly dynamic opsin gene evolution in percomorph fishes Fabio Cortesia,b,c,1,2, Zuzana Musilov\E1a,1,2, Sara M. Stieba,c, Nathan S. Hartd,e, Ulrike E. Siebeckf, Martin Malmstr\F8mg, Ole K. T\F8rreseng, Sissel Jentoftg, Karen L. Cheneyb, N. Justin Marshallc, Karen L. Carletonh, and Walter Salzburgera,g PNAS December 29 doi: 10.1073/pnas.1417803112 Single-gene and whole-genome duplications are important evolutionary mechanisms that contribute to biological diversification by launching new genetic raw material. For example, the evolution of animal vision is tightly linked to the expansion of the opsin gene family encoding light-absorbing visual pigments. In teleost fishes, the most species-rich vertebrate group, opsins are particularly diverse and key to the successful colonization of habitats ranging from the bioluminescence-biased but basically dark deep sea to clear mountain streams. In this study, we report a previously unnoticed duplication of the violet-blue short wavelength-sensitive 2 (SWS2) opsin, which coincides with the radiation of highly diverse percomorph fishes, permitting us to reinterpret the evolution of this gene family. The inspection of close to 100 fish genomes revealed that, triggered by frequent gene conversion between duplicates, the evolutionary history of SWS2 is rather complex and difficult to predict. Coincidentally, we also report potential cases of gene resurrection in vertebrate opsins, whereby pseudogenized genes were found to convert with their functional paralogs. We then identify multiple novel amino acid substitutions that are likely to have contributed to the adaptive differentiation between SWS2 copies. Finally, using the dusky dottyback Pseudochromis fuscus, we show that the newly discovered SWS2A duplicates can contribute to visual adaptation in two ways: by gaining sensitivities to different wavelengths of light and by being differentially expressed between ontogenetic stages. Thus, our study highlights the importance of comparative approaches in gaining a comprehensive view of the dynamics underlying gene family evolution and ultimately, animal diversification. , doi: 10.1073/pnas.1416212112 CRISPR------------------------------------------------------------------------------------------------------------------------------------------- Programmable RNA recognition and cleavage by CRISPR/Cas9 Mitchell R. O’Connell, Benjamin L. Oakes, Samuel H. Sternberg, Alexandra East-Seletsky, Matias Kaplan & Jennifer A. Doudna Nature 516, 263–266 (11 December 2014) doi:10.1038/nature13769 Published online 28 September 2014 The CRISPR-associated protein Cas9 is an RNA-guided DNA endonuclease that uses RNA–DNA complementarity to identify target sites for sequence-specific double-stranded DNA (dsDNA) cleavage1, 2, 3, 4, 5. In its native context, Cas9 acts on DNA substrates exclusively because both binding and catalysis require recognition of a short DNA sequence, known as the protospacer adjacent motif (PAM), next to and on the strand opposite the twenty-nucleotide target site in dsDNA4, 5, 6, 7. Cas9 has proven to be a versatile tool for genome engineering and gene regulation in a large range of prokaryotic and eukaryotic cell types, and in whole organisms8, but it has been thought to be incapable of targeting RNA5. Here we show that Cas9 binds with high affinity to single-stranded RNA (ssRNA) targets matching the Cas9-associated guide RNA sequence when the PAM is presented in trans as a separate DNA oligonucleotide. Furthermore, PAM-presenting oligonucleotides (PAMmers) stimulate site-specific endonucleolytic cleavage of ssRNA targets, similar to PAM-mediated stimulation of Cas9-catalysed DNA cleavage7. Using specially designed PAMmers, Cas9 can be specifically directed to bind or cut RNA targets while avoiding corresponding DNA sequences, and we demonstrate that this strategy enables the isolation of a specific endogenous messenger RNA from cells. These results reveal a fundamental connection between PAM binding and substrate selection by Cas9, and highlight the utility of Cas9 for programmable transcript recognition without the need for tags. In vivo engineering of oncogenic chromosomal rearrangements with the CRISPR/Cas9 system Danilo Maddalo, Eusebio Manchado, Carla P. Concepcion, Ciro Bonetti, Joana A. Vidigal, Yoon-Chi Han, Paul Ogrodowski, Alessandra Crippa, Natasha Rekhtman, Elisa de Stanchina, Scott W. Lowe & Andrea Ventura Nature 516, 423-427 (18 December 2014) doi:10.1038/nature13902 Published online, 22 October 2014 Chromosomal rearrangements have a central role in the pathogenesis of human cancers and often result in the expression of therapeutically actionable gene fusions1. A recently discovered example is a fusion between the genes echinoderm microtubule-associated protein like 4 (EML4) and anaplastic lymphoma kinase (ALK), generated by an inversion on the short arm of chromosome 2: inv(2)(p21p23). The EML4-ALK oncogene is detected in a subset of human non-small cell lung cancers (NSCLC)2 and is clinically relevant because it confers sensitivity to ALK inhibitors3. Despite their importance, modelling such genetic events in mice has proven challenging and requires complex manipulation of the germ line. Here we describe an efficient method to induce specific chromosomal rearrangements in vivo using viral-mediated delivery of the CRISPR/Cas9 system to somatic cells of adult animals. We apply it to generate a mouse model of Eml4-Alk-driven lung cancer. The resulting tumours invariably harbour the Eml4-Alk inversion, express the Eml4-Alk fusion gene, display histopathological and molecular features typical of ALK+ human NSCLCs, and respond to treatment with ALK inhibitors. The general strategy described here substantially expands our ability to model human cancers in mice and potentially in other organisms. Human - ape evolution ------------------------------------------------------------------------------------------------------------------------------- The African Genome Variation Project shapes medical genetics in Africa Deepti Gurdasani, Tommy Carstensen, Fasil Tekola-Ayele, Luca Pagani, Ioanna Tachmazidou, Konstantinos Hatzikotoulas, Savita Karthikeyan, Louise Iles, Martin O. Pollard, Ananyo Choudhury, Graham R. S. Ritchie, Yali Xue, Jennifer Asimit, Rebecca N. Nsubuga, Elizabeth H. Young, Cristina Pomilla, Katja Kivinen, Kirk Rockett, Anatoli Kamali, Ayo P. Doumatey, Gershim Asiki, Janet Seeley, Fatoumatta Sisay-Joof, Muminatou Jallow, Stephen Tollman et al. Nature (2014), 03 December 2014 doi:10.1038/nature13997 Given the importance of Africa to studies of human origins and disease susceptibility, detailed characterization of African genetic diversity is needed. The African Genome Variation Project provides a resource with which to design, implement and interpret genomic studies in sub-Saharan Africa and worldwide. The African Genome Variation Project represents dense genotypes from 1,481 individuals and whole-genome sequences from 320 individuals across sub-Saharan Africa. Using this resource, we find novel evidence of complex, regionally distinct hunter-gatherer and Eurasian admixture across sub-Saharan Africa. We identify new loci under selection, including loci related to malaria susceptibility and hypertension. We show that modern imputation panels (sets of reference genotypes from which unobserved or missing genotypes in study sets can be inferred) can identify association signals at highly differentiated loci across populations in sub-Saharan Africa. Using whole-genome sequencing, we demonstrate further improvements in imputation accuracy, strengthening the case for large-scale sequencing efforts of diverse African haplotypes. Finally, we present an efficient genotype array design capturing common genetic variation in Africa. Homo erectus at Trinil on Java used shells for tool production and engraving Josephine C. A. Joordens, Francesco d’Errico, Frank P. Wesselingh, Stephen Munro, John de Vos, Jakob Wallinga, Christina Ankjærgaard, Tony Reimann, Jan R. Wijbrans, Klaudia F. Kuiper, Herman J. Mücher, Hélène Coqueugniot, Vincent Prié, Ineke Joosten, Bertil van Os, Anne S. Schulp, Michel Panuel, Victoria van der Haas, Wim Lustenhouwer, John J. G. Reijmer & Wil Roebroeks Nature (2014), 03 December 2014 doi:10.1038/nature13962 The manufacture of geometric engravings is generally interpreted as indicative of modern cognition and behaviour1. Key questions in the debate on the origin of such behaviour are whether this innovation is restricted to Homo sapiens, and whether it has a uniquely African origin1. Here we report on a fossil freshwater shell assemblage from the Hauptknochenschicht (‘main bone layer’) of Trinil (Java, Indonesia), the type locality of Homo erectus discovered by Eugène Dubois in 1891 (refs 2 and 3). In the Dubois collection (in the Naturalis museum, Leiden, The Netherlands) we found evidence for freshwater shellfish consumption by hominins, one unambiguous shell tool, and a shell with a geometric engraving. We dated sediment contained in the shells with 40Ar/39Ar and luminescence dating methods, obtaining a maximum age of 0.54 ± 0.10 million years and a minimum age of 0.43 ± 0.05 million years. This implies that the Trinil Hauptknochenschicht is younger than previously estimated. Together, our data indicate that the engraving was made by Homo erectus, and that it is considerably older than the oldest geometric engravings described so far4, 5. Although it is at present not possible to assess the function or meaning of the engraved shell, this discovery suggests that engraving abstract patterns was in the realm of Asian Homo erectus cognition and neuromotor control. Hominids adapted to metabolize ethanol long before human-directed fermentation Matthew A. Carrigana,b,1, Oleg Uryasevb, Carole B. Fryeb, Blair L. Eckmanb, Candace R. Myersc, Thomas D. Hurleyc, and Steven A. Bennerb PNAS December 1, 2014 doi: 10.1073/pnas.1404167111 Paleogenetics is an emerging field that resurrects ancestral proteins from now-extinct organisms to test, in the laboratory, models of protein function based on natural history and Darwinian evolution. Here, we resurrect digestive alcohol dehydrogenases (ADH4) from our primate ancestors to explore the history of primate–ethanol interactions. The evolving catalytic properties of these resurrected enzymes show that our ape ancestors gained a digestive dehydrogenase enzyme capable of metabolizing ethanol near the time that they began using the forest floor, about 10 million y ago. The ADH4 enzyme in our more ancient and arboreal ancestors did not efficiently oxidize ethanol. This change suggests that exposure to dietary sources of ethanol increased in hominids during the early stages of our adaptation to a terrestrial lifestyle. Because fruit collected from the forest floor is expected to contain higher concentrations of fermenting yeast and ethanol than similar fruits hanging on trees, this transition may also be the first time our ancestors were exposed to (and adapted to) substantial amounts of dietary ethanol. Static network structure can stabilize human cooperation David G. Randa,b,c,d,1, Martin A. Nowake,f,g, James H. Fowlerh,i, and Nicholas A. Christakisd,j,k,l vol. 111 no. 48, 17093-17098 December 2 doi: 10.1073/pnas.1400406111 The evolution of cooperation in network-structured populations has been a major focus of theoretical work in recent years. When players are embedded in fixed networks, cooperators are more likely to interact with, and benefit from, other cooperators. In theory, this clustering can foster cooperation on fixed networks under certain circumstances. Laboratory experiments with humans, however, have thus far found no evidence that fixed network structure actually promotes cooperation. Here, we provide such evidence and help to explain why others failed to find it. First, we show that static networks can lead to a stable high level of cooperation, outperforming well-mixed populations. We then systematically vary the benefit that cooperating provides to one\92s neighbors relative to the cost required to cooperate (b/c), as well as the average number of neighbors in the network (k). When b/c > k, we observe high and stable levels of cooperation. Conversely, when b/c = k or players are randomly shuffled, cooperation decays. Our results are consistent with a quantitative evolutionary game theoretic prediction for when cooperation should succeed on networks and, for the first time to our knowledge, provide an experimental demonstration of the power of static network structure for stabilizing human cooperation. Phylogenetic reconstruction of Bantu kinship challenges Main Sequence Theory of human social evolution Christopher Opiea,1, Susanne Shultzb, Quentin D. Atkinsonc, Thomas Curried, and Ruth Macea PNAS vol. 111 no. 49, 17414-17419, December 9 doi: 10.1073/pnas.1415744111 Kinship provides the fundamental structure of human society: descent determines the inheritance pattern between generations, whereas residence rules govern the location a couple moves to after they marry. In turn, descent and residence patterns determine other key relationships such as alliance, trade, and marriage partners. Hunter-gatherer kinship patterns are viewed as flexible, whereas agricultural societies are thought to have developed much more stable kinship patterns as they expanded during the Holocene. Among the Bantu farmers of sub-Saharan Africa, the ancestral kinship patterns present at the beginning of the expansion are hotly contested, with some arguing for matrilineal and matrilocal patterns, whereas others maintain that any kind of lineality or sex-biased dispersal only emerged much later. Here, we use Bayesian phylogenetic methods to uncover the history of Bantu kinship patterns and trace the interplay between descent and residence systems. The results suggest a number of switches in both descent and residence patterns as Bantu farming spread, but that the first Bantu populations were patrilocal with patrilineal descent. Across the phylogeny, a change in descent triggered a switch away from patrifocal kinship, whereas a change in residence triggered a switch back from matrifocal kinship. These results challenge \93Main Sequence Theory,\94 which maintains that changes in residence rules precede change in other social structures. We also indicate the trajectory of kinship change, shedding new light on how this fundamental structure of society developed as farming spread across the globe during the Neolithic. Impact of HLA-driven HIV adaptation on virulence in populations of high HIV seroprevalence Rebecca Paynea,1, Maximilian Muenchhoffa,1, Jaclyn Mannb, Hannah E. Robertsc,d, Philippa Matthewsa, Emily Adlanda, Allison Hempenstalla, Kuan-Hsiang Huangc,d, Mark Brockmane,f, Zabrina Brummee,f, Marc Sinclaira, Toshiyuki Miurag, John Fraterc,d,h, Myron Essexi,j, Roger Shapiroi,j, Bruce D. Walkerb,k, Thumbi Ndung\92ub,k, Angela R. McLeanc,l, Jonathan M. Carlsonm, and Philip J. R. Gouldera,b,2 PNAS vol. 111 no. 50, E5393-E5400, December 16 doi: 10.1073/pnas.1413339111 It is widely believed that epidemics in new hosts diminish in virulence over time, with natural selection favoring pathogens that cause minimal disease. However, a tradeoff frequently exists between high virulence shortening host survival on the one hand but allowing faster transmission on the other. This is the case in HIV infection, where high viral loads increase transmission risk per coital act but reduce host longevity. We here investigate the impact on HIV virulence of HIV adaptation to HLA molecules that protect against disease progression, such as HLA-B*57 and HLA-B*58:01. We analyzed cohorts in Botswana and South Africa, two countries severely affected by the HIV epidemic. In Botswana, where the epidemic started earlier and adult seroprevalence has been higher, HIV adaptation to HLA including HLA-B*57/58:01 is greater compared with South Africa (P = 7 \D7 10-82), the protective effect of HLA-B*57/58:01 is absent (P = 0.0002), and population viral replicative capacity is lower (P = 0.03). These data suggest that viral evolution is occurring relatively rapidly, and that adaptation of HIV to the most protective HLA alleles may contribute to a lowering of viral replication capacity at the population level, and a consequent reduction in HIV virulence over time. The potential role in this process played by increasing antiretroviral therapy (ART) access is also explored. Models developed here suggest distinct benefits of ART, in addition to reducing HIV disease and transmission, in driving declines in HIV virulence over the course of the epidemic, thereby accelerating the effects of HLA-mediated viral adaptation. Early social exposure in wild chimpanzees: Mothers with sons are more gregarious than mothers with daughters Carson M. Murraya,1, Elizabeth V. Lonsdorfb, Margaret A. Stantona, Kaitlin R. Wellensa, Jordan A. Millera, Jane Goodallc, and Anne E. Puseyd PNAS vol. 111 no. 51, 18189-18194 December 23 doi: 10.1073/pnas.1409507111 In many mammals, early social experience is critical to developing species-appropriate adult behaviors. Although mother-infant interactions play an undeniably significant role in social development, other individuals in the social milieu may also influence infant outcomes. Additionally, the social skills necessary for adult success may differ between the sexes. In chimpanzees (Pan troglodytes), adult males are more gregarious than females and rely on a suite of competitive and cooperative relationships to obtain access to females. In fission-fusion species, including humans and chimpanzees, subgroup composition is labile and individuals can vary the number of individuals with whom they associate. Thus, mothers in these species have a variety of social options. In this study, we investigated whether wild chimpanzee maternal subgrouping patterns differed based on infant sex. Our results show that mothers of sons were more gregarious than mothers of daughters; differences were especially pronounced during the first 6 mo of life, when infant behavior is unlikely to influence maternal subgrouping. Furthermore, mothers with sons spent significantly more time in parties containing males during the first 6 mo. These early differences foreshadow the well-documented sex differences in adult social behavior, and maternal gregariousness may provide sons with important observational learning experiences and social exposure early in life. The presence of these patterns in chimpanzees raises questions concerning the evolutionary history of differential social exposure and its role in shaping sex-typical behavior in humans. Responses to social and environmental stress are attenuated by strong male bonds in wild macaques Christopher Younga,b,1, Bonaventura Majoloc, Michael Heistermannd, Oliver Sch\FClkea,2, and Julia Ostnera,2 PNAS vol. 111 no. 51, 18195-18200, December 23 doi: 10.1073/pnas.1411450111 In humans and obligatory social animals, individuals with weak social ties experience negative health and fitness consequences. The social buffering hypothesis conceptualizes one possible mediating mechanism: During stressful situations the presence of close social partners buffers against the adverse effects of increased physiological stress levels. We tested this hypothesis using data on social (rate of aggression received) and environmental (low temperatures) stressors in wild male Barbary macaques (Macaca sylvanus) in Morocco. These males form strong, enduring, and equitable affiliative relationships similar to human friendships. We tested the effect of the strength of a male\92s top three social bonds on his fecal glucocorticoid metabolite (fGCM) levels as a function of the stressors\92 intensity. The attenuating effect of stronger social bonds on physiological stress increased both with increasing rates of aggression received and with decreasing minimum daily temperature. Ruling out thermoregulatory and immediate effects of social interactions on fGCM levels, our results indicate that male Barbary macaques employ a tend-and-befriend coping strategy in the face of increased environmental as well as social day-to-day stressors. This evidence of a stress-ameliorating effect of social bonding among males under natural conditions and beyond the mother-offspring, kin or pair bond broadens the generality of the social buffering hypothesis. Hominids adapted to metabolize ethanol long before human-directed fermentation Matthew A. Carrigana,b,1, Oleg Uryasevb, Carole B. Fryeb, Blair L. Eckmanb, Candace R. Myersc, Thomas D. Hurleyc, and Steven A. Bennerb PNAS, published online 1 December doi: 10.1073/pnas.1404167111 Paleogenetics is an emerging field that resurrects ancestral proteins from now-extinct organisms to test, in the laboratory, models of protein function based on natural history and Darwinian evolution. Here, we resurrect digestive alcohol dehydrogenases (ADH4) from our primate ancestors to explore the history of primate-ethanol interactions. The evolving catalytic properties of these resurrected enzymes show that our ape ancestors gained a digestive dehydrogenase enzyme capable of metabolizing ethanol near the time that they began using the forest floor, about 10 million y ago. The ADH4 enzyme in our more ancient and arboreal ancestors did not efficiently oxidize ethanol. This change suggests that exposure to dietary sources of ethanol increased in hominids during the early stages of our adaptation to a terrestrial lifestyle. Because fruit collected from the forest floor is expected to contain higher concentrations of fermenting yeast and ethanol than similar fruits hanging on trees, this transition may also be the first time our ancestors were exposed to (and adapted to) substantial amounts of dietary ethanol. curious---------------------------------------------------------------------------------------------------------------------------------------------- Summer jobs reduce violence among disadvantaged youth Sara B. Heller1,2,* Science 5 December 2014: Vol. 346 no. 6214 pp. 1219-1223 DOI: 10.1126/science.1257809 Every day, acts of violence injure more than 6000 people in the United States. Despite decades of social science arguing that joblessness among disadvantaged youth is a key cause of violent offending, programs to remedy youth unemployment do not consistently reduce delinquency. This study tests whether summer jobs, which shift focus from remediation to prevention, can reduce crime. In a randomized controlled trial among 1634 disadvantaged high school youth in Chicago, assignment to a summer jobs program decreases violence by 43% over 16 months (3.95 fewer violent-crime arrests per 100 youth). The decline occurs largely after the 8-week intervention ends. The results suggest the promise of using low-cost, well-targeted programs to generate meaningful behavioral change, even with a problem as complex as youth violence. When contact changes minds: An experiment on transmission of support for gay equality Michael J. LaCour1, Donald P. Green2 Science 12 December 2014: Vol. 346 no. 6215 pp. 1366-1369 DOI: 10.1126/science.1256151 Can a single conversation change minds on divisive social issues, such as same-sex marriage? A randomized placebo-controlled trial assessed whether gay (n = 22) or straight (n = 19) messengers were effective at encouraging voters (n = 972) to support same-sex marriage and whether attitude change persisted and spread to others in voters\92 social networks. The results, measured by an unrelated panel survey, show that both gay and straight canvassers produced large effects initially, but only gay canvassers\92 effects persisted in 3-week, 6-week, and 9-month follow-ups. We also find strong evidence of within-household transmission of opinion change, but only in the wake of conversations with gay canvassers. Contact with gay canvassers further caused substantial change in the ratings of gay men and lesbians more generally. These large, persistent, and contagious effects were confirmed by a follow-up experiment. Contact with minorities coupled with discussion of issues pertinent to them is capable of producing a cascade of opinion change. Identification of the remains of King Richard III Turi E. King, Gloria Gonzalez Fortes, Patricia Balaresque, Mark G. Thomas, David Balding, Pierpaolo Maisano Delser, Rita Neumann, Walther Parson, Michael Knapp, Susan Walsh, Laure Tonasso, John Holt, Manfred Kayser, Jo Appleby, Peter Forster, David Ekserdjian, Michael Hofreiter & Kevin Sch\FCrer Nature Communications 5, Article number: 5631 doi:10.1038/ncomms6631 Published 02 December 2014 In 2012, a skeleton was excavated at the presumed site of the Grey Friars friary in Leicester, the last-known resting place of King Richard III. Archaeological, osteological and radiocarbon dating data were consistent with these being his remains. Here we report DNA analyses of both the skeletal remains and living relatives of Richard III. We find a perfect mitochondrial DNA match between the sequence obtained from the remains and one living relative, and a single-base substitution when compared with a second relative. Y-chromosome haplotypes from male-line relatives and the remains do not match, which could be attributed to a false-paternity event occurring in any of the intervening generations. DNA-predicted hair and eye colour are consistent with Richard\92s appearance in an early portrait. We calculate likelihood ratios for the non-genetic and genetic data separately, and combined, and conclude that the evidence for the remains being those of Richard III is overwhelming. student course-------------------------------------------------------------------------------------------------------------------------------------- Structured Inquiry-Based Learning: Drosophila GAL4 Enhancer Trap Characterization in an Undergraduate Laboratory Course Christopher R. Dunne, Anthony R. Cillo, Danielle R. Glick, Katherine John, Cody Johnson, Jaspinder Kanwal, Brian T. Malik, Kristina Mammano, Stefan Petrovic, William Pfister, Alexander S. Rascoe, Diane Schrom, Scott Shapiro, Jeffrey W. Simkins, David Strauss, Rene Talai, John P. Tomtishen III, Josephine Vargas, Tony Veloz, Thomas O. Vogler, Michael E. Clenshaw, Devin T. Gordon-Hamm, Kathryn L. Lee, Elizabeth C. Marin PLoS Biology December 30, 2014 DOI: 10.1371/journal.pbio.1002030 We have developed and tested two linked but separable structured inquiry exercises using a set of Drosophila melanogaster GAL4 enhancer trap strains for an upper-level undergraduate laboratory methods course at Bucknell University. In the first, students learn to perform inverse PCR to identify the genomic location of the GAL4 insertion, using FlyBase to identify flanking sequences and the primary literature to synthesize current knowledge regarding the nearest gene. In the second, we cross each GAL4 strain to a UAS-CD8-GFP reporter strain, and students perform whole mount CNS dissection, immunohistochemistry, confocal imaging, and analysis of developmental expression patterns. We have found these exercises to be very effective in teaching the uses and limitations of PCR and antibody-based techniques as well as critical reading of the primary literature and scientific writing. Students appreciate the opportunity to apply what they learn by generating novel data of use to the wider research community. Helicornus------------------------------------------------------------------------------------------------------------------------------------------ Warning signals are seductive: Relative contributions of color and pattern to predator avoidance and mate attraction in Heliconius butterflies Susan D. Finkbeiner1,2, Adriana D. Briscoe1 and Robert D. Reed1,2,3 Article first published online: 14 OCT 2014 DOI: 10.1111/evo.12524 Evolution Volume 68, Issue 12, pages 3410-3420, December 2014 Visual signaling in animals can serve many uses, including predator deterrence and mate attraction. In many cases, signals used to advertise unprofitability to predators are also used for intraspecific communication. Although aposematism and mate choice are significant forces driving the evolution of many animal phenotypes, the interplay between relevant visual signals remains little explored. Here, we address this question in the aposematic passion-vine butterfly Heliconius erato by using color- and pattern-manipulated models to test the contributions of different visual features to both mate choice and warning coloration. We found that the relative effectiveness of a model at escaping predation was correlated with its effectiveness at inducing mating behavior, and in both cases wing color was more predictive of presumptive fitness benefits than wing pattern. Overall, however, a combination of the natural (local) color and pattern was most successful for both predator deterrence and mate attraction. By exploring the relative contributions of color versus pattern composition in predation and mate preference studies, we have shown how both natural and sexual selection may work in parallel to drive the evolution of specific animal color patterns. Stable Heliconius butterfly hybrid zones are correlated with a local rainfall peak at the edge of the Amazon basin Neil Rosser1,2, Kanchon K. Dasmahapatra2 and James Mallet1,3 Article first published online: 24 NOV 2014 DOI: 10.1111/evo.12539 Evolution Volume 68, Issue 12, pages 3470-3484, December 2014 Multilocus clines between M\FCllerian mimetic races of Heliconius butterflies provide a classic example of the maintenance of hybrid zones and their importance in speciation. Concordant hybrid zones in the mimics Heliconius erato and H. melpomene in northern Peru were carefully documented in the 1980s, and this prior work now permits a historical analysis of the movement or stasis of the zones. Previous work predicted that these zones might be moving toward the Andes due to selective asymmetry. Extensive deforestation and climate change might also be expected to affect the positions and widths of the hybrid zones. We show that the positions and shapes of these hybrid zones have instead remained remarkably stable between 1985 and 2012. The stability of this interaction strongly implicates continued selection, rather than neutral mixing following secondary contact. The stability of cline widths and strong linkage disequilibria (gametic correlation coefficients Rmax = 0.35-0.56 among unlinked loci) over 25 years suggest that mimetic selection pressures on each color pattern locus have remained approximately constant (s \98 0.13-0.40 per locus in both species). Exceptionally high levels of precipitation at the edge of the easternmost Andes may act as a population density trough for butterflies, trapping the hybrid zones at the foot of the mountains, and preventing movement. As such, our results falsify one prediction of the Pleistocene Refugium theory: That the ranges of divergent species or subspecies should be centered on regions characterized by maxima of rainfall, with hybrid zones falling in more arid regions between them.