Press report, July 2016 asymmetric genitalia Unique set of copulatory organs in mantises: Concealed female genital opening and extremely asymmetric male genitalia Hashimoto K, Suzuki K, Hayashi F Entomological Sciences First published: 8 July 2016Full publication history DOI: 10.1111/ens.12219View/save citation Abstract Several insects exhibit strong asymmetry in male genital shape, but the functions of this asymmetry is unknown. In the four species of the family Mantidae belonging to the genera Tenodera, Statilia and Hierodula, male genitalia consist of a more complex left-side lobe, with two well-pointed sclerotized processes, the apical process (paa) and the distal process (pda). Female genitalia are symmetric, and the genital opening (gonopore) is concealed by placement of the ovipositor (ovi) into the subgenital plate (sgp). Mating with experimental males, in which either paa or pda was cut, demonstrated that paa is essential for successful copulation. By fluorescence detection of the surface of females mated with males in which the paa was coated with fine fluorescent beads, the paa attachment site was determined to be the left edge of the female sgp. This finding suggests that copulation begins with exposure of the female gonopore by the male hooking the paa to the sgp and unfastening the ovi from the sgp, as associated with other parts of the male genitalia. The extremely asymmetric male genitalia also determine their mating posture. The male, mounting the female, bends his abdomen from the right side of his mate to attach his paa to her sgp. We found no antisymmetry in male genitalia, and never observed reversal (leftward) abdominal bending by the males. This was the fixed mating posture, even in virgin males, suggesting its innateness. left-right asymmetry Development Wtip is required for proepicardial organ specification and cardiac left/right asymmetry in zebrafish Rebecca Powell, Ekaterina Bubenshchikova, Yayoi Fukuyo, Chaonan Hsu, Olga Lakiza, Hiroki Nomura, Erin Renfrew, Deborah Garrity, Tomoko Obara Molecular Medicine Reports Published online on: Wednesday, July 27, 2016 Pages: 2665-2678 DOI: 10.3892/mmr.2016.5550 Abstract Wilm's tumor 1 interacting protein (Wtip) was identified as an interacting partner of Wilm's tumor protein (WT1) in a yeast two-hybrid screen. WT1 is expressed in the proepicardial organ (PE) of the heart, and mouse and zebrafish wt1 knockout models appear to lack the PE. Wtip's role in the heart remains unexplored. In the present study, we demonstrate that wtip expression is identical in wt1a‑, tcf21‑, and tbx18‑positive PE cells, and that Wtip protein localizes to the basal body of PE cells. We present the first genetic evidence that Wtip signaling in conjunction with WT1 is essential for PE specification in the zebrafish heart. By overexpressing wtip mRNA, we observed ectopic expression of PE markers in the cardiac and pharyngeal arch regions. Furthermore, wtip knockdown embryos showed perturbed cardiac looping and lacked the atrioventricular (AV) boundary. However, the chamber‑specific markers amhc and vmhc were unaffected. Interestingly, knockdown of wtip disrupts early left‑right (LR) asymmetry. Our studies uncover new roles for Wtip regulating PE cell specification and early LR asymmetry, and suggest that the PE may exert non‑autonomous effects on heart looping and AV morphogenesis. The presence of cilia in the PE, and localization of Wtip in the basal body of ciliated cells, raises the possibility of cilia-mediated PE signaling in the embryonic heart. Transcriptional regulation Enhancer Control of Transcriptional Bursting Takashi Fukaya, Bomyi Lim, Michael Levine Cell Published: June 9 DOI: http://dx.doi.org/10.1016/j.cell.2016.05.025 | Summary Transcription is episodic, consisting of a series of discontinuous bursts. Using live-imaging methods and quantitative analysis, we examine transcriptional bursting in living Drosophila embryos. Different developmental enhancers positioned downstream of synthetic reporter genes produce transcriptional bursts with similar amplitudes and duration but generate very different bursting frequencies, with strong enhancers producing more bursts than weak enhancers. Insertion of an insulator reduces the number of bursts and the corresponding level of gene expression, suggesting that enhancer regulation of bursting frequency is a key parameter of gene control in development. We also show that linked reporter genes exhibit coordinated bursting profiles when regulated by a shared enhancer, challenging conventional models of enhancer-promoter looping. Gene expression / sex- / fecundity / genitalia evolution Sex Chromosome-wide Transcriptional Suppression and Compensatory Cis-Regulatory Evolution Mediate Gene Expression in the Drosophila Male Germline Emily L. Landeen, Christina A. Muirhead, Lori Wright, Colin D. Meiklejohn, Daven C. Presgraves PLOS Biology Published: July 12, 2016 http://dx.doi.org/10.1371/journal.pbio.1002499 Abstract The evolution of heteromorphic sex chromosomes has repeatedly resulted in the evolution of sex chromosome-specific forms of regulation, including sex chromosome dosage compensation in the soma and meiotic sex chromosome inactivation in the germline. In the male germline of Drosophila melanogaster, a novel but poorly understood form of sex chromosome-specific transcriptional regulation occurs that is distinct from canonical sex chromosome dosage compensation or meiotic inactivation. Previous work shows that expression of reporter genes driven by testis-specific promoters is considerably lower—approximately 3-fold or more—for transgenes inserted into X chromosome versus autosome locations. Here we characterize this transcriptional suppression of X-linked genes in the male germline and its evolutionary consequences. Using transgenes and transpositions, we show that most endogenous X-linked genes, not just testis-specific ones, are transcriptionally suppressed several-fold specifically in the Drosophila male germline. In wild-type testes, this sex chromosome-wide transcriptional suppression is generally undetectable, being effectively compensated by the gene-by-gene evolutionary recruitment of strong promoters on the X chromosome. We identify and experimentally validate a promoter element sequence motif that is enriched upstream of the transcription start sites of hundreds of testis-expressed genes; evolutionarily conserved across species; associated with strong gene expression levels in testes; and overrepresented on the X chromosome. These findings show that the expression of X-linked genes in the Drosophila testes reflects a balance between chromosome-wide epigenetic transcriptional suppression and long-term compensatory adaptation by sex-linked genes. Our results have broad implications for the evolution of gene expression in the Drosophila male germline and for genome evolution. A maleness gene in the malaria mosquito Anopheles gambiae Elzbieta Krzywinska, Nathan J. Dennison, Gareth J. Lycett, Jaroslaw Krzywinski Science 01 Jul 2016: Vol. 353, Issue 6294, pp. 67-69 DOI: 10.1126/science.aaf5605 The molecular pathways controlling gender are highly variable and have been identified in only a few nonmammalian model species. In many insects, maleness is conferred by a Y chromosome–linked M factor of unknown nature. We have isolated and characterized a gene, Yob, for the M factor in the malaria mosquito Anopheles gambiae. Yob, activated at the beginning of zygotic transcription and expressed throughout a male’s life, controls male-specific splicing of the doublesex gene. Silencing embryonic Yob expression is male-lethal, whereas ectopic embryonic delivery of Yob transcripts yields male-only broods. This female-killing property may be an invaluable tool for creation of conditional male-only transgenic Anopheles strains for malaria control programs. Expression Quantitative Trait Locus Mapping Studies in Mid-secretory Phase Endometrial Cells Identifies HLA-F and TAP2 as Fecundability-Associated Genes Courtney K. Burrows, Gülüm Kosova, Catherine Herman, Kristen Patterson, Katherine E. Hartmann, Digna R. Velez Edwards, Mary D. Stephenson, Vincent J. Lynch, Carole Ober PLOS Genetics Published: July 22, 2016 http://dx.doi.org/10.1371/journal.pgen.1005858 Abstract Fertility traits in humans are heritable, however, little is known about the genes that influence reproductive outcomes or the genetic variants that contribute to differences in these traits between individuals, particularly women. To address this gap in knowledge, we performed an unbiased genome-wide expression quantitative trait locus (eQTL) mapping study to identify common regulatory (expression) single nucleotide polymorphisms (eSNPs) in mid-secretory endometrium. We identified 423 cis-eQTLs for 132 genes that were significant at a false discovery rate (FDR) of 1%. After pruning for strong LD (r2 >0.95), we tested for associations between eSNPs and fecundability (the ability to get pregnant), measured as the length of the interval to pregnancy, in 117 women. Two eSNPs were associated with fecundability at a FDR of 5%; both were in the HLA region and were eQTLs for the TAP2 gene (P = 1.3x10-4) and the HLA-F gene (P = 4.0x10-4), respectively. The effects of these SNPs on fecundability were replicated in an independent sample. The two eSNPs reside within or near regulatory elements in decidualized human endometrial stromal cells. Our study integrating eQTL mapping in a primary tissue with association studies of a related phenotype revealed novel genes and associated alleles with independent effects on fecundability, and identified a central role for two HLA region genes in human implantation success. Significance of constraints on genital coevolution: Why do female Drosophila appear to cooperate with males by accepting harmful matings? Authors Evolution First published: 30 May 2016Full publication history DOI: 10.1111/evo.12955 Kamimura Y Abstract The mechanisms driving the coevolution of male and female genital morphologies are still debated. Female genitalia in Drosophila species bear membranous “pouches” or hardened “shields,” which the male genital armature contact during copulation. Although shield-like structures likely serve to mitigate the effects of harmful mating, some authors have suggested that soft pouches, which do not prevent male genitalia from inflicting wounds, represent a congruent sensory organ. To elucidate the evolutionary forces responsible for the development of such organs, I examined the effects of artificial damage to various genital parts of female Drosophila erecta on reproductive success. Despite a high survival rate among females, damage to the ovipositor plate resulted in frequent failure of insemination and in the embedment of eggs into the substrate. Damage to the vaginal shield resulted in increased mortality and frequent failure of egg embedment, with an egg blocking the vagina under the damaged shield in some females. Wounding of the pouch had less of an effect on both mating and oviposition success, suggesting that the structure “lures” the male trauma-causing organs to areas where the resultant wounds do not interfere with insemination or oviposition. These data show that the dual functions of female genitalia (mating and oviposition) mediate genital coevolution. Evolution / Genetics The Evolution of Olfactory Gene Families in Drosophila and the Genomic Basis of chemical-Ecological Adaptation in Drosophila suzukii Sukanya Ramasamy, Lino Ometto, Cristina M. Crava, Santosh Revadi, Rupinder Kaur, David S. Horner, Davide Pisani, Teun Dekker, Gianfranco Anfora and Omar Rota-Stabelli Genome Biol Evol (2016) 8 (8): 2297-2311. doi: 10.1093/gbe/evw160 First published online: July 19, 2016 Abstract How the evolution of olfactory genes correlates with adaption to new ecological niches is still a debated topic. We explored this issue in Drosophila suzukii, an emerging model that reproduces on fresh fruit rather than in fermenting substrates like most other Drosophila. We first annotated the repertoire of odorant receptors (ORs), odorant binding proteins (OBPs), and antennal ionotropic receptors (aIRs) in the genomes of two strains of D. suzukii and of its close relative Drosophila biarmipes. We then analyzed these genes on the phylogeny of 14 Drosophila species: whereas ORs and OBPs are characterized by higher turnover rates in some lineages including D. suzukii, aIRs are conserved throughout the genus. Drosophila suzukii is further characterized by a non-random distribution of OR turnover on the gene phylogeny, consistent with a change in selective pressures. In D. suzukii, we found duplications and signs of positive selection in ORs with affinity for short-chain esters, and loss of function of ORs with affinity for volatiles produced during fermentation. These receptors—Or85a and Or22a—are characterized by divergent alleles in the European and American genomes, and we hypothesize that they may have been replaced by some of the duplicated ORs in corresponding neurons, a hypothesis reciprocally confirmed by electrophysiological recordings. Our study quantifies the evolution of olfactory genes in Drosophila and reveals an array of genomic events that can be associated with the ecological adaptations of D. suzukii. Evolution of domain–peptide interactions to coadapt specificity and affinity to functional diversity Abdellali Kelil, Emmanuel D. Levy, and Stephen W. Michnickc PNAS vol. 113 no. 27 doi: 10.1073/pnas.1518469113 Abstract Evolution of complexity in eukaryotic proteomes has arisen, in part, through emergence of modular independently folded domains mediating protein interactions via binding to short linear peptides in proteins. Over 30 years, structural properties and sequence preferences of these peptides have been extensively characterized. Less successful, however, were efforts to establish relationships between physicochemical properties and functions of domain–peptide interactions. To our knowledge, we have devised the first strategy to exhaustively explore the binding specificity of protein domain–peptide interactions. We applied the strategy to SH3 domains to determine the properties of their binding peptides starting from various experimental data. The strategy identified the majority (∼70%) of experimentally determined SH3 binding sites. We discovered mutual relationships among binding specificity, binding affinity, and structural properties and evolution of linear peptides. Remarkably, we found that these properties are also related to functional diversity, defined by depth of proteins within hierarchies of gene ontologies. Our results revealed that linear peptides evolved to coadapt specificity and affinity to functional diversity of domain–peptide interactions. Thus, domain–peptide interactions follow human-constructed gene ontologies, which suggest that our understanding of biological process hierarchies reflect the way chemical and thermodynamic properties of linear peptides and their interaction networks, in general, have evolved. Allele-Specific Transcriptome and Methylome Analysis Reveals Stable Inheritance and Cis-Regulation of DNA Methylation in Nasonia Xu Wang, John H. Werren, Andrew G. Clark PLOS Biology Published: July 5, 2016 http://dx.doi.org/10.1371/journal.pbio.1002500 Abstract Gene expression divergence between closely related species could be attributed to both cis- and trans- DNA sequence changes during evolution, but it is unclear how the evolutionary dynamics of epigenetic marks are regulated. In eutherian mammals, biparental DNA methylation marks are erased and reset during gametogenesis, resulting in paternal or maternal imprints, which lead to genomic imprinting. Whether DNA methylation reprogramming exists in insects is not known. Wasps of the genus Nasonia are non-social parasitoids that are emerging as a model for studies of epigenetic processes in insects. In this study, we quantified allele-specific expression and methylation genome-wide in Nasonia vitripennis and Nasonia giraulti and their reciprocal F1 hybrids. No parent-of-origin effect in allelic expression was found for >8,000 covered genes, suggesting a lack of genomic imprinting in adult Nasonia. As we expected, both significant cis- and trans- effects are responsible for the expression divergence between N. vitripennis and N. giraulti. Surprisingly, all 178 differentially methylated genes are also differentially methylated between the two alleles in F1 hybrid offspring, recapitulating the parental methylation status with nearly 100% fidelity, indicating the presence of strong cis-elements driving the target of gene body methylation. In addition, we discovered that total and allele-specific expression are positively correlated with allele-specific methylation in a subset of the differentially methylated genes. The 100% cis-regulation in F1 hybrids suggests the methylation machinery is conserved and DNA methylation is targeted by cis features in Nasonia. The lack of genomic imprinting and parent-of-origin differentially methylated regions in Nasonia, together with the stable inheritance of methylation status between generations, suggests either a cis-regulatory motif for methylation at the DNA level or highly stable inheritance of an epigenetic signal in Nasonia. Buffering of Genetic Regulatory Networks in Drosophila melanogaster Justin M. Fear, Luis G. León-Novelo, Alison M. Morse, Alison R. Gerken, Kjong Van Lehmann, John Tower, Sergey V. Nuzhdin, Lauren M. McIntyre Genetics July 1, 2016 vol. 203 no. 3 1177-1190; DOI: 10.1534/genetics.116.188797 Abstract Regulatory variation in gene expression can be described by cis- and trans-genetic components. Here we used RNA-seq data from a population panel of Drosophila melanogaster test crosses to compare allelic imbalance (AI) in female head tissue between mated and virgin flies, an environmental change known to affect transcription. Indeed, 3048 exons (1610 genes) are differentially expressed in this study. A Bayesian model for AI, with an intersection test, controls type I error. There are ∼200 genes with AI exclusively in mated or virgin flies, indicating an environmental component of expression regulation. On average 34% of genes within a cross and 54% of all genes show evidence for genetic regulation of transcription. Nearly all differentially regulated genes are affected in cis, with an average of 63% of expression variation explained by the cis-effects. Trans-effects explain 8% of the variance in AI on average and the interaction between cis and trans explains an average of 11% of the total variance in AI. In both environments cis- and trans-effects are compensatory in their overall effect, with a negative association between cis- and trans-effects in 85% of the exons examined. We hypothesize that the gene expression level perturbed by cis-regulatory mutations is compensated through trans-regulatory mechanisms, e.g., trans and cis by trans-factors buffering cis-mutations. In addition, when AI is detected in both environments, cis-mated, cis-virgin, and trans-mated–trans-virgin estimates are highly concordant with 99% of all exons positively correlated with a median correlation of 0.83 for cis and 0.95 for trans. We conclude that the gene regulatory networks (GRNs) are robust and that trans-buffering explains robustness. Resolving the Conflict Between Associative Overdominance and Background Selection Lei Zhao, View ORCID ProfileBrian Charlesworth Genetics July 1, 2016 vol. 203 no. 3 1315-1334; DOI: 10.1534/genetics.116.188912 Abstract In small populations, genetic linkage between a polymorphic neutral locus and loci subject to selection, either against partially recessive mutations or in favor of heterozygotes, may result in an apparent selective advantage to heterozygotes at the neutral locus (associative overdominance) and a retardation of the rate of loss of variability by genetic drift at this locus. In large populations, selection against deleterious mutations has previously been shown to reduce variability at linked neutral loci (background selection). We describe analytical, numerical, and simulation studies that shed light on the conditions under which retardation vs. acceleration of loss of variability occurs at a neutral locus linked to a locus under selection. We consider a finite, randomly mating population initiated from an infinite population in equilibrium at a locus under selection. With mutation and selection, retardation occurs only when S, the product of twice the effective population size and the selection coefficient, is of order 1. With S >> 1, background selection always causes an acceleration of loss of variability. Apparent heterozygote advantage at the neutral locus is, however, always observed when mutations are partially recessive, even if there is an accelerated rate of loss of variability. With heterozygote advantage at the selected locus, loss of variability is nearly always retarded. The results shed light on experiments on the loss of variability at marker loci in laboratory populations and on the results of computer simulations of the effects of multiple selected loci on neutral variability. Epistasis and the Dynamics of Reversion in Molecular Evolution David M. McCandlish, Premal Shah, Joshua B. Plotkin Genetics July 1, 2016 vol. 203 no. 3 1335-1351; DOI: 10.1534/genetics.116.188961 Abstract Recent studies of protein evolution contend that the longer an amino acid substitution is present at a site, the less likely it is to revert to the amino acid previously occupying that site. Here we study this phenomenon of decreasing reversion rates rigorously and in a much more general context. We show that, under weak mutation and for arbitrary fitness landscapes, reversion rates decrease with time for any site that is involved in at least one epistatic interaction. Specifically, we prove that, at stationarity, the hazard function of the distribution of waiting times until reversion is strictly decreasing for any such site. Thus, in the presence of epistasis, the longer a particular character has been absent from a site, the less likely the site will revert to its prior state. We also explore several examples of this general result, which share a common pattern whereby the probability of having reverted increases rapidly at short times to some substantial value before becoming almost flat after a few substitutions at other sites. This pattern indicates a characteristic tendency for reversion to occur either almost immediately after the initial substitution or only after a very long time. Drosophila dany is essential for transcriptional control and nuclear architecture in spermatocytes Martina Trost, Ariane C. Blattner, Stefano Leo, Christian F. Lehner Development 2016 143: 2664-2676; doi: 10.1242/dev.134759 Abstract The terminal differentiation of adult stem cell progeny depends on transcriptional control. A dramatic change in gene expression programs accompanies the transition from proliferating spermatogonia to postmitotic spermatocytes, which prepare for meiosis and subsequent spermiogenesis. More than a thousand spermatocyte-specific genes are transcriptionally activated in early Drosophila spermatocytes. Here we describe the identification and initial characterization of dany, a gene required in spermatocytes for the large-scale change in gene expression. Similar to tMAC and tTAFs, the known major activators of spermatocyte-specific genes, dany has a recent evolutionary origin, but it functions independently. Like dan and danr, its primordial relatives with functions in somatic tissues, dany encodes a nuclear Psq domain protein. Dany associates preferentially with euchromatic genome regions. In dany mutant spermatocytes, activation of spermatocyte-specific genes and silencing of non-spermatocyte-specific genes are severely compromised and the chromatin no longer associates intimately with the nuclear envelope. Therefore, as suggested recently for Dan/Danr, we propose that Dany is essential for the coordination of change in cell type-specific expression programs and large-scale spatial chromatin reorganization. Malik Recurrent Gene Duplication Diversifies Genome Defense Repertoire in Drosophila Mia T. Levine, Helen M. Vander Wende, Emily Hsieh, EmilyClare P. Baker, and Harmit S. Mol Biol Evol (2016) 33 (7): 1641-1653 first published online March 14, 2016 doi:10.1093/molbev/msw053 Abstract Transposable elements (TEs) comprise large fractions of many eukaryotic genomes and imperil host genome integrity. The host genome combats these challenges by encoding proteins that silence TE activity. Both the introduction of new TEs via horizontal transfer and TE sequence evolution requires constant innovation of host-encoded TE silencing machinery to keep pace with TEs. One form of host innovation is the adaptation of existing, single-copy host genes. Indeed, host suppressors of TE replication often harbor signatures of positive selection. Such signatures are especially evident in genes encoding the piwi-interacting-RNA pathway of gene silencing, for example, the female germline-restricted TE silencer, HP1D/Rhino. Host genomes can also innovate via gene duplication and divergence. However, the importance of gene family expansions, contractions, and gene turnover to host genome defense has been largely unexplored. Here, we functionally characterize Oxpecker, a young, tandem duplicate gene of HP1D/rhino. We demonstrate that Oxpecker supports female fertility in Drosophila melanogaster and silences several TE families that are incompletely silenced by HP1D/Rhino in the female germline. We further show that, like Oxpecker, at least ten additional, structurally diverse, HP1D/rhino-derived daughter and “granddaughter” genes emerged during a short 15-million year period of Drosophila evolution. These young paralogs are transcribed primarily in germline tissues, where the genetic conflict between host genomes and TEs plays out. Our findings suggest that gene family expansion is an underappreciated yet potent evolutionary mechanism of genome defense diversification. Widespread Impact of Chromosomal Inversions on Gene Expression Uncovers Robustness via Phenotypic Buffering Samina Naseeb, Zorana Carter, David Minnis, Ian Donaldson, Leo Zeef, and Daniela Delneri Mol Biol Evol (2016) 33 (7): 1679-1696 first published online February 28, 2016 doi:10.1093/molbev/msw045 Abstract The nonrandom gene organization in eukaryotes plays a significant role in genome evolution and function. Chromosomal structural changes impact meiotic fitness and, in several organisms, are associated with speciation and rapid adaptation to different environments. Small sized chromosomal inversions, encompassing few genes, are pervasive in Saccharomyces “sensu stricto” species, while larger inversions are less common in yeasts compared with higher eukaryotes. To explore the effect of gene order on phenotype, reproductive isolation, and gene expression, we engineered 16 Saccharomyces cerevisiae strains carrying all possible paracentric and pericentric inversions between Ty1 elements, a natural substrate for rearrangements. We found that 4 inversions were lethal, while the other 12 did not show any fitness advantage or disadvantage in rich and minimal media. At meiosis, only a weak negative correlation with fitness was seen with the size of the inverted region. However, significantly lower fertility was seen in heterozygote invertant strains carrying recombination hotspots within the breakpoints. Altered transcription was observed throughout the genome rather than being overrepresented within the inversions. In spite of the large difference in gene expression in the inverted strains, mitotic fitness was not impaired in the majority of the 94 conditions tested, indicating that the robustness of the expression network buffers the deleterious effects of structural changes in several environments. Overall, our results support the notion that transcriptional changes may compensate for Ty-mediated rearrangements resulting in the maintenance of a constant phenotype, and suggest that large inversions in yeast are unlikely to be a selectable trait during vegetative growth. Gene X Environment x Organism Caenorhabditis elegans responses to bacteria from its natural habitats Buck S. Samuel, Holli Rowedder, Christian Braendle, Marie-Anne Félix, and Gary Ruvkun PNAS vol. 113 no. 27 doi: 10.1073/pnas.1607183113 Abstract Most Caenorhabditis elegans studies have used laboratory Escherichia coli as diet and microbial environment. Here we characterize bacteria of C. elegans' natural habitats of rotting fruits and vegetation to provide greater context for its physiological responses. By the use of 16S ribosomal DNA (rDNA)-based sequencing, we identified a large variety of bacteria in C. elegans habitats, with phyla Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria being most abundant. From laboratory assays using isolated natural bacteria, C. elegans is able to forage on most bacteria (robust growth on ∼80% of >550 isolates), although ∼20% also impaired growth and arrested and/or stressed animals. Bacterial community composition can predict wild C. elegans population states in both rotting apples and reconstructed microbiomes: alpha-Proteobacteria-rich communities promote proliferation, whereas Bacteroidetes or pathogens correlate with nonproliferating dauers. Combinatorial mixtures of detrimental and beneficial bacteria indicate that bacterial influence is not simply nutritional. Together, these studies provide a foundation for interrogating how bacteria naturally influence C. elegans physiology. Gene-Environment Interactions in Stress Response Contribute Additively to a Genotype-Environment Interaction Takeshi Matsui, Ian M. Ehrenreich PLOS Genetics Published: July 20, 2016 http://dx.doi.org/10.1371/journal.pgen.1006158 Abstract How combinations of gene-environment interactions collectively give rise to genotype-environment interactions is not fully understood. To shed light on this problem, we genetically dissected an environment-specific poor growth phenotype in a cross of two budding yeast strains. This phenotype is detectable when certain segregants are grown on ethanol at 37°C (‘E37’), a condition that differs from the standard culturing environment in both its carbon source (ethanol as opposed to glucose) and temperature (37°C as opposed to 30°C). Using recurrent backcrossing with phenotypic selection, we identified 16 contributing loci. To examine how these loci interact with each other and the environment, we focused on a subset of four loci that together can lead to poor growth in E37. We measured the growth of all 16 haploid combinations of alleles at these loci in all four possible combinations of carbon source (ethanol or glucose) and temperature (30 or 37°C) in a nearly isogenic population. This revealed that the four loci act in an almost entirely additive manner in E37. However, we also found that these loci have weaker effects when only carbon source or temperature is altered, suggesting that their effect magnitudes depend on the severity of environmental perturbation. Consistent with such a possibility, cloning of three causal genes identified factors that have unrelated functions in stress response. Thus, our results indicate that polymorphisms in stress response can show effects that are intensified by environmental stress, thereby resulting in major genotype-environment interactions when multiple of these variants co-occur. function and form The evolutionary path of least resistance P. S. Ungar, L. J. Hlusko Science 01 Jul 2016: Vol. 353, Issue 6294, pp. 29-30 DOI: 10.1126/science.aaf8398 Summary Paleontologists typically reconstruct past behavior by assuming that function follows form. But there can be more than one function for a given form, and different forms can serve the same function. Deconstructing these relationships can be complicated. Here, we use an example from human evolution—markedly different tooth morphologies in early hominins—to show that insights about the underlying genetic architecture of form can help us to better infer function and deepen our understanding of evolution. Hybrid sterility Neighboring genes for DNA-binding proteins rescue male sterility in Drosophila hybrids Marjorie A. Liénard, Luciana O. Araripe, and Daniel L. Hartl PNAS vol. 113 no. 29, E4200–E4207, doi: 10.1073/pnas.1608337113 Abstract Crosses between closely related animal species often result in male hybrids that are sterile, and the molecular and functional basis of genetic factors for hybrid male sterility is of great interest. Here, we report a molecular and functional analysis of HMS1, a region of 9.2 kb in chromosome 3 of Drosophila mauritiana, which results in virtually complete hybrid male sterility when homozygous in the genetic background of sibling species Drosophila simulans. The HMS1 region contains two strong candidate genes for the genetic incompatibility, agt and Taf1. Both encode unrelated DNA-binding proteins, agt for an alkyl-cysteine-S-alkyltransferase and Taf1 for a subunit of transcription factor TFIID that serves as a multifunctional transcriptional regulator. The contribution of each gene to hybrid male sterility was assessed by means of germ-line transformation, with constructs containing complete agt and Taf1 genomic sequences as well as various chimeric constructs. Both agt and Taf1 contribute about equally to HMS1 hybrid male sterility. Transgenes containing either locus rescue sterility in about one-half of the males, and among fertile males the number of offspring is in the normal range. This finding suggests compensatory proliferation of the rescued, nondysfunctional germ cells. Results with chimeric transgenes imply that the hybrid incompatibilities result from interactions among nucleotide differences residing along both agt and Taf1. Our results challenge a number of preliminary generalizations about the molecular and functional basis of hybrid male sterility, and strongly reinforce the role of DNA-binding proteins as a class of genes contributing to the maintenance of postzygotic reproductive isolation. Development Patterned Contractile Forces Promote Epidermal Spreading and Regulate Segment Positioning during Drosophila Head Involution Natalia Dorota Czerniak, Kai Dierkes, Arturo D’Angelo, Julien Colombelli, Jérôme Solon Current Biology Volume 26, Issue 14, p1895–1901, 25 July 2016 DOI: http://dx.doi.org/10.1016/j.cub.2016.05.027 Summary Epithelial spreading is a fundamental mode of tissue rearrangement occurring during animal development and wound closure. It has been associated either with the collective migration of cells [ 1, 2 ] or with actomyosin-generated forces acting at the leading edge (LE) and pulling the epithelial tissue [ 3, 4 ]. During the process of Drosophila head involution (HI), the epidermis spreads anteriorly to envelope the head tissues and fully cover the embryo [ 5 ]. This results in epidermal segments of equal width that will give rise to the different organs of the fly [ 6 ]. Here we perform a quantitative analysis of tissue spreading during HI. Combining high-resolution live microscopy with laser microsurgery and genetic perturbations, we show that epidermal movement is in part, but not solely, driven by a contractile actomyosin cable at the LE. Additional driving forces are generated within each segment by a gradient of actomyosin-based circumferential tension. Interfering with Hedgehog (Hh) signaling can modulate this gradient, thus suggesting the involvement of polarity genes in the regulation of HI. In particular, we show that disruption of these contractile forces alters segment widths and leads to a mispositioning of segments. Within the framework of a physical description, we confirm that given the geometry of the embryo, a patterned profile of active circumferential tensions can indeed generate propelling forces and control final segment position. Our study thus unravels a mechanism by which patterned tensile forces can regulate spreading and positioning of epithelial tissues. Setting the Stage for Notch: The Drosophila Su(H)-Hairless Repressor Complex Tilman Borggrefe, Franz Oswald PLOS Biology Published: July 26, 2016 http://dx.doi.org/10.1371/journal.pbio.1002524 Abstract Notch signaling is iteratively used throughout development to maintain stem cell potential or in other instances allow differentiation. The central transcription factor in Notch signaling is CBF-1/RBP-J, Su(H), Lag-1 (CSL)—Su(H) in Drosophila—which functions as a molecular switch between transcriptional activation and repression. Su(H) represses transcription by forming a complex with the corepressor Hairless (H). The Su(H)-repressor complex not only competes with the Notch intracellular domain (NICD) but also configures the local chromatin landscape. In this issue, Yuan and colleagues determined the structure of the Su(H)/H complex, showing that a major conformational change within Su(H) explains why the binding of NICD and H is mutually exclusive. Functional Dissection of the Blocking and Bypass Activities of the Fab-8 Boundary in the Drosophila Bithorax Complex Olga Kyrchanova, Vladic Mogila, Daniel Wolle, Girish Deshpande, Alexander Parshikov, Fabienne Cléard, Francois Karch, Paul Schedl, Pavel Georgiev PLOS Genetics Published: July 18, 2016 http://dx.doi.org/10.1371/journal.pgen.1006188 Abstract Functionally autonomous regulatory domains direct the parasegment-specific expression of the Drosophila Bithorax complex (BX-C) homeotic genes. Autonomy is conferred by boundary/insulator elements that separate each regulatory domain from its neighbors. For six of the nine parasegment (PS) regulatory domains in the complex, at least one boundary is located between the domain and its target homeotic gene. Consequently, BX-C boundaries must not only block adventitious interactions between neighboring regulatory domains, but also be permissive (bypass) for regulatory interactions between the domains and their gene targets. To elucidate how the BX-C boundaries combine these two contradictory activities, we have used a boundary replacement strategy. We show that a 337 bp fragment spanning the Fab-8 boundary nuclease hypersensitive site and lacking all but 83 bp of the 625 bp Fab-8 PTS (promoter targeting sequence) fully rescues a Fab-7 deletion. It blocks crosstalk between the iab-6 and iab-7 regulatory domains, and has bypass activity that enables the two downstream domains, iab-5 and iab-6, to regulate Abdominal-B (Abd-B) transcription in spite of two intervening boundary elements. Fab-8 has two dCTCF sites and we show that they are necessary both for blocking and bypass activity. However, CTCF sites on their own are not sufficient for bypass. While multimerized dCTCF (or Su(Hw)) sites have blocking activity, they fail to support bypass. Moreover, this bypass defect is not rescued by the full length PTS. Finally, we show that orientation is critical for the proper functioning the Fab-8 replacement. Though the inverted Fab-8 boundary still blocks crosstalk, it disrupts the topology of the Abd-B regulatory domains and does not support bypass. Importantly, altering the orientation of the Fab-8 dCTCF sites is not sufficient to disrupt bypass, indicating that orientation dependence is conferred by other factors. Regulation of the BMP Signaling-Responsive Transcriptional Network in the Drosophila Embryo Lisa Deignan, Marco T. Pinheiro, Catherine Sutcliffe, Abbie Saunders, Scott G. Wilcockson, Leo A. H. Zeef, Ian J. Donaldson, Hilary L. Ashe PLOS Genetics Published: July 5, 2016 http://dx.doi.org/10.1371/journal.pgen.1006164 Abstract The BMP signaling pathway has a conserved role in dorsal-ventral axis patterning during embryonic development. In Drosophila, graded BMP signaling is transduced by the Mad transcription factor and opposed by the Brinker repressor. In this study, using the Drosophila embryo as a model, we combine RNA-seq with Mad and Brinker ChIP-seq to decipher the BMP-responsive transcriptional network underpinning differentiation of the dorsal ectoderm during dorsal-ventral axis patterning. We identify multiple new BMP target genes, including positive and negative regulators of EGF signaling. Manipulation of EGF signaling levels by loss- and gain-of-function studies reveals that EGF signaling negatively regulates embryonic BMP-responsive transcription. Therefore, the BMP gene network has a self-regulating property in that it establishes a balance between its activity and that of the antagonistic EGF signaling pathway to facilitate correct patterning. In terms of BMP-dependent transcription, we identify key roles for the Zelda and Zerknüllt transcription factors in establishing the resulting expression domain, and find widespread binding of insulator proteins to the Mad and Brinker-bound genomic regions. Analysis of embryos lacking the BEAF-32 insulator protein shows reduced transcription of a peak BMP target gene and a reduction in the number of amnioserosa cells, the fate specified by peak BMP signaling. We incorporate our findings into a model for Mad-dependent activation, and discuss its relevance to BMP signal interpretation in vertebrates. Drosophila wing modularity revisited through a quantitative genetic approach Munoz Munoz F, Carreira VP, Martinez-Abadias N, Ortiz V, Gonzales-Jose R, Soto IM Evolution First published: 24 June 2016 DOI: 10.1111/evo.12975 Abstract To predict the response of complex morphological structures to selection it is necessary to know how the covariation among its different parts is organized. Two key features of covariation are modularity and integration. The Drosophila wing is currently considered a fully integrated structure. Here, we study the patterns of integration of the Drosophila wing and test the hypothesis of the wing being divided into two modules along the proximo-distal axis, as suggested by developmental, biomechanical, and evolutionary evidence. To achieve these goals we perform a multilevel analysis of covariation combining the techniques of geometric morphometrics and quantitative genetics. Our results indicate that the Drosophila wing is indeed organized into two main modules, the wing base and the wing blade. The patterns of integration and modularity were highly concordant at the phenotypic, genetic, environmental, and developmental levels. Besides, we found that modularity at the developmental level was considerably higher than modularity at other levels, suggesting that in the Drosophila wing direct developmental interactions are major contributors to total phenotypic shape variation. We propose that the precise time at which covariance-generating developmental processes occur and/or the magnitude of variation that they produce favor proximo-distal, rather than anterior-posterior, modularity in the Drosophila wing. Taxonomy/Phylogeny/Phylogeography Phylogeography of the Subgenus Drosophila (Diptera: Drosophilidae): Evolutionary History of Faunal Divergence between the Old and the New Worlds Hiroyuki F. Izumitani, Yohei Kusaka, Shigeyuki Koshikawa, Masanori J. Toda, Toru Katoh PLOS ONE Published: July 27, 2016 http://dx.doi.org/10.1371/journal.pone.0160051 Abstract The current subgenus Drosophila (the traditional immigrans-tripunctata radiation) includes major elements of temperate drosophilid faunas in the northern hemisphere. Despite previous molecular phylogenetic analyses, the phylogeny of the subgenus Drosophila has not fully been resolved: the resulting trees have more or less varied in topology. One possible factor for such ambiguous results is taxon-sampling that has been biased towards New World species in previous studies. In this study, taxon sampling was balanced between Old and New World species, and phylogenetic relationships among 45 ingroup species selected from ten core species groups of the subgenus Drosophila were analyzed using nucleotide sequences of three nuclear and two mitochondrial genes. Based on the resulting phylogenetic tree, ancestral distributions and divergence times were estimated for each clade to test Throckmorton’s hypothesis that there was a primary, early-Oligocene disjunction of tropical faunas and a subsequent mid-Miocene disjunction of temperate faunas between the Old and the New Worlds that occurred in parallel in separate lineages of the Drosophilidae. Our results substantially support Throckmorton’s hypothesis of ancestral migrations via the Bering Land Bridge mainly from the Old to the New World, and subsequent vicariant divergence of descendants between the two Worlds occurred in parallel among different lineages of the subgenus Drosophila. However, our results also indicate that these events took place multiple times over a wider time range than Throckmorton proposed, from the late Oligocene to the Pliocene. Going beyond the tip of the Drosophilidae iceberg: New Cladochaeta Coquillett, 1900 (Diptera: Drosophilidae) from Brazil. Pirani G, Amorim Dde S. Zootaxa. 2016 Jul 21;4139(3):301-44. doi: 10.11646/zootaxa.4139.3.1. Abstract Drosophilidae comprises more than 4,000 described species worldwide. Despite the huge number of papers published on the genus Drosophila Fallén, 1823, large parts of the family are still poorly known. The drosophiline genus Cladochaeta Coquillet, 1900 has more than 100 Neotropical and several southern Nearctic described species, but there is quite a large number of undescribed species. The Brazilian fauna of the genus was studied and 12 new species are herein described-Cladochaeta armatopsis nov. sp., C. balbiae nov. sp., C. paraitinga nov. sp., C. asapha nov. sp., C.chauliodactyla nov. sp., C. conicophallus nov. sp., C. dicrophallus nov. sp., C.grimaldii nov. sp., C. atlantica nov. sp., C. periotoi nov. sp., C. phallotrixa nov. sp. and C. stigmata nov. sp. We set the first record of C. arthrostyla Grimaldi & Nguyen, 1999 for northeastern Brazil a species otherwise known from Costa Rica, and the first record of C. bomplandi (Malloch, 1934) for the state of Minas Gerais, a species known for northeastern Argentina and southern Brazil. The descriptions include photographs for each species and detailed illustrations of the male terminalia in different views. A synopsis on the taxonomy and natural history of the genus is provided, as well as comments about the relationships of species in the genus, a discussion on problems of male terminalia sclerite homology and the problem of association between males and females. Multiple origins of Hawaiian drosophilids: Phylogeography of Scaptomyza Hardy (Diptera: Drosophilidae) Katoh T, Izumitani HF, Yamashita S, Watada M Entomological Sciences First published: 13 July 2016Full publication history DOI: 10.1111/ens.12222View/save citation Abstract Scaptomyza is a highly diversified genus in the family Drosophilidae, having undergone an explosive radiation, along with the Hawaiian-endemic genus Idiomyia in the Hawaiian Islands: about 60% of 269 Scaptomyza species so far described are endemic to the Hawaiian Islands. Two hypotheses have been proposed for the origin and diversification of Hawaiian drosophilids. One is the “single Hawaiian origin” hypothesis: Scaptomyza and Idiomyia diverged from a single common ancestor that had once colonized the Hawaiian Islands, and then non-Hawaiian Scaptomyza migrated back to continents. The other is the “multiple origins” hypothesis: Hawaiian Scaptomyza and Idiomyia derived from different ancestors that independently colonized the Hawaiian Islands. A key issue for testing these two hypotheses is to clarify the phylogenetic relationships between Hawaiian and non-Hawaiian species in Scaptomyza. Toward this goal, we sampled additional non-Hawaiian Scaptomyza species, particularly in the Old World, and determined the nucleotide sequences of four mitochondrial and seven nuclear genes for these species. Combining these sequence data with published data for 79 species, we reconstructed the phylogeny and estimated ancestral distributions and divergence times. In the resulting phylogenetic trees, non-Hawaiian Scaptomyza species were interspersed in two Hawaiian clades. From a reconstruction of ancestral biogeography, we inferred that Idiomyia and Scaptomyza diverged outside the Hawaiian Islands and then independently colonized the Hawaiian Islands, twice in Scaptomyza, thus supporting the “multiple origins” hypothesis. In the light of evolution X: Comparative phylogeography PNAS vol. 113 no. 29, 7957–7961, doi: 10.1073/pnas.1604338113 John C. Avise, Brian W. Bowen, and Francisco J. Ayala Phylogeography is the study of the spatial arrangement of genealogical lineages, especially within and among conspecific populations and closely related species (10). Ever since its inception in the late 1970s (11, 12) and mid-1980s (13), the field has sought to extend phylogenetic reasoning to the intraspecific level, and thereby build empirical and conceptual bridges between the formerly separate disciplines of microevolutionary population genetics and macroevolutionary phylogenetics. In the early years, phylogeographers relied on data from restriction-site surveys of mitochondrial (mt) DNA to draw inferences about population structure and historical demography, but stunning improvements in molecular techniques (14, 15) and extensions of coalescent theory and other analytical methods (16) later broadened the field’s scope dramatically (17). Phylogeographic perspectives have transformed aspects of population biology, biogeography, systematics, ecology, genetics, and biodiversity conservation. One aim of this colloquium was to bring together leading scientists to address the current state of phylogeography as the discipline enters its fourth decade. The broader goal was to update a wide audience on recent developments in phylogeographic research and their relevance to past accomplishments and future research directions. Many of the advancements in phylogeography have entailed comparative appraisals of one sort or another (18). (See refs. 1⇓⇓⇓⇓⇓⇓⇓–9 for papers from previous colloquia in the series and Box 1 for an overview of the series.) Papers in Section I of this colloquium emphasize the word “comparative” in a spatial sense, where the phylogeographic assessments entail various species (sometimes generally codistributed) that may be representative of particular kinds of environmental settings, such as oceanic versus continental realms. Section II deals with comparative phylogeography in a genomic sense. Nonrecombining cytoplasmic genomes have been the standard workhorses of genealogical analyses, but in principle the primary library of evolutionary histories is ensconced … otherwise interesting Whole-organism lineage tracing by combinatorial and cumulative genome editing Aaron McKenna, Gregory M. Findlay, James A. Gagnon, Marshall S. Horwitz, Alexander F. Schier, Jay Shendure Science 29 Jul 2016: Vol. 353, Issue 6298, DOI: 10.1126/science.aaf7907 Abstract Multicellular systems develop from single cells through distinct lineages. However, current lineage-tracing approaches scale poorly to whole, complex organisms. Here, we use genome editing to progressively introduce and accumulate diverse mutations in a DNA barcode over multiple rounds of cell division. The barcode, an array of clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 target sites, marks cells and enables the elucidation of lineage relationships via the patterns of mutations shared between cells. In cell culture and zebrafish, we show that rates and patterns of editing are tunable and that thousands of lineage-informative barcode alleles can be generated. By sampling hundreds of thousands of cells from individual zebrafish, we find that most cells in adult organs derive from relatively few embryonic progenitors. In future analyses, genome editing of synthetic target arrays for lineage tracing (GESTALT) can be used to generate large-scale maps of cell lineage in multicellular systems for normal development and disease. Teaching accreditation exams reveal grading biases favor women in male-dominated disciplines in France Thomas Breda, Mélina Hillion Science 29 Jul 2016: Vol. 353, Issue 6298, pp. 474-478 DOI: 10.1126/science.aaf4372 Abstract Discrimination against women is seen as one of the possible causes behind their underrepresentation in certain STEM (science, technology, engineering, and mathematics) subjects. We show that this is not the case for the competitive exams used to recruit almost all French secondary and postsecondary teachers and professors. Comparisons of oral non–gender-blind tests with written gender-blind tests for about 100,000 individuals observed in 11 different fields over the period 2006–2013 reveal a bias in favor of women that is strongly increasing with the extent of a field’s male-domination. This bias turns from 3 to 5 percentile ranks for men in literature and foreign languages to about 10 percentile ranks for women in math, physics, or philosophy. These findings have implications for the debate over what interventions are appropriate to increase the representation of women in fields in which they are currently underrepresented. Genetic evidence for natural selection in humans in the contemporary United States Jonathan P. Beauchamp PNAS vol. 113 no. 28 7774–7779, doi: 10.1073/pnas.1600398113 Abstract Recent findings from molecular genetics now make it possible to test directly for natural selection by analyzing whether genetic variants associated with various phenotypes have been under selection. I leverage these findings to construct polygenic scores that use individuals’ genotypes to predict their body mass index, educational attainment (EA), glucose concentration, height, schizophrenia, total cholesterol, and (in females) age at menarche. I then examine associations between these scores and fitness to test whether natural selection has been occurring. My study sample includes individuals of European ancestry born between 1931 and 1953 who participated in the Health and Retirement Study, a representative study of the US population. My results imply that natural selection has been slowly favoring lower EA in both females and males, and are suggestive that natural selection may have favored a higher age at menarche in females. For EA, my estimates imply a rate of selection of about −1.5 mo of education per generation (which pales in comparison with the increases in EA observed in contemporary times). Although they cannot be projected over more than one generation, my results provide additional evidence that humans are still evolving—albeit slowly, especially compared with the rapid changes that have occurred over the past few generations due to cultural and environmental factors. What Is a Genome? Aaron David Goldman, Laura F. Landweber PLOS Genetics Published: July 21, 2016 http://dx.doi.org/10.1371/journal.pgen.1006181 Abstract The genome is often described as the information repository of an organism. Whether millions or billions of letters of DNA, its transmission across generations confers the principal medium for inheritance of organismal traits. Several emerging areas of research demonstrate that this definition is an oversimplification. Here, we explore ways in which a deeper understanding of genomic diversity and cell physiology is challenging the concepts of physical permanence attached to the genome as well as its role as the sole information source for an organism. Complex Ancestries of Lager-Brewing Hybrids Were Shaped by Standing Variation in the Wild Yeast Saccharomyces eubayanus David Peris, Quinn K. Langdon, Ryan V. Moriarty, Kayla Sylvester, Martin Bontrager, Guillaume Charron, Jean-Baptiste Leducq, Christian R. Landry, Diego Libkind, Chris Todd Hittinger PLOS Genetics Published: July 6, 2016 http://dx.doi.org/10.1371/journal.pgen.1006155 Abstract Lager-style beers constitute the vast majority of the beer market, and yet, the genetic origin of the yeast strains that brew them has been shrouded in mystery and controversy. Unlike ale-style beers, which are generally brewed with Saccharomyces cerevisiae, lagers are brewed at colder temperatures with allopolyploid hybrids of Saccharomyces eubayanus x S. cerevisiae. Since the discovery of S. eubayanus in 2011, additional strains have been isolated from South America, North America, Australasia, and Asia, but only interspecies hybrids have been isolated in Europe. Here, using genome sequence data, we examine the relationships of these wild S. eubayanus strains to each other and to domesticated lager strains. Our results support the existence of a relatively low-diversity (π = 0.00197) lineage of S. eubayanus whose distribution stretches across the Holarctic ecozone and includes wild isolates from Tibet, new wild isolates from North America, and the S. eubayanus parents of lager yeasts. This Holarctic lineage is closely related to a population with higher diversity (π = 0.00275) that has been found primarily in South America but includes some widely distributed isolates. A second diverse South American population (π = 0.00354) and two early-diverging Asian subspecies are more distantly related. We further show that no single wild strain from the Holarctic lineage is the sole closest relative of lager yeasts. Instead, different parts of the genome portray different phylogenetic signals and ancestry, likely due to outcrossing and incomplete lineage sorting. Indeed, standing genetic variation within this wild Holarctic lineage of S. eubayanus is responsible for genetic variation still segregating among modern lager-brewing hybrids. We conclude that the relationships among wild strains of S. eubayanus and their domesticated hybrids reflect complex biogeographical and genetic processes. The genetics of speciation: Insights from Fisher's geometric model Fraisse C, Gunnarsson PA, Roze D, Bierne N, Welch JJ Evolution First published: 5 July 2016 DOI: 10.1111/evo.12968View/save citation Abstract Research in speciation genetics has uncovered many robust patterns in intrinsic reproductive isolation, and fitness landscape models have been useful in interpreting these patterns. Here, we examine fitness landscapes based on Fisher's geometric model. Such landscapes are analogous to models of optimizing selection acting on quantitative traits, and have been widely used to study adaptation and the distribution of mutational effects. We show that, with a few modifications, Fisher's model can generate all of the major findings of introgression studies (including “speciation genes” with strong deleterious effects, complex epistasis and asymmetry), and the major patterns in overall hybrid fitnesses (including Haldane's Rule, the speciation clock, heterosis, hybrid breakdown, and male–female asymmetry in the F1). We compare our approach to alternative modeling frameworks that assign fitnesses to genotypes by identifying combinations of incompatible alleles. In some cases, the predictions are importantly different. For example, Fisher's model can explain conflicting empirical results about the rate at which incompatibilities accumulate with genetic divergence. In other cases, the predictions are identical. For example, the quality of reproductive isolation is little affected by the manner in which populations diverge. Alfred Sturtevant and George Beadle Untangle Inversions R. Scott Hawley, Barry Ganetzky Genetics July 1, 2016 vol. 203 no. 3 1001-1003; DOI: 10.1534/genetics.116.191825 MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets Sudhir Kumar, Glen Stecher, and Koichiro Tamura Mol Biol Evol (2016) 33 (7): 1870-1874 first published online March 22, 2016 doi:10.1093/molbev/msw054 Abstract We present the latest version of the Molecular Evolutionary Genetics Analysis (Mega) software, which contains many sophisticated methods and tools for phylogenomics and phylomedicine. In this major upgrade, Mega has been optimized for use on 64-bit computing systems for analyzing larger datasets. Researchers can now explore and analyze tens of thousands of sequences in Mega. The new version also provides an advanced wizard for building timetrees and includes a new functionality to automatically predict gene duplication events in gene family trees. The 64-bit Mega is made available in two interfaces: graphical and command line. The graphical user interface (GUI) is a native Microsoft Windows application that can also be used on Mac OS X. The command line Mega is available as native applications for Windows, Linux, and Mac OS X. They are intended for use in high-throughput and scripted analysis. Both versions are available from www.megasoftware.net free of charge.