1. Curr Top Dev Biol. 2016;117:237-51. doi: 10.1016/bs.ctdb.2015.12.014. Epub 2016 Feb 1. Implications of Developmental Gene Regulatory Networks Inside and Outside Developmental Biology. Peter IS(1), Davidson EH(2). Author information: (1)Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA. Electronic address: ipeter@caltech.edu. (2)Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA. The insight that the genomic control of developmental process is encoded in the form of gene regulatory networks has profound impacts on many areas of modern bioscience. Most importantly, it affects developmental biology itself, as it means that a causal understanding of development requires knowledge of the architecture of regulatory network interactions. Furthermore, it follows that functional changes in developmental gene regulatory networks have to be considered as a primary mechanism for evolutionary process. We here discuss some of the recent advances in gene regulatory network biology and how they have affected our current understanding of development, evolution, and regulatory genomics. © 2016 Elsevier Inc. All rights reserved. PMID: 26969981 [PubMed - in process] 2. Integr Biol (Camb). 2016 Feb 29. [Epub ahead of print] Conserved roles for cytoskeletal components in determining laterality. McDowell GS(1), Lemire JM(2), Paré JF(2), Cammarata G(3), Lowery LA(3), Levin M(2). Author information: (1)Biology Department, and Center for Regenerative and Developmental Biology, Tufts University, 200 Boston Avenue, Suite 4600, Medford, MA 02155-4243, USA. michael.levin@tufts.edu and Biology Department, Boston College, Chestnut Hill, MA, USA. (2)Biology Department, and Center for Regenerative and Developmental Biology, Tufts University, 200 Boston Avenue, Suite 4600, Medford, MA 02155-4243, USA. michael.levin@tufts.edu. (3)Biology Department, Boston College, Chestnut Hill, MA, USA. Consistently-biased left-right (LR) patterning is required for the proper placement of organs including the heart and viscera. The LR axis is especially fascinating as an example of multi-scale pattern formation, since here chiral events at the subcellular level are integrated and amplified into asymmetric transcriptional cascades and ultimately into the anatomical patterning of the entire body. In contrast to the other two body axes, there is considerable controversy about the earliest mechanisms of embryonic laterality. Many molecular components of asymmetry have not been widely tested among phyla with diverse bodyplans, and it is unknown whether parallel (redundant) pathways may exist that could reverse abnormal asymmetry states at specific checkpoints in development. To address conservation of the early steps of LR patterning, we used the Xenopus laevis (frog) embryo to functionally test a number of protein targets known to direct asymmetry in plants, fruit fly, and rodent. Using the same reagents that randomize asymmetry in Arabidopsis, Drosophila, and mouse embryos, we show that manipulation of the microtubule and actin cytoskeleton immediately post-fertilization, but not later, results in laterality defects in Xenopus embryos. Moreover, we observed organ-specific randomization effects and a striking dissociation of organ situs from effects on the expression of left side control genes, which parallel data from Drosophila and mouse. Remarkably, some early manipulations that disrupt laterality of transcriptional asymmetry determinants can be subsequently "rescued" by the embryo, resulting in normal organ situs. These data reveal the existence of novel corrective mechanisms, demonstrate that asymmetric expression of Nodal is not a definitive marker of laterality, and suggest the existence of amplification pathways that connect early cytoskeletal processes to control of organ situs bypassing Nodal. Counter to alternative models of symmetry breaking during neurulation (via ciliary structures absent in many phyla), our data suggest a widely-conserved role for the cytoskeleton in regulating left-right axis formation immediately after fertilization of the egg. The novel mechanisms that rescue organ situs, even after incorrect expression of genes previously considered to be left-side master regulators, suggest LR patterning as a new context in which to explore multi-scale redundancy and integration of patterning from the subcellular structure to the entire bodyplan. PMID: 26928161 [PubMed - as supplied by publisher] 3. PLoS Genet. 2016 Feb 29;12(2):e1005887. doi: 10.1371/journal.pgen.1005887. eCollection 2016. Genomics of Rapid Incipient Speciation in Sympatric Threespine Stickleback. Marques DA(1,)(2,)(3), Lucek K(1,)(2,)(4), Meier JI(1,)(2,)(3), Mwaiko S(1,)(2), Wagner CE(1,)(2,)(5), Excoffier L(3,)(6), Seehausen O(1,)(2). Author information: (1)Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland. (2)Department of Fish Ecology and Evolution, Centre of Ecology, Evolution & Biogeochemistry, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland. (3)Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland. (4)Department of Animal and Plant Science, University of Sheffield, Sheffield, United Kingdom. (5)Biodiversity Institute, University of Wyoming, Wyoming, United States of America. (6)Swiss Institute of Bioinformatics, Lausanne, Switzerland. Ecological speciation is the process by which reproductively isolated populations emerge as a consequence of divergent natural or ecologically-mediated sexual selection. Most genomic studies of ecological speciation have investigated allopatric populations, making it difficult to infer reproductive isolation. The few studies on sympatric ecotypes have focused on advanced stages of the speciation process after thousands of generations of divergence. As a consequence, we still do not know what genomic signatures of the early onset of ecological speciation look like. Here, we examined genomic differentiation among migratory lake and resident stream ecotypes of threespine stickleback reproducing in sympatry in one stream, and in parapatry in another stream. Importantly, these ecotypes started diverging less than 150 years ago. We obtained 34,756 SNPs with restriction-site associated DNA sequencing and identified genomic islands of differentiation using a Hidden Markov Model approach. Consistent with incipient ecological speciation, we found significant genomic differentiation between ecotypes both in sympatry and parapatry. Of 19 islands of differentiation resisting gene flow in sympatry, all were also differentiated in parapatry and were thus likely driven by divergent selection among habitats. These islands clustered in quantitative trait loci controlling divergent traits among the ecotypes, many of them concentrated in one region with low to intermediate recombination. Our findings suggest that adaptive genomic differentiation at many genetic loci can arise and persist in sympatry at the very early stage of ecotype divergence, and that the genomic architecture of adaptation may facilitate this. PMCID: PMC4771382 PMID: 26925837 [PubMed - in process] 4. Fly (Austin). 2016 Feb 29:0. [Epub ahead of print] Enhancer Modularity and the Evolution of New Traits. Koshikawa S(1). Author information: (1)a The Hakubi Center for Advanced Research and Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-Cho , Sakyo-Ku , Kyoto 606-8502 , Japan. Animals have modular cis-regulatory regions in their genomes, and expression of a single gene is often regulated by multiple enhancers residing in such a region. In the laboratory, and also in natural populations, loss of an enhancer can result in a loss of gene expression. Although only a few examples have been well characterized to date, some studies have suggested that an evolutionary gain of a new enhancer function can establish a new gene expression domain. Our recent study showed that Drosophila guttifera has more enhancers and additional expression domains of the wingless gene during the pupal stage, compared to D. melanogaster, and that these new features appear to have evolved in the ancestral lineage leading to D. guttifera. (1) Gain of a new expression domain of a developmental regulatory gene (toolkit gene), such as wingless, can cause co-option of the expression of its downstream genes to the new domain, resulting in duplication of a preexisting structure at this new body position. Recently, with the advancement of evo-devo studies, we have learned that the developmental regulatory systems are strikingly similar across various animal taxa, in spite of the great diversity of the animals' morphology. Even behind "new" traits, co-options of essential developmental genes from known systems are very common. We previously provided concrete evidence of gains of enhancer activities of a developmental regulatory gene underlying gains of new traits. (1) Broad occurrence of this scenario is testable and should be validated in the future. PMID: 26925592 [PubMed - as supplied by publisher] 5. Ecol Evol. 2016 Feb 16. doi: 10.1002/ece3.2015. [Epub ahead of print] Introduced Drosophila subobscura populations perform better than native populations during an oviposition choice task due to increased fecundity but similar learning ability. Foucaud J(1), Moreno C(1), Pascual M(2), Rezende EL(3), Castañeda LE(4), Gibert P(5), Mery F(1). Author information: (1)Laboratoire Evolution, Génomes, Comportement et Ecologie UMR-CNRS 9191 Gif/Yvette France. (2)Department of Genetics and IrBio Universitat de Barcelona Av. Diagonal 643 08028 Barcelona Spain. (3)Department of Life Sciences University of Roehampton Holybourne Avenue London SW15 4JD UK. (4)Instituto de Ciencias Ambientales y Evolutivas Universidad Austral de Chile PO 5090000 Valdivia Chile. (5)Université de Lyon Université Lyon1 Laboratoire de Biométrie et Biologie Evolutive UMR CNRS 5558 43 Bd du 11 Novembre 1918 69622 Villeurbanne Cedex France. The success of invasive species is tightly linked to their fitness in a putatively novel environment. While quantitative components of fitness have been studied extensively in the context of invasive species, fewer studies have looked at qualitative components of fitness, such as behavioral plasticity, and their interaction with quantitative components, despite intuitive benefits over the course of an invasion. In particular, learning is a form of behavioral plasticity that makes it possible to finely tune behavior according to environmental conditions. Learning can be crucial for survival and reproduction of introduced organisms in novel areas, for example, for detecting new predators, or finding mates or oviposition sites. Here we explored how oviposition performance evolved in relation to both fecundity and learning during an invasion, using native and introduced Drosophila subobscura populations performing an ecologically relevant task. Our results indicated that, under comparable conditions, invasive populations performed better during our oviposition task than did native populations. This was because invasive populations had higher fecundity, together with similar cognitive performance when compared to native populations, and that there was no interaction between learning and fecundity. Unexpectedly, our study did not reveal an allocation trade-off (i.e., a negative relationship) between learning and fecundity. On the contrary, the pattern we observed was more consistent with an acquisition trade-off, meaning that fecundity could be limited by availability of resources, unlike cognitive ability. This pattern might be the consequence of escaping natural enemies and/or competitors during the introduction. The apparent lack of evolution of learning may indicate that the introduced population did not face novel cognitive challenges in the new environment (i.e., cognitive "pre-adaptation"). Alternatively, the evolution of learning may have been transient and therefore not detected. PMCID: PMC4755011 PMID: 26925216 [PubMed - as supplied by publisher] 6. Science. 2016 Feb 26;351(6276):aad4234. doi: 10.1126/science.aad4234. Direct CRISPR spacer acquisition from RNA by a natural reverse transcriptase-Cas1 fusion protein. Silas S(1), Mohr G(2), Sidote DJ(2), Markham LM(2), Sanchez-Amat A(3), Bhaya D(4), Lambowitz AM(2), Fire AZ(5). Author information: (1)Department of Pathology, Stanford University, Stanford, CA 94305, USA. Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA. (2)Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, University of Texas-Austin, Austin, TX 78712, USA. (3)Department of Genetics and Microbiology, Universidad de Murcia, Murcia 30100, Spain. (4)Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA. (5)Department of Pathology, Stanford University, Stanford, CA 94305, USA. Comment in Science. 2016 Feb 26;351(6276):920-1. CRISPR systems mediate adaptive immunity in diverse prokaryotes. CRISPR-associated Cas1 and Cas2 proteins have been shown to enable adaptation to new threats in type I and II CRISPR systems by the acquisition of short segments of DNA (spacers) from invasive elements. In several type III CRISPR systems, Cas1 is naturally fused to a reverse transcriptase (RT). In the marine bacterium Marinomonas mediterranea (MMB-1), we showed that a RT-Cas1 fusion protein enables the acquisition of RNA spacers in vivo in a RT-dependent manner. In vitro, the MMB-1 RT-Cas1 and Cas2 proteins catalyze the ligation of RNA segments into the CRISPR array, which is followed by reverse transcription. These observations outline a host-mediated mechanism for reverse information flow from RNA to DNA. Copyright © 2016, American Association for the Advancement of Science. PMID: 26917774 [PubMed - in process] 7. J Evol Biol. 2016 Feb 23. doi: 10.1111/jeb.12851. [Epub ahead of print] Testing for a genetic response to sexual selection in a wild Drosophila population. Gosden TP(1), Thomson JR(1), Blows MW(1), Schaul A(1), Chenoweth SF(1). Author information: (1)School of Biological Sciences, The University of Queensland, St. Lucia, Qld, AUSTRALIA, 4072. In accordance with the consensus that sexual selection is responsible for the rapid evolution of display traits on macroevolutionary scales, microevolutionary studies suggest sexual selection is a widespread and often strong form of directional selection in nature. However, empirical evidence for the contemporary evolution of sexually selected traits remains weak. In this study we used a novel application of quantitative genetic breeding designs to test for a genetic response to sexual selection on eight chemical display traits in a field population of the fly, Drosophila serrata. Using our quantitative genetic approach, we were able to detect a genetically-based difference in means between groups of males descended from either successful or random wild males for one of these display traits, the diene (Z,Z)-5,9-C27:2 . Our experimental results, in combination with previous lab studies on this system, suggest that both natural selection and sexual selection may be influencing the evolutionary trajectories of these traits in nature, limiting the capacity for a contemporary evolutionary response. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved. PMID: 26914275 [PubMed - as supplied by publisher] 8. Science. 2016 Feb 5;351(6273):569-70. doi: 10.1126/science.351.6273.569-c. Epub 2016 Feb 4. False positives are statistically inevitable. Fricker RD Jr(1). Author information: (1)Department of Statistics, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA. rf@vt.edu. PMID: 26912694 [PubMed - in process] 9. Proc Biol Sci. 2016 Feb 24;283(1825). pii: 20152726. doi: 10.1098/rspb.2015.2726. Evolution under dietary restriction increases male reproductive performance without survival cost. Zajitschek F(1), Zajitschek SR(2), Canton C(3), Georgolopoulos G(3), Friberg U(4), Maklakov AA(3). Author information: (1)School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia Department of Animal Ecology, Evolutionary Biology Centre, Uppsala University, Uppsala 75236, Sweden felix@zajitschek.net. (2)Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala 75236, Sweden Doñana Biological Station, Spanish Research Council CSIC, c/ Americo Vespucio, s/n, Isla de la Cartuja, 41092 Sevilla, Spain. (3)Department of Animal Ecology, Evolutionary Biology Centre, Uppsala University, Uppsala 75236, Sweden. (4)Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala 75236, Sweden IFM Biology, AVIAN Behavioural, Genomics and Physiology Group, Linköping University, Linköping 58183, Sweden. Dietary restriction (DR), a reduction in nutrient intake without malnutrition, is the most reproducible way to extend lifespan in a wide range of organisms across the tree of life, yet the evolutionary underpinnings of the DR effect on lifespan are still widely debated. The leading theory suggests that this effect is adaptive and results from reallocation of resources from reproduction to somatic maintenance, in order to survive periods of famine in nature. However, such response would cease to be adaptive when DR is chronic and animals are selected to allocate more resources to reproduction. Nevertheless, chronic DR can also increase the strength of selection resulting in the evolution of more robust genotypes. We evolved Drosophila melanogaster fruit flies on 'DR', 'standard' and 'high' adult diets in replicate populations with overlapping generations. After approximately 25 generations of experimental evolution, male 'DR' flies had higher fitness than males from 'standard' and 'high' populations. Strikingly, this increase in reproductive success did not come at a cost to survival. Our results suggest that sustained DR selects for more robust male genotypes that are overall better in converting resources into energy, which they allocate mostly to reproduction. © 2016 The Author(s). PMID: 26911958 [PubMed - in process] 10. PLoS Biol. 2016 Feb 24;14(2):e1002388. doi: 10.1371/journal.pbio.1002388. eCollection 2016. Adaptation to Temporally Fluctuating Environments by the Evolution of Maternal Effects. Dey S(1), Proulx SR(2), Teotónio H(1). Author information: (1)Institut de Biologie de l´École Normale Supérieure, INSERM U1024, CNRS UMR 8197, Paris, France. (2)Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, California, United States of America. All organisms live in temporally fluctuating environments. Theory predicts that the evolution of deterministic maternal effects (i.e., anticipatory maternal effects or transgenerational phenotypic plasticity) underlies adaptation to environments that fluctuate in a predictably alternating fashion over maternal-offspring generations. In contrast, randomizing maternal effects (i.e., diversifying and conservative bet-hedging), are expected to evolve in response to unpredictably fluctuating environments. Although maternal effects are common, evidence for their adaptive significance is equivocal since they can easily evolve as a correlated response to maternal selection and may or may not increase the future fitness of offspring. Using the hermaphroditic nematode Caenorhabditis elegans, we here show that the experimental evolution of maternal glycogen provisioning underlies adaptation to a fluctuating normoxia-anoxia hatching environment by increasing embryo survival under anoxia. In strictly alternating environments, we found that hermaphrodites evolved the ability to increase embryo glycogen provisioning when they experienced normoxia and to decrease embryo glycogen provisioning when they experienced anoxia. At odds with existing theory, however, populations facing irregularly fluctuating normoxia-anoxia hatching environments failed to evolve randomizing maternal effects. Instead, adaptation in these populations may have occurred through the evolution of fitness effects that percolate over multiple generations, as they maintained considerably high expected growth rates during experimental evolution despite evolving reduced fecundity and reduced embryo survival under one or two generations of anoxia. We develop theoretical models that explain why adaptation to a wide range of patterns of environmental fluctuations hinges on the existence of deterministic maternal effects, and that such deterministic maternal effects are more likely to contribute to adaptation than randomizing maternal effects. PMCID: PMC4766184 PMID: 26910440 [PubMed - in process] 11. Nature. 2016 Mar 10;531(7593):233-6. doi: 10.1038/nature17143. Epub 2016 Feb 24. Sex speeds adaptation by altering the dynamics of molecular evolution. McDonald MJ(1,)(2), Rice DP(1,)(2), Desai MM(1,)(2,)(3). Author information: (1)Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA. (2)FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138, USA. (3)Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA. Comment in Nature. 2016 Mar 10;531(7593):176-7. Sex and recombination are pervasive throughout nature despite their substantial costs. Understanding the evolutionary forces that maintain these phenomena is a central challenge in biology. One longstanding hypothesis argues that sex is beneficial because recombination speeds adaptation. Theory has proposed several distinct population genetic mechanisms that could underlie this advantage. For example, sex can promote the fixation of beneficial mutations either by alleviating interference competition (the Fisher-Muller effect) or by separating them from deleterious load (the ruby in the rubbish effect). Previous experiments confirm that sex can increase the rate of adaptation, but these studies did not observe the evolutionary dynamics that drive this effect at the genomic level. Here we present the first, to our knowledge, comparison between the sequence-level dynamics of adaptation in experimental sexual and asexual Saccharomyces cerevisiae populations, which allows us to identify the specific mechanisms by which sex speeds adaptation. We find that sex alters the molecular signatures of evolution by changing the spectrum of mutations that fix, and confirm theoretical predictions that it does so by alleviating clonal interference. We also show that substantially deleterious mutations hitchhike to fixation in adapting asexual populations. In contrast, recombination prevents such mutations from fixing. Our results demonstrate that sex both speeds adaptation and alters its molecular signature by allowing natural selection to more efficiently sort beneficial from deleterious mutations. PMID: 26909573 [PubMed - in process] 12. Proc Natl Acad Sci U S A. 2016 Mar 8;113(10):E1352-61. doi: 10.1073/pnas.1601232113. Epub 2016 Feb 22. Rare recombination events generate sequence diversity among balancer chromosomes in Drosophila melanogaster. Miller DE(1), Cook KR(2), Yeganeh Kazemi N(3), Smith CB(3), Cockrell AJ(3), Hawley RS(4), Bergman CM(5). Author information: (1)Stowers Institute for Medical Research, Kansas City, MO 64110; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS 66160; (2)Department of Biology, Indiana University, Bloomington, IN 47405; (3)Stowers Institute for Medical Research, Kansas City, MO 64110; (4)Stowers Institute for Medical Research, Kansas City, MO 64110; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS 66160; rsh@stowers.org casey.bergman@manchester.ac.uk. (5)Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom rsh@stowers.org casey.bergman@manchester.ac.uk. Multiply inverted balancer chromosomes that suppress exchange with their homologs are an essential part of the Drosophila melanogaster genetic toolkit. Despite their widespread use, the organization of balancer chromosomes has not been characterized at the molecular level, and the degree of sequence variation among copies of balancer chromosomes is unknown. To map inversion breakpoints and study potential diversity in descendants of a structurally identical balancer chromosome, we sequenced a panel of laboratory stocks containing the most widely used X chromosome balancer, First Multiple 7 (FM7). We mapped the locations of FM7 breakpoints to precise euchromatic coordinates and identified the flanking sequence of breakpoints in heterochromatic regions. Analysis of SNP variation revealed megabase-scale blocks of sequence divergence among currently used FM7 stocks. We present evidence that this divergence arose through rare double-crossover events that replaced a female-sterile allele of the singed gene (sn(X2)) on FM7c with a sequence from balanced chromosomes. We propose that although double-crossover events are rare in individual crosses, many FM7c chromosomes in the Bloomington Drosophila Stock Center have lost sn(X2) by this mechanism on a historical timescale. Finally, we characterize the original allele of the Bar gene (B(1)) that is carried on FM7, and validate the hypothesis that the origin and subsequent reversion of the B(1) duplication are mediated by unequal exchange. Our results reject a simple nonrecombining, clonal mode for the laboratory evolution of balancer chromosomes and have implications for how balancer chromosomes should be used in the design and interpretation of genetic experiments in Drosophila. PMID: 26903656 [PubMed - in process] 13. Insect Sci. 2016 Feb 22. doi: 10.1111/1744-7917.12327. [Epub ahead of print] The Distal-less homeobox genes of insects and spiders: genomic organization, function, regulation and evolution. Chen B(1), Piel WH(2,)(3), Monteiro A(2,)(3). Author information: (1)Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Shapingba, Chongqing, 400047, P.R. China. (2)Yale-NUS College, 16 College Avenue West #02-221, Singapore, 138527. (3)Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543. The Distal-less (Dll) genes are homeodomain transcription factors that are present in most Metazoa and in representatives of all investigated arthropod groups. In Drosophila, the best studied insect, Distal-less plays an essential role in forming the proximodistal axis of the legs, antennae and analia, and in specifying antennal identity. The initiation of Dll expression in clusters of cells in mid-lateral regions of the Drosophila embryo represents the earliest genetic marker of limbs. Dll genes are involved in the development of the peripheral nervous system and sensitive organs, and they also function as master regulators of black pigmentation in some insect lineages. Here we analyze the complete genomes of six insects, the nematode Caenorhabditis elegans and Homo sapiens, as well as multiple Dll sequences available in databases in order to examine the structure and protein features of these genes. We also review the function, expression, regulation, and evolution of arthropod Dll genes with emphasis on insects and spiders. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved. PMID: 26898323 [PubMed - as supplied by publisher] 14. Genetics. 2016 Feb 19. pii: genetics.116.186783. [Epub ahead of print] Quantitative Single-Embryo Profile of Drosophila Genome Activation and the Dorsal-Ventral Patterning Network. Sandler JE(1), Stathopoulos A(2). Author information: (1)California Institute of Technology; (2)California Insitute of Technology angelike@caltech.edu. During embryonic development of Drosophila melanogaster, the Maternal to Zygotic Transition (MZT) marks a significant and rapid turning point when zygotic transcription begins and control of development is transferred from maternally deposited transcripts. Characterizing the sequential activation of the genome during the MZT requires precise timing and a sensitive assay to measure changes in expression. We utilized the NanoString nCounter instrument, which directly counts mRNA transcripts without reverse transcription or amplification, to study over 70 genes expressed along the dorsal-ventral (DV) axis of early Drosophila embryos, dividing the MZT into 10 time points. Transcripts were quantified for every gene studied at all time points, providing the first data set of absolute numbers of transcripts during Drosophila development. We found that gene expression changes quickly during the MZT, with early Nuclear Cycle (NC) 14 the most dynamic time for the embryo. twist is one of the most abundant genes in the entire embryo and we use mutants to quantitatively demonstrate how it cooperates with Dorsal to activate transcription and is responsible for some of the rapid changes in transcription observed during early NC14. We also uncovered elements within the gene regulatory network that maintain precise transcript levels for sets of genes that are spatiotemporally co-transcribed within the presumptive mesoderm or dorsal ectoderm. Using this new data, we show that a fine-scale, quantitative analysis of temporal gene expression can provide new insights into developmental biology by uncovering trends in gene networks including coregulation of target genes and specific temporal input by transcription factors. Copyright © 2016, The Genetics Society of America. PMID: 26896327 [PubMed - as supplied by publisher] 15. Nature. 2016 Feb 18;530(7590):344-8. doi: 10.1038/nature16953. The sexual identity of adult intestinal stem cells controls organ size and plasticity. Hudry B(1), Khadayate S(1), Miguel-Aliaga I(1). Author information: (1)MRC Clinical Sciences Centre, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, UK. Comment in Nature. 2016 Feb 18;530(7590):289-90. Sex differences in physiology and disease susceptibility are commonly attributed to developmental and/or hormonal factors, but there is increasing realization that cell-intrinsic mechanisms play important and persistent roles. Here we use the Drosophila melanogaster intestine to investigate the nature and importance of cellular sex in an adult somatic organ in vivo. We find that the adult intestinal epithelium is a cellular mosaic of different sex differentiation pathways, and displays extensive sex differences in expression of genes with roles in growth and metabolism. Cell-specific reversals of the sexual identity of adult intestinal stem cells uncovers the key role this identity has in controlling organ size, reproductive plasticity and response to genetically induced tumours. Unlike previous examples of sexually dimorphic somatic stem cell activity, the sex differences in intestinal stem cell behaviour arise from intrinsic mechanisms that control cell cycle duration and involve a new doublesex- and fruitless-independent branch of the sex differentiation pathway downstream of transformer. Together, our findings indicate that the plasticity of an adult somatic organ is reversibly controlled by its sexual identity, imparted by a new mechanism that may be active in more tissues than previously recognized. PMID: 26887495 [PubMed - indexed for MEDLINE] 16. Nature. 2016 Feb 17. doi: 10.1038/nature16994. [Epub ahead of print] The mid-developmental transition and the evolution of animal body plans. Levin M(1), Anavy L(1), Cole AG(1), Winter E(1), Mostov N(1), Khair S(1), Senderovich N(1), Kovalev E(1), Silver DH(1), Feder M(1), Fernandez-Valverde SL(2), Nakanishi N(2), Simmons D(3), Simakov O(4), Larsson T(4), Liu SY(5), Jerafi-Vider A(6), Yaniv K(6), Ryan JF(3), Martindale MQ(3), Rink JC(5), Arendt D(4), Degnan SM(2), Degnan BM(2), Hashimshony T(1), Yanai I(1). Author information: (1)Department of Biology, Technion - Israel Institute of Technion, Haifa 32000, Israel. (2)School of Biological Sciences, University of Queensland, Brisbane, Queensland, Australia. (3)Whitney Laboratory for Marine Bioscience, University of Florida, 9505 N Ocean Shore Blvd, St Augustine, Florida 32080-8610 USA. (4)Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany. (5)Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany. (6)Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel. Animals are grouped into ~35 'phyla' based upon the notion of distinct body plans. Morphological and molecular analyses have revealed that a stage in the middle of development-known as the phylotypic period-is conserved among species within some phyla. Although these analyses provide evidence for their existence, phyla have also been criticized as lacking an objective definition, and consequently based on arbitrary groupings of animals. Here we compare the developmental transcriptomes of ten species, each annotated to a different phylum, with a wide range of life histories and embryonic forms. We find that in all ten species, development comprises the coupling of early and late phases of conserved gene expression. These phases are linked by a divergent 'mid-developmental transition' that uses species-specific suites of signalling pathways and transcription factors. This mid-developmental transition overlaps with the phylotypic period that has been defined previously for three of the ten phyla, suggesting that transcriptional circuits and signalling mechanisms active during this transition are crucial for defining the phyletic body plan and that the mid-developmental transition may be used to define phylotypic periods in other phyla. Placing these observations alongside the reported conservation of mid-development within phyla, we propose that a phylum may be defined as a collection of species whose gene expression at the mid-developmental transition is both highly conserved among them, yet divergent relative to other species. PMID: 26886793 [PubMed - as supplied by publisher] 17. J Evol Biol. 2016 Feb 16. doi: 10.1111/jeb.12847. [Epub ahead of print] Parallel effects of the inversion In(3R)Payne on body size across the North American and Australian clines in Drosophila melanogaster. Kapun M(1), Schmidt C(1), Durmaz E(1), Schmidt PS(2), Flatt T(1). Author information: (1)Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland. (2)Department of Biology, University of Pennsylvania, Philadelphia, USA. Chromosomal inversions are thought to play a major role in climatic adaptation. In D. melanogaster, the cosmopolitan inversion In(3R)Payne exhibits latitudinal clines on multiple continents. Since many fitness traits show similar clines, it is tempting to hypothesize that In(3R)P underlies observed clinal patterns for some of these traits. In support of this idea, previous work in Australian populations has demonstrated that In(3R)P affects body size but not development time or cold resistance. However, similar data from other clines of this inversion are largely lacking; finding parallel effects of In(3R)P across multiple clines would considerably strengthen the case for clinal selection. Here, we have analyzed the phenotypic effects of In(3R)P in populations originating from the endpoints of the latitudinal cline along the North American east coast. We measured development time, egg-to-adult survival, several size-related traits (femur and tibia length, wing area and shape), chill coma recovery, oxidative stress resistance and triglyceride content in homokaryon lines carrying In(3R)P or the standard arrangement. Our central finding is that the effects of In(3R)P along the North American cline match those observed in Australia: standard arrangement lines were larger than inverted lines, but the inversion did not influence development time or cold resistance. Similarly, In(3R)P did not affect egg-to-adult survival, oxidative stress resistance and lipid content. In(3R)P thus seems to specifically affect size traits in populations from both continents. This parallelism strongly suggests an adaptive pattern, whereby the inversion has captured alleles associated with growth regulation and clinal selection acts on size across both continents. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved. PMID: 26881839 [PubMed - as supplied by publisher] 18. J Econ Entomol. 2016 Feb 14. pii: tow006. [Epub ahead of print] Thermal Tolerances of the Spotted-Wing Drosophila Drosophila suzukii (Diptera: Drosophilidae). Ryan GD(1), Emiljanowicz L(2), Wilkinson F(2), Kornya M(2), Newman JA(2). Author information: (1)School of Environmental Sciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada (geraldinedryan@gmail.com; lemiljan@gmail.com; cescawilkinson_123_@hotmail.co.uk; mkornya2@uwo.ca; jnewma01@uoguelph.ca) geraldinedryan@gmail.com. (2)School of Environmental Sciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada (geraldinedryan@gmail.com; lemiljan@gmail.com; cescawilkinson_123_@hotmail.co.uk; mkornya2@uwo.ca; jnewma01@uoguelph.ca). The spotted-wing drosophila (Drosophila suzukii Matsumura) is an invasive species of Asian origin that is now widely distributed in North America and Europe. Because of the female's serrated ovipositor, eggs are laid in preharvest fruit, causing large economic losses in cultivated berries and stone fruit. Modeling D. suzukii population dynamics and potential distribution will require information on its thermal tolerance. Large summer populations have been found in regions with severe winter conditions, though little is known about responses to prolonged low-temperature exposure. We used controlled chambers to examine D. suzukii fecundity, development rate, and mortality across a range of temperatures encompassing the upper and lower thresholds (5-35°C). Optimal temperatures (Topt) were found to be 28.2°C for the development of the egg-to-adult stage, and 22.9°C for reproductive output. No adult eclosion occurred below 8.1°C (Tlower) or above 30.9°C (Tupper). We also investigated survival outcomes following prolonged (42-d) low-temperature exposure to a simulated cold winter (-5, -3, -1, 1, 3, and 5°C). Adult survival was dependent on temperature, with a mean LT50 of 4.9°C. There were no effects of sex, mating status, geographic strain, and photoperiod preexposure on overwintering survival. Thirty-eight percent of females that were mated prior, but not after, prolonged low-temperature exposure produced viable offspring, suggesting that this species may undergo sperm storage. This study provides data on the thermal tolerances of D. suzukii, which can be used for models of D. suzukii population dynamics, degree-day, and distribution models. © The Authors 2016. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com. PMID: 26880397 [PubMed - as supplied by publisher] 19. Mol Biol Evol. 2016 Feb 12. pii: msw027. [Epub ahead of print] Codon usage selection can bias estimation of the fraction of adaptive amino acid fixations. Matsumoto T(1), John A(1), Baeza-Centurion P(1), Li B(1), Akashi H(2). Author information: (1)Division of Evolutionary Genetics, National Institute of Genetics, 1111, Yata, Mishima, Shizuoka-ken, 411-8540 Japan. (2)Division of Evolutionary Genetics, National Institute of Genetics, 1111, Yata, Mishima, Shizuoka-ken, 411-8540 Japan Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI), 1111, Yata, Mishima, Shizuoka 411-8540, Japan. hiakashi@nig.ac.jp. A growing number of molecular evolutionary studies are estimating the proportion of adaptive amino acid substitutions (alpha) from comparisons of ratios of polymorphic and fixed DNA mutations. Here, we examine how violations of two of the model assumptions, neutral evolution of synonymous mutations and stationary base composition, affect alpha estimation. We simulated the evolution of coding sequences assuming weak selection on synonymous codon usage bias and neutral protein evolution, alpha = 0. We show that weak selection on synonymous mutations can give polymorphism/divergence ratios that yield alpha-hat (estimated alpha) considerably larger than its true value. Non-stationary evolution (changes in population size, selection or mutation) can exacerbate such biases or, in some scenarios, give biases in the opposite direction, alpha-hat < alpha. These results demonstrate that two factors that appear to be prevalent among taxa, weak selection on synonymous mutations and non-steady-state nucleotide composition, should be considered when estimating alpha. Estimates of the proportion of adaptive amino acid fixations from large-scale analyses of Drosophila melanogaster polymorphism and divergence data are positively correlated with codon usage bias. Such patterns are consistent with alpha-hat inflation from weak selection on synonymous mutations and/or mutational changes within the examined gene trees. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com. PMID: 26873577 [PubMed - as supplied by publisher] 20. Genome Biol Evol. 2016 Feb 11;8(3):507-18. doi: 10.1093/gbe/evw018. Duplication and Diversification of Dipteran Argonaute Genes, and the Evolutionary Divergence of Piwi and Aubergine. Lewis SH(1), Salmela H(2), Obbard DJ(3). Author information: (1)Institute of Evolutionary Biology, University of Edinburgh, United Kingdom Present Address: Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH sam.lewis@gen.cam.ac.uk. (2)Department of Biosciences, Centre of Excellence in Biological Interactions, University of Helsinki, Helsinki, Finland. (3)Institute of Evolutionary Biology, University of Edinburgh, United Kingdom Centre for Immunity, Infection and Evolution, University of Edinburgh, United Kingdom. Genetic studies of Drosophila melanogaster have provided a paradigm for RNA interference (RNAi) in arthropods, in which the microRNA and antiviral pathways are each mediated by a single Argonaute (Ago1 and Ago2) and germline suppression of transposable elements is mediated by a trio of Piwi-subfamily Argonaute proteins (Ago3, Aub, and Piwi). Without a suitable evolutionary context, deviations from this can be interpreted as derived or idiosyncratic. Here we analyze the evolution of Argonaute genes across the genomes and transcriptomes of 86 Dipteran species, showing that variation in copy number can occur rapidly, and that there is constant flux in some RNAi mechanisms. The lability of the RNAi pathways is illustrated by the divergence of Aub and Piwi (182-156 Ma), independent origins of multiple Piwi-family genes in Aedes mosquitoes (less than 25Ma), and the recent duplications of Ago2 and Ago3 in the tsetse fly Glossina morsitans. In each case the tissue specificity of these genes has altered, suggesting functional divergence or innovation, and consistent with the action of dynamic selection pressures across the Argonaute gene family. We find there are large differences in evolutionary rates and gene turnover between pathways, and that paralogs of Ago2, Ago3, and Piwi/Aub show contrasting rates of evolution after duplication. This suggests that Argonautes undergo frequent evolutionary expansions that facilitate functional divergence. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. PMID: 26868596 [PubMed - in process] 21. BMC Evol Biol. 2016 Feb 9;16(1):35. doi: 10.1186/s12862-016-0606-3. Natural selection in a population of Drosophila melanogaster explained by changes in gene expression caused by sequence variation in core promoter regions. Sato MP(1), Makino T(2), Kawata M(3). Author information: (1)Department of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, 6-3, Aramaki Aza Aoba, Aoba-ku, Sendai, 980-8578, Japan. mitsuhikoevolution@gmail.com. (2)Department of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, 6-3, Aramaki Aza Aoba, Aoba-ku, Sendai, 980-8578, Japan. tamakino@m.tohoku.ac.jp. (3)Department of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, 6-3, Aramaki Aza Aoba, Aoba-ku, Sendai, 980-8578, Japan. kawata@m.tohoku.ac.jp. BACKGROUND: Understanding the evolutionary forces that influence variation in gene regulatory regions in natural populations is an important challenge for evolutionary biology because natural selection for such variations could promote adaptive phenotypic evolution. Recently, whole-genome sequence analyses have identified regulatory regions subject to natural selection. However, these studies could not identify the relationship between sequence variation in the detected regions and change in gene expression levels. We analyzed sequence variations in core promoter regions, which are critical regions for gene regulation in higher eukaryotes, in a natural population of Drosophila melanogaster, and identified core promoter sequence variations associated with differences in gene expression levels subjected to natural selection. RESULTS: Among the core promoter regions whose sequence variation could change transcription factor binding sites and explain differences in expression levels, three core promoter regions were detected as candidates associated with purifying selection or selective sweep and seven as candidates associated with balancing selection, excluding the possibility of linkage between these regions and core promoter regions. CHKov1, which confers resistance to the sigma virus and related insecticides, was identified as core promoter regions that has been subject to selective sweep, although it could not be denied that selection for variation in core promoter regions was due to linked single nucleotide polymorphisms in the regulatory region outside core promoter regions. Nucleotide changes in core promoter regions of CHKov1 caused the loss of two basal transcription factor binding sites and acquisition of one transcription factor binding site, resulting in decreased gene expression levels. Of nine core promoter regions regions associated with balancing selection, brat, and CG9044 are associated with neuromuscular junction development, and Nmda1 are associated with learning, behavioral plasticity, and memory. Diversity of neural and behavioral traits may have been maintained by balancing selection. CONCLUSIONS: Our results revealed the evolutionary process occurring by natural selection for differences in gene expression levels caused by sequence variation in core promoter regions in a natural population. The sequences of core promoter regions were diverse even within the population, possibly providing a source for natural selection. PMCID: PMC4748610 PMID: 26860869 [PubMed - in process] 22. Behav Processes. 2016 Apr;125:76-84. doi: 10.1016/j.beproc.2016.02.002. Epub 2016 Feb 3. Mate-choice copying in Drosophila melanogaster: Impact of demonstration conditions and male-male competition. Germain M(1), Blanchet S(2), Loyau A(3), Danchin É(4). Author information: (1)Université de Lyon, F-69000, Lyon; Université Lyon 1; CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne, France; CNRS, Université Paul Sabatier, ENFA, UMR5174 EDB (Laboratoire Évolution & Diversité Biologique), 118 route de Narbonne, 31062 Toulouse, France; Université de Toulouse, UMR5174 EDB, F-31062 Toulouse, France. Electronic address: marion.germain@univ-lyon1.fr. (2)CNRS, Université Paul Sabatier, ENFA, UMR5174 EDB (Laboratoire Évolution & Diversité Biologique), 118 route de Narbonne, 31062 Toulouse, France; CNRS, 09200 Moulis, France. (3)Helmholtz Centre for Environmental Research-UFZ, Department of Conservation Biology, Permoserstrasse 15, 04318 Leipzig, Germany; Helmholtz Centre for Environmental Research-UFZ, Department of System Ecotoxicology, Permoserstrasse 15, 04138 Leipzig, Germany; ECOLAB, Université de Toulouse, CNRS, INPT, UPS, France. (4)CNRS, Université Paul Sabatier, ENFA, UMR5174 EDB (Laboratoire Évolution & Diversité Biologique), 118 route de Narbonne, 31062 Toulouse, France; Université de Toulouse, UMR5174 EDB, F-31062 Toulouse, France. Individuals of many species, including invertebrates, have been shown to use social information in mate choice, notably by extracting information from the mating performance of opposite sex conspecifics, a process called "mate-choice copying" (MCC). Here, we performed four experiments with Drosophila melanogaster to investigate two aspects of MCC methodology: whether (i) providing positive and negative social information simultaneously or sequentially during the demonstration phase of the protocol, and (ii) male-male competition during the mate-choice test, affect MCC. We found that the simultaneous provision of positive and negative information during demonstrations hampered female MCC performance, compared to the sequential provision of information. This can be interpreted in two alternative, yet not exclusive, ways: (i) attentional mechanisms may restrict the focus of the brain to one source of information at a time, and/or (ii) the shorter duration of demonstrations in the simultaneous protocol may have not permit full social learning use and may explain the non-detection of MCC in that protocol. Moreover, we did not detect any significant effect of male-male competition on female choice. This study thus provides further evidence for MCC in D. melanogaster and expands on the necessary methodology for detailed studies. Copyright © 2016 Elsevier B.V. All rights reserved. PMID: 26851455 [PubMed - in process] 23. Biol Sex Differ. 2016 Feb 3;7:10. doi: 10.1186/s13293-016-0064-z. eCollection 2016. The phenotypic impact of the male-specific region of chromosome-Y in inbred mating: the role of genetic variants and gene duplications in multiple inbred rat strains. Prokop JW(1), Tsaih SW(2), Faber AB(3), Boehme S(4), Underwood AC(5), Troyer S(4), Playl L(4), Milsted A(4), Turner ME(4), Ely D(4), Martins AS(6), Tutaj M(2), Lazar J(1), Dwinell MR(3), Jacob HJ(1). Author information: (1)HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA ; Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI 53226 USA ; Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226 USA. (2)Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI 53226 USA. (3)Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI 53226 USA ; Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226 USA. (4)Department of Biology, The University of Akron, Akron, OH 44325 USA. (5)Department of Mathematics and Science, Walsh University, North Canton, OH 44720 USA. (6)Núcleo de Fisiologia Geral e Genômica Funcional-ICB-Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais Brazil. BACKGOUND: The male-specific region of chromosome-Y (MSY) contributes to phenotypes outside of testis development and has a high rate of evolution between mammalian species. With a lack of genomic crossover, MSY is one of the few genomic areas under similar variation and evolutionary selection in inbred and outbred animal populations, allowing for an assessment of evolutionary mechanisms to translate between the populations. METHODS: Using next-generation sequencing, MSY consomic strains, molecular characterization, and large-scale phenotyping, we present here regions of MSY that contribute to inbred strain phenotypes. RESULTS: We have shown that (1) MSY of rat has nine autosomal gene transposition events with strain-specific selection; (2) sequence variants in MSY occur with a 1.98-fold higher number of variants than other chromosomes in seven sequenced rat strains; (3) Sry, the most studied MSY gene, has undergone extensive gene duplications, driving ubiquitous expression not seen in human or mouse; (4) the expression profile of Sry in the rat is driven by the insertion of the Sry2 copy into an intron of the ubiquitously expressed Kdm5d gene in antisense orientation, but due to several loss of function mutations in the Sry2 protein, nuclear localization and transcriptional control are decreased; (5) expression of Sry copies other than Sry2 in the rat overlaps with the expression profile for human SRY; (6) gene duplications and sequence variants (P76T) of Sry can be selected for phenotypes such as high blood pressure and androgen receptor signaling within inbred mating; and most importantly, (7) per chromosome size, MSY contributes to higher strain-specific phenotypic variation relative to all other chromosomes, with 53 phenotypes showing both a male to female and consomic cross significance. CONCLUSION: The data presented supports a high probability of MSY genetic variation altering a broad range of inbred rat phenotypes. PMCID: PMC4740989 PMID: 26848384 [PubMed] 24. Nature. 2016 Feb 18;530(7590):331-5. doi: 10.1038/nature16548. Epub 2016 Jan 27. The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea. Olsen JL(1), Rouzé P(2), Verhelst B(2), Lin YC(2), Bayer T(3), Collen J(4), Dattolo E(5), De Paoli E(6), Dittami S(4), Maumus F(7), Michel G(4), Kersting A(8,)(9), Lauritano C(5), Lohaus R(2), Töpel M(10), Tonon T(4), Vanneste K(2), Amirebrahimi M(11), Brakel J(3), Boström C(12), Chovatia M(11), Grimwood J(11,)(13), Jenkins JW(11,)(13), Jueterbock A(14), Mraz A(15), Stam WT(1), Tice H(11), Bornberg-Bauer E(8), Green PJ(16), Pearson GA(17), Procaccini G(5), Duarte CM(18), Schmutz J(11,)(13), Reusch TB(3,)(19), Van de Peer Y(2,)(20,)(21). Author information: (1)Groningen Institute of Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103, 9700 CC Groningen, The Netherlands. (2)Department of Plant Systems Biology, VIB and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium. (3)GEOMAR Helmholtz Centre for Ocean Research-Kiel, Evolutionary Ecology, Düsternbrooker Weg 20, D-24105 Kiel, Germany. (4)Sorbonne Université, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff cedex, France. (5)Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy. (6)Dipartimento di Scienze Agrarie e Ambientali, University of Udine, Via delle Scienze 206, 33100 Udine, Italy. (7)INRA, UR1164 URGI-Research Unit in Genomics-Info, INRA de Versailles-Grignon, Route de Saint-Cyr, Versailles 78026, France. (8)Institute for Evolution and Biodiversity, Westfälische Wilhelms-University of Münster, Hüfferstrasse 1, D-48149 Münster, Germany. (9)Institute for Computer Science, Heinrich Heine University, D-40255 Duesseldorf, Germany. (10)Department of Biological and Environmental Sciences, Bioinformatics Infrastructure for Life Sciences (BILS), University of Gothenburg, Medicinaregatan 18A, 40530 Gothenburg, Sweden. (11)Department of Energy Joint Genome Institute, 2800 Mitchell Dr., #100, Walnut Creek, California 94598, USA. (12)Environmental and Marine Biology, Faculty of Science and Engineering, Åbo Akademi University, Artillerigatan 6, FI-20520 Turku/Åbo, Finland. (13)HudsonAlpha Institute for Biotechnology, 601 Genome Way NW, Huntsville, Alabama 35806, USA. (14)Marine Ecology Group, Nord University, Postbox 1490, 8049 Bodø, Norway. (15)Amplicon Express, 2345 NE Hopkins Ct., Pullman, Washington 99163, USA. (16)School of Marine Science and Policy, Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, 15-Innovation Way, Newark, Delaware 19711, USA. (17)Marine Ecology and Evolution, Centre for Marine Sciences (CCMAR), University of Algarve, 8005-139 Faro, Portugal. (18)King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Thuwal 23955-6900, Saudi Arabia. (19)University of Kiel, Faculty of Mathematics and Natural Sciences, Christian-Albrechts-Platz 4, 24118 Kiel, Germany. (20)Genomics Research Institute, University of Pretoria, Hatfield Campus, Pretoria 0028, South Africa. (21)Bioinformatics Institute Ghent, Ghent University, Ghent B-9000, Belgium. Comment in Nature. 2016 Feb 18;530(7590):290-1. Seagrasses colonized the sea on at least three independent occasions to form the basis of one of the most productive and widespread coastal ecosystems on the planet. Here we report the genome of Zostera marina (L.), the first, to our knowledge, marine angiosperm to be fully sequenced. This reveals unique insights into the genomic losses and gains involved in achieving the structural and physiological adaptations required for its marine lifestyle, arguably the most severe habitat shift ever accomplished by flowering plants. Key angiosperm innovations that were lost include the entire repertoire of stomatal genes, genes involved in the synthesis of terpenoids and ethylene signalling, and genes for ultraviolet protection and phytochromes for far-red sensing. Seagrasses have also regained functions enabling them to adjust to full salinity. Their cell walls contain all of the polysaccharides typical of land plants, but also contain polyanionic, low-methylated pectins and sulfated galactans, a feature shared with the cell walls of all macroalgae and that is important for ion homoeostasis, nutrient uptake and O2/CO2 exchange through leaf epidermal cells. The Z. marina genome resource will markedly advance a wide range of functional ecological studies from adaptation of marine ecosystems under climate warming, to unravelling the mechanisms of osmoregulation under high salinities that may further inform our understanding of the evolution of salt tolerance in crop plants. PMID: 26814964 [PubMed - indexed for MEDLINE] 25. Evolution. 2016 Feb;70(2):456-64. doi: 10.1111/evo.12843. Epub 2016 Jan 12. Increases in the evolutionary potential of upper thermal limits under warmer temperatures in two rainforest Drosophila species. van Heerwaarden B(1), Malmberg M(1,)(2), Sgrò CM(3). Author information: (1)School of Biological Sciences, Monash University, Clayton 3800, Melbourne, Australia. (2)Department of Applied Systems Biology, La Trobe University, Bundoora 3083, Melbourne, Australia. (3)School of Biological Sciences, Monash University, Clayton 3800, Melbourne, Australia. carla.sgro@monash.edu. Tropical and subtropical species represent the majority of biodiversity. These species are predicted to lack the capacity to evolve higher thermal limits in response to selection imposed by climatic change. However, these assessments have relied on indirect estimates of adaptive capacity, using conditions that do not reflect environmental changes projected under climate change. Using a paternal half-sib full-sib breeding design, we estimated the additive genetic variance and narrow-sense heritability for adult upper thermal limits in two rainforest-restricted species of Drosophila reared under two thermal regimes, reflecting increases in seasonal temperature projected for the Wet Tropics of Australia and under standard laboratory conditions (constant 25°C). Estimates of additive genetic variation and narrow-sense heritability for adult heat tolerance were significantly different from zero in both species under projected summer, but not winter or constant, thermal regimes. In contrast, significant broad-sense genetic variation was apparent in all thermal regimes for egg-to-adult viability. Environment-dependent changes in the expression of genetic variation for adult upper thermal limits suggest that predicting adaptive responses to climate change will be difficult. Estimating adaptive capacity under conditions that do not reflect future environmental conditions may provide limited insight into evolutionary responses to climate change. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution. PMID: 26703976 [PubMed - in process] 26. Genetics. 2016 Feb;202(2):675-87. doi: 10.1534/genetics.115.183822. Epub 2015 Nov 27. Differential Masking of Natural Genetic Variation by miR-9a in Drosophila. Cassidy JJ(1), Straughan AJ(1), Carthew RW(2). Author information: (1)Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208. (2)Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208 r-carthew@northwestern.edu. Genetic variation is prevalent among individuals of the same species and yet the potential effects of genetic variation on developmental outcomes are frequently suppressed. Understanding the mechanisms that are responsible for this suppression is an important goal. Previously, we found that the microRNA miR-9a mitigates the impact of natural genetic variants that promote the development of scutellar bristles in adult Drosophila. Here we find that miR-9a does not affect the impact of genetic variants that inhibit the development of scutellar bristles. We show this using both directional and stabilizing selection in the laboratory. This specificity of action suggests that miR-9a does not interact with all functional classes of developmental genetic variants affecting sensory organ development. We also investigate the impact of miR-9a on a fitness trait, which is adult viability. At elevated physiological temperatures, miR-9a contributes to viability through masking genetic variants that hinder adult viability. We conclude that miR-9a activity in different developmental networks contributes to suppression of natural variants from perturbing development. Copyright © 2016 by the Genetics Society of America. PMID: 26614743 [PubMed - in process] 27. J Evol Biol. 2016 Feb;29(2):407-17. doi: 10.1111/jeb.12795. Epub 2015 Dec 16. Evolution of increased adult longevity in Drosophila melanogaster populations selected for adaptation to larval crowding. Shenoi VN(1), Ali SZ(1), Prasad NG(1). Author information: (1)Indian Institute of Science Education and Research Mohali, Mohali, India. In holometabolous animals such as Drosophila melanogaster, larval crowding can affect a wide range of larval and adult traits. Adults emerging from high larval density cultures have smaller body size and increased mean life span compared to flies emerging from low larval density cultures. Therefore, adaptation to larval crowding could potentially affect adult longevity as a correlated response. We addressed this issue by studying a set of large, outbred populations of D. melanogaster, experimentally evolved for adaptation to larval crowding for 83 generations. We assayed longevity of adult flies from both selected (MCUs) and control populations (MBs) after growing them at different larval densities. We found that MCUs have evolved increased mean longevity compared to MBs at all larval densities. The interaction between selection regime and larval density was not significant, indicating that the density dependence of mean longevity had not evolved in the MCU populations. The increase in longevity in MCUs can be partially attributed to their lower rates of ageing. It is also noteworthy that reaction norm of dry body weight, a trait probably under direct selection in our populations, has indeed evolved in MCU populations. To the best of our knowledge, this is the first report of the evolution of adult longevity as a correlated response of adaptation to larval crowding. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology. PMID: 26575793 [PubMed - in process] 28. J Evol Biol. 2016 Feb;29(2):455-60. doi: 10.1111/jeb.12784. Epub 2015 Nov 22. Within-species reproductive costs affect the asymmetry of satyrization in Drosophila. Yassin A(1), David JR(2,)(3). Author information: (1)Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA. (2)Laboratoire Evolution, Génomes, Comportement, Ecologie (EGCE), CNRS, IRD, Université Paris Sud, Université Paris-Saclay, Gif-sur-Yvette, France. (3)CNRS UMR7205, Institut de Systématique, Evolution et Biodiversité (ISyEB), Muséum National d'Histoire Naturelle, Paris, France. Understanding how species interactions influence their distribution and evolution is a fundamental question in evolutionary biology. Theory suggests that asymmetric reproductive interference, in which one species induces higher reproductive costs on another species, may be more important in delimiting species boundaries than interspecific competition over resources. However, the underlying mechanisms of such asymmetry remain unclear. Here, we test whether differences in within-species reproductive costs determine the between-species asymmetry of costs using three allopatric Drosophila species belonging to the melanogaster subgroup. Our results support this hypothesis, especially in a pair of insular species. Males of one species that induce costs to their conspecific females led to a 5-fold increase of heterospecific females mortality with dead flies bearing spectacular large melanized wounds on their genitalia. Males of the other species were harmful neither to their conspecific nor heterospecific females. Comparative studies of within-species reproductive costs may therefore be a valuable tool for predicting between-species interactions and community structures. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology. PMID: 26538290 [PubMed - in process] 29. Mol Biol Evol. 2016 Feb;33(2):367-74. doi: 10.1093/molbev/msv221. Epub 2015 Oct 22. Ancient Male Recombination Shaped Genetic Diversity of Neo-Y Chromosome in Drosophila albomicans. Satomura K(1), Tamura K(2). Author information: (1)Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan. (2)Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan Research Center for Genomics and Bioinformatics, Tokyo Metropolitan University, Tokyo, Japan ktamura@tmu.ac.jp. Researchers studying Y chromosome evolution have drawn attention to neo-Y chromosomes in Drosophila species due to their resembling the initial stage of Y chromosome evolution. In the studies of neo-Y chromosome of Drosophila miranda, the extremely low genetic diversity observed suggested various modes of natural selection acting on the nonrecombining genome. However, alternative possibility may come from its peculiar origin from a single chromosomal fusion event with male achiasmy, which potentially caused and maintained the low genetic diversity of the neo-Y chromosome. Here, we report a real case where a neo-Y chromosome is in transition from an autosome to a typical Y chromosome. The neo-Y chromosome of Drosophila albomicans harbored a rich genetic diversity comparable to its gametologous neo-X chromosome and an autosome in the same genome. Analyzing sequence variations in 53 genes and measuring recombination rates between pairs of loci by cross experiments, we elucidated the evolutionary scenario of the neo-Y chromosome of D. albomicans having high genetic diversity without assuming selective force, i.e., it originated from a single chromosomal fusion event, experienced meiotic recombination during the initial stage of evolution and diverged from neo-X chromosome by the suppression of recombination tens or a few hundreds of thousand years ago. Consequently, the observed high genetic diversity on the neo-Y chromosome suggested a strong effect of meiotic recombination to introduce genetic variations into the newly arisen sex chromosome. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com. PMID: 26494844 [PubMed - in process] 30. Mol Biol Evol. 2016 Feb;33(2):413-28. doi: 10.1093/molbev/msv227. Epub 2015 Oct 20. Drosophila X-Linked Genes Have Lower Translation Rates than Autosomal Genes. Zhang Z(1), Presgraves DC(2). Author information: (1)Department of Biology, University of Rochester zhangz.sci@gmail.com. (2)Department of Biology, University of Rochester. In Drosophila, X-linked and autosomal genes achieve comparable expression at the mRNA level. Whether comparable X-autosome gene expression is realized at the translational and, ultimately, the protein levels is, however, unknown. Previous studies suggest the possibility of higher translation rates for X-linked genes owing to stronger usage of preferred codons. In this study, we use public ribosome profiling data from Drosophila melanogaster to infer translation rates on the X chromosome versus the autosomes. We find that X-linked genes have consistently lower ribosome densities than autosomal genes in S2 cells, early embryos, eggs, and mature oocytes. Surprisingly, the lower ribosome densities of X-linked genes are not consistent with faster translation elongation but instead imply slower translation initiation. In particular, X-linked genes have sequence features known to slow translation initiation such as stronger mRNA structure near start codons and longer 5'-UTRs. Comparison to outgroup species suggests that stronger mRNA structure is an evolved feature of Drosophila X chromosomes. Finally, we find that the magnitude of the X-autosome difference in ribosome densities is smaller for genes encoding members of protein complexes, suggesting that stoichiometry constrains the evolution of translation rates. In sum, our analyses suggest that Drosophila X-linked genes have evolved lower translation rates than autosomal genes despite stronger usage of preferred codons. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com. PMID: 26486873 [PubMed - in process] 31. Dev Neurobiol. 2016 Feb;76(2):225-37. doi: 10.1002/dneu.22309. Epub 2015 Jun 8. Epithelial microRNA-9a regulates dendrite growth through Fmi-Gq signaling in Drosophila sensory neurons. Wang Y(1,)(2), Wang H(1,)(3), Li X(1,)(3), Li Y(1). Author information: (1)State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. (2)Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China. (3)University of Chinese Academy of Sciences, Beijing, 100049, China. microRNA-9 (miR-9) is highly expressed in the nervous system across species and plays essential roles in neurogenesis and axon growth; however, little is known about the mechanisms that link miR-9 with dendrite growth. Using an in vivo model of Drosophila class I dendrite arborization (da) neurons, we show that miR-9a, a Drosophila homolog of mammalian miR-9, downregulates the cadherin protein Flamingo (Fmi) thereby attenuating dendrite development in a non-cell autonomous manner. In miR-9a knockout mutants, the dendrite length of a sensory neuron ddaE was significantly increased. Intriguingly, miR-9a is specifically expressed in epithelial cells but not in neurons, thus the expression of epithelial but not neuronal Fmi is greatly elevated in miR-9a mutants. In contrast, overexpression of Fmi in the neuron resulted in a reduction in dendrite growth, suggesting that neuronal Fmi plays a suppressive role in dendrite growth, and that increased epithelial Fmi might promote dendrite growth by competitively binding to neuronal Fmi. Fmi has been proposed as a G protein-coupled receptor (GPCR), we find that neuronal G protein Gαq (Gq), but not Go, may function downstream of Fmi to negatively regulate dendrite growth. Taken together, our results reveal a novel function of miR-9a in dendrite morphogenesis. Moreover, we suggest that Gq might mediate the intercellular signal of Fmi in neurons to suppress dendrite growth. Our findings provide novel insights into the complex regulatory mechanisms of microRNAs in dendrite development, and further reveal the interplay between the different components of Fmi, functioning in cadherin adhesion and GPCR signalling. © 2015 Wiley Periodicals, Inc. Develop Neurobiol 76: 225-237, 2016. © 2015 Wiley Periodicals, Inc. PMID: 26016469 [PubMed - in process]