1. Nature. 2015 Oct 1;526(7571):75-81. doi: 10.1038/nature15394. An integrated map of structural variation in 2,504 human genomes. Sudmant PH et al. Structural variants are implicated in numerous diseases and make up the majority of varying nucleotides among human genomes. Here we describe an integrated set of eight structural variant classes comprising both balanced and unbalanced variants, which we constructed using short-read DNA sequencing data and statistically phased onto haplotype blocks in 26 human populations. Analysing this set, we identify numerous gene-intersecting structural variants exhibiting population stratification and describe naturally occurring homozygous gene knockouts that suggest the dispensability of a variety of human genes. We demonstrate that structural variants are enriched on haplotypes identified by genome-wide association studies and exhibit enrichment for expression quantitative trait loci. Additionally, we uncover appreciable levels of structural variant complexity at different scales, including genic loci subject to clusters of repeated rearrangement and complex structural variants with multiple breakpoints likely to have formed through individual mutational events. Our catalogue will enhance future studies into structural variant demography, functional impact and disease association. PMID: 26432246 [PubMed - in process] 2. Nature. 2015 Oct 1;526(7571):68-74. doi: 10.1038/nature15393. A global reference for human genetic variation. 1000 Genomes Project Consortium, Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA, Abecasis GR. The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-genome sequencing, deep exome sequencing, and dense microarray genotyping. We characterized a broad spectrum of genetic variation, in total over 88 million variants (84.7 million single nucleotide polymorphisms (SNPs), 3.6 million short insertions/deletions (indels), and 60,000 structural variants), all phased onto high-quality haplotypes. This resource includes >99% of SNP variants with a frequency of >1% for a variety of ancestries. We describe the distribution of genetic variation across the global sample, and discuss the implications for common disease studies. PMID: 26432245 [PubMed - in process] 3. Evolution. 2015 Sep 30. doi: 10.1111/evo.12788. [Epub ahead of print] Intergenomic interactions between mitochondrial and Y-linked genes shape male mating patterns and fertility in Drosophila melanogaster. Yee WK(1), Rogell B(2,)(3), Lemos B(4), Dowling DK(2). Under maternal inheritance, mitochondrial genomes are prone to accumulate mutations that exhibit male-biased effects. Such mutations should, however, place selection on the nuclear genome for modifier adaptations that mitigate mitochondrial-incurred male harm. One gene region that might harbor such modifiers is the Y-chromosome, given the abundance of Y-linked variation for male fertility, and because Y-linked modifiers would not exert antagonistic effects in females because they would be found only in males. Recent studies in Drosophila revealed a set of nuclear genes whose expression is sensitive to allelic variation among mtDNA- and Y-haplotypes, suggesting these genes might be entwined in evolutionary conflict between mtDNA and Y. Here, we test whether genetic variation across mtDNA and Y haplotypes, sourced from three disjunct populations, interacts to affect male mating patterns and fertility across 10 days of early life in D. melanogaster. We also investigate whether coevolved mito-Y combinations outperform their evolutionarily novel counterparts, as predicted if the interacting Y-linked variance is comprised of modifier adaptations. Although we found no evidence that coevolved mito-Y combinations outperformed their novel counterparts, interactions between mtDNA and Y-chromosomes affected male mating patterns. These interactions were dependent on male age; thus male reproductive success was shaped by G×G×E interactions. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved. PMID: 26419212 [PubMed - as supplied by publisher] 4. Mol Biol Evol. 2015 Sep 28. pii: msv206. [Epub ahead of print] The roles of compensatory evolution and constraint in aminoacyl tRNA synthetase evolution. Adrion JR(1), White PS(2), Montooth KL(3). Mitochondrial protein translation requires interactions between transfer RNAs encoded by the mitochondrial genome (mt-tRNAs) and mitochondrial aminoacyl tRNA synthetase proteins (mt-aaRS) encoded by the nuclear genome. It has been argued that animal mt-tRNAs have higher deleterious substitution rates relative to their nuclear-encoded counterparts, the cytoplasmic tRNAs (cyt-tRNAs). This dynamic predicts elevated rates of compensatory evolution of mt-aaRS that interact with mt-tRNAs, relative to aaRS that interact with cyt-tRNAs (cyt-aaRS). We find that mt-aaRS do evolve at significantly higher rates (exemplified by higher dN and dN/dS) relative to cyt-aaRS, across mammals, birds, and Drosophila. While this pattern supports a model of compensatory evolution, the level at which a gene is expressed is a more general predictor of protein evolutionary rate. We find that gene expression level explains 10-56% of the variance in aaRS dN/dS, and that cyt-aaRS are more highly expressed in addition to having have lower dN/dS values relative to mt-aaRS, consistent with more highly expressed genes being more evolutionarily constrained. Furthermore, we find no evidence of positive selection acting on either class of aaRS protein, as would be expected under a model of compensatory evolution. Nevertheless, the signature of faster mt-aaRS evolution persists in mammalian, but not bird or Drosophila, lineages after controlling for gene expression, suggesting some additional effect of compensatory evolution for mammalian mt-aaRS. We conclude that gene expression is the strongest factor governing differential amino acid substitution rates in proteins interacting with mitochondrial versus cytoplasmic factors, with important differences in mt-aaRS molecular evolution among taxonomic groups. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. PMID: 26416980 [PubMed - as supplied by publisher] 5. J Evol Biol. 2015 Sep 23. doi: 10.1111/jeb.12763. [Epub ahead of print] Evolution of reduced postcopulatory molecular interactions in Drosophila populations lacking sperm competition. Hollis B(1), Houle D(2), Kawecki TJ(1). In many species with internal fertilization, molecules transferred in the male ejaculate trigger and interact with physiological changes in females. It is controversial to what extent these interactions between the sexes act synergistically to mediate the female switch to a reproductive state or instead reflect sexual antagonism evolved as a byproduct of sexual selection on males. To address this question, we eliminated sexual selection by enforcing monogamy in populations of Drosophila melanogaster for 65 generations and then measured the expression of male seminal fluid protein genes and genes involved in the female response to mating. In the absence of sperm competition, male and female reproductive interests are perfectly aligned and any antagonism should be reduced by natural selection. Consistent with this idea, males from monogamous populations showed reduced expression of seminal fluid protein genes, 16% less on average than in polygamous males. Further, we identified 428 genes that responded to mating in females. After mating, females with an evolutionary history of monogamy exhibited lower relative expression of genes that were upregulated in response to mating and higher expression of genes that were downregulated-in other words, their post-mating transcriptome appeared more virgin-like. Surprisingly, these genes showed a similar pattern even before mating, suggesting that monogamous females evolved to be less poised for mating and the accompanying receipt of male seminal fluid proteins. This reduced investment by both monogamous males and females in molecules involved in postcopulatory interactions points to a pervasive role of sexual conflict in shaping these interactions. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved. PMID: 26395588 [PubMed - as supplied by publisher] 6. Development. 2015 Sep 15;142(18):3100-12. doi: 10.1242/dev.120048. Genomic approaches to studying human-specific developmental traits. Franchini LF(1), Pollard KS(2). Changes in developmental regulatory programs drive both disease and phenotypic differences among species. Linking human-specific traits to alterations in development is challenging, because we have lacked the tools to assay and manipulate regulatory networks in human and primate embryonic cells. This field was transformed by the sequencing of hundreds of genomes - human and non-human - that can be compared to discover the regulatory machinery of genes involved in human development. This approach has identified thousands of human-specific genome alterations in developmental genes and their regulatory regions. With recent advances in stem cell techniques, genome engineering, and genomics, we can now test these sequences for effects on developmental gene regulation and downstream phenotypes in human cells and tissues. © 2015. Published by The Company of Biologists Ltd. PMID: 26395139 [PubMed - in process] 7. BMC Evol Biol. 2015 Sep 21;15(1):203. doi: 10.1186/s12862-015-0472-4. The effects of natural selection across molecular pathways in Drosophila melanogaster. Vedanayagam JP(1), Garrigan D(2). BACKGROUND: Whole-genome RNA interference post-transcriptional silencing (RNAi) is a widely used method for studying the phenotypic effects of knocking down individual genes. In this study, we use a population genomic approach to characterize the rate of evolution for proteins affecting 26 RNAi knockdown phenotypes in Drosophila melanogaster. RESULTS: We find that only two of the 26 RNAi knockdown phenotypes are enriched for rapidly evolving proteins: innate immunity and regulation of Hedgehog signaling. Among all genes associated with an RNAi knockdown phenotype, we note examples in which the adaptively evolving proteins play a well-defined role in a given molecular pathway. However, most adaptively evolving proteins are found to perform more general cellular functions. When RNAi phenotypes are grouped into categories according to cellular function, we find that genes involved in the greatest number of phenotypic categories are also significantly more likely to have a history of rapid protein evolution. CONCLUSIONS: We show that genes that have been demonstrated to have a measurable effect on multiple molecular phenotypes show higher rates of protein evolution than genes having an effect on a single category of phenotype. Defining pleiotropy in this way yields very different results than previous studies that define pleiotropy by the number of physical interactions, which show highly connected proteins tend to evolve more slowly than lowly connected proteins. We suggest that a high degree of pleiotropy may increase the likelihood of compensatory substitution, consistent with modern theoretical work on adaptation. PMCID: PMC4578789 PMID: 26391223 [PubMed - in process] 8. Evolution. 2015 Sep 21. doi: 10.1111/evo.12778. [Epub ahead of print] Transcriptome-wide effects of sexual selection on the fate of new mutations. Collet JM(1), Blows MW(2), McGuigan K(2). Sexual selection on males is predicted to have widespread effects on genetic variation as a consequence of the pleiotropic allelic effects on sexual and nonsexual traits. We manipulated the opportunity for sexual selection on males during 27 generations of mutation accumulation in inbred lines of Drosophila serrata, and used a microarray platform to investigate the effect of sexual selection on the expression of 2689 genes. While gene expression signal was, on average, higher in the absence of sexual selection, this difference was small (0.1%). In contrast, sexual selection impacted substantially on the mutational variance in gene expression. Over all genes, mutational variance in gene expression was, on average, 42% higher when sexual selection operated than when it was absent. Our results indicate that sexual selection on males can generate widespread effects across the genome. An increase in mutational variance without a corresponding change in mean suggested that most expression traits were unlikely to be under direct sexual selection. Instead, the mutational variance in gene expression traits is consistent with divergence generated by widespread pleiotropic associations with traits affecting male mating success. © 2015 The Author(s). PMID: 26389669 [PubMed - as supplied by publisher] 9. Evolution. 2015 Sep 16. doi: 10.1111/evo.12775. [Epub ahead of print] Alleles versus mutations: Understanding the evolution of genetic architecture requires a molecular perspective on allelic origins. Remington DL(1). Perspectives on the role of large-effect quantitative trait loci (QTL) in the evolution of complex traits have shifted back and forth over the past few decades. Different sets of studies have produced contradictory insights on the evolution of genetic architecture. I argue that much of the confusion results from a failure to distinguish mutational and allelic effects, a limitation of using the Fisherian model of adaptive evolution as the lens through which the evolution of adaptive variation is examined. A molecular-based perspective reveals that allelic differences can involve the cumulative effects of many mutations plus intragenic recombination, a model that is supported by extensive empirical evidence. I discuss how different selection regimes could produce very different architectures of allelic effects under a molecular-based model, which may explain conflicting insights on genetic architecture from studies of variation within populations versus between divergently selected populations. I address shortcomings of genome-wide association study (GWAS) practices in light of more suitable models of allelic evolution, and suggest alternate GWAS strategies to generate more valid inferences about genetic architecture. Finally, I discuss how adopting more suitable models of allelic evolution could help redirect research on complex trait evolution toward addressing more meaningful questions in evolutionary biology. © 2015 The Author(s). PMID: 26374707 [PubMed - as supplied by publisher] 10. Evolution. 2015 Sep 16. doi: 10.1111/evo.12764. [Epub ahead of print] Sexual selection has minimal impact on effective population sizes in species with high rates of random offspring mortality: An empirical demonstration using fitness distributions. Pischedda A(1), Friberg U(2), Stewart AD(3), Miller PM(4), Rice WR(5). The effective population size (Ne ) is a fundamental parameter in population genetics that influences the rate of loss of genetic diversity. Sexual selection has the potential to reduce Ne by causing the sex-specific distributions of individuals that successfully reproduce to diverge. To empirically estimate the effect of sexual selection on Ne , we obtained fitness distributions for males and females from an outbred, laboratory-adapted population of Drosophila melanogaster. We observed strong sexual selection in this population (the variance in male reproductive success was ∼14 times higher than that for females), but found that sexual selection had only a modest effect on Ne , which was 75% of the census size. This occurs because the substantial random offspring mortality in this population diminishes the effects of sexual selection on Ne , a result that necessarily applies to other high fecundity species. The inclusion of this random offspring mortality creates a scaling effect that reduces the variance/mean ratios for male and female reproductive success and causes them to converge. Our results demonstrate that measuring reproductive success without considering offspring mortality can underestimate Ne and overestimate the genetic consequences of sexual selection. Similarly, comparing genetic diversity among different genomic components may fail to detect strong sexual selection. © 2015 The Author(s). PMID: 26374275 [PubMed - as supplied by publisher] 11. Proc Natl Acad Sci U S A. 2015 Sep 14. pii: 201505357. [Epub ahead of print] Complex constraints on allometry revealed by artificial selection on the wing of Drosophila melanogaster. Bolstad GH(1), Cassara JA(2), Márquez E(2), Hansen TF(3), van der Linde K(2), Houle D(2), Pélabon C(4). Precise exponential scaling with size is a fundamental aspect of phenotypic variation. These allometric power laws are often invariant across taxa and have long been hypothesized to reflect developmental constraints. Here we test this hypothesis by investigating the evolutionary potential of an allometric scaling relationship in drosophilid wing shape that is nearly invariant across 111 species separated by at least 50 million years of evolution. In only 26 generations of artificial selection in a population of Drosophila melanogaster, we were able to drive the allometric slope to the outer range of those found among the 111 sampled species. This response was rapidly lost when selection was suspended. Only a small proportion of this reversal could be explained by breakup of linkage disequilibrium, and direct selection on wing shape is also unlikely to explain the reversal, because the more divergent wing shapes produced by selection on the allometric intercept did not revert. We hypothesize that the reversal was instead caused by internal selection arising from pleiotropic links to unknown traits. Our results also suggest that the observed selection response in the allometric slope was due to a component expressed late in larval development and that variation in earlier development did not respond to selection. Together, these results are consistent with a role for pleiotropic constraints in explaining the remarkable evolutionary stability of allometric scaling. PMID: 26371319 [PubMed - as supplied by publisher] 12. Evolution. 2015 Sep 12. doi: 10.1111/evo.12771. [Epub ahead of print] Quantitative genetic variance in experimental fly populations evolving with or without environmental heterogeneity. Huang Y(1), Stinchcombe JR(2), Agrawal AF(2). Heterogeneous environments are typically expected to maintain more genetic variation in fitness within populations than homogeneous environments. However, the accuracy of this claim depends on the form of heterogeneity as well as the genetic basis of fitness traits and how similar the assay environment is to the environment of past selection. Here, we measure quantitative genetic (QG) variance for three traits important for fitness using replicated experimental populations of Drosophila melanogaster evolving under four selective regimes: constant salt-enriched medium (Salt), constant cadmium-enriched medium (Cad), and two heterogeneous regimes that vary either temporally (Temp) or spatially (Spatial). As theory predicts, we found that Spatial populations tend to harbor more genetic variation than Temp populations or those maintained in a constant environment that is the same as the assay environment. Contrary to expectation, Salt populations tend to have more genetic variation than Cad populations in both assay environments. We discuss the patterns for QG variances across regimes in relation to previously reported data on genome-wide sequence diversity. For some traits, the QG patterns are similar to the diversity patterns of ecological selected SNPs, whereas the QG patterns for some other traits resembled that of neutral SNPs. © 2015 The Author(s). PMID: 26362112 [PubMed - as supplied by publisher] 13. Comp Biochem Physiol C Toxicol Pharmacol. 2015 Sep 7;179:72-78. doi: 10.1016/j.cbpc.2015.09.002. [Epub ahead of print] A single-point mutation enhances dual functionality of a scorpion toxin. Wang X(1), Gao B(1), Zhu S(2). Scorpion venom represents a tremendous, hitherto partially explored peptide library that has been proven to be useful not only for understanding ion channels but also for drug design. MeuTXKα3 is a functionally unknown scorpion toxin-like peptide. Here we describe new transcripts of this gene arising from alternative polyadenylation and its biological function as well as a mutant with a single-point substitution at site 30. Native-like MeuTXKα3 and its mutant were produced in Escherichia coli and their toxic function against Drosophila Shaker K(+) channel and its mammalian counterparts (rKv1.1-rKv1.3) were assayed by two-electrode voltage clamp technique. The results show that MeuTXKα3 is a weak toxin with a wide-spectrum of activity on both Drosophila and mammalian K(+) channels. The substitution of a proline at site 30 by an asparagine, an evolutionarily conserved functional residue in the scorpion α-KTx family, led to an increased activity on rKv1.2 and rKv1.3 but a decreased activity on the Shaker channel without changing the potency on rKv1.1, suggesting a key role of this site in species selectivity of scorpion toxins. MeuTXKα3 was also active on a variety of bacteria with lethal concentrations ranging from 4.66 to 52.01μM and the mutant even had stronger activity on some of these bacterial species. To the best of our knowledge, this is the first report on a bi-functional short-chain peptide in the lesser Asian scorpion venom. Further extensive mutations of MeuTXKα3 at site 30 could help improve its K(+) channel-blocking and antibacterial functions. Copyright © 2015 Elsevier Inc. All rights reserved. PMID: 26358403 [PubMed - as supplied by publisher] 14. Nat Rev Genet. 2015 Oct;16(10):567-82. doi: 10.1038/nrg3937. Epub 2015 Sep 8. Elucidating the molecular architecture of adaptation via evolve and resequence experiments. Long A(1), Liti G(2), Luptak A(3), Tenaillon O(4). Evolve and resequence (E&R) experiments use experimental evolution to adapt populations to a novel environment, then next-generation sequencing to analyse genetic changes. They enable molecular evolution to be monitored in real time on a genome-wide scale. Here, we review the field of E&R experiments across diverse systems, ranging from simple non-living RNA to bacteria, yeast and the complex multicellular organism Drosophila melanogaster. We explore how different evolutionary outcomes in these systems are largely consistent with common population genetics principles. Differences in outcomes across systems are largely explained by different starting population sizes, levels of pre-existing genetic variation, recombination rates and adaptive landscapes. We highlight emerging themes and inconsistencies that future experiments must address. PMID: 26347030 [PubMed - in process] 15. Ann Bot. 2015 Sep 7. pii: mcv134. [Epub ahead of print] Species diversity vs. morphological disparity in the light of evolutionary developmental biology. Minelli A(1). BACKGROUND: Two indicators of a clade's success are its diversity (number of included species) and its disparity (extent of morphospace occupied by its members). Many large genera show high diversity with low disparity, while others such as Euphorbia and Drosophila are highly diverse but also exhibit high disparity. The largest genera are often characterized by key innovations that often, but not necessarily, coincide with their diagnostic apomorphies. In terms of their contribution to speciation, apomorphies are either permissive (e.g. flightlessness) or generative (e.g. nectariferous spurs). SCOPE: Except for Drosophila, virtually no genus among those with the highest diversity or disparity includes species currently studied as model species in developmental genetics or evolutionary developmental biology (evo-devo). An evo-devo approach is, however, potentially important to understand how diversity and disparity could rapidly increase in the largest genera currently accepted by taxonomists. The most promising directions for future research and a set of key questions to be addressed are presented in this review. CONCLUSIONS: From an evo-devo perspective, the evolution of clades with high diversity and/or disparity can be addressed from three main perspectives: (1) evolvability, in terms of release from previous constraints and of the presence of genetic or developmental conditions favouring multiple parallel occurrences of a given evolutionary transition and its reversal; (2) phenotypic plasticity as a facilitator of speciation; and (3) modularity, heterochrony and a coupling between the complexity of the life cycle and the evolution of diversity and disparity in a clade. This simple preliminary analysis suggests a set of topics that deserve priority for scrutiny, including the possible role of saltational evolution in the origination of high diversity and/or disparity, the predictability of morphological evolution following release from a former constraint, and the extent and the possible causes of a positive correlation between diversity and disparity and the complexity of the life cycle. © The Author 2015. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com. PMID: 26346718 [PubMed - as supplied by publisher] 16. Cell Rep. 2015 Sep 22;12(11):1740-7. doi: 10.1016/j.celrep.2015.08.021. Epub 2015 Sep 3. Krüppel Expression Levels Are Maintained through Compensatory Evolution of Shadow Enhancers. Wunderlich Z(1), Bragdon MD(1), Vincent BJ(1), White JA(2), Estrada J(1), DePace AH(3). Many developmental genes are controlled by shadow enhancers-pairs of enhancers that drive overlapping expression patterns. We hypothesized that compensatory evolution can maintain the total expression of a gene, while individual shadow enhancers diverge between species. To test this hypothesis, we analyzed expression driven by orthologous pairs of shadow enhancers from Drosophila melanogaster, Drosophila yakuba, and Drosophila pseudoobscura that control expression of Krüppel, a transcription factor that patterns the anterior-posterior axis of blastoderm embryos. We found that the expression driven by the pair of enhancers is conserved between these three species, but expression levels driven by the individual enhancers are not. Using sequence analysis and experimental perturbation, we show that each shadow enhancer is regulated by different transcription factors. These results support the hypothesis that compensatory evolution can occur between shadow enhancers, which has implications for mechanistic and evolutionary studies of gene regulation. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved. PMCID: PMC4581983 [Available on 2016-09-22] PMID: 26344774 [PubMed - in process] 17. Philos Trans R Soc Lond B Biol Sci. 2015 Sep 26;370(1678). pii: 20140332. doi: 10.1098/rstb.2014.0332. New genes from non-coding sequence: the role of de novo protein-coding genes in eukaryotic evolutionary innovation. McLysaght A(1), Guerzoni D(2). The origin of novel protein-coding genes de novo was once considered so improbable as to be impossible. In less than a decade, and especially in the last five years, this view has been overturned by extensive evidence from diverse eukaryotic lineages. There is now evidence that this mechanism has contributed a significant number of genes to genomes of organisms as diverse as Saccharomyces, Drosophila, Plasmodium, Arabidopisis and human. From simple beginnings, these genes have in some instances acquired complex structure, regulated expression and important functional roles. New genes are often thought of as dispensable late additions; however, some recent de novo genes in human can play a role in disease. Rather than an extremely rare occurrence, it is now evident that there is a relatively constant trickle of proto-genes released into the testing ground of natural selection. It is currently unknown whether de novo genes arise primarily through an 'RNA-first' or 'ORF-first' pathway. Either way, evolutionary tinkering with this pool of genetic potential may have been a significant player in the origins of lineage-specific traits and adaptations. © 2015 The Authors. PMCID: PMC4571571 PMID: 26323763 [PubMed - in process] 18. Evolution. 2015 Sep;69(9):2468-81. doi: 10.1111/evo.12747. Epub 2015 Sep 8. Speciation and reduced hybrid female fertility in house mice. Suzuki TA(1,)(2), Nachman MW(3,)(4). In mammals, intrinsic postzygotic isolation has been well studied in males but has been less studied in females, despite the fact that female gametogenesis and pregnancy provide arenas for hybrid sterility or inviability that are absent in males. Here, we asked whether inviability or sterility is observed in female hybrids of Mus musculus domesticus and M. m. musculus, taxa which hybridize in nature and for which male sterility has been well characterized. We looked for parent-of-origin growth phenotypes by measuring adult body weights in F1 hybrids. We evaluated hybrid female fertility by crossing F1 females to a tester male and comparing multiple reproductive parameters between intrasubspecific controls and intersubspecific hybrids. Hybrid females showed no evidence of parent-of-origin overgrowth or undergrowth, providing no evidence for reduced viability. However, hybrid females had smaller litter sizes, reduced embryo survival, fewer ovulations, and fewer small follicles relative to controls. Significant variation in reproductive parameters was seen among different hybrid genotypes, suggesting that hybrid incompatibilities are polymorphic within subspecies. Differences in reproductive phenotypes in reciprocal genotypes were observed and are consistent with cyto-nuclear incompatibilities or incompatibilities involving genomic imprinting. These findings highlight the potential importance of reduced hybrid female fertility in the early stages of speciation. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution. PMCID: PMC4573315 [Available on 2016-09-08] PMID: 26299202 [PubMed - in process] 19. Evolution. 2015 Sep;69(9):2452-67. doi: 10.1111/evo.12748. Epub 2015 Aug 26. Origins of female genital diversity: Predation risk and lock-and-key explain rapid divergence during an adaptive radiation. Anderson CM(1), Langerhans RB(2). The study of male genital diversity has long overshadowed evolutionary inquiry of female genitalia, despite its nontrivial diversity. Here, we identify four nonmutually exclusive mechanisms that could lead to genital divergence in females, and potentially generate patterns of correlated male-female genital evolution: (1) ecological variation alters the context of sexual selection ("ecology hypothesis"), (2) sexually antagonistic selection ("sexual-conflict hypothesis"), (3) female preferences for male genitalia mediated by female genital traits ("female-choice hypothesis"), and (4) selection against inter-population mating ("lock-and-key hypothesis"). We performed an empirical investigation of all four hypotheses using the model system of Bahamas mosquitofish inhabiting blue holes that vary in predation risk. We found unequivocal support for the ecology hypothesis, with females exhibiting a smaller genital opening in blue holes containing piscivorous fish. This is consistent with stronger postmating female choice/conflict when predators are present, but greater premating female choice in their absence. Our results additionally supported the lock-and-key hypothesis, uncovering a pattern of reproductive character displacement for genital shape. We found no support for the sexual conflict or female choice hypotheses. Our results demonstrate a strong role for ecology in generating female genital diversity, and suggest that lock-and-key may provide a viable cause of female genital diversification. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution. PMID: 26259062 [PubMed - in process] 20. Evolution. 2015 Sep;69(9):2525-32. doi: 10.1111/evo.12744. Epub 2015 Aug 27. An integrated analysis of phenotypic selection on insect body size and development time. Eck DJ(1), Shaw RG(2), Geyer CJ(1), Kingsolver JG(3). Most studies of phenotypic selection do not estimate selection or fitness surfaces for multiple components of fitness within a unified statistical framework. This makes it difficult or impossible to assess how selection operates on traits through variation in multiple components of fitness. We describe a new generation of aster models that can evaluate phenotypic selection by accounting for timing of life-history transitions and their effect on population growth rate, in addition to survival and reproductive output. We use this approach to estimate selection on body size and development time for a field population of the herbivorous insect, Manduca sexta (Lepidoptera: Sphingidae). Estimated fitness surfaces revealed strong and significant directional selection favoring both larger adult size (via effects on egg counts) and more rapid rates of early larval development (via effects on larval survival). Incorporating the timing of reproduction and its influence on population growth rate into the analysis resulted in larger values for size in early larval development at which fitness is maximized, and weaker selection on size in early larval development. These results illustrate how the interplay of different components of fitness can influence selection on size and development time. This integrated modeling framework can be readily applied to studies of phenotypic selection via multiple fitness components in other systems. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution. PMID: 26257167 [PubMed - in process] 21. Evolution. 2015 Sep;69(9):2345-58. doi: 10.1111/evo.12732. Epub 2015 Aug 27. Robustness to noise in gene expression evolves despite epistatic constraints in a model of gene networks. Draghi J(1), Whitlock M(2). Stochastic noise in gene expression causes variation in the development of phenotypes, making such noise a potential target of stabilizing selection. Here, we develop a new simulation model of gene networks to study the adaptive landscape underlying the evolution of robustness to noise. We find that epistatic interactions between the determinants of the expression of a gene and its downstream effect impose significant constraints on evolution, but these interactions do allow the gradual evolution of increased robustness. Despite strong sign epistasis, adaptation rarely proceeds via deleterious intermediate steps, but instead occurs primarily through small beneficial mutations. A simple mathematical model captures the relevant features of the single-gene fitness landscape and explains counterintuitive patterns, such as a correlation between the mean and standard deviation of phenotypes. In more complex networks, mutations in regulatory regions provide evolutionary pathways to increased robustness. These results chart the constraints and possibilities of adaptation to reduce expression noise and demonstrate the potential of a novel modeling framework for gene networks. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution. PMID: 26200818 [PubMed - in process] 22. Dev Biol. 2015 Sep 15;405(2):328-39. doi: 10.1016/j.ydbio.2015.07.003. Epub 2015 Jul 14. How complexity increases in development: An analysis of the spatial-temporal dynamics of 1218 genes in Drosophila melanogaster. Salvador-Martínez I(1), Salazar-Ciudad I(2). One of the most apparent phenomena in development is that it starts with something apparently simple and leads to something clearly complex with a specific and functional structure. At the level of gene expression it seems also clear that the embryo becomes progressively compartmentalized over time and space. However, there have not been any systematic attempts to quantify how this occurs. Here, we present a quantitative analysis of the compartmentalization and spatial complexity of gene expression in Drosophila melanogaster over developmental time by analyzing thousands of gene expression spatial patterns from FlyExpress database. We use three different mathematical measures of compartmentalization of gene expression in space. All these measures show a similar non-linear increase in compartmentalization over time, with the most dramatic change occurring from the maternal to the early gastrula stage. Transcription factors and growth factors showed an earlier compartmentalization. Finally, we partitioned the embryo space in 257 equally sized regions and clustered them depending on their expression similarity, within and between stages. This provides a global overview about the effective degree of differentiation and compartmentalization between body parts at each developmental stage and when and where in the embryo there are more changes, due to signaling or movement. Copyright © 2015 Elsevier Inc. All rights reserved. PMID: 26187198 [PubMed - in process] 23. Dev Biol. 2015 Sep 1;405(1):173-81. doi: 10.1016/j.ydbio.2015.06.019. Epub 2015 Jun 27. Natural variation of the expression pattern of the segmentation gene even-skipped in melanogaster. Jiang P(1), Ludwig MZ(2), Kreitman M(2), Reinitz J(3). The evolution of canalized traits is a central question in evolutionary biology. Natural variation in highly conserved traits can provide clues about their evolutionary potential. Here we investigate natural variation in a conserved trait-even-skipped (eve) expression at the cellular blastoderm stage of embryonic development in Drosophila melanogaster. Expression of the pair-rule gene eve was quantitatively measured in three inbred lines derived from a natural population of D. melanogaster. One line showed marked differences in the spacing, amplitude and timing of formation of the characteristic seven-striped pattern over a 50-min period prior to the onset of gastrulation. Stripe 5 amplitude and the width of the interstripe between stripes 4 and 5 were both reduced in this line, while the interstripe distance between stripes 3 and 4 was increased. Engrailed expression in stage 10 embryos revealed a statistically significant increase in the length of parasegment 6 and a decrease in the length of parasegments 8 and 9. These changes are larger than those previously reported between D. melanogaster and D. pseudoobscura, two species that are thought to have diverged from a common ancestor over 25 million years ago. This line harbors a rare 448 bp deletion in the first intron of knirps (kni). This finding suggested that reduced Kni levels caused the deviant eve expression, and indeed we observed lower levels of Kni protein at early cycle 14A in L2 compared to the other two lines. A second of the three lines displayed an approximately 20% greater level of expression for all seven eve stripes. The three lines are each viable and fertile, and none display a segmentation defect as adults, suggesting that early-acting variation in eve expression is ameliorated by developmental buffering mechanisms acting later in development. Canalization of the segmentation pathway may reduce the fitness consequences of genetic variation, thus allowing the persistence of mutations with unexpectedly strong gene expression phenotypes. Copyright © 2015 Elsevier Inc. All rights reserved. PMCID: PMC4529771 [Available on 2016-09-01] PMID: 26129990 [PubMed - in process]