Origin and evolution of the vertebrate vomeronasal system viewed through system-specific genes

Tetrapods have two distinct nasal chemosensory systems, the main olfactory system and the vomeronasal system (VNS). Defined by certain morphological components, the main olfactory system is present in all groups of vertebrates, while the VNS is found only in tetrapods. Previous attempts to identify a VNS precursor in teleost fish were limited by functional and morphological characters that could not clearly distinguish between homologous and analogous systems. In the past decade, several genes that specifically function in the VNS have been discovered. Here we first describe recent evolutionary studies of mammalian VNS-specific genes. We then review evidence showing the presence and tissue-specific expression of the VNS-specific genes in teleosts, as well as co-expression patterns of these genes in specific regions of the teleost olfactory epithelium. We propose that a VNS precursor exists in teleosts and that its evolutionary origin predated the separation between teleosts and tetrapods.     

海洋哺乳动物信息素嗅觉的分子进化

研究感觉基因的进化规律是动物进化领域长期探索的重要问题.哺乳动物通常具有2套嗅觉系统:主要嗅觉系统(MOS)和犁鼻器系统(VNS).其中,VNS主要感知动物个体释放的信息素分子,而信息素在动物的生殖和社会行为中起重要调节作用.为了研究动物信息素嗅觉进化的背后推动力,对海洋哺乳动物的代表物种进行了Trpc2基因(VNS功能的分子标记)的序列测定和进化分析.以前的研究表明,Trpc2基因仅在VNS中表达,其序列完整/缺失与VNS的功能完整/退化完全一致.本研究结果显示,鲸类和海牛类的Trpc2为假基因,鳍脚类的1个分支类群(海豹类)和水獭类的Trpc2也是假基因,提示VNS功能丢失,即信息素嗅觉功能退化;而北极熊和鳍脚类的另一个分支类群(海狮类)保留了1个完整的Trpc2,并且这个基因仍受强烈的净化选择和功能限制,提示信息素嗅觉功能仍然保留.进一步分析表明,信息素嗅觉退化的海兽主要在水中交配,而信息素嗅觉保留的海兽主要在陆地上交配.本研究提出了一个新的科学假说:交配场所的选择可能推动了海洋哺乳动物信息素嗅觉的进化.     

Distinct evolutionary patterns between chemoreceptors of 2 vertebrate olfactory systems and the differential tuning hypothesis

Most tetrapod vertebrates have 2 olfactory systems, the main olfactory system (MOS) and the vomeronasal system (VNS). According to the dual olfactory hypothesis, the MOS detects environmental odorants, whereas the VNS recognizes intraspecific pheromonal cues. However, this strict functional distinction has been blurred by recent reports that both systems can perceive both types of signals. Studies of a limited number of receptors suggest that MOS receptors are broadly tuned generalists, whereas VNS receptors are narrowly tuned specialists. However, whether this distinction applies to all MOS and VNS receptors remains unknown. The differential tuning hypothesis predicts that generalist MOS receptors detect an overlapping set of ligands and thus are more likely to be conserved over evolutionary time than specialist VNS receptors, which would evolve in a more lineage-specific manner. Here we test this prediction for all olfactory chemoreceptors by examining the evolutionary patterns of MOS-expressed odorant receptors (ORs) and trace amine-associated receptors (TAARs) and VNS-expressed vomeronasal type 1 receptors (V1Rs) and vomeronasal type 2 receptors (V2Rs) in 7 tetrapods (mouse, rat, dog, opossum, platypus, chicken, and frog). The phylogenies of V1Rs and V2Rs show abundant lineage-specific gene gains/losses and virtually no one-to-one orthologs between species. Opposite patterns are found for ORs and TAARs. Analysis of functional data and ligand-binding sites of ORs confirms that paralogous chemoreceptors are more likely than orthologs to have different ligands and that functional divergence between paralogous chemoreceptors is established relatively quickly following gene duplication. Together, these results strongly suggest that the functional profile of the VNS chemoreceptor repertoire evolves much faster than that of the MOS chemoreceptor repertoire and that the differential tuning hypothesis applies to the majority, if not all, of MOS and VNS receptors.     

Sexual selection on brain size in shorebirds (Charadriiformes)

Natural selection is considered a major force shaping brain size evolution in vertebrates, whereas the influence of sexual selection remains controversial. On one hand, sexual selection could promote brain enlargement by enhancing cognitive skills needed to compete for mates. On the other hand, sexual selection could favour brain size reduction due to trade‐offs between investing in brain tissue and in sexually selected traits. These opposed predictions are mirrored in contradictory relationships between sexual selection proxies and brain size relative to body size. Here, we report a phylogenetic comparative analysis that highlights potential flaws in interpreting relative brain size‐mating system associations as effects of sexual selection on brain size in shorebirds (Charadriiformes), a taxonomic group with an outstanding diversity in breeding systems. Considering many ecological effects, relative brain size was not significantly correlated with testis size. In polyandrous species, however, relative brain sizes of males and females were smaller than in monogamous species, and females had smaller brain size than males. Although these findings are consistent with sexual selection reducing brain size, they could also be due to females deserting parental care, which is a common feature of polyandrous species. Furthermore, our analyses suggested that body size evolved faster than brain size, and thus the evolution of body size may be confounding the effect of the mating system on relative brain size. The brain size‐mating system association in shorebirds is thus not only due to sexual selection on brain size but rather, to body size evolution and other multiple simultaneous effects.     

Investment in visual system predicted by floral associations in sap beetles (Coleoptera: Nitidulidae)

Patterns in morphological variation are a central theme of evolution. Uncovering links between morphological character evolution and natural history, specifically feeding behaviour, is important to understanding biological diversity. Species within the sap beetles (Nitidulidae) exhibit a tremendous diversity of feeding behaviours. This immense diversity of feeding can be seen both between major lineages and very closely related taxa. Feeding behaviour diversity may drive morphological variation in several character systems (e.g., eyes). For example, in a shift from feeding on rotting fruit to flower-visiting (anthophily), selective pressures on the visual system may vary and ultimately lead to differences in eye morphology. We tested for potential morphological shifts in relative eye size among adult beetles. We specifically tested for significant relationships between relative eye size and the following factors flower-visiting and sex. We also tested for the influence of phylogeny on the evolution of relative eye size, implementing tests of trait correlation across a topology. We found greater relative eye size in taxa exhibiting anthophilous behaviour, regardless of phylogenetic relatedness or feeding behaviour of sister taxa. We were unable to recover a relationship between relative eye size and sex. Thus, feeding behaviour is currently the strongest predictor of eye size in sap beetles.     

A trajectory of increasing activity and the elaboration of chemosensory modality: a new perspective on vertebrate origins

This article reviews recent advances in comparative biological studies of vertebrate origins, with the aim of revisiting the long-standing controversy concerning these origins. Since early vertebrate evolution is paralleled by an evolutionary trend towards increasing activity, I focus on the evolution of respiratory and circulatory systems and discuss their potential roles in early vertebrate evolution. I give particular attention to the nasohypophyseal duct, an orifice characteristically found in agnathan vertebrates, and hypothesize that this duct originally functioned to convey oxygen dissolved in seawater to the respiratory gills. The chemosensory cell population that originated from the wall of the duct became the incipient olfactory organ and played a role in the organization of feeding behavior. An increase in chemosensory receptor genes via large-scale genomic evolution in the vertebrate lineage caused the repertoire of chemosensory cells to diversify and led to the appearance of the integrative center, including telencephalic structures typically lacking in protochordates.     

The demography and population genomics of evolutionary transitions to self-fertilization in plants

The evolution of self-fertilization from outcrossing has occurred on numerous occasions in flowering plants. This shift in mating system profoundly influences the morphology, ecology, genetics and evolution of selfing lineages. As a result, there has been sustained interest in understanding the mechanisms driving the evolution of selfing and its environmental context. Recently, patterns of molecular variation have been used to make inferences about the selective mechanisms associated with mating system transitions. However, these inferences can be complicated by the action of linked selection following the transition. Here, using multilocus simulations and comparative molecular data from related selfers and outcrossers, we demonstrate that there is little evidence for strong bottlenecks associated with initial transitions to selfing, and our simulation results cast doubt on whether it is possible to infer the role of bottlenecks associated with reproductive assurance in the evolution of selfing. They indicate that the effects of background selection on the loss of diversity and efficacy of selection occur rapidly following the shift to high selfing. Future comparative studies that integrate explicit ecological and genomic details are necessary for quantifying the independent and joint effects of selection and demography on transitions to selfing and the loss of genetic diversity.     

Linked selection,demography and the evolution of correlated genomic landscapes in birds and beyond

Selection has a deep impact on the distribution of genetic diversity and population differentiation along the genome (the genomic landscapes of diversity and differentiation), reducing diversity and elevating differentiation not only at the sites it targets, but also at linked neutral sites. Fuelled by the high‐throughput sequencing revolution, these genomic footprints of selection have been extensively exploited over the past decade with the aim to identify genomic regions involved in adaptation and speciation. However, while this research has shown that the genomic landscapes of diversity and differentiation are usually highly heterogeneous, it has also led to the increasing realization that this heterogeneity may evolve under processes other than adaptation or speciation. In particular, instead of being an effect of selective sweeps or barriers to gene flow, accentuated differentiation can evolve by any process reducing genetic diversity locally within the genome (Charlesworth, 1998 ), including purifying selection at linked sites (background selection). In particular, in genomic regions where recombination is infrequent, accentuated differentiation can evolve as a by‐product of diversity reductions unrelated to adaptation or speciation (Cruickshank & Hahn, 2014 ; Nachman & Payseur, 2012 ; Noor & Bennett, 2009 ). In such genomic regions, linkage extends over physically larger genome stretches, and selection affects a particularly high number of linked neutral sites. Even though the effects of selection on linked neutral diversity (linked selection) within populations are well documented (Cutter & Payseur, 2013 ), recent observations of diversity and differentiation landscapes that are highly correlated even among independent lineages suggest that the effects of long‐term linked selection may have a deeper impact on the evolution of the genomic landscapes of diversity and differentiation than previously anticipated. The study on Saxicola stonechats by Van Doren et al. ( 2017 ) reported in the current issue of Molecular Ecology lines in with a rapidly expanding body of evidence in this direction. Correlations of genomic landscapes extending from within stonechats to comparisons with Ficedula flycatchers add to recent insights into the timescales across which the effects of linked selection persist. Absent and inverted correlations of genomic landscapes in comparisons involving an island taxon, on the other hand, provide important empirical clues about the role of demographic constraints in the evolution of the genomic landscapes of diversity and differentiation.     

Effective population size is positively correlated with levels of adaptive divergence among annual sunflowers

The role of adaptation in the divergence of lineages has long been a central question in evolutionary biology, and as multilocus sequence data sets have become available for a wide range of taxa, empirical estimates of levels of adaptive molecular evolution are increasingly common. Estimates vary widely among taxa, with high levels of adaptive evolution in Drosophila, bacteria, and viruses but very little evidence of widespread adaptive evolution in hominids. Although estimates in plants are more limited, some recent work has suggested that rates of adaptive evolution in a range of plant taxa are surprisingly low and that there is little association between adaptive evolution and effective population size in contrast to patterns seen in other taxa. Here, we analyze data from 35 loci for six sunflower species that vary dramatically in effective population size. We find that rates of adaptive evolution are positively correlated with effective population size in these species, with a significant fraction of amino acid substitutions driven by positive selection in the species with the largest effective population sizes but little or no evidence of adaptive evolution in species with smaller effective population sizes. Although other factors likely contribute as well, in sunflowers effective population size appears to be an important determinant of rates of adaptive evolution.     

Convergent vomeronasal system reduction in mammals coincides with convergent losses of calcium signalling and odorant‐degrading genes

The vomeronasal system (VNS) serves crucial functions for detecting olfactory clues often related to social and sexual behaviour. Intriguingly, two of the main components of the VNS, the vomeronasal organ (VNO) and the accessory olfactory bulb, are regressed in aquatic mammals, several bats and primates, likely due to adaptations to different ecological niches. To detect genomic changes that are associated with the convergent reduction of the VNS, we performed the first systematic screen for convergently inactivated protein‐coding genes associated with convergent VNS reduction, considering 106 mammalian genomes. Extending previous studies, our results support that Trpc2, a cation channel that is important for calcium signalling in the VNO, is a predictive molecular marker for the presence of a VNS. Our screen also detected the convergent inactivation of the calcium‐binding protein S100z, the aldehyde oxidase Aox2 that is involved in odorant degradation, and the uncharacterized Mslnl gene that is expressed in the VNO and olfactory epithelium. Furthermore, we found that Trpc2 and S100z or Aox2 are also inactivated in otters and Phocid seals for which no morphological data about the VNS are available yet. This predicts a VNS reduction in these semi‐aquatic mammals. By examining the genomes of 115 species in total, our study provides a detailed picture of how the convergent reduction of the VNS coincides with gene inactivation in placental mammals. These inactivated genes provide experimental targets for studying the evolution and biological significance of the olfactory system under different environmental conditions.     

Taste and pheromone perception in mammals and flies

The olfactory systems of insects and mammals have analogous anatomical features and use similar molecular logic for olfactory coding. The molecular underpinnings of the chemosensory systems that detect taste and pheromone cues have only recently been characterized. Comparison of these systems in Drosophila and mouse uncovers clear differences and a few surprising similarities.     

Emerging views on the distinct but related roles of the main and accessory olfactory systems in responsiveness to chemosensory signals in mice

In rodents, the nasal cavity contains two separate chemosensory epithelia, the main olfactory epithelium, located in the posterior dorsal aspect of the nasal cavity, and the vomeronasal/accessory olfactory epithelium, located in a capsule in the anterior aspect of the ventral floor of the nasal cavity. Both the main and accessory olfactory systems play a role in detection of biologically relevant odors. The accessory olfactory system has been implicated in response to pheromones, while the main olfactory system is thought to be a general molecular analyzer capable of detecting subtle differences in molecular structure of volatile odorants. However, the role of the two systems in detection of biologically relevant chemical signals appears to be partially overlapping. Thus, while it is clear that the accessory olfactory system is responsive to putative pheromones, the main olfactory system can also respond to some pheromones. Conversely, while the main olfactory system can mediate recognition of differences in genetic makeup by smell, the vomeronasal organ (VNO) also appears to participate in recognition of chemosensory differences between genetically distinct individuals. The most salient feature of our review of the literature is that there are no general rules that allow classification of the accessory olfactory system as a pheromone detector and the main olfactory system as a detector of general odorants. Instead, each behavior must be considered within a specific behavioral context to determine the role of these two chemosensory systems. In each case, one system or the other (or both) participates in a specific behavioral or hormonal response.     

Sexual selection impacts brain anatomy in frogs and toads

Natural selection is a major force in the evolution of vertebrate brain size, but the role of sexual selection in brain size evolution remains enigmatic. At least two opposing schools of thought predict a relationship between sexual selection and brain size. Sexual selection should facilitate the evolution of larger brains because better cognitive abilities may aid the competition for mates. However, it may also restrict brain size evolution due to energetic trade‐offs between brain tissue and sexually selected traits. Here, we examined the patterns of selection on brain size and brain anatomy in male anurans (frogs and toads), a group where the strength of sexual selection differs markedly among species, using a phylogenetically controlled generalized least‐squared (PGLS) regression analyses. The analysis revealed that in 43 Chinese anuran species, neither mating system, nor type of courtship, or testes mass was significantly associated with relative brain size. While none of those factors related to the relative size of olfactory nerves, optic tecta, telencephalon, and cerebellum, the olfactory bulbs were relatively larger in monogamous species and those using calls during courtship. Our findings support the mosaic model of brain evolution and suggest that while the investigated aspects of sexual selection do not seem to play a prominent role in the evolution of brain size of anurans, they do impact their brain anatomy.     

Sexual selection and the adaptive evolution of mammalian ejaculate proteins

An elevated rate of substitution characterizes the molecular evolution of reproductive proteins from a wide range of taxa. Although the selective pressures explaining this rapid evolution are yet to be resolved, recent evidence implicates sexual selection as a potentially important explanatory factor. To investigate this hypothesis, we sought evidence of a high rate of adaptive gene evolution linked to postcopulatory sexual selection in muroid rodents, a model vertebrate group displaying a broad range of mating systems. Specifically, we sequenced 7 genes from diverse rodents that are expressed in the testes, prostate, or seminal vesicles, products of which have the potential to act in sperm competition. We inferred positive Darwinian selection in these genes by estimation of the ratio of nonsynonymous (d(N), amino acid changing) to synonymous (d(S), amino acid retaining) substitution rates (omega = d(N)/d(S)). Next, we tested whether variation in this ratio among lineages could be attributed to interspecific variation in mating systems, as inferred from the variation in these rodents' relative testis sizes (RTS). Four of the 7 genes examined (Prm1, Sva, Acrv1, and Svs2, but not Svp2, Msmb, or Spink3) exhibit unambiguous evidence of positive selection. One of these, the seminal vesicle-derived protein Svs2, also shows some evidence for a concentration of positive selection in those lineages in which sperm competition is common. However, this was not a general trend among all the rodent genes we examined. Using the same methods, we then reanalyzed previously published data on 2 primate genes, SEMG1 and SEMG2. Although SEMG2 also shows evidence of positive selection concentrated in lineages subject to high levels of sperm competition, no such trend was found for SEMG1. Overall, despite a high rate of positive selection being a feature of many ejaculate proteins, these results indicate that the action of sexual selection potentially responsible for elevated evolutionary rates may be difficult to detect on a gene-by-gene basis. Although the extreme diversity of reproductive phenotypes exhibited in nature attests to the power of sexual selection, the extent to which this force predominates in driving the rapid molecular evolution of reproductive genes therefore remains to be determined.     

Olfactory receptor gene evolution is unusually rapid across Tetrapoda and outpaces chemosensory phenotypic change

Chemosensation is the most ubiquitous sense in animals, enacted by the products of complex gene families that detect environmental chemical cues and larger-scale sensory structures that process these cues. While there is a general conception that olfactory receptor (OR) genes evolve rapidly, the universality of this phenomenon across vertebrates, and its magnitude, are unclear. The supposed correlation between molecular rates of chemosensory evolution and phenotypic diversity of chemosensory systems is largely untested. We combine comparative genomics and sensory morphology to test whether OR genes and olfactory phenotypic traits evolve at faster rates than other genes or traits. Using published genomes, we identified ORs in 21 tetrapods, including amphibians, reptiles, birds, and mammals and compared their rates of evolution to those of orthologous non-OR protein-coding genes. We found that, for all clades investigated, most OR genes evolve nearly an order of magnitude faster than other protein-coding genes, with many OR genes showing signatures of diversifying selection across nearly all taxa in this study. This rapid rate of evolution suggests that chemoreceptor genes are in “evolutionary overdrive,” perhaps evolving in response to the ever-changing chemical space of the environment. To obtain complementary morphological data, we stained whole fixed specimens with iodine, µCT-scanned the specimens, and digitally segmented chemosensory and nonchemosensory brain regions. We then estimated phenotypic variation within traits and among tetrapods. While we found considerable variation in chemosensory structures, they were no more diverse than nonchemosensory regions. We suggest chemoreceptor genes evolve quickly in reflection of an ever-changing chemical space, whereas chemosensory phenotypes and processing regions are more conserved because they use a standardized or constrained architecture to receive and process a range of chemical cues.     

Brain reorganization,not relative brain size,primarily characterizes anthropoid brain evolution

Comparative analyses of primate brain evolution have highlighted changes in size and internal organization as key factors underlying species diversity. It remains, however, unclear (i) how much variation in mosaic brain reorganization versus variation in relative brain size contributes to explaining the structural neural diversity observed across species, (ii) which mosaic changes contribute most to explaining diversity, and (iii) what the temporal origin, rates and processes are that underlie evolutionary shifts in mosaic reorganization for individual branches of the primate tree of life. We address these questions by combining novel comparative methods that allow assessing the temporal origin, rate and process of evolutionary changes on individual branches of the tree of life, with newly available data on volumes of key brain structures (prefrontal cortex, frontal motor areas and cerebrocerebellum) for a sample of 17 species (including humans). We identify patterns of mosaic change in brain evolution that mirror brain systems previously identified by electrophysiological and anatomical tract-tracing studies in non-human primates and functional connectivity MRI studies in humans. Across more than 40 Myr of anthropoid primate evolution, mosaic changes contribute more to explaining neural diversity than changes in relative brain size, and different mosaic patterns are differentially selected for when brains increase or decrease in size. We identify lineage-specific evolutionary specializations for all branches of the tree of life covered by our sample and demonstrate deep evolutionary roots for mosaic patterns associated with motor control and learning.     

Sexual size dimorphism of the tongue in a North American pitviper

Sexual dimorphisms – phenotypic dissimilarities between the sexes – are common and widespread among plants and animals, and classical examples include differences in body size, colour, shape, ornamentation and behaviour. In general, sexual dimorphisms are hypothesized to evolve by way of sexual selection acting on one sex through priority-of-access for sexual partners via mate choice and/or intra-sexual competition. In snakes, males are the mate-searching sex and one form of sexual selection involves male–male competition in locating females by following pheromone trails using their forked tongues, the structure used to sample environmental chemicals for transduction in the vomeronasal chemosensory system (VNS). Based on several lines of empirical evidence, increased tongue forking (bifurcation) in snakes (and some lizard taxa) appears to enhance chemical trail-following abilities through tropotaxis (the simultaneous comparison of stimulus intensities on two sides of the body) and thus aids in prey location and mate searching in males. We predicted that male copperheads, Agkistrodon contortrix , a North American pitviper, should have more deeply forked tongues than females owing to male–male competition for priority-of-access to widely dispersed females during the mating seasons. We examined formalin-fixed, ethanol-preserved museum specimens of adult A. contortrix for sexual size dimorphism (SSD) of the tongue. Tongue dimensions showed differences indicative of SSD, and the degree of bifurcation (i.e. mean tine length) was significantly greater in males. Various structures of the VNS and associated regions (e.g. muscles) in some vertebrate taxa show sexual dimorphism, but our study is the first to document dimorphism in the tongue of a tetrapod vertebrate.     

Adaptive evolution of four microcephaly genes and the evolution of brain size in anthropoid primates

The anatomical basis and adaptive function of the expansion in primate brain size have long been studied; however, we are only beginning to understand the genetic basis of these evolutionary changes. Genes linked to human primary microcephaly have received much attention as they have accelerated evolutionary rates along lineages leading to humans. However, these studies focus narrowly on apes, and the link between microcephaly gene evolution and brain evolution is disputed. We analyzed the molecular evolution of four genes associated with microcephaly (ASPM, CDK5RAP2, CENPJ, MCPH1) across 21 species representing all major clades of anthropoid primates. Contrary to prevailing assumptions, positive selection was not limited to or intensified along the lineage leading to humans. In fact we show that all four loci were subject to positive selection across the anthropoid primate phylogeny. We developed clearly defined hypotheses to explicitly test if selection on these loci was associated with the evolution of brain size. We found positive relationships between both CDK5RAP2 and ASPM and neonatal brain mass and somewhat weaker relationships between these genes and adult brain size. In contrast, there is no evidence linking CENPJ and MCPH1 to brain size evolution. The stronger association of ASPM and CDK5RAP2 evolution with neonatal brain size than with adult brain size is consistent with these loci having a direct effect on prenatal neuronal proliferation. These results suggest that primate brain size may have at least a partially conserved genetic basis. Our results contradict a previous study that linked adaptive evolution of ASPM to changes in relative cortex size; however, our analysis indicates that this conclusion is not robust. Our finding that the coding regions of two widely expressed loci has experienced pervasive positive selection in relation to a complex, quantitative developmental phenotype provides a notable counterexample to the commonly asserted hypothesis that cis-regulatory regions play a dominant role in phenotypic evolution.     

How to Infer Relative Fitness from a Sample of Genomic Sequences

Mounting evidence suggests that natural populations can harbor extensive fitness diversity with numerous genomic loci under selection. It is also known that genealogical trees for populations under selection are quantifiably different from those expected under neutral evolution and described statistically by Kingman’s coalescent. While differences in the statistical structure of genealogies have long been used as a test for the presence of selection, the full extent of the information that they contain has not been exploited. Here we demonstrate that the shape of the reconstructed genealogical tree for a moderately large number of random genomic samples taken from a fitness diverse, but otherwise unstructured, asexual population can be used to predict the relative fitness of individuals within the sample. To achieve this we define a heuristic algorithm, which we test in silico, using simulations of a Wright–Fisher model for a realistic range of mutation rates and selection strength. Our inferred fitness ranking is based on a linear discriminator that identifies rapidly coalescing lineages in the reconstructed tree. Inferred fitness ranking correlates strongly with actual fitness, with a genome in the top 10% ranked being in the top 20% fittest with false discovery rate of 0.1–0.3, depending on the mutation/selection parameters. The ranking also enables us to predict the genotypes that future populations inherit from the present one. While the inference accuracy increases monotonically with sample size, samples of 200 nearly saturate the performance. We propose that our approach can be used for inferring relative fitness of genomes obtained in single-cell sequencing of tumors and in monitoring viral outbreaks.     

Natural Selection Constrains Neutral Diversity across A Wide Range of Species

The neutral theory of molecular evolution predicts that the amount of neutral polymorphisms within a species will increase proportionally with the census population size (Nc). However, this prediction has not been borne out in practice: while the range of Nc spans many orders of magnitude, levels of genetic diversity within species fall in a comparatively narrow range. Although theoretical arguments have invoked the increased efficacy of natural selection in larger populations to explain this discrepancy, few direct empirical tests of this hypothesis have been conducted. In this work, we provide a direct test of this hypothesis using population genomic data from a wide range of taxonomically diverse species. To do this, we relied on the fact that the impact of natural selection on linked neutral diversity depends on the local recombinational environment. In regions of relatively low recombination, selected variants affect more neutral sites through linkage, and the resulting correlation between recombination and polymorphism allows a quantitative assessment of the magnitude of the impact of selection on linked neutral diversity. By comparing whole genome polymorphism data and genetic maps using a coalescent modeling framework, we estimate the degree to which natural selection reduces linked neutral diversity for 40 species of obligately sexual eukaryotes. We then show that the magnitude of the impact of natural selection is positively correlated with Nc, based on body size and species range as proxies for census population size. These results demonstrate that natural selection removes more variation at linked neutral sites in species with large Nc than those with small Nc and provides direct empirical evidence that natural selection constrains levels of neutral genetic diversity across many species. This implies that natural selection may provide an explanation for this longstanding paradox of population genetics.