The genomic rate of adaptive amino acid substitution in Drosophila

The rate of molecular adaptation in a changing environment

It is currently unclear whether the amino acid substitutions that occur during protein evolution are primarily driven by adaptation, or reflect the random accumulation of neutral changes. When estimated from genomic data, the proportion of adaptive amino acid substitutions, called α, was found to vary greatly across species, from nearly zero in humans to above 0.5 in Drosophila. These variations have been interpreted as reflecting differences in effective population size, adaptation being supposedly more efficient in large populations. Here, we investigate the influence of effective population size and other biological parameters on the rate of adaptive evolution by simulating the evolution of a coding sequence under Fisher's geometric formalism. We explicitly model recurrent environmental changes and the subsequent adaptive walks, followed by periods of stasis during which purifying selection dominates. We show that, under a variety of conditions, the effective population size has only a moderate influence on α, and an even weaker influence on the per generation rate of selective sweeps, modifying the prevalent view in current literature. The rate of environmental change and, interestingly, the dimensionality of the phenotypic space (organismal complexity) affect the adaptive rate more deeply than does the effective population size. We discuss the reasons why verbal arguments have been misleading on that subject and revisit the empirical evidence. Our results question the relevance of the "α" parameter as an indicator of the efficiency of molecular adaptation.

Inference of natural selection from interspersed genomic elements based on polymorphism and divergence

Complete genome sequences contain valuable information about natural selection, but this information is difficult to access for short, widely scattered noncoding elements such as transcription factor binding sites or small noncoding RNAs. Here, we introduce a new computational method, called Inference of Natural Selection from Interspersed Genomically coHerent elemenTs (INSIGHT), for measuring the influence of natural selection on such elements. INSIGHT uses a generative probabilistic model to contrast patterns of polymorphism and divergence in the elements of interest with those in flanking neutral sites, pooling weak information from many short elements in a manner that accounts for variation among loci in mutation rates and coalescent times. The method is able to disentangle the contributions of weak negative, strong negative, and positive selection based on their distinct effects on patterns of polymorphism and divergence. It obtains information about divergence from multiple outgroup genomes using a general statistical phylogenetic approach. The INSIGHT model is efficiently fitted to genome-wide data using an approximate expectation maximization algorithm. Using simulations, we show that the method can accurately estimate the parameters of interest even in complex demographic scenarios, and that it significantly improves on methods based on summary statistics describing polymorphism and divergence. To demonstrate the usefulness of INSIGHT, we apply it to several classes of human noncoding RNAs and to GATA2-binding sites in the human genome.

A high load of non-neutral amino-acid polymorphisms explains high protein diversity despite moderate effective population size in a marine bivalve with sweepstakes reproduction

Marine bivalves show among the greatest allozyme diversity ever reported in Eukaryotes, putting them historically at the heart of the neutralist-selectionist controversy on the maintenance of genetic variation. Although it is now acknowledged that this high diversity is most probably a simple consequence of a large population size, convincing support for this explanation would require a rigorous assessment of the silent nucleotide diversity in natural populations of marine bivalves, which has not yet been done. This study investigated DNA sequence polymorphism in a set of 37 nuclear loci in wild samples of the flat oyster Ostrea edulis. Silent diversity was found to be only moderate (0.7%), and there was no departure from demographic equilibrium under the Wright-Fisher model, suggesting that the effective population size might not be as large as might have been expected. In accordance with allozyme heterozygosity, nonsynonymous diversity was comparatively very high (0.3%), so that the nonsynonymous to silent diversity ratio reached a value rarely observed in any other organism. We estimated that one-quarter of amino acid-changing mutations behave as neutral in O. edulis, and as many as one-third are sufficiently weakly selected to segregate at low frequency in the polymorphism. Finally, we inferred that one oyster is expected to carry more than 4800 non-neutral alleles (or 4.2 cM(-1)). We conclude that a high load of segregating non-neutral amino-acid polymorphisms contributes to high protein diversity in O. edulis. The high fecundity of marine bivalves together with an unpredictable and highly variable success of reproduction and recruitment (sweepstakes reproduction) might produce a greater decoupling between Ne and N than in other organisms with lower fecundities, and we suggest this could explain why a higher segregating load could be maintained for a given silent mutation effective size.

SnIPRE: selection inference using a Poisson random effects model

We present an approach for identifying genes under natural selection using polymorphism and divergence data from synonymous and non-synonymous sites within genes. A generalized linear mixed model is used to model the genome-wide variability among categories of mutations and estimate its functional consequence. We demonstrate how the model's estimated fixed and random effects can be used to identify genes under selection. The parameter estimates from our generalized linear model can be transformed to yield population genetic parameter estimates for quantities including the average selection coefficient for new mutations at a locus, the synonymous and non-synynomous mutation rates, and species divergence times. Furthermore, our approach incorporates stochastic variation due to the evolutionary process and can be fit using standard statistical software. The model is fit in both the empirical Bayes and Bayesian settings using the lme4 package in R, and Markov chain Monte Carlo methods in WinBUGS. Using simulated data we compare our method to existing approaches for detecting genes under selection: the McDonald-Kreitman test, and two versions of the Poisson random field based method MKprf. Overall, we find our method universally outperforms existing methods for detecting genes subject to selection using polymorphism and divergence data.

Why are male malaria parasites in such a rush?

Host immunity selects for the rapid, adaptive, evolution of genes expressed exclusively in male malaria parasites. Analyses of genomic and proteomic data across multiple malaria species reveals rapid adaptive evolution of genes with sex-biased expression in unicellular parasites. Accelerated evolution enables parasites to cope with host immune responses that reduce fertility.

Background: Disease-causing organisms are notorious for fast rates of molecular evolution and the ability to adapt rapidly to changes in their ecology. Sex plays a key role in evolution, and recent studies, in humans and other multicellular organisms, document that genes expressed principally or exclusively in males exhibit the fastest rates of adaptive evolution. However, despite the importance of sexual reproduction for many unicellular taxa, sex-biased gene expression and its evolutionary implications have been overlooked.

Methods: We analyse genomic data from multiple malaria parasite (Plasmodium) species and proteomic data sets from different parasite life cycle stages.

Results: The accelerated evolution of male-biased genes has only been examined in multicellular taxa, but our analyses reveal that accelerated evolution in genes with male-specific expression is also a feature of unicellular organisms. This ‘fast-male’ evolution is adaptive and likely facilitated by the male-biased sex ratio of gametes in the mating pool. Furthermore, we propose that the exceptional rates of evolution we observe are driven by interactions between males and host immune responses.

Conclusions: We reveal a novel form of host–parasite coevolution that enables parasites to evade host immune responses that negatively impact upon fertility. The identification of parasite genes with accelerated evolution has important implications for the identification of drug and vaccine targets. Specifically, vaccines targeting males will be more vulnerable to parasite evolution than those targeting females or both sexes.

Modeling the effect of changing selective pressures on polymorphism and divergence

The most common models of sequence evolution used to make inferences about adaptation rely on the assumption that selective pressures at a site remain constant through time. Instead, one might plausibly imagine that a change in the environment renders an allele beneficial and that when it fixes, the site is now constrained-until another change in the environment occurs that affects the selective pressures at that site. With this view in mind, we introduce a simple dynamic model for the evolution of coding regions, in which non-synonymous sites alternate between being fixed for the favored allele and being neutral with respect to other alleles. We use the pruning algorithm to derive closed forms for observable patterns of polymorphism and divergence in terms of the model parameters. Using our model, estimates of the fraction of beneficial substitutions α would remain similar to those obtained from existing approaches. In this framework, however, it becomes natural to ask how often adaptive substitutions originate from previously constrained or previously neutral sites, i.e., about the source of adaptive substitutions. We show that counts of coding sites that are both polymorphic in a sample from one species and divergent between two others carry information about this parameter. We also extend the basic model to include the effects of weakly deleterious mutations and discuss the importance of assumptions about the distribution of deleterious mutations among constrained non-synonymous sites. Finally, we derive a likelihood function for the parameters and apply it to a toy example, variation data for coding regions from chromosome 2 of the Drosophila melanogaster subgroup. This modeling work underscores how restrictive assumptions about adaptation have been to date, and how further work in this area will help to reveal unexplored and yet basic characteristics of adaptation.

Adaptive evolution and the birth of CTCF binding sites in the Drosophila genome

Comparative ChIP-seq data reveal adaptive evolution of insulator protein CTCF binding in multiple Drosophila species.

Changes in the physical interaction between cis-regulatory DNA sequences and proteins drive the evolution of gene expression. However, it has proven difficult to accurately quantify evolutionary rates of such binding change or to estimate the relative effects of selection and drift in shaping the binding evolution. Here we examine the genome-wide binding of CTCF in four species of Drosophila separated by between ∼2.5 and 25 million years. CTCF is a highly conserved protein known to be associated with insulator sequences in the genomes of human and Drosophila. Although the binding preference for CTCF is highly conserved, we find that CTCF binding itself is highly evolutionarily dynamic and has adaptively evolved. Between species, binding divergence increased linearly with evolutionary distance, and CTCF binding profiles are diverging rapidly at the rate of 2.22% per million years (Myr). At least 89 new CTCF binding sites have originated in the Drosophila melanogaster genome since the most recent common ancestor with Drosophila simulans. Comparing these data to genome sequence data from 37 different strains of Drosophila melanogaster, we detected signatures of selection in both newly gained and evolutionarily conserved binding sites. Newly evolved CTCF binding sites show a significantly stronger signature for positive selection than older sites. Comparative gene expression profiling revealed that expression divergence of genes adjacent to CTCF binding site is significantly associated with the gain and loss of CTCF binding. Further, the birth of new genes is associated with the birth of new CTCF binding sites. Our data indicate that binding of Drosophila CTCF protein has evolved under natural selection, and CTCF binding evolution has shaped both the evolution of gene expression and genome evolution during the birth of new genes.

A large proportion of the diversity of living organisms results from differential regulation of gene transcription. Transcriptional regulation is thought to differ between species because of evolutionary changes in the physical interactions between regulatory DNA elements and DNA-binding proteins; these can generate variation in the spatial and temporal patterns of gene expression. The mechanisms by which these protein–DNA interactions evolve is therefore an important question in evolutionary biology. Does adaptive evolution play a role, or is the process dominated by neutral genetic drift? Insulator proteins are a special group of DNA-binding proteins—instead of directly serving to activate or repress genes, they can function to coordinate the interactions between other regulatory elements (such as enhancers and promoters). Additionally, insulator proteins can limit the spreading of chromatin condensation and help to demarcate the boundaries of regulatory domains in the genome. In spite of their critical role in genome regulation, little is known about the evolution of interactions between insulator proteins and DNA. Here, we use ChIP-seq to examine the distribution of binding sites for CTCF, a highly conserved insulator protein, in four closely related Drosophila species. We find that genome-wide binding profiles of CTCF are highly dynamic across evolutionary time, with frequent births of new CTCF-DNA interactions, and we demonstrate that this evolutionary process is driven by natural selection. By comparing these with RNA-seq data, we find that gain or loss of CTCF binding impacts the expression levels of nearby genes and correlates with structural evolution of the genome. Together these results suggest a potential mechanism of regulatory re-wiring through adaptive evolution of CTCF binding.

Weak selection and protein evolution

The "nearly neutral" theory of molecular evolution proposes that many features of genomes arise from the interaction of three weak evolutionary forces: mutation, genetic drift, and natural selection acting at its limit of efficacy. Such forces generally have little impact on allele frequencies within populations from generation to generation but can have substantial effects on long-term evolution. The evolutionary dynamics of weakly selected mutations are highly sensitive to population size, and near neutrality was initially proposed as an adjustment to the neutral theory to account for general patterns in available protein and DNA variation data. Here, we review the motivation for the nearly neutral theory, discuss the structure of the model and its predictions, and evaluate current empirical support for interactions among weak evolutionary forces in protein evolution. Near neutrality may be a prevalent mode of evolution across a range of functional categories of mutations and taxa. However, multiple evolutionary mechanisms (including adaptive evolution, linked selection, changes in fitness-effect distributions, and weak selection) can often explain the same patterns of genome variation. Strong parameter sensitivity remains a limitation of the nearly neutral model, and we discuss concave fitness functions as a plausible underlying basis for weak selection.

Colon cancer associated genes exhibit signatures of positive selection at functionally significant positions

Background

Cancer, much like most human disease, is routinely studied by utilizing model organisms. Of these model organisms, mice are often dominant. However, our assumptions of functional equivalence fail to consider the opportunity for divergence conferred by ~180 Million Years (MY) of independent evolution between these species. For a given set of human disease related genes, it is therefore important to determine if functional equivalency has been retained between species. In this study we test the hypothesis that cancer associated genes have different patterns of substitution akin to adaptive evolution in different mammal lineages.

Results

Our analysis of the current literature and colon cancer databases identified 22 genes exhibiting colon cancer associated germline mutations. We identified orthologs for these 22 genes across a set of high coverage (>6X) vertebrate genomes. Analysis of these orthologous datasets revealed significant levels of positive selection. Evidence of lineage-specific positive selection was identified in 14 genes in both ancestral and extant lineages. Lineage-specific positive selection was detected in the ancestral Euarchontoglires and Hominidae lineages for STK11, in the ancestral primate lineage for CDH1, in the ancestral Murinae lineage for both SDHC and MSH6 genes and the ancestral Muridae lineage for TSC1.

Conclusion

Identifying positive selection in the Primate, Hominidae, Muridae and Murinae lineages suggests an ancestral functional shift in these genes between the rodent and primate lineages. Analyses such as this, combining evolutionary theory and predictions - along with medically relevant data, can thus provide us with important clues for modeling human diseases.

The population genomics of a fast evolver: high levels of diversity, functional constraint, and molecular adaptation in the tunicate Ciona intestinalis

Phylogenomics has revealed the existence of fast-evolving animal phyla in which the amino acid substitution rate, averaged across many proteins, is consistently higher than in other lineages. The reasons for such differences in proteome-wide evolutionary rates are still unknown, largely because only a handful of species offer within-species genomic data from which molecular evolutionary processes can be deduced. In this study, we use next-generation sequencing technologies and individual whole-transcriptome sequencing to gather extensive polymorphism sequence data sets from Ciona intestinalis. Ciona is probably the best-characterized member of the fast-evolving Urochordata group (tunicates), which was recently identified as the sister group of the slow-evolving vertebrates. We introduce and validate a maximum-likelihood framework for single-nucleotide polymorphism and genotype calling, based on high-throughput short-read typing. We report that the C. intestinalis proteome is characterized by a high level of within-species diversity, efficient purifying selection, and a substantial percentage of adaptive amino acid substitutions. We conclude that the increased rate of amino acid sequence evolution in tunicates, when compared with vertebrates, is the consequence of both a 2–6 times higher per-year mutation rate and prevalent adaptive evolution.

Major role of positive selection in the evolution of conservative segments of Drosophila proteins

Slow evolution of conservative segments of coding and non-coding DNA is caused by the action of negative selection, which removes new mutations. However, the mode of selection that affects the few substitutions that do occur within such segments remains unclear. Here, we show that the fraction of allele replacements that were driven by positive selection, and the strength of this selection, is the highest within the conservative segments of Drosophila protein-coding genes. The McDonald–Kreitman test, applied to the data on variation in Drosophila melanogaster and in Drosophila simulans, indicates that within the most conservative protein segments, approximately 72 per cent (approx. 80%) of allele replacements were driven by positive selection, as opposed to only approximately 44 per cent (approx. 53%) at rapidly evolving segments. Data on multiple non-synonymous substitutions at a codon lead to the same conclusion and additionally indicate that positive selection driving allele replacements at conservative sites is the strongest, as it accelerates evolution by a factor of approximately 40, as opposed to a factor of approximately 5 at rapidly evolving sites. Thus, random drift plays only a minor role in the evolution of conservative DNA segments, and those relatively rare allele replacements that occur within such segments are mostly driven by substantial positive selection.

Reshaping of global gene expression networks and sex-biased gene expression by integration of a young gene

New genes originate frequently across diverse taxa. Given that genetic networks are typically comprised of robust, co-evolved interactions, the emergence of new genes raises an intriguing question: how do new genes interact with pre-existing genes? Here, we show that a recently originated gene rapidly evolved new gene networks and impacted sex-biased gene expression in Drosophila. This 4-6 million-year-old factor, named Zeus for its role in male fecundity, originated through retroposition of a highly conserved housekeeping gene, Caf40. Zeus acquired male reproductive organ expression patterns and phenotypes. Comparative expression profiling of mutants and closely related species revealed that Zeus has recruited a new set of downstream genes, and shaped the evolution of gene expression in germline. Comparative ChIP-chip revealed that the genomic binding profile of Zeus diverged rapidly from Caf40. These data demonstrate, for the first time, how a new gene quickly evolved novel networks governing essential biological processes at the genomic level.

The effect of variation in the effective population size on the rate of adaptive molecular evolution in eukaryotes

The role of adaptation is a fundamental question in molecular evolution. Theory predicts that species with large effective population sizes should undergo a higher rate of adaptive evolution than species with low effective population sizes if adaptation is limited by the supply of mutations. Previous analyses have appeared to support this conjecture because estimates of the proportion of nonsynonymous substitutions fixed by adaptive evolution, α, tend to be higher in species with large N_e. However, α is a function of both the number of advantageous and effectively neutral substitutions, either of which might depend on N_e. Here, we investigate the relationship between N_e and ω_a, the rate of adaptive evolution relative to the rate of neutral evolution, using nucleotide polymorphism and divergence data from 13 independent pairs of eukaryotic species. We find a highly significant positive correlation between ω_a and N_e. We also find some evidence that the rate of adaptive evolution varies between groups of organisms for a given N_e. The correlation between ω_a and N_e does not appear to be an artifact of demographic change or selection on synonymous codon use. Our results suggest that adaptation is to some extent limited by the supply of mutations and that at least some adaptation depends on newly occurring mutations rather than on standing genetic variation. Finally, we show that the proportion of nearly neutral nonadaptive substitutions declines with increasing N_e. The low rate of adaptive evolution and the high proportion of effectively neutral substitution in species with small N_e are expected to combine to make it difficult to detect adaptive molecular evolution in species with small N_e.

The nearly neutral and selection theories of molecular evolution under the fisher geometrical framework: substitution rate, population size, and complexity

The general theories of molecular evolution depend on relatively arbitrary assumptions about the relative distribution and rate of advantageous, deleterious, neutral, and nearly neutral mutations. The Fisher geometrical model (FGM) has been used to make distributions of mutations biologically interpretable. We explored an FGM-based molecular model to represent molecular evolutionary processes typically studied by nearly neutral and selection models, but in which distributions and relative rates of mutations with different selection coefficients are a consequence of biologically interpretable parameters, such as the average size of the phenotypic effect of mutations and the number of traits (complexity) of organisms. A variant of the FGM-based model that we called the static regime (SR) represents evolution as a nearly neutral process in which substitution rates are determined by a dynamic substitution process in which the population's phenotype remains around a suboptimum equilibrium fitness produced by a balance between slightly deleterious and slightly advantageous compensatory substitutions. As in previous nearly neutral models, the SR predicts a negative relationship between molecular evolutionary rate and population size; however, SR does not have the unrealistic properties of previous nearly neutral models such as the narrow window of selection strengths in which they work. In addition, the SR suggests that compensatory mutations cannot explain the high rate of fixations driven by positive selection currently found in DNA sequences, contrary to what has been previously suggested. We also developed a generalization of SR in which the optimum phenotype can change stochastically due to environmental or physiological shifts, which we called the variable regime (VR). VR models evolution as an interplay between adaptive processes and nearly neutral steady-state processes. When strong environmental fluctuations are incorporated, the process becomes a selection model in which evolutionary rate does not depend on population size, but is critically dependent on the complexity of organisms and mutation size. For SR as well as VR we found that key parameters of molecular evolution are linked by biological factors, and we showed that they cannot be fixed independently by arbitrary criteria, as has usually been assumed in previous molecular evolutionary models.

Estimating the rate of adaptive molecular evolution when the evolutionary divergence between species is small

We investigate the extent by which the estimates of the rate of adaptive molecular evolution obtained by extending the McDonald-Kreitman test are biased if the species, subjected to analysis, diverged recently. We show that estimates can be biased if the nucleotide divergence between the species is low relative to within species variation, and that the magnitude of the bias depends on the rate of adaptive evolution and the distribution of fitness effects of new mutations. Bias appears to be because of three factors: (1) misattribution of polymorphism to divergence; (2) the contribution of ancestral polymorphism to divergence; and (3) different rates of fixation of neutral and advantageous mutations. If there is little adaptive molecular evolution, then slightly deleterious mutations inflate estimates of the rate of adaptive evolution, because these contribute proportionately more to polymorphism than to nucleotide divergence than neutral mutations. However, if there is substantial adaptive evolution, polymorphism contributing to apparent divergence may downwardly bias estimates. We propose a simple method for correcting the different contributions of slightly deleterious and neutral mutations to polymorphism and divergence, and apply it to datasets from several species. We find that estimates of the rate of adaptive molecular evolution from closely related species may be underestimates by ~10% or more. However, after the contribution of polymorphism to divergence is removed, the rate of adaptive evolution may still be overestimated as a consequence of ancestral polymorphism and time for fixation effects. This bias may be substantial if branch lengths are less than 10N (e) generations.

Evidence for widespread positive and purifying selection across the European rabbit (Oryctolagus cuniculus) genome

The nearly neutral theory of molecular evolution predicts that the efficacy of both positive and purifying selection is a function of the long-term effective population size (N(e)) of a species. Under this theory, the efficacy of natural selection should increase with N(e). Here, we tested this simple prediction by surveying ~1.5 to 1.8 Mb of protein coding sequence in the two subspecies of the European rabbit (Oryctolagus cuniculus algirus and O. c. cuniculus), a mammal species characterized by high levels of nucleotide diversity and N(e) estimates for each subspecies on the order of 1 × 10(6). When the segregation of slightly deleterious mutations and demographic effects were taken into account, we inferred that >60% of amino acid substitutions on the autosomes were driven to fixation by positive selection. Moreover, we inferred that a small fraction of new amino acid mutations (<4%) are effectively neutral (defined as 0 < N(e)s < 1) and that this fraction was negatively correlated with a gene's expression level. Consistent with models of recurrent adaptive evolution, we detected a negative correlation between levels of synonymous site polymorphism and the rate of protein evolution, although the correlation was weak and nonsignificant. No systematic X chromosome-autosome difference was found in the efficacy of selection. For example, the proportion of adaptive substitutions was significantly higher on the X chromosome compared with the autosomes in O. c. algirus but not in O. c. cuniculus. Our findings support widespread positive and purifying selection in rabbits and add to a growing list of examples suggesting that differences in N(e) among taxa play a substantial role in determining rates and patterns of protein evolution.

Methods to detect selection on noncoding DNA

Vast tracts of noncoding DNA contain elements that regulate gene expression in higher eukaryotes. Describing these regulatory elements and understanding how they evolve represent major challenges for biologists. Advances in the ability to survey genome-scale DNA sequence data are providing unprecedented opportunities to use evolutionary models and computational tools to identify functionally important elements and the mode of selection acting on them in multiple species. This chapter reviews some of the current methods that have been developed and applied on noncoding DNA, what they have shown us, and how they are limited. Results of several recent studies reveal that a significantly larger fraction of noncoding DNA in eukaryotic organisms is likely to be functional than previously believed, implying that the functional annotation of most noncoding DNA in these organisms is largely incomplete. In Drosophila, recent studies have further suggested that a large fraction of noncoding DNA divergence observed between species may be the product of recurrent adaptive substitution. Similar studies in humans have revealed a more complex pattern, with signatures of recurrent positive selection being largely concentrated in conserved noncoding DNA elements. Understanding these patterns and the extent to which they generalize to other organisms awaits the analysis of forthcoming genome-scale polymorphism and divergence data from more species.

Selection on the protein-coding genome

Populations evolve as mutations arise in individual organisms and, through hereditary transmission, may become "fixed" (shared by all individuals) in the population. Most mutations are lethal or have negative fitness consequences for the organism. Others have essentially no effect on organismal fitness and can become fixed through the neutral stochastic process known as random drift. However, mutations may also produce a selective advantage that boosts their chances of reaching fixation. Regions of genes where new mutations are beneficial, rather than neutral or deleterious, tend to evolve more rapidly due to positive selection. Genes involved in immunity and defense are a well-known example; rapid evolution in these genes presumably occurs because new mutations help organisms to prevail in evolutionary "arms races" with pathogens. In recent years, genome-wide scans for selection have enlarged our understanding of the evolution of the protein-coding regions of the various species. In this chapter, we focus on the methods to detect selection in protein-coding genes. In particular, we discuss probabilistic models and how they have changed with the advent of new genome-wide data now available.

Temporally variable selection on proteolysis-related reproductive tract proteins in Drosophila

In order to gain further insight into the processes underlying rapid reproductive protein evolution, we have conducted a population genetic survey of 44 reproductive tract-expressed proteases, protease inhibitors, and targets of proteolysis in Drosophila melanogaster and Drosophila simulans. Our findings suggest that positive selection on this group of genes is temporally heterogeneous, with different patterns of selection inferred using tests sensitive at different time scales. Such variation in the strength and targets of selection through time may be expected under models of sexual conflict and/or host-pathogen interaction. Moreover, available functional information concerning the genes that show evidence of selection suggests that both sexual selection and immune processes have been important in the evolutionary history of this group of molecules.

Genomic determinants of protein evolution and polymorphism in Arabidopsis

Recent results from Drosophila suggest that positive selection has a substantial impact on genomic patterns of polymorphism and divergence. However, species with smaller population sizes and/or stronger population structure may not be expected to exhibit Drosophila-like patterns of sequence variation. We test this prediction and identify determinants of levels of polymorphism and rates of protein evolution using genomic data from Arabidopsis thaliana and the recently sequenced Arabidopsis lyrata genome. We find that, in contrast to Drosophila, there is no negative relationship between nonsynonymous divergence and silent polymorphism at any spatial scale examined. Instead, synonymous divergence is a major predictor of silent polymorphism, which suggests variation in mutation rate as the main determinant of silent variation. Variation in rates of protein divergence is mainly correlated with gene expression level and breadth, consistent with results for a broad range of taxa, and map-based estimates of recombination rate are only weakly correlated with nonsynonymous divergence. Variation in mutation rates and the strength of purifying selection seem to be major drivers of patterns of polymorphism and divergence in Arabidopsis. Nevertheless, a model allowing for varying negative and positive selection by functional gene category explains the data better than a homogeneous model, implying the action of positive selection on a subset of genes. Genes involved in disease resistance and abiotic stress display high proportions of adaptive substitution. Our results are important for a general understanding of the determinants of rates of protein evolution and the impact of selection on patterns of polymorphism and divergence.

Weighing the evidence for adaptation at the molecular level

The abundance of genome polymorphism and divergence data has provided unprecedented insight into how mutation, drift and natural selection shape genome evolution. Application of the McDonald-Kreitman (MK) test to such data indicates a pervasive influence of positive selection, particularly in Drosophila species. However, evidence for positive selection in other species ranging from yeast to humans is often weak or absent. Although evidence for positive selection could be obscured in some species, there is also reason to believe that the frequency of adaptive substitutions could be overestimated as a result of epistatic fitness effects or hitchhiking of deleterious mutations. Based on these considerations it is argued that the common assumption of independence among sites must be relaxed before abandoning the neutral theory of molecular evolution.

Characterizing the influence of effective population size on the rate of adaptation: Gillespie's Darwin domain

Characterizing the role of effective population size in dictating the rate of adaptive evolution remains a major challenge in evolutionary biology. Depending on the underlying distribution of fitness effects of new mutations, populations of different sizes may differ vastly in their rate of adaptation. Here, we collect polymorphism data at over 100 loci for two closely related Drosophila species with different current effective population sizes (N_e), Drosophila miranda and D. pseudoobscura, to evaluate the prevalence of adaptive evolution versus genetic drift in molecular evolution. Utilizing these large and consistently sampled data sets, we obtain greatly improved estimates of the demographic histories of both species. Specifically, although current N_e differs between these species, their ancestral sizes were much more similar. We find that statistical approaches capturing recent adaptive evolution (using patterns of polymorphisms) detect higher rates of adaptive evolution in the larger D. pseudoobscura population. In contrast, methods aimed at detecting selection over longer time periods (i.e., those relying on divergence data) estimate more similar rates of adaptation between the two species. Thus, our results suggest an important role of effective population size in dictating rates of adaptation and highlight how complicated population histories—as is probably the case for most species—can effect rates of adaptation. Additionally, we also show how different methodologies to detect positive selection can reveal information about different timescales of adaptive evolution.

Accelerated and adaptive evolution of yeast sexual adhesins

There is a recent emergence of interest in the genes involved in gametic recognition as drivers of reproductive isolation. The recent population genomic sequencing of two species of sexually primitive yeasts (Liti G, Carter DM, Moses AM, Warringer J, Parts L, James SA, Davey RP, Roberts IN, Burt A, Koufopanou V et al. [23 co-authors]. 2009. Population genomics of domestic and wild yeasts. Nature 458:337-341.) has provided data for systematic study of the roles these genes play in the early evolution of sex and speciation. Here, we discovered that among genes encoding cell surface proteins, the sexual adhesin genes have evolved significantly more rapidly than others, both within and between Saccharomyces cerevisiae and its closest relative S. paradoxus. This result was supported by analyses using the PAML pairwise model, a modified McDonald-Kreitman test, and the PAML branch model. Moreover, using a combination of a new statistic of neutrality, an information theory-based measure of evolutionary variability, and functional characterization of amino acid changes, we found that a higher proportion of amino acid changes are fixed in the sexual adhesins than in other proteins and a greater proportion of the fixed amino acid changes either between the two species or the two subgroups of S. paradoxus are functionally dissimilar or radically different. These results suggest that the accelerated evolution of sexual adhesin genes may facilitate speciation, or incipient speciation, and promote sexual selection in general.

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.

Positive and negative selection on noncoding DNA close to protein-coding genes in wild house mice

During the past two decades, evidence has accumulated of adaptive evolution within protein-coding genes in a variety of species. However, with the exception of Drosophila and humans, little is known about the extent of adaptive evolution in noncoding DNA. Here, we study regions upstream and downstream of protein-coding genes in the house mouse Mus musculus castaneus, a species that has a much larger effective population size (N(e)) than humans. We analyze polymorphism data for 78 genes from 15 wild-caught M. m. castaneus individuals and divergence to a closely related species, Mus famulus. We find high levels of nucleotide diversity and moderate levels of selective constraint in upstream and downstream regions compared with nonsynonymous sites of protein-coding genes. From the polymorphism data, we estimate the distribution of fitness effects (DFE) of new mutations and infer that most new mutations in upstream and downstream regions behave as effectively neutral and that only a small fraction is strongly negatively selected. We also estimate the fraction of substitutions that have been driven to fixation by positive selection (α) and the ratio of adaptive to neutral divergence (ω(α)). We find that α for upstream and downstream regions (∼ 10%) is much lower than α for nonsynonymous sites (∼ 50%). However, ω(α) estimates are very similar for nonsynonymous sites (∼ 10%) and upstream and downstream regions (∼ 5%). We conclude that negative selection operating in upstream and downstream regions of M. m. castaneus is weak and that the low values of α for upstream and downstream regions relative to nonsynonymous sites are most likely due to the presence of a higher proportion of neutrally evolving sites and not due to lower absolute rates of adaptive substitution.

Molecular evolution, mutation size and gene pleiotropy: a geometric reexamination

The influence of phenotypic effects of genetic mutations on molecular evolution is not well understood. Neutral and nearly neutral theories of molecular evolution predict a negative relationship between the evolutionary rate of proteins and their functional importance; nevertheless empirical studies seeking relationships between evolutionary rate and the phenotypic role of proteins have not produced conclusive results. In particular, previous studies have not found the expected negative correlation between evolutionary rate and gene pleiotropy. Here, we studied the effect of gene pleiotropy and the phenotypic size of mutations on the evolutionary rate of genes in a geometrical model, in which gene pleiotropy was characterized by n molecular phenotypes that affect organismal fitness. For a nearly neutral process, we found a negative relationship between evolutionary rate and mutation size but pleiotropy did not affect the evolutionary rate. Further, for a selection model, where most of the substitutions were fixed by natural selection in a randomly fluctuating environment, we also found a negative relationship between evolutionary rate and mutation size, but interestingly, gene pleiotropy increased the evolutionary rate as √n. These findings may explain part of the disagreement between empirical data and traditional expectations.

Gene duplication and ectopic gene conversion in Drosophila

The evolutionary impact of gene duplication events has been a theme of Drosophila genetics dating back to the Morgan School. While considerable attention has been placed on the genetic novelties that duplicates are capable of introducing, and the role that positive selection plays in their early stages of duplicate evolution, much less attention has been given to the potential consequences of ectopic (non-allelic) gene conversion on these evolutionary processes. In this paper we consider the historical origins of ectopic gene conversion models and present a synthesis of the current Drosophila data in light of several primary questions in the field.

The distinctive footprints of local hitchhiking in a varied environment and global hitchhiking in a subdivided population

Loci with higher levels of population differentiation than the neutral expectation are traditionally interpreted as evidence of ongoing selection that varies in space. This article emphasizes an alternative explanation that has been largely overlooked to date: in species subdivided into large subpopulations, enhanced differentiation can also be the signature left by the fixation of an unconditionally favorable mutation on its chromosomal neighborhood. This is because the hitchhiking effect is expected to diminish as the favorable mutation spreads from the deme in which it originated to other demes. To discriminate among the two alternative scenarios one needs to investigate how genetic structure varies along the chromosomal region of the locus. Local hitchhiking is shown to generate a single sharp peak of differentiation centered on the adaptive polymorphism and the standard signature of a selective sweep only in those subpopulations in which the allele is favored. Global hitchhiking produces two domes of differentiation on either side of the fixed advantageous mutation and signatures of a selective sweep in every subpopulation, albeit of different magnitude. Investigating population differentiation around a locus that strongly differentiates two otherwise genetically similar populations of the marine mussel Mytilus edulis, plausible evidence for the global hitchhiking hypothesis has been obtained. Global hitchhiking is a neglected phenomenon that might prove to be important in species with large population sizes such as many marine invertebrates.

Recent and recurrent selective sweeps of the antiviral RNAi gene Argonaute-2 in three species of Drosophila

Antagonistic host-parasite interactions can drive rapid adaptive evolution in genes of the immune system, and such arms races may be an important force shaping polymorphism in the genome. The RNA interference pathway gene Argonaute-2 (AGO2) is a key component of antiviral defense in Drosophila, and we have previously shown that genes in this pathway experience unusually high rates of adaptive substitution. Here we study patterns of genetic variation in a 100-kbp region around AGO2 in three different species of Drosophila. Our data suggest that recent independent selective sweeps in AGO2 have reduced genetic variation across a region of more than 50 kbp in Drosophila melanogaster, D. simulans, and D. yakuba, and we estimate that selection has fixed adaptive substitutions in this gene every 30-100 thousand years. The strongest signal of recent selection is evident in D. simulans, where we estimate that the most recent selective sweep involved an allele with a selective advantage of the order of 0.5-1% and occurred roughly 13-60 Kya. To evaluate the potential consequences of the recent substitutions on the structure and function of AGO2, we used fold-recognition and homology-based modeling to derive a structural model for the Drosophila protein, and this suggests that recent substitutions in D. simulans are overrepresented at the protein surface. In summary, our results show that selection by parasites can consistently target the same genes in multiple species, resulting in areas of the genome that have markedly reduced genetic diversity.

Nonadaptive processes in primate and human evolution

Evolutionary biology has tended to focus on adaptive evolution by positive selection as the primum mobile of evolutionary trajectories in species while underestimating the importance of nonadaptive evolutionary processes. In this review, I describe evidence that suggests that primate and human evolution has been strongly influenced by nonadaptive processes, particularly random genetic drift and mutation. This is evidenced by three fundamental effects: a relative relaxation of selective constraints (i.e., purifying selection), a relative increase in the fixation of slightly deleterious mutations, and a general reduction in the efficacy of positive selection. These effects are observed in protein-coding, regulatory regions, and in gene expression data, as well as in an augmentation of fixation of large-scale mutations, including duplicated genes, mobile genetic elements, and nuclear mitochondrial DNA. The evidence suggests a general population-level explanation such as a reduction in effective population size (N(e)). This would have tipped the balance between the evolutionary forces of natural selection and random genetic drift toward genetic drift for variants having small selective effects. After describing these proximate effects, I describe the potential consequences of these effects for primate and human evolution. For example, an increase in the fixation of slightly deleterious mutations could potentially have led to an increase in the fixation rate of compensatory mutations that act to suppress the effects of slightly deleterious substitutions. The potential consequences of compensatory evolution for the evolution of novel gene functions and in potentially confounding the detection of positively selected genes are explored. The consequences of the passive accumulation of large-scale genomic mutations by genetic drift are unclear, though evidence suggests that new gene copies as well as insertions of transposable elements into genes can potentially lead to adaptive phenotypes. Finally, because a decrease in selective constraint at the genetic level is expected to have effects at the morphological level, I review studies that compare rates of morphological change in various mammalian and island populations where N(e) is reduced. Furthermore, I discuss evidence that suggests that craniofacial morphology in the Homo lineage has shifted from an evolutionary rate constrained by purifying selection toward a neutral evolutionary rate.

Fitness effects of derived deleterious mutations in four closely related wild tomato species with spatial structure

A key issue in evolutionary biology is an improved understanding of the genetic mechanisms by which species adapt to various environments. Using DNA sequence data, it is possible to quantify the number of adaptive and deleterious mutations, and the distribution of fitness effects of new mutations (its mean and variance) by simultaneously taking into account the demography of a given species. We investigated how selection functions at eight housekeeping genes of four closely related, outcrossing species of wild tomatoes that are native to diverse environments in western South America (Solanum arcanum, S. chilense, S. habrochaites and S. peruvianum). We found little evidence for adaptive mutations but pervasive evidence for strong purifying selection in coding regions of the four species. In contrast, the strength of purifying selection seems to vary among the four species in non-coding (NC) regions (introns). Using F(ST)-based measures of fixation in subdivided populations, we suggest that weak purifying selection has affected the NC regions of S. habrochaites, S. chilense and S. peruvianum. In contrast, NC regions in S. arcanum show a distribution of fitness effects with mutations being either nearly neutral or very strongly deleterious. These results suggest that closely related species with similar genetic backgrounds but experiencing contrasting environments differ in the variance of deleterious fitness effects.

Effective population size and the efficacy of selection on the X chromosomes of two closely related Drosophila species

The prevalence of natural selection relative to genetic drift is of central interest in evolutionary biology. Depending on the distribution of fitness effects of new mutations, the importance of these evolutionary forces may differ in species with different effective population sizes. Here, we survey population genetic variation at 105 orthologous X-linked protein coding regions in Drosophila melanogaster and its sister species D. simulans, two closely related species with distinct demographic histories. We observe significantly higher levels of polymorphism and evidence for stronger selection on codon usage bias in D. simulans, consistent with a larger historical effective population size on average for this species. Despite these differences, we estimate that <10% of newly arising nonsynonymous mutations have deleterious fitness effects in the nearly neutral range (i.e., -10 < N(e)s < 0) in both species. The inferred distributions of fitness effects and demographic models translate into surprisingly high estimates of the fraction of "adaptive" protein divergence in both species (∼ 85-90%). Despite evidence for different demographic histories, differences in population size have apparently played little role in the dynamics of protein evolution in these two species, and estimates of the adaptive fraction (α) of protein divergence in both species remain high even if we account for recent 10-fold growth. Furthermore, although several recent studies have noted strong signatures of recurrent adaptive protein evolution at genes involved in immunity, reproduction, sexual conflict, and intragenomic conflict, our finding of high levels of adaptive protein divergence at randomly chosen proteins (with respect to function) suggests that many other factors likely contribute to the adaptive protein divergence signature in Drosophila.

Chromosomal redistribution of male-biased genes in mammalian evolution with two bursts of gene gain on the X chromosome

Mammalian X chromosomes evolved under various mechanisms including sexual antagonism, the faster-X process, and meiotic sex chromosome inactivation (MSCI). These forces may contribute to nonrandom chromosomal distribution of sex-biased genes. In order to understand the evolution of gene content on the X chromosome and autosome under these forces, we dated human and mouse protein-coding genes and miRNA genes on the vertebrate phylogenetic tree. We found that the X chromosome recently acquired a burst of young male-biased genes, which is consistent with fixation of recessive male-beneficial alleles by sexual antagonism. For genes originating earlier, however, this pattern diminishes and finally reverses with an overrepresentation of the oldest male-biased genes on autosomes. MSCI contributes to this dynamic since it silences X-linked old genes but not X-linked young genes. This demasculinization process seems to be associated with feminization of the X chromosome with more X-linked old genes expressed in ovaries. Moreover, we detected another burst of gene originations after the split of eutherian mammals and opossum, and these genes were quickly incorporated into transcriptional networks of multiple tissues. Preexisting X-linked genes also show significantly higher protein-level evolution during this period compared to autosomal genes, suggesting positive selection accompanied the early evolution of mammalian X chromosomes. These two findings cast new light on the evolutionary history of the mammalian X chromosome in terms of gene gain, sequence, and expressional evolution.

The neutral theory of molecular evolution in the genomic era

The neutral theory of molecular evolution has been widely accepted and is the guiding principle for studying evolutionary genomics and the molecular basis of phenotypic evolution. Recent data on genomic evolution are generally consistent with the neutral theory. However, many recently published papers claim the detection of positive Darwinian selection via the use of new statistical methods. Examination of these methods has shown that their theoretical bases are not well established and often result in high rates of false-positive and false-negative results. When the deficiencies of these statistical methods are rectified, the results become largely consistent with the neutral theory. At present, genome-wide analyses of natural selection consist of collections of single-locus analyses. However, because phenotypic evolution is controlled by the interaction of many genes, the study of natural selection ought to take such interactions into account. Experimental studies of evolution will also be crucial.

Local effects of limited recombination: historical perspective and consequences for population estimates of adaptive evolution

Recent years have witnessed the integration of theoretical advances in population genetics with large-scale analyses of complete genomes, with a growing number of studies suggesting pervasive natural selection that includes frequent deleterious as well as adaptive mutations. In finite populations, however, mutations under selection alter the fate of genetically linked mutations (the so-called Hill-Robertson effect). Here we review the evolutionary consequences of selection at linked sites (linked selection) focusing on its effects on nearby nucleotides in genomic regions with nonreduced recombination. We argue that these local effects of linkage may account for differences in selection intensity among genes. We also show that even high levels of recombination are unlikely to remove all effects of linked selection, causing a reduction in the polymorphism to divergence ratio (r(pd)) at neutral sites. Because a number of methods employed to estimate the magnitude and frequency of adaptive mutations take reduced r(pd) as evidence of positive selection, ignoring local linkage effects may lead to misleading estimates of the proportion of adaptive substitutions and estimates of positive selection. These biases are caused by employing methods that do not account for local variation in the relative effective population size (N(e)) caused by linked selection.

Estimation of the neutrality index

The McDonald-Kreitman (MK) test is a simple and widely used test of selection in which the numbers of nonsilent and silent substitutions (D(n) and D(s)) are compared with the numbers of nonsilent and silent polymorphisms (P(n) and P(s)). The neutrality index (NI = D(s)P(n)/D(n)P(s)), the odds ratio (OR) of the MK table, measures the direction and degree of departure from neutral evolution. The mean of NI values across genes is often taken to summarize patterns of selection in a species. Here, we show that this leads to statistical bias in both simulated and real data to the extent that species, which show a pattern of adaptive evolution, can apparently be subject to weak purifying selection and vice versa. We show that this bias can be removed by using a variant of the Cochran-Mantel-Haenszel procedure for estimating a weighted average OR. We also show that several point estimators of NI are statistically biased even when cutoff values are employed. We therefore suggest that a new statistic be used to study patterns of selection when data are sparse, the direction of selection: DoS = D(n)/(D(n) + D(s)) - P(n)/(P(n) + P(s)).

Shifts in the intensity of purifying selection: an analysis of genome-wide polymorphism data from two closely related yeast species

How much does the intensity of purifying selection vary among populations and species? How uniform are the shifts in selective pressures across the genome? To address these questions, we took advantage of a recent, whole-genome polymorphism data set from two closely related species of yeast, Saccharomyces cerevisiae and S. paradoxus, paying close attention to the population structure within these species. We found that the average intensity of purifying selection on amino acid sites varies markedly among populations and between species. As expected in the presence of extensive weakly deleterious mutations, the effect of purifying selection is substantially weaker on single nucleotide polymorphisms (SNPs) segregating within populations than on SNPs fixed between population samples. Also in accordance with a Nearly Neutral model, the variation in the intensity of purifying selection across populations corresponds almost perfectly to simple measures of their effective size. As a first step toward understanding the processes generating these patterns, we sought to tease apart the relative importance of systematic, genome-wide changes in the efficacy of selection, such as those expected from demographic processes and of gene-specific changes, which may be expected after a shift in selective pressures. For that purpose, we developed a new model for the evolution of purifying selection between populations and inferred its parameters from the genome-wide data using a likelihood approach. We found that most, but not all changes seem to be explained by systematic shifts in the efficacy of selection. One population, the sake-derived strains of S. cerevisiae, however, also shows extensive gene-specific changes, plausibly associated with domestication. These findings have important implications for our understanding of purifying selection as well as for estimates of the rate of molecular adaptation in yeast and in other species.

Age-dependent chromosomal distribution of male-biased genes in Drosophila

We investigated the correlation between the chromosomal location and age distribution of new male-biased genes formed by duplications via DNA intermediates (DNA-level) or by de novo origination in Drosophila. Our genome-wide analysis revealed an excess of young X-linked male-biased genes. The proportion of X-linked male-biased genes then diminishes through time, leading to an autosomal excess of male-biased genes. The switch between X-linked and autosomal enrichment of male-biased genes was also present in the distribution of both protein-coding genes on the D. pseudoobscura neo-X chromosome and microRNA genes of D. melanogaster. These observations revealed that the evolution of male-biased genes is more complicated than the previously detected one-step X→A gene traffic and the enrichment of the male-biased genes on autosomes. The pattern we detected suggests that the interaction of various evolutionary forces such as the meiotic sex chromosome inactivation (MSCI), faster-X effect, and sexual antagonism in the male germline might have shaped the chromosomal distribution of male-biased genes on different evolutionary time scales.

Genome wide analyses reveal little evidence for adaptive evolution in many plant species

The relative contribution of advantageous and neutral mutations to the evolutionary process is a central problem in evolutionary biology. Current estimates suggest that whereas Drosophila, mice, and bacteria have undergone extensive adaptive evolution, hominids show little or no evidence of adaptive evolution in protein-coding sequences. This may be a consequence of differences in effective population size. To study the matter further, we have investigated whether plants show evidence of adaptive evolution using an extension of the McDonald-Kreitman test that explicitly models slightly deleterious mutations by estimating the distribution of fitness effects of new mutations. We apply this method to data from nine pairs of species. Altogether more than 2,400 loci with an average length of approximately 280 nucleotides were analyzed. We observe very similar results in all species; we find little evidence of adaptive amino acid substitution in any comparison except sunflowers. This may be because many plant species have modest effective population sizes.

Estimating the parameters of selection on nonsynonymous mutations in Drosophila pseudoobscura and D. miranda

We present the results of surveys of diversity in sets of >40 X-linked and autosomal loci in samples from natural populations of Drosophila miranda and D. pseudoobscura, together with their sequence divergence from D. affinis. Mean silent site diversity in D. miranda is approximately one-quarter of that in D. pseudoobscura; mean X-linked silent diversity is about three-quarters of that for the autosomes in both species. Estimates of the distribution of selection coefficients against heterozygous, deleterious nonsynonymous mutations from two different methods suggest a wide distribution, with coefficients of variation greater than one, and with the average segregating amino acid mutation being subject to only very weak selection. Only a small fraction of new amino acid mutations behave as effectively neutral, however. A large fraction of amino acid differences between D. pseudoobscura and D. affinis appear to have been fixed by positive natural selection, using three different methods of estimation; estimates between D. miranda and D. affinis are more equivocal. Sources of bias in the estimates, especially those arising from selection on synonymous mutations and from the choice of genes, are discussed and corrections for these applied. Overall, the results show that both purifying selection and positive selection on nonsynonymous mutations are pervasive.

Recombination yet inefficient selection along the Drosophila melanogaster subgroup's fourth chromosome

A central goal of evolutionary genetics is an understanding of the forces responsible for the observed variation, both within and between species. Theoretical and empirical work have demonstrated that genetic recombination contributes to this variation by breaking down linkage between nucleotide sites, thus allowing them to behave independently and for selective forces to act efficiently on them. The Drosophila fourth chromosome, which is believed to experience no-or very low-rates of recombination has been an important model for investigating these effects. Despite previous efforts, central questions regarding the extent of recombination and the predominant modes of selection acting on it remain open. In order to more comprehensively test hypotheses regarding recombination and its potential influence on selection along the fourth chromosome, we have resequenced regions from most of its genes from Drosophila melanogaster, D. simulans, and D. yakuba. These data, along with available outgroup sequence, demonstrate that recombination is low but significantly greater than zero for the three species. Despite there being recombination, there is strong evidence that its frequency is low enough to have rendered selection relatively inefficient. The signatures of relaxed constraint can be detected at both the level of polymorphism and divergence.

The role of advantageous mutations in enhancing the evolution of a recombination modifier

Although the evolution of recombination is still a major problem in evolutionary genetics, recent theoretical studies have shown that recombination can evolve by breaking down interference ("Hill-Robertson effects") among multiple loci. This leads to selection on a recombination modifier in a population subject to recurrent deleterious mutation. Here, we use computer simulations to investigate the evolution of a recombination modifier under three different scenarios of recurrent mutation in a finite population: (1) mutations are deleterious only, (2) mutations are advantageous only, and (3) there is a mixture of deleterious and advantageous mutations. We also investigate how linkage disequilibrium, the strength of selection acting on a modifier, and effective population size change under the different scenarios. We observe that adding even a small number of advantageous mutations increases the fixation rate of modifiers that increase recombination, especially if the effects of deleterious mutations are weak. However, the strength of selection on a modifier is less than the summed strengths had there been deleterious mutations only and advantageous mutations only.

Genome-wide evidence for efficient positive and purifying selection in Capsella grandiflora, a plant species with a large effective population size

Recent studies comparing genome-wide polymorphism and divergence in Drosophila have found evidence for a surprisingly high proportion of adaptive amino acid fixations, but results for other taxa are mixed. In particular, few studies have found convincing evidence for adaptive amino acid substitution in plants. To assess the generality of this finding, we have sequenced 257 loci in the outcrossing crucifer Capsella grandiflora, which has a large effective population size and low population structure. Using a new method that jointly infers selective and demographic effects, we estimate that 40% of amino acid substitutions were fixed by positive selection in this species, and we also infer a low proportion of slightly deleterious amino acid mutations. We contrast these estimates with those for a similar data set from the closely related Arabidopsis thaliana and find significantly higher rates of adaptive evolution and fewer nearly neutral mutations in C. grandiflora. In agreement with results for other taxa, genes involved in reproduction show the strongest evidence for positive selection in C. grandiflora. Taken together, these results imply that both positive and purifying selection are more effective in C. grandiflora than in A. thaliana, consistent with the contrasting demographic history and effective population sizes of these species.

On the utility of short intron sequences as a reference for the detection of positive and negative selection in Drosophila

The detection of selection, both positive and negative, acting on a DNA sequence or class of nucleotide sites requires comparison with a reference sequence that is unaffected by selection. In Drosophila, recent findings of widespread selective constraint, as well as adaptive evolution, in both coding and noncoding regions highlight the difficulties in choosing such a reference sequence. Here, we investigate the utility of short intron sequences as a reference for the detection of selection. For a set of 119 Drosophila melanogaster genes containing 195 short introns (<or=120 bp), we analyzed polymorphism and divergence at 1) 4-fold synonymous sites, 2) all sites of introns <or=120 bp, 3) all sites of introns <or=65 bp, 4) bases 8-30 of introns <or=120 bp, and 5) bases 8-30 of introns <or=65 bp. The last class of sites shows the highest levels of both interspecific divergence and intraspecific polymorphism, suggesting that these sites are under the least selective constraint. Bases 8-30 of introns <or=65 bp also have the lowest ratio of divergence to polymorphism, which may indicate that a small proportion of substitutions in the other classes of sites are the result of adaptive evolution. Although there is little signal of selection on the primary sequence of short introns, patterns of insertion-deletion polymorphism and divergence suggest that both positive and negative selection act to maintain an optimal intron length.