Genome-wide Scan of 29,141 African Americans Finds No Evidence of Directional Selection since Admixture

The extent of recent selection in admixed populations is currently an unresolved question. We scanned the genomes of 29,141 African Americans and failed to find any genome-wide-significant deviations in local ancestry, indicating no evidence of selection influencing ancestry after admixture. A recent analysis of data from 1,890 African Americans reported that there was evidence of selection in African Americans after their ancestors left Africa, both before and after admixture. Selection after admixture was reported on the basis of deviations in local ancestry, and selection before admixture was reported on the basis of allele-frequency differences between African Americans and African populations. The local-ancestry deviations reported by the previous study did not replicate in our very large sample, and we show that such deviations were expected purely by chance, given the number of hypotheses tested. We further show that the previous study’s conclusion of selection in African Americans before admixture is also subject to doubt. This is because the F_ST statistics they used were inflated and because true signals of unusual allele-frequency differences between African Americans and African populations would be best explained by selection that occurred in Africa prior to migration to the Americas.     

Detecting Selection in Multiple Populations by Modeling Ancestral Admixture Components

One of the most powerful and commonly used approaches for detecting local adaptation in the genome is the identification of extreme allele frequency differences between populations. In this article, we present a new maximum likelihood method for finding regions under positive selection. It is based on a Gaussian approximation to allele frequency changes and it incorporates admixture between populations. The method can analyze multiple populations simultaneously and retains power to detect selection signatures specific to ancestry components that are not representative of any extant populations. Using simulated data, we compare our method to related approaches, and show that it is orders of magnitude faster than the state-of-the-art, while retaining similar or higher power for most simulation scenarios. We also apply it to human genomic data and identify loci with extreme genetic differentiation between major geographic groups. Many of the genes identified are previously known selected loci relating to hair pigmentation and morphology, skin, and eye pigmentation. We also identify new candidate regions, including various selected loci in the Native American component of admixed Mexican-Americans. These involve diverse biological functions, such as immunity, fat distribution, food intake, vision, and hair development.     

Strong Reinforcing Selection in a Texas Wildflower

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Selection maintains MHC diversity through a natural population bottleneck

A perceived consequence of a population bottleneck is the erosion of genetic diversity and concomitant reduction in individual fitness and evolutionary potential. Although reduced genetic variation associated with demographic perturbation has been amply demonstrated for neutral molecular markers, the effective management of genetic resources in natural populations is hindered by a lack of understanding of how adaptive genetic variation will respond to population fluctuations, given these are affected by selection as well as drift. Here, we demonstrate that selection counters drift to maintain polymorphism at a major histocompatibility complex (MHC) locus through a population bottleneck in an inbred island population of water voles. Before and after the bottleneck, MHC allele frequencies were close to balancing selection equilibrium but became skewed by drift when the population size was critically low. MHC heterozygosity generally conformed to Hardy-Weinberg expectations except in one generation during the population recovery where there was a significant excess of heterozygous genotypes, which simulations ascribed to strong differential MHC-dependent survival. Low allelic diversity and highly skewed frequency distributions at microsatellite loci indicated potent genetic drift due to a strong founder affect and/or previous population bottlenecks. This study is a real-time examination of the predictions of fundamental evolutionary theory in low genetic diversity situations. The findings highlight that conservation efforts to maintain the genetic health and evolutionary potential of natural populations should consider the genetic basis for fitness-related traits, and how such adaptive genetic diversity will vary in response to both the demographic fluctuations and the effects of selection.     

Pleiotropic Mutations Are Subject to Strong Stabilizing Selection

The assumption that pleiotropic mutations are more deleterious than mutations with more restricted phenotypic effects is an important premise in models of evolution. However, empirical evidence supporting this assumption is limited. Here, we estimated the strength of stabilizing selection on mutations affecting gene expression in male Drosophila serrata. We estimated the mutational variance (V_M) and the standing genetic variance (V_G) from two well-matched panels of inbred lines: a panel of mutation accumulation (MA) lines derived from a single inbred ancestral line and a panel of inbred lines derived from an outbred population. For 855 gene-expression traits, we estimated the strength of stabilizing selection as s = V_M/V_G. Selection was observed to be relatively strong, with 17% of traits having s > 0.02, a magnitude typically associated with life-history traits. Randomly assigning expression traits to five-trait sets, we used factor analytic mixed modeling in the MA data set to identify covarying traits that shared pleiotropic mutations. By assigning traits to the same trait sets in the outbred line data set, we then estimated s for the combination of traits affected by pleiotropic mutation. For these pleiotropic combinations, the median s was three times greater than s acting on the individual component traits, and 46% of the pleiotropic trait combinations had s > 0.02. Although our analytical approach was biased toward detecting mutations with relatively large effects, likely overestimating the average strength of selection, our results provide widespread support for the prediction that stronger selection can act against mutations with pleiotropic effects.THE extent to which new mutations have pleiotropic effects on multiple traits, and ultimately on fitness is central to our understanding of the maintenance of genetic variation and the process of adaptation (Kondrashov and Turelli 1992; Otto 2004; Johnson and Barton 2005; Zhang and Hill 2005). Analyses of Fisher’s (1930) geometric model of adaptation have shown that a mutation with effects on many traits will have a reduced probability of contributing to adaptive evolution (Orr 2000; Welch and Waxman 2003; see also Haygood 2006). For a population close to its optimum under mutation–selection balance, a direct corollary of this is that selection must act more strongly against mutations with wider pleiotropic effects (Zhang 2012).Evidence for the strength of selection increasing with the number of traits that are pleiotropically affected by a mutation is limited. At a phenotypic level, nonlinear (stabilizing) selection is much stronger on combinations of metric traits than on each individual trait contributing to the combination (Blows and Brooks 2003; Walsh and Blows 2009). Given that genetic correlations among such traits are expected to be a consequence of pleiotropic alleles (Lande 1980), stronger selection on trait combinations is consistent with stronger selection on pleiotropic mutations that are likely to underlie the genetic covariance among such traits. There is some evidence that per-trait allelic effects might be greater for alleles with more widespread pleiotropic effects (Wagner et al. 2008; Wang et al. 2010); as mutations with larger phenotypic effects might be more effectively targeted by selection, this also suggests stronger selection against more pleiotropic mutation.Mutation accumulation (MA) breeding designs, in which the opportunity for selection is reduced, allowing new mutations to drift to fixation, provide an opportunity to characterize the strength of selection acting directly against new mutations. Rice and Townsend (2012) proposed an approach for determining the strength of selection acting against mutations at individual loci, combining information from QTL mapping and MA studies. This approach could conceivably be extended to associate the strength of selection with the number of traits a QTL affects. More typically, estimates of selection from MA designs are focused on traits, rather than alleles. Under the assumption that most mutations are deleterious, an assumption supported by MA studies (Halligan and Keightley 2009), the strength of selection acting on mutations affecting quantitative traits can be measured as the ratio of the mutational to the standing genetic variance, s = V_M/V_G, where s is the selection coefficient of the mutation in heterozygous form (Barton 1990; Houle et al. 1996). While estimating s in this way provides a framework for estimating selection on pleiotropic combinations of traits, we are not aware of any studies adopting this approach to directly estimate the strength of selection acting on mutations affecting multiple traits.Within an MA framework, Estes and Phillips (2006) manipulated the opportunity for selection, providing rare direct evidence of stronger selection against mutations with pleiotropic effects. In a DNA repair-deficient strain of Caenorhabditis elegans, Estes and Phillips (2006) observed lower mutational covariance among life-history components when selection was allowed (larger populations) than when the opportunity for selection was limited (small populations). Similarly, McGuigan et al. (2011) compared Drosophila serrata MA lines accumulating mutations in the presence or absence of sexual selection on males, reporting reduced covariance between two fitness components in the selection treatment. These studies reveal that selection can eliminate nonlethal alleles with pleiotropic effects, but whether traits other than life-history components exhibit similar evidence of selection against pleiotropic alleles remains unknown.In parallel to the quantitative genetic predictions that pleiotropic alleles will be under stronger selection, molecular genetic theory predicts that the rate of gene evolution will be negatively correlated with pleiotropy (Pal et al. 2006; Salathe et al. 2006). More highly pleiotropic genes, as identified through the extent of connectivity (the number of interactions) in protein–protein interaction networks (Jeong et al. 2001), or the number of gene ontology (GO) terms (Jovelin and Phillips 2009) are more likely to be essential (i.e., knockout mutations result in lethality), suggesting that selection is stronger against large-effect (knockout) mutations in more highly pleiotropic genes. However, the selection acting against small-effect, nonlethal mutations in pleiotropic genes is less clear (Pal et al. 2006). Several studies have found an association between gene pleiotropy indices, such GO annotation of the number of biological processes or tissue specificity of expression, and the rate of sequence evolution (e.g., Pal et al. 2001; Salathe et al. 2006; Jovelin and Phillips 2009; Su et al. 2010). These pleiotropy indices typically explain little of the variation in sequence evolutionary rates, and it remains unclear whether more highly pleiotropic mutations are typically under stronger selection (Pal et al. 2006; Salathe et al. 2006).Here, we estimate the selection coefficients acting against naturally occurring mutations affecting gene-expression traits in male D. serrata to quantitatively test if selection is stronger on mutations that affect multiple traits. Gene-expression phenotypes are uniquely positioned to enable detailed investigations of pleiotropy: there are many of them, they represent a broad coverage of biological function, they can be analyzed to quantify developmental pleiotropy in the same way as traits traditionally considered in quantitative genetics, and GO information can be used to index molecular genetic pleiotropy. We use multivariate mixed-model analyses of expression traits in a set of inbred lines from a mutation accumulation experiment to estimate the mutational variance in individual expression traits, and the pleiotropic mutational covariance among random sets of five expression traits. Using a second panel of inbred lines, derived from a natural, outbred, population, we estimate the standing genetic variance in the same individual traits and five-trait combinations. From these estimates of mutational and standing genetic variance, we calculate s for each of the individual traits and trait combinations to determine whether selection has typically been stronger on mutations with pleiotropic effects than on other mutations affecting each trait. We complement this quantitative genetic analysis of developmental pleiotropy with an analysis of molecular genetic pleiotropy (Paaby and Rockman 2013), determining whether the strength of selection acting on individual expression traits can be predicted from the number of biological functions that the gene annotates to in the GO database or to the range of tissues in which the gene is expressed.     

Coalescent Size Versus Coalescent Time with Strong Selection

This work studies the coalescent (ancestral pedigree, genealogy) of the entire population. The coalescent structure (topology) is robust, but selection changes the rate of coalescence (the time between branching events). The change in the rate of coalescence is not uniform, rather the reduction in the time between branching events is greatest when the coalescent is small (immediately after the common ancestor is the only member of the coalescent) with little change when the coalescent is large (immediately preceding when that common ancestor becomes fixed and the size of the coalescent is N). This provides that the reduction in the coalescent time due to selection is much greater than the reduction in the cumulative size of the coalescent (total number of ancestors of the present population after and including the most recent common ancestor) due to selection. If Ns≫1, the coalescent and fixation times are approximately equal to , which is much less than the value N which would result from neutral drift (N rather than the canonical haploid neutral fixation time 2N is the appropriate comparison for the model considered here), in particular, it is 70% less for Ns=10 and 95% less for Ns=100. However, for those values of Ns, and N ranging between 10³ and 10⁶, the reduction in the cumulative size of the coalescent of the entire population compared to the neutral case ranges from 17% to 65% (depending on the values of N and s). The coalescent time for two individuals for Ns of 10 and 100 is reduced by approximately 70% and 94%, respectively, compared with the neutral case. Because heterozygosity is proportional to the coalescent time for two individuals and the number of segregating alleles is proportional to the cumulative size of the coalescent, selection reduces heterozygosity more than it reduces the number of segregating alleles.     

Population Genetics Inference for Longitudinally-Sampled Mutants Under Strong Selection

Longitudinal allele frequency data are becoming increasingly prevalent. Such samples permit statistical inference of the population genetics parameters that influence the fate of mutant variants. To infer these parameters by maximum likelihood, the mutant frequency is often assumed to evolve according to the Wright–Fisher model. For computational reasons, this discrete model is commonly approximated by a diffusion process that requires the assumption that the forces of natural selection and mutation are weak. This assumption is not always appropriate. For example, mutations that impart drug resistance in pathogens may evolve under strong selective pressure. Here, we present an alternative approximation to the mutant-frequency distribution that does not make any assumptions about the magnitude of selection or mutation and is much more computationally efficient than the standard diffusion approximation. Simulation studies are used to compare the performance of our method to that of the Wright–Fisher and Gaussian diffusion approximations. For large populations, our method is found to provide a much better approximation to the mutant-frequency distribution when selection is strong, while all three methods perform comparably when selection is weak. Importantly, maximum-likelihood estimates of the selection coefficient are severely attenuated when selection is strong under the two diffusion models, but not when our method is used. This is further demonstrated with an application to mutant-frequency data from an experimental study of bacteriophage evolution. We therefore recommend our method for estimating the selection coefficient when the effective population size is too large to utilize the discrete Wright–Fisher model.     

Strong Positive Selection Drives Rapid Diversification of R-Genes in Arabidopsis Relatives

Although plant resistance (R) genes are extremely diverse and evolve rapidly, little is known about the mechanisms that generate this sequence divergence. To investigate these forces, we compared all nucleotide binding sites and leucine-rich repeat R-genes between two closely related species, Arabidopsis thaliana and Arabidopsis lyrata. Our analyses revealed two distinct evolutionary patterns driven by either positive or stabilizing selection. Most R-genes (>50%) were evolving under strong positive selection characterized by high Ka/Ks ratios (>1), frequent recombination, copy number variation, and extremely high sequence divergence between the two species. The stably selected R-genes (<30%) have exactly the opposite four characters as the positively selected genes. The remaining R-genes (about 20%) are present in only one genome and absent from the other. A higher proportion of such genes were found to be part of TNL class (23.5%) compared to the non-TNL class (5.6%), suggesting different evolutionary patterns between these two groups. A significant correlation between Ka and divergence was revealed, indicating that the rapid evolution and diversification of R-genes were initiated by selectively generated, frequently shuffled and selectively maintained non-synonymous substitutions. Our genome-wide analyses confirmed an amazing mechanism by which plants to selectively accumulate and efficiently exploit these non-synonymous substitutions for their resistance to various pathogens.     

Unique Pathogen Peptidomes Facilitate Pathogen-Specific Selection and Specialization of MHC Alleles

A key component of pathogen-specific adaptive immunity in vertebrates is the presentation of pathogen-derived antigenic peptides by major histocompatibility complex (MHC) molecules. The excessive polymorphism observed at MHC genes is widely presumed to result from the need to recognize diverse pathogens, a process called pathogen-driven balancing selection. This process assumes that pathogens differ in their peptidomes—the pool of short peptides derived from the pathogen’s proteome—so that different pathogens select for different MHC variants with distinct peptide-binding properties. Here, we tested this assumption in a comprehensive data set of 51.9 Mio peptides, derived from the peptidomes of 36 representative human pathogens. Strikingly, we found that 39.7% of the 630 pairwise comparisons among pathogens yielded not a single shared peptide and only 1.8% of pathogen pairs shared more than 1% of their peptides. Indeed, 98.8% of all peptides were unique to a single pathogen species. Using computational binding prediction to characterize the binding specificities of 321 common human MHC class-I variants, we investigated quantitative differences among MHC variants with regard to binding peptides from distinct pathogens. Our analysis showed signatures of specialization toward specific pathogens especially by MHC variants with narrow peptide-binding repertoires. This supports the hypothesis that such fastidious MHC variants might be maintained in the population because they provide an advantage against particular pathogens. Overall, our results establish a key selection factor for the excessive allelic diversity at MHC genes observed in natural populations and illuminate the evolution of variable peptide-binding repertoires among MHC variants.     

Parasite mediated homogenizing selection at the MHC in guppies

Understanding the selective forces influencing genetic diversity is a fundamental goal of evolutionary ecology. The genes of the major histocompatibility complex (MHC) play a key role in the adaptive immune response of vertebrates and thus provide an excellent opportunity to examine the agents of selection on a functionally important gene. Here we examine the genetic architecture of the MHC class IIB genes in 10 wild populations of guppies (Poecilia reticulata) in Northern Trinidad. We have previously shown that these populations are significantly less diverged at the class IIB locus than expected based on neutral (microsatellite) loci. We now survey infection by Gyrodactylus turnbulli and G. bullatarudis, common parasitic worms that infect guppies, as a potential agent of homogenizing selection. We used a genetic algorithm to partition both additive and non-additive genetic effects of the five most common MHC allele types as well as a rare allele category. Although we found no evidence for non-additive effects, across the populations we found that one allele type (the a-type) had a significant negative additive effect on parasite load. Thus, individuals who had more copies of the a-type allele were infected with fewer gyrodactylus than individuals with fewer copies of the allele. These results not only link parasite infection with MHC genotype, they provide a mechanism of homogenizing selection across these otherwise disparate populations.     

Application of cDNA Selection Techniques to Regions of the Human MHC

Identification of transcribed sequences by cDNA selection is a potentially rapid and efficient way of scanning large genomic DNA fragments for the presence of genes. To evaluate this approach further, we have applied it to three yeast artificial chromosomes (YACs) and examined the products obtained from a total of about 1100 kb from two regions of the human major histocompatibility complex (MHC). One YAC was derived from an extensively studied portion of the Class II region of the MHC. The cDNAs recovered from this YAC included representatives of the previously described genes as well as one or more cDNA clones not described in the databases. A second YAC spanned about 330 kb of DNA surrounding the Class I gene HLA-A. In addition to Class I clones, 10 distinct cDNA products were identified from this YAC. A third YAC contained about 700 kb of human DNA, including 260 kb of overlap with the second YAC, and recovered an additional cDNA complementary to YAC B30 H3 DNA. Overall, the method is shown to be able to detect very scarce cDNAs and to detect a large fraction of coding sequences in YAC clones. Advantages and limitations of the approach are discussed.     

Strong Epistatic Selection on the RNA Secondary Structure of HIV

A key question in evolutionary genomics is how populations navigate the adaptive landscape in the presence of epistasis, or interactions among loci. This problem can be directly addressed by studying the evolution of RNA secondary structures, for which there is constraint to maintain pairing between Watson-Crick (WC) sites. Replacement of a nucleotide at one site of a WC pair reduces fitness by disrupting binding, which can be restored via a compensatory replacement at the interacting site. Here, I present the first genome-scale analysis of epistasis on the RNA secondary structure of human immunodeficiency virus type 1 (HIV-1). Comparison of polymorphism frequencies at ancestrally conserved sites reveals that selection against replacements is ∼2.7 times stronger at WC than at non-WC sites, such that nearly 50% of constraint can be attributed to epistasis. However, almost all epistatic constraint is due to selection against conversions of WC pairs to unpaired (UP) nucleotides, whereas conversions to GU wobbles are only slightly deleterious. This disparity is also evident in pairs with second-site compensatory replacements; conversions from UP nucleotides to WC pairs increase median fitness by ∼4.2%, whereas conversions from GU wobbles to WC pairs only increase median fitness by ∼0.3%. Moreover, second-site replacements that convert UP nucleotides to GU wobbles also increase median fitness by ∼4%, indicating that such replacements are nearly as compensatory as those that restore WC pairing. Thus, WC peaks of the HIV-1 epistatic adaptive landscape are connected by high GU ridges, enabling the viral population to rapidly explore distant peaks without traversing deep UP valleys.     

Selection and recombination drive the evolution of MHC class II DRB diversity in ungulates

Major histocompatibility complex (MHC) antigen-presenting genes are the most variable loci in vertebrate genomes. Host-parasite co-evolution is assumed to maintain the excessive polymorphism in the MHC loci. However, the molecular mechanisms underlying the striking diversity in the MHC remain contentious. The extent to which recombination contributes to the diversity at MHC loci in natural populations is still controversial, and there have been only few comparative studies that make quantitative estimates of recombination rates. In this study, we performed a comparative analysis for 15 different ungulates species to estimate the population recombination rate, and to quantify levels of selection. As expected for all species, we observed signatures of strong positive selection, and identified individual residues experiencing selection that were congruent with those constituting the peptide-binding region of the human DRB gene. However, in addition for each species, we also observed recombination rates that were significantly different from zero on the basis of likelihood-permutation tests, and in other non-quantitative analyses. Patterns of synonymous and non-synonymous sequence diversity were consistent with differing demographic histories between species, but recent simulation studies by other authors suggest inference of selection and recombination is likely to be robust to such deviations from standard models. If high rates of recombination are common in MHC genes of other taxa, re-evaluation of many inference-based phylogenetic analyses of MHC loci, such as estimates of the divergence time of alleles and trans-specific polymorphism, may be required.     

Trans-Species Polymorphism and Selection in the MHC Class II DRA Genes of Domestic Sheep

Highly polymorphic genes with central roles in lymphocyte mediated immune surveillance are grouped together in the major histocompatibility complex (MHC) in higher vertebrates. Generally, across vertebrate species the class II MHC DRA gene is highly conserved with only limited allelic variation. Here however, we provide evidence of trans-species polymorphism at the DRA locus in domestic sheep (Ovis aries). We describe variation at the Ovar-DRA locus that is far in excess of anything described in other vertebrate species. The divergent DRA allele (Ovar-DRA*0201) differs from the sheep reference sequences by 20 nucleotides, 12 of which appear non-synonymous. Furthermore, DRA*0201 is paired with an equally divergent DRB1 allele (Ovar-DRB1*0901), which is consistent with an independent evolutionary history for the DR sub-region within this MHC haplotype. No recombination was observed between the divergent DRA and B genes in a range of breeds and typical levels of MHC class II DR protein expression were detected at the surface of leukocyte populations obtained from animals homozygous for the DRA*0201, DRB1*0901 haplotype. Bayesian phylogenetic analysis groups Ovar-DRA*0201 with DRA sequences derived from species within the Oryx and Alcelaphus genera rather than clustering with other ovine and caprine DRA alleles. Tests for Darwinian selection identified 10 positively selected sites on the branch leading to Ovar-DRA*0201, three of which are predicted to be associated with the binding of peptide antigen. As the Ovis, Oryx and Alcelaphus genera have not shared a common ancestor for over 30 million years, the DRA*0201 and DRB1*0901 allelic pair is likely to be of ancient origin and present in the founding population from which all contemporary domestic sheep breeds are derived. The conservation of the integrity of this unusual DR allelic pair suggests some selective advantage which is likely to be associated with the presentation of pathogen antigen to T-cells and the induction of protective immunity.     

鸡痘病毒载体启动子的优化

要提高外源基因在鸡痘病毒（ＦＰＶ）载体的表达量,必须使用强启动子来控制表达。为构建较强的启动子组合,根据痘苗病毒天然启动子Ｐ７．５的结构,人工合成４条寡核苷酸,形成一个早期启动子和一个晚期启动子,其首尾可相互连接。利用分子生物学常用实验方法把合成的启动子进行不同组合,最终形成１０个较有代表性的启动子组合ＰＳ１￣１０。在其下游插入大肠杆菌β－半乳糖苷酸基因ＬａｃＺ,并进一步构建成鸡痘病毒转移载体ｐＦ     

Pathogen resistance and genetic variation at MHC loci

Abstract.— Balancing selection in the form of heterozygote advantage, frequency-dependent selection, or selection that varies in time and/or space, has been proposed to explain the high variation at major histocompatibility complex (MHC) genes. Here the effect of variation of the presence and absence of pathogens over time on genetic variation at multiallelic loci is examined. In the basic model, resistance to each pathogen is conferred by a given allele, and this allele is assumed to be dominant. Given that s is the selective disadvantage for homozygotes (and heterozygotes) without the resistance allele and the proportion of generations, which a pathogen is present, is e , fitnesses for homozygotes become (1 — s )^(n-1)e and the fitnesses for heterozygotes become (1 — s )^(n-2)e, where n is the number of alleles. In this situation, the conditions for a stable, multiallelic polymorphism are met even though there is no intrinsic heterozygote advantage. The distribution of allele frequencies and consequently heterozygosity are a function of the autocorrelation of the presence of the pathogen in subsequent generations. When there is a positive autocorrelation over generations, the observed heterozygosity is reduced. In addition, the effects of lower levels of selection and dominance and the influence of genetic drift were examined. These effects were compared to the observed heterozygosity for two MHC genes in several South American Indian samples. Overall, resistance conferred by specific alleles to temporally variable pathogens may contribute to the observed polymorphism at MHC genes and other similar host defense loci.