Stabilizing Selection,Purifying Selection,and Mutational Bias in Finite Populations

Genomic traits such as codon usage and the lengths of noncoding sequences may be subject to stabilizing selection rather than purifying selection. Mutations affecting these traits are often biased in one direction. To investigate the potential role of stabilizing selection on genomic traits, the effects of mutational bias on the equilibrium value of a trait under stabilizing selection in a finite population were investigated, using two different mutational models. Numerical results were generated using a matrix method for calculating the probability distribution of variant frequencies at sites affecting the trait, as well as by Monte Carlo simulations. Analytical approximations were also derived, which provided useful insights into the numerical results. A novel conclusion is that the scaled intensity of selection acting on individual variants is nearly independent of the effective population size over a wide range of parameter space and is strongly determined by the logarithm of the mutational bias parameter. This is true even when there is a very small departure of the mean from the optimum, as is usually the case. This implies that studies of the frequency spectra of DNA sequence variants may be unable to distinguish between stabilizing and purifying selection. A similar investigation of purifying selection against deleterious mutations was also carried out. Contrary to previous suggestions, the scaled intensity of purifying selection with synergistic fitness effects is sensitive to population size, which is inconsistent with the general lack of sensitivity of codon usage to effective population size.     

The Genomic Impacts of Drift and Selection for Hybrid Performance in Maize

Although maize is naturally an outcrossing organism, modern breeding utilizes highly inbred lines in controlled crosses to produce hybrids. The U.S. Department of Agriculture’s reciprocal recurrent selection experiment between the Iowa Stiff Stalk Synthetic (BSSS) and the Iowa Corn Borer Synthetic No. 1 (BSCB1) populations represents one of the longest running experiments to understand the response to selection for hybrid performance. To investigate the genomic impact of this selection program, we genotyped the progenitor lines and >600 individuals across multiple cycles of selection using a genome-wide panel of ∼40,000 SNPs. We confirmed previous results showing a steady temporal decrease in genetic diversity within populations and a corresponding increase in differentiation between populations. Thanks to detailed historical information on experimental design, we were able to perform extensive simulations using founder haplotypes to replicate the experiment in the absence of selection. These simulations demonstrate that while most of the observed reduction in genetic diversity can be attributed to genetic drift, heterozygosity in each population has fallen more than expected. We then took advantage of our high-density genotype data to identify extensive regions of haplotype fixation and trace haplotype ancestry to single founder inbred lines. The vast majority of regions showing such evidence of selection differ between the two populations, providing evidence for the dominance model of heterosis. We discuss how this pattern is likely to occur during selection for hybrid performance and how it poses challenges for dissecting the impacts of modern breeding and selection on the maize genome.     

Natural selection. III. Selection versus transmission and the levels of selection

George Williams defined an evolutionary unit as hereditary information for which the selection bias between competing units dominates the informational decay caused by imperfect transmission. In this article, I extend Williams' approach to show that the ratio of selection bias to transmission bias provides a unifying framework for diverse biological problems. Specific examples include Haldane and Lande's mutation-selection balance, Eigen's error threshold and quasispecies, Van Valen's clade selection, Price's multilevel formulation of group selection, Szathmáry and Demeter's evolutionary origin of primitive cells, Levin and Bull's short-sighted evolution of HIV virulence, Frank's timescale analysis of microbial metabolism and Maynard Smith and Szathmáry's major transitions in evolution. The insights from these diverse applications lead to a deeper understanding of kin selection, group selection, multilevel evolutionary analysis and the philosophical problems of evolutionary units and individuality.     

Selection and microevolution of coat pattern are cryptic in a wild population of sheep

Understanding the maintenance of genetic variation in natural populations is a core aim of evolutionary genetics. Insight can be gained by quantifying selection at the level of the genotype, as opposed to the phenotype. Here, we show that in a natural population of Soay sheep which is polymorphic for coat pattern, recessive genetic variants at the causal gene, agouti signalling protein (ASIP) are associated with reduced lifetime fitness. This was due primarily to a reduction in juvenile survival of uniformly coloured (self-type) sheep, which are homozygous recessive, and occurs despite significantly higher reproductive success in surviving self-type adults. Consistent with their relatively low fitness, we show that the frequency of self-type individuals has declined from 1985 to 2008. Remarkably though, the frequency of the underlying self-allele has increased, because the frequency of heterozygous individuals (who harbour the majority of all self-alleles) has increased. Indeed, the ratio of observed/expected heterozygous individuals has increased during the study, such that there is now a significant excess of heterozygotyes. By employing gene-dropping simulations, we show that microevolutionary trends in the frequency and excess of ASIP heterozygotes are too pronounced to be caused by genetic drift. Studying this polymorphism at the level of phenotype rather than underlying genotype would have failed to detect cryptic fitness differences. We would also have been unable to rule out genetic drift as an evolutionary force driving genetic change. This highlights the importance of resolving the underlying genetic basis of phenotypic variation in explaining evolutionary dynamics.     

Demographic History and Natural Selection Shape Patterns of Deleterious Mutation Load and Barriers to Introgression across Populus Genome

Hybridization and resulting introgression are important processes shaping the tree of life and appear to be far more common than previously thought. However, how the genome evolution was shaped by various genetic and evolutionary forces after hybridization remains unresolved. Here we used whole-genome resequencing data of 227 individuals from multiple widespread Populus species to characterize their contemporary patterns of hybridization and to quantify genomic signatures of past introgression. We observe a high frequency of contemporary hybridization and confirm that multiple previously ambiguous species are in fact F₁ hybrids. Seven species were identified, which experienced different demographic histories that resulted in strikingly varied efficacy of selection and burdens of deleterious mutations. Frequent past introgression has been found to be a pervasive feature throughout the speciation of these Populus species. The retained introgressed regions, more generally, tend to contain reduced genetic load and to be located in regions of high recombination. We also find that in pairs of species with substantial differences in effective population size, introgressed regions are inferred to have undergone selective sweeps at greater than expected frequencies in the species with lower effective population size, suggesting that introgression likely have higher potential to provide beneficial variation for species with small populations. Our results, therefore, illustrate that demography and recombination have interplayed with both positive and negative selection in determining the genomic evolution after hybridization.     

光皮桦优树子代性状遗传变异及选择

在福建省选择101株光皮桦(Betula luminifera H. Winkl.)优树,利用其中55株优树的种子在福建省邵武卫闽林场开展子代测定分析. 结果表明, 光皮桦种内存在丰富的遗传变异, 优树子代间差异显著, 这些差异主要由遗传因素控制; 3 a生树高家系遗传力、单株遗传力分别为0.446和0.327, 胸径的家系遗传力和单株遗传力分别为 0.431和0.291;各生长性状与冠幅间存在紧密的相关性;以3a生树高为主要指标,从参试的家系中初步选出12个优良家系和31株优良个体,优良家系的树高和胸径的平均遗传增益分别为7.95%和11.87%;优良个体的树高和胸径的平均遗传增益分别高达26.60%和40.37%,选择效果非常明显.这些优良家系和个体可用作种子园建园材料或无性繁殖材料.     

长白落叶松群体遗传变异及优良家系选择的研究

以黑龙江省林口县青山林场21年生长白落叶松(Larix olgensis Henry)异地保存林为材料,分析白刀山种源优良木和劣等木群体的生长变异情况。结果发现优势木群体和劣等木群体差异不显著。树高、胸径、材积都存在丰富的变异,其中变异系数最大的是材积,其次是胸径,最小的是树高,其变异系数分别为46.24%、19.82%和12.25%;优势木群体树高、胸径、材积的变异系数分别是12.98%、20.77%和49.36%;劣等木群体树高、胸径、材积的变异系数分别是11.47%、18.79%和43.16%。同一性状树高、胸径、材积优势木群体变异高出劣等木群体变异系数分别为1.51%、1.98%和6.2%。方差分析表明家系间差异显著,选择了856、859、563、552、567、864号6个优良家系,优良木与劣等木群体各占3个;6个家系平均值分别超过优势木群体平均值和劣等木群体平均值0.017 7和0.013 6 m3。按照各自群体10%入选率,则遗传增益分别是38.74%和30.04%。     

Dynamics of drift, gene flow, and selection during speciation in Silene

The mechanics of speciation with gene flow are still unclear. Disparity among genes in population differentiation (F(ST)) between diverging species is often interpreted as evidence for semipermeable species boundaries, with selection preventing "key" genes from introgressing despite ongoing gene flow. However, F(ST) can remain high before it reaches equilibrium between the lineage sorting of species divergence and the homogenizing effects of gene flow (via secondary contact). Thus, when interpreting F(ST), the dynamics of drift, gene flow, and selection need to be taken into account. We illustrate this view with a multigenic analyses of gene flow and selection in three closely related Silene species, S. latifolia, S. dioica, and S. diclinis. We report that although S. diclinis appears to have evolved in allopatry, isolation with (bidirectional) gene flow between S. latifolia and S. dioica is likely, perhaps as a result of parapatric speciation followed by more extensive sympatry. Interestingly, we detected the signatures of apparently independent instances of positive selection at the same locus in S. latifolia and S. dioica. Despite gene flow between the species, the adaptive alleles have not crossed the species boundary, suggesting that this gene has independently undergone species-specific (diversifying or parallel) selection.     

Rapid loss of MHC class II variation in a bottlenecked population is explained by drift and loss of copy number variation

Population bottlenecks may reduce genetic variation and potentially increase the risk of extinction. Here, we present the first study to use historic samples to analyse loss of variation at the major histocompatibility complex (MHC), which plays a central role in vertebrate disease resistance. Balancing selection acts on the MHC and could moderate the loss of variation expected from drift; however, in a Wisconsin population of greater prairie-chickens (Tympanuchus cupido), the number of MHC class II B alleles per individual declined by 44% following a population bottleneck, compared to a loss of only 8% at microsatellites. Simulations indicate that drift likely reduced MHC variation at the population level, as well as within individuals by reducing the number of gene copies per individual or by fixing the same alleles across multiple loci. These multiple effects of genetic drift on MHC variation could have important implications for immunity and fitness.     

长白落叶松半同胞家系生长和木材性状遗传变异与联合选择

长白落叶松（Larix olgensis）是我国东北重要的用材树种,根据生长和木材性状对其进行综合选择至关重要。本研究以吉林省延边自治区汪清林业局32年生的49个长白落叶松半同胞家系为材料,对其9个生长性状（树高、地径、胸径、3 m径、材积、尖削度、冠幅、分枝角和通直度）和4个木材性状（木材基本密度、管胞长度、管胞宽度和管胞长宽比）进行测定与分析。结果表明：不同变异来源间所有性状差异均达极显著水平（P<0.01）;各性状家系遗传力均较高（0.51~0.96）;表型变异系数为3.04%（分枝角）~23.15%（冠幅）;各性状相关系数为-0.367（管胞宽度与管胞长宽比）~0.994（胸径与材积）;主成分分析结果表明,4个主成分的累计贡献率达到78.46%,包含了家系生长性状和木材性状的大部分信息;分别以生长和木材性状对家系进行综合评价,初步筛选出5个生长性状优良家系（S78、S81、S80、S84和S83）和5个木材性状优良家系（S37、S51、S6、S30和S19）,结合生长和木材性状初步筛选出5个优良家系（S89、S74、S76、S82和S83）。本研究初选的材料可以为良种选育提供基础,亲本可以为改良种子园营建提供材料。     

Selection and drift influence genetic differentiation of insular Canada lynx (Lynx canadensis) on Newfoundland and Cape Breton Island

Island populations have long been important for understanding the dynamics and mechanisms of evolution in natural systems. While genetic drift is often strong on islands due to founder events and population bottlenecks, the strength of selection can also be strong enough to counteract the effects of drift. Here, we used several analyses to identify the roles of genetic drift and selection on genetic differentiation and diversity of Canada lynx (Lynx canadensis) across eastern Canada, including the islands of Cape Breton and Newfoundland. Specifically, we assessed whether we could identify a genetic component to the observed morphological differentiation that has been reported across insular and mainland lynx. We used a dinucleotide repeat within the promoter region of a functional gene that has been linked to mammalian body size, insulin‐like growth factor‐1 (IGF‐1). We found high genetic differentiation at neutral molecular markers but convergence of allele frequencies at the IGF‐1 locus. Thus, we showed that while genetic drift has influenced the observed genetic structure of lynx at neutral molecular markers, natural selection has also played a role in the observed patterns of genetic diversity at the IGF‐1 locus of insular lynx.     

天然次生林植物叶片生态化学计量特征及光合特性对长期N沉降的响应

2006年5月于吉林省抚松县露水河林业局实验林场布设了人工模拟氮沉降控制试验,共设置3个氮（N）添加梯度,分别为对照（CK 0 g·N·m^-2·a^-1）、低N（LN 2.5 g·N·m^-2·a^-1）和高N（HN 5.0 g·N·m^-2·a^-1）,旨在探讨N沉降对天然次生林先锋树种白桦（Betula platyphylla）和山杨（Populus davidiana）鲜叶、凋落叶化学计量特征、养分重吸收的影响,以及鲜叶光合特性的变化和各性状之间的相互关系。结果表明：（1）模拟N沉降处理下白桦、山杨鲜叶的C含量较对照均无显著影响,LN处理显著降低了山杨鲜叶N、P含量（P<0.05）,显著增加了C：N、C：P和N：P（P<0.05）;HN处理显著增加了白桦鲜叶N含量和N：P,显著降低了C：N（P<0.05）。（2）白桦、山杨鲜叶N、P重吸收率在两个梯度N添加下均显著下降（P<0.05）,且均为负值。山杨鲜叶N重吸收率与P重吸收率呈显著正相关关系（P<0.05）,与鲜叶C：N呈显著负相关关系（P<0.05）。（3）N添加可以提高2种树木叶片氮素光合利用效率（PNUE）（P<0.05）、净光合速率（P_n）（P<0.05）。白桦鲜叶N含量与P_n、PNUE呈显著正相关（P<0.05）;白桦、山杨鲜叶比叶重（LMA）与N含量呈显著负相关（P<0.05）;P_n与PNUE呈显著正相关（P<0.05）。本试验研究表明：在生长季,白桦、山杨鲜叶中N、P均表现为富集状态,土壤养分及外源N可供林木较快吸收并促进其生长,无需从凋落叶中吸收养分。N添加可以增强白桦、山杨鲜叶的光合性能,进而促进植物养分吸收和叶片发育。HN对长白山天然次生林的生长有促进作用。     

Genetic parameters of sow feed efficiency during lactation and its underlying traits in a Duroc population

As a result of the genetic selection for prolificacy and the improvements in the environment and farms management, litter size has increased in the last few years so that energy requirements of the lactating sow are greater. In addition, selection for feed efficiency of growing pigs is also conducted in maternal lines, and this has led to a decrease in appetite and feed intake that is extended to the lactation period, so the females are not able to obtain the necessary energy and nutrients for milk production and they mobilize their energetic reserves. When this mobilization is excessive, reproductive and health problems occur which ends up in an early sow culling. In this context, it has been suggested to improve feed efficiency at lactation through genetic selection. The aim of this study is to know, in a Duroc population, the genetic determinism of sow feed efficiency during lactation and traits involved in its definition, as well as genetic and environmental associations between them. The studied traits are daily lactation feed intake (dLFI), daily sow weight balance (dSWB), backfat thickness balance (BFTB), daily litter weight gain (dLWG), sow residual feed intake (RFI) and sow restricted residual feed intake (RRFI) during lactation. Data corresponded to 851 parities from 581 Duroc sows. A Bayesian analysis was performed using Gibbs sampling. A four-trait repeatability animal model was implemented including the systematic factors of batch and parity order, the standardized covariates of sow weight (SW_f) and litter weight (LWs) at farrowing for all traits and lactation length for BFTB. The posterior mean (posterior SD) of heritabilities were: 0.09 (0.03) for dLFI, 0.37 (0.07) for dSWB, 0.09 (0.03) for BFTB, 0.22 (0.05) for dLWG, 0.04 (0.02) for RFI and null for RRFI. The genetic correlation between dLFI and dSWB was high and positive (0.74 (0.11)) and null between dLFI and BFTB. Genetic correlation was favourable between RFI and dLFI and BFTB (0.71 (0.16) and −0.69 (0.18)), respectively. The other genetic correlations were not statistically different from zero. The phenotypic correlations were low and positive between dLFI and dSWB (0.27 (0.03), dSWB and BFTB (0.25 (0.04)), and between dLFI and dLWG (0.16 (0.03)). Therefore, in the population under study, the improvement of the lactation feed efficiency would be possible either using RFI, which would not have unfavourable correlated effects, or through an index including its component traits.     

Contrasting patterns of body shape and neutral genetic divergence in marine and lake populations of threespine sticklebacks

Comparisons of neutral marker and quantitative trait divergence can provide important insights into the relative roles of natural selection and neutral genetic drift in population differentiation. We investigated phenotypic and genetic differentiation among Fennoscandian threespine stickleback (Gasterosteus aculeatus) populations, and found that the highest degree of differentiation occurred between sea and freshwater habitats. Within habitats, morphological divergence was highest among the different freshwater populations. Pairwise phenotypic and neutral genetic distances among populations were positively correlated, suggesting that genetic drift may have contributed to the morphological differentiation among habitats. On the other hand, the degree of phenotypic differentiation (PST) clearly surpassed the neutral expectation set by FST, suggesting a predominant role for natural selection over genetic drift as an explanation for the observed differentiation. However, separate PST/FST comparisons by habitats revealed that body shape divergence between lake and marine populations, and even among marine populations, can be strongly influenced by natural selection. On the other hand, genetic drift can play an important role in the differentiation among lake populations.     

Drift,selection and adaptive variation in small populations of a threatened rattlesnake

An important goal of conservation genetics is to determine if the viability of small populations is reduced by a loss of adaptive variation due to genetic drift. Here, we assessed the impact of drift and selection on direct measures of adaptive variation (toxin loci encoding venom proteins) in the eastern massasauga rattlesnake (Sistrurus catenatus), a threatened reptile that exists in small isolated populations. We estimated levels of individual polymorphism in 46 toxin loci and 1,467 control loci across 12 populations of this species, and compared the results with patterns of selection on the same loci following speciation of S. catenatus and its closest relative, the western massasauga (S. tergeminus). Multiple lines of evidence suggest that both drift and selection have had observable impacts on standing adaptive variation. In support of drift effects, we found little evidence for selection on toxin variation within populations and a significant positive relationship between current levels of adaptive variation and long‐ and short‐term estimates of effective population size. However, we also observed levels of directional selection on toxin loci among populations that are broadly similar to patterns predicted from interspecific selection analyses that pre‐date the effects of recent drift, and that functional variation in these loci persists despite small short‐term effective sizes. This suggests that much of the adaptive variation present in populations may represent an example of “drift debt,” a nonequilibrium state where present‐day levels of variation overestimate the amount of functional genetic diversity present in future populations.     

Changes in composition of cuticular biochemicals of the facultatively polygynous ant Petalomyrmex phylax during range expansion in Cameroon with respect to social, spatial and genetic variation

In social insects, biochemicals found at the surface of the cuticle are involved in the recognition process and in protection against desiccation and pathogens. However, the relative contribution of evolutionary forces in shaping diversity of these biochemicals remains largely unresolved in ants. We determined the composition of epicuticular biochemicals for workers sampled in 12 populations of the ant Petalomyrmex phylax from Cameroon. Genetic variation at 12 microsatellite markers was used to infer population history and to provide null expectations under the neutrality hypothesis. Genetic data suggest a recent southward range expansion of this ant species. Furthermore, there is a decline southward in the numbers of queens present in mature colonies. Here, we contrast the pattern of biochemical variation against genetic, social and spatial parameters. We thus provide the first estimates of the relative contribution of neutral and selective processes on variation of ant cuticular profile. Populations in migration-drift disequilibrium showed reduction of within-population variation for genetic markers as well as for cuticular profiles. In these populations, the cuticular profile became biased towards a limited number of high molecular weight molecules. Within- and among-population biochemical variation was explained by both genetic and social variation and by the spatial distribution of populations. We therefore propose that during range expansion of P. phylax, the composition of epicuticular compounds has been affected by a combination of neutral processes - genetic drift and spatially limited dispersal - and spatially varying selection, social organization and environmental effects.     

Contrasting patterns of selection and drift between two categories of immune genes in prairie‐chickens

Immune‐receptor genes of the adaptive immune system, such as the major histocompatibility complex (MHC), are involved in recognizing specific pathogens and are known to have high rates of adaptive evolution, presumably as a consequence of rapid co‐evolution between hosts and pathogens. In contrast, many ‘mediating’ genes of the immune system do not interact directly with specific pathogens and are involved in signalling (e.g. cytokines) or controlling immune cell growth. As a consequence, we might expect stronger selection at immune‐receptor than mediating genes, but these two types of genes have not been compared directly in wild populations. Here, we tested the hypothesis that selection differs between MHC (class I and II) and mediating genes by comparing levels of population differentiation across the range of greater prairie‐chickens (Tympanuchus cupido). As predicted, there was stronger population differentiation and isolation by distance at immune receptor (MHC) than at either mediating genes or neutral microsatellites, suggesting a stronger role of local adaptation at the MHC. In contrast, mediating genes displayed weaker differentiation between populations than neutral microsatellites, consistent with selection favouring similar alleles across populations for mediating genes. In addition to selection, drift also had a stronger effect on immune receptor (MHC) than mediating genes as indicated by the stronger decline of MHC variation in relation to population size. This is the first study in the wild to show that the effects of selection and drift on immune genes vary across populations depending on their functional role.     

白桦半同胞家系苗期生长和光合特性及其选育评价指标筛选

对6个白桦半同胞家系苗期生长、光合和叶绿素荧光参数进行测定,分析各指标的变异状况,并探讨白桦苗期选育评价的主要因子。结果表明:(1)白桦半同胞家系间生长性状(苗高、地径、叶片长度、叶片宽度、叶片数量、叶片长宽比)和光合指标(Pn、Gs、Ci、Tr、WUE)差异极显著,除Ci外各光合指标的变异系数和遗传变异系数均超过了10%。(2)白桦半同胞家系间叶绿素荧光参数F0、F0′、Fs、Fv′/Fm′、NPQ和Yield差异显著,除NPQ外所有叶绿素荧光参数变异系数和遗传变异系数均不超过10%,表明白桦半同胞家系叶片光合潜在能力差异不大。(3)白桦半同胞家系叶绿素荧光参数各指标遗传力H2均大于0.4,属中度遗传力,而生长指标和光合指标遗传力均大于0.7,属于较高遗传力,表明白桦半同胞家系生长和光合变异主要由遗传因素控制,有利于苗期选择评价。(4)白桦半同胞家系苗高、地径与WUE显著正相关,而与Yield显著负相关;叶片数量和叶片宽度对白桦苗期苗高和地径影响较大,可以作为苗期选择评价的主要因子。     

Comparison of genetic differentiation at marker loci and quantitative traits

The comparison of the degree of differentiation in neutral marker loci and genes coding quantitative traits with standardized and equivalent measures of genetic differentiation (F_ST and Q_ST, respectively) can provide insights into two important but seldom explored questions in evolutionary genetics: (i) what is the relative importance of random genetic drift and directional natural selection as causes of population differentiation in quantitative traits, and (ii) does the degree of divergence in neutral marker loci predict the degree of divergence in genes coding quantitative traits? Examination of data from 18 independent studies of plants and animals using both standard statistical and meta‐analytical methods revealed a number of interesting points. First, the degree of differentiation in quantitative traits (Q_ST) typically exceeds that observed in neutral marker genes (F_ST), suggesting a prominent role for natural selection in accounting for patterns of quantitative trait differentiation among contemporary populations. Second, the F_ST – Q_ST difference is more pronounced for allozyme markers and morphological traits, than for other kinds of molecular markers and life‐history traits. Third, very few studies reveal situations were Q_ST < F_ST, suggesting that selection pressures, and hence optimal phenotypes, in different populations of the same species are unlikely to be often similar. Fourth, there is a strong correlation between Q_ST and F_ST indices across the different studies for allozyme (r=0.81), microsatellite (r=0.87) and combined (r=0.75) marker data, suggesting that the degree of genetic differentiation in neutral marker loci is closely predictive of the degree of differentiation in loci coding quantitative traits. However, these interpretations are subject to a number of assumptions about the data and methods used to derive the estimates of population differentiation in the two sets of traits.     

The Interaction of Protein Structure, Selection, and Recombination on the Evolution of the Type-1 Fimbrial Major Subunit (fimA) from Escherichia coli

Fimbrial adhesins allow bacteria to interact with and attach to their environment. The bacteria possibly benefit from these interactions, but all external structures including adhesins also allow bacteria to be identified by other organisms. Thus adhesion molecules might be under multiple forms of selection including selection to constrain functional interactions or evolve novel epitopes to avoid recognition. We address these issues by studying genetic diversity in the Escherichia coli type-1 fimbrial major subunit, fimA. Overall, sequence diversity in fimA is high (π= 0.07) relative to that in other E. coli genes. High diversity is a function of positive diversifying selection, as detected by d _N/d _S ratios higher than 1.0, and amino acid residuces subject to diversifying selection are nonrandomly clustered on the exterior surface of the peptide. In addition, McDonald and Kreitman tests suggest that there has been historical but not current directional selection at fimA between E. coli and Salmonella. Finally, some regions of the fimA peptide appear to be under strong structural constraint within E. coli, particularly the interior regions of the molecule that is involved in subunit to subunit interaction. Recombination also plays a major role contributing to E. coli fimA allelic variation and estimates of recombination (2N _e c) and mutation (2N _eμ) are about the same. Recombination may act to separate the diverse evolutionary forces in different regions of the fimA peptide. Received: 13 April 2000 / Accepted: 28 October 2000