Interpreting population differentiation in terms of drift and selection

Summary Many empirical studies demonstrate some degree of genetic differentiation among populations of the same species. Understanding the relative importance of the processes causing this genetic differentiation has proven to be a difficult task. In particular, population differentiation can be influenced primarily by selection, genetic drift, and migration. We review the effect of drift and migration on patterns of genetic variation, with special reference to the conditions necessary for population differentiation. Conceptually, selection may be implicated in cases of population differentiation if the effect of drift and migration can be shown to be insufficient to cause the observed patterns. We examine some of the pitfalls of this approach when used with allozyme data, and revise a previous conclusion concerning the relative importance of selection in poulations of scale insects.     

Fixation of new alleles and the extinction of small populations: drift load, beneficial alleles, and sexual selection

With a small effective population size, random genetic drift is more important than selection in determining the fate of new alleles. Small populations therefore accumulate deleterious mutations. Left unchecked, the effect of these fixed alleles is to reduce the reproductive capacity of a species, eventually to the point of extinction. New beneficial mutations, if fixed by selection, can restore some of this lost fitness. This paper derives the overall change in fitness due to fixation of new deleterious and beneficial alleles, as a function of the distribution of effects of new mutations and the effective population size. There is a critical effective size below which a population will on average decline in fitness, but above which beneficial mutations allow the population to persist. With reasonable estimates of the relevant parameters, this critical effective size is likely to be a few hundred. Furthermore, sexual selection can act to reduce the fixation probability of deleterious new mutations and increase the probability of fixing new beneficial mutations. Sexual selection can therefore reduce the risk of extinction of small populations.     

Molecular and quantitative genetic differentiation across Europe in yellow dung flies

Relating geographic variation in quantitative traits to underlying population structure is crucial for understanding processes driving population differentiation, isolation and ultimately speciation. Our study represents a comprehensive population genetic survey of the yellow dung fly Scathophaga stercoraria, an important model organism for evolutionary and ecological studies, over a broad geographic scale across Europe (10 populations from the Swiss Alps to Iceland). We simultaneously assessed differentiation in five quantitative traits (body size, development time, growth rate, proportion of diapausing individuals and duration of diapause), to compare differentiation in neutral marker loci (F(ST)) to that of quantitative traits (Q(ST)). Despite long distances and uninhabitable areas between sampled populations, population structuring was very low but significant (F(ST) = 0.007, 13 microsatellite markers; F(ST) = 0.012, three allozyme markers; F(ST) = 0.007, markers combined). However, only two populations (Iceland and Sweden) showed significant allelic differentiation to all other populations. We estimated high levels of gene flow [effective number of migrants (Nm) = 6.2], there was no isolation by distance, and no indication of past genetic bottlenecks (i.e. founder events) and associated loss of genetic diversity in any northern or island population. In contrast to the low population structure, quantitative traits were strongly genetically differentiated among populations, following latitudinal clines, suggesting that selection is responsible for life history differentiation in yellow dung flies across Europe.     

Drift load in populations of small size and low density

According to theory, drift load in randomly mating populations is determined by past population size, because enhanced genetic drift in small populations causes accumulation and fixation of recessive deleterious mutations of small effect. In contrast, segregating load due to mutations of low frequency should decline in smaller populations, at least when mutations are highly recessive and strongly deleterious. Strong local selection generally reduces both types of load. We tested these predictions in 13 isolated, outcrossing populations of Arabidopsis lyrata that varied in population size and plant density. Long-term size was estimated by expected heterozygosity at 20 microsatellite loci. Segregating load was assessed by comparing performance of offspring from selfings versus within-population crosses. Drift load was the heterosis effect created by interpopulation outbreeding. Results showed that segregating load was unrelated to long-term size. However, drift load was significantly higher in populations of small effective size and low density. Drift load was mostly expressed late in development, but started as early as germination and accumulated thereafter. The study largely confirms predictions of theory and illustrates that mutation accumulation can be a threat to natural populations.     

一个实用的群体遗传学分析软件包——GENEPOP 3.1版

ＧＥＮＥＰＯＰ是一个非常实用的群体遗传学分析软件包,适用于对大量的群体遗传学数据进行分析。它主要有以下３个方面的用途：１）进行正合检验,如对哈迪－温伯格平衡、种群差异和位点间的连锁不平衡进行检验;２）估算经典的群体遗传学参数,如Ｆｓｔ和其它相关指数及基因频率等;３）可把ＧＥＮＥＰＯＰ的文件转换为常用的群体遗传学分析软件包（如ＢＩＳＹＳ、ＦＳＴＡＴ和ＬＩＮＫＤＯＳ）所要求的输入文件格式。与软件ＢＩＯ     

New insights into the interplay between codon bias determinants in plants

Codon bias is the non-random use of synonymous codons, a phenomenon that has been observed in species as diverse as bacteria, plants and mammals. The preferential use of particular synonymous codons may reflect neutral mechanisms (e.g. mutational bias, G|C-biased gene conversion, genetic drift) and/or selection for mRNA stability, translational efficiency and accuracy. The extent to which these different factors influence codon usage is unknown, so we dissected the contribution of mutational bias and selection towards codon bias in genes from 15 eudicots, 4 monocots and 2 mosses. We analysed the frequency of mononucleotides, dinucleotides and trinucleotides and investigated whether the compositional genomic background could account for the observed codon usage profiles. Neutral forces such as mutational pressure and G|C-biased gene conversion appeared to underlie most of the observed codon bias, although there was also evidence for the selection of optimal translational efficiency and mRNA folding. Our data confirmed the compositional differences between monocots and dicots, with the former featuring in general a lower background compositional bias but a higher overall codon bias.     

Evolutionary mechanisms of senescence

This paper reviews theories of the evolution of senescence. The population genetic basis for the decline with age in sensitivity of fitness to changes in survival and fecundity is discussed. It is shown that this creates a presure of selection that disproportionately favors performance early in life. The extent of this bias is greater when there is a high level of extrinsic mortality; this accounts for much the diversity in life-history patterns among different taxa. The implications of quantitative genetic theory for experimental tests of alternative population genetic models of senescence are discussed. In particular, the negative genetic correlations between traits predicted by the antagonistic pleiotropy model may be obscured by positive correlations that are inevitable in a multivariate system, or by the effects of variation due to deleterious mutations. The status of the genetic evidence relevant to these theories is discussed.     

QUANTITATIVE GENETICS OF BRYOZOAN PHENOTYPIC EVOLUTION. II. ANALYSIS OF SELECTION AND RANDOM CHANGE IN FOSSIL SPECIES USING RECONSTRUCTED GENETIC PARAMETERS

The roles of natural selection and random genetic change in the punctuated phenotypic evolution of eight Miocene-Pliocene tropical American species of the cheilostome bryozoan Metrarabdotos are analyzed by quantitative genetic methods. Trait heritabilities and genetic covariances reconstructed by partitioning within- and among-colony phenotypic variance are similar to those previously obtained for living species of the cheilostome Stylopoma using breeding data. The hypothesis that differences in skeletal morphology between species of Metrarabdotos are entirely due to mutation and genetic drift cannot be rejected for reasonable rates of mutation maintained for periods brief enough to account for the geologically abrupt appearances of these species in the fossil record. Except for one pair of species, separated by the largest morphologic distance, directional selection acting alone would require unrealistically high rates of selective mortality to be maintained for these periods. Thus, directional selection is not strongly implicated in the divergence of Metrarabdotos species. Within species, rates of net phenotypic change are slow enough to require stabilizing selection, but mask large, relatively rapid fluctuations, all of which, however, can be attributed to chance departures from the mean phenotype by mutation and genetic drift, rather than to tracking environmental fluctuation by directional selection. The results are consistent with genetic models involving shifts between multiple adaptive peaks on which phenotypes remain more or less static through long-term stabilizing selection. Regardless of the degree to which directional selection may be involved in peak shifts, phenotypic differentiation is thus related to processes different than the pervasive stabilizing selection acting within species.     

Low levels of nucleotide diversity in mammalian Y chromosomes

Sex chromosomes provide a useful context for the study of the relative importance of evolutionary forces affecting genetic diversity. The human Y chromosome shows levels of nucleotide diversity 20% that of autosomes, which is significantly less than expected when differences in effective population size and sex-specific mutation rates are taken into account. To study the generality of low levels of Y chromosome variability in mammalian genomes, we investigated nucleotide diversity in intron sequences of X (1.1-3.0 kb) and Y (0.7-3.5 kb) chromosome genes of five mammals: lynx, wolf, reindeer, cattle, and field vole. For all species, nucleotide diversity was found to be lower on Y than on X, with no segregating site observed in Y-linked sequences of lynx, reindeer, and cattle. For X chromosome sequences, nucleotide diversity was in the range of 1.6 x 10(-4) (lynx) to 8.0 x 10(-4) (field vole). When differences in effective population size and the extent of the male mutation bias were taken into account, all five species showed evidence of reduced levels of Y chromosome variability. Reduced levels of Y chromosome variability have also been observed in Drosophila and in plants, as well as in the female-specific W chromosome of birds. Among the different factors proposed to explain low levels of genetic variability in the sex-limited chromosome (Y/W), we note that selection is the only factor that is broadly applicable irrespective of mode of reproduction and whether there is male or female heterogamety.     

群体融合对选择有效性的影响

探讨了群体融合对选择有效性的影响⒚显性完全且选择不利于纯合子 ａａ 时,当群体中隐性基因的频率 ０≤ｑ＜ １／３,群体融合导致选择有效性增加;而当 １／３＜ ｑ≤１ 时,融合使选择有效性减小⒚无显性即选择不利于 Ａａ 和 ａａ 时,群体融合导致选择有效性减小⒚超显性即选择有利于杂合子 Ａａ 而不利于纯合子 Ａ Ａ 和 ａａ 时,当 ０≤ｑ＜ １／２,融合导致选择有效性增加;当 １／２＜ ｑ≤１,融合导致选择有效性减小⒚