EPISTASIS AND THE EFFECT OF FOUNDER EVENTS ON THE ADDITIVE GENETIC VARIANCE

Models of founder events have focused on the reduction in the genetic variation following a founder event. However, recent work (Bryant et al., 1986; Goodnight, 1987) suggests that when there is epistatic genetic variance in a population, the total genetic variance within demes may actually increase following a founder event. Since the additive genetic variance is a statistical property of a population and can change with the level of inbreeding, some of the epistatic genetic variance may be converted to additive genetic variance during a founder event. The model presented here demonstrates that some of the additive-by-additive epistatic genetic variance is converted to additive genetic variance following a founder event. Furthermore, the amount of epistasis converted to additive genetic variance is a function of the recombination rate and the propagule size. For a single founder event of two individuals, as much as 75% of the epistatic variance in the ancestral population may become additive genetic variance following the founder event. For founder events involving two individuals with free recombination, the relative contribution of epistasis to the additive genetic variance following a founder event is equal to its proportion of the total genetic variance prior to the founder event. Traits closely related to fitness are expected to have relatively little additive genetic variance but may have substantial nonadditive genetic variance. Founder events may be important in the evolution of fitness traits, not because they lead to a reduction in the genetic variance, but rather because they lead to an increase in the additive genetic variance.     

NEUTRAL THEORY OF QUANTITATIVE GENETIC VARIANCE IN AN ISLAND MODEL WITH LOCAL EXTINCTION AND COLONIZATION

Additive genetic variance maintained by mutation in a selectively neutral quantitative character is analyzed for an ideal population distributed on n islands, each with local effective size N, that exchange migrants at a small rate, m. In a stable population structure, the expected genetic variance maintained within islands is identical to that in a panmictic population of the same total size, regardless of the migration rate (m > 0). This result contrasts with Wright's classical conclusion, based on inbreeding coefficients, that at least one immigrant per island every other generation (Nm > ½) is necessary for the genetic variance within local populations to approach that under panmixia. The expected genetic variance maintained among islands is inversely proportional to m and increases with the number of islands, but is independent of N. Local extinction and colonization diminish the genetic variance maintained within islands by reducing the effective size of island populations through the founder effect, although the expected genetic variance within islands is nearly as large as that in a panmictic population of the same total effective size. If the founders of new colonies originate from more than one island, rates of local extinction and colonization larger than about twice the migration rate will substantially reduce the genetic variance maintained among islands. These results indicate the importance of mutation and migration in maintaining quantitative genetic variance within small local populations.     

WILL POPULATION BOTTLENECKS AND MULTILOCUS EPISTASIS INCREASE ADDITIVE GENETIC VARIANCE?

We apply new analytical methods to understand the consequences of population bottlenecks for expected additive genetic variance. We analyze essentially all models for multilocus epistasis that have been numerically simulated to demonstrate increased additive variance. We conclude that for biologically plausible models, large increases in expected additive variance--attributable to epistasis rather than dominance--are unlikely. Naciri-Graven and Goudet (2003) found that as the number of epistatically interacting loci increases, additive variance tends to be inflated more after a bottleneck. We argue that this result reflects biologically unrealistic aspects of their models. Specifically, as the number of loci increases, higher-order epistatic interactions become increasingly important in these models, with an increasing fraction of the genetic variance becoming nonadditive, contrary to empirical observations. As shown by Barton and Turelli (2004), without dominance, conversion of nonadditive to additive variance depends only on the variance components and not on the number of loci per se. Numerical results indicating that more inbreeding is needed to produce maximal release of additive variance with more loci follow directly from our analytical results, which show that high levels of inbreeding (F > 0.5) are needed for significant conversion of higher-order components. We discuss alternative approaches to modeling multilocus epistasis and understanding its consequences.     

MULTIPLE EQUILIBRIA AND MAINTENANCE OF ADDITIVE GENETIC VARIANCE IN A MODEL OF PLEIOTROPY

We describe a multilocus model that incorporates pleiotropic stabilizing selection on a large number of characters. We find many different stable equilibria with different levels of polymorphism and additive genetic variability. The results lend support to Wright's concept of a complex adaptive surface with many peaks of different heights. The model assumes that alleles contribute additively to the characters. We analyze the multilocus model by first considering a two-locus model. The two-locus model depends critically on having loci of different effect and on having the optimum phenotype not be that of a completely heterozygous individual. The effects of different loci need to differ only by less than a factor of two. For the multilocus, multicharacter model, we assume that completely heterozygous individuals do not have the optimum phenotype. By restricting attention to a two-allele model, we also assume that there are no alleles that can affect all characters in all possible combinations of directions.     

INBREEDING AND VARIANCE EFFECTIVE SIZES FOR NONRANDOM MATING POPULATIONS

Following an inbreeding approach and assuming discrete generations and autosomal inheritance involving genes that do not affect viability or reproductive ability, I have derived expressions for the inbreeding effective size, N_eI, for a finite diploid population with variable census sizes for three cases: monoecious populations with partial selfing; dioecious populations of equal numbers of males and females with partial sib mating; and unequal numbers of males and females with random mating. For the first two cases, recurrence equations for the inbreeding coefficient are also obtained, which allow inbreeding coefficients to be predicted exactly in both early and late generations. Following the variance of change in gene frequency approach, a general expression for variance effective size, N_eV, is obtained for a population with unequal numbers of male and female individuals, arbitrary family size distribution, and nonrandom mating. All the parameters involved are allowed to change over generations. For some special cases, the equation reduces to the simple expressions approximately as derived by previous authors. Comparisons are made between equations derived by the present study and those obtained by previous authors. Some of the published equations for N_eI and N_eV are shown to be incomplete or incorrect. Stochastic simulations are run to check the results where disagreements with others are involved.     

ON GENETIC SEGREGATION AND THE EVOLUTION OF SEX

It has recently been argued that because the genetic load borne by an asexual species resulting from segregation, relative to a comparable sexual population, is greater than two, sex can overcome its twofold disadvantage and succeed. We evaluate some of the assumptions underlying this argument and discuss alternative assumptions. Further, we simulate the dynamics of competition between sexual and asexual types. We find that for populations of size 100 and 500 the advantages of segregation do not outweigh the cost of producing males. We conclude that, at least for small populations, drift and the cost of sex govern the evolution of sexuality, not selection or segregation. We believe, however, that if sexual and asexual populations were isolated for a sufficiently long period, segregation might impart a fitness advantage upon sexuals that could compensate for the cost of sex and allow sexuals to outcompete asexuals upon their reunion.     

GENETIC RELATEDNESS OF TWO POPULATIONS OF THE SOUTHERN ELEPHANT SEAL, MIROUNGA LEONINA

Blood samples from southern elephant seals ( Mirounga leonina ) from Heard and Macquarie Islands were surveyed electrophoretically for protein variation. Thirty proteins encoded by a minimum of 35 loci were screened, four of which were found to be polymorphic. Statistically significant differences in allele frequencies were found between the two populations at three loci. Heterozygosity estimates for the Heard and Macquarie island populations were 0.034 ± 0.020 (mean ± standard error) and O.029 ± 0.017 respectively, with a Nei distance of 0.007. The findings suggest that the two populations may have diverged genetically and very limited gene flow exists between the islands, a finding consistent with limited information from mark-recapture studies.     

草鱼野生与选育群体线粒体DNA控制区D-loop遗传变异分析

为探究经过2个选育世代后选育群体遗传多样性和遗传结构的变化, 研究对4个野生群体(邗江、九江、石首和吴江)和2个选育世代(F1和F2)进行了线粒体DNA控制区(D-loop)序列的遗传变异分析。实验结果表明, 4个野生群体在单倍型数目(H)、单倍型多样性(H_d)、核苷酸多样性(π)、平均核苷酸差异数(K)水平上均高于2个选育世代, 在2个选育世代内表现为F1代群体的核苷酸多样性(π)和平均核苷酸差异数(K)大于F2代群体, 但单倍型多样性(H_d)小于F2代群体; 单倍型分析结果表明, 6个群体间无共享单倍型, 4个野生群体间共发现2种共享单倍型(Hap1和Hap3), 石首群体和2个选育世代共享1种单倍型(Hap15); 遗传分化指数(F_st)分析结果表明, 邗江、九江、吴江3个野生群体和2个选育世代间存在较大的遗传分化(F_st范围为0.41475—0.55128), 石首群体与F1代群体之间存在较小的遗传分化, 与F2代群体之间存在中等水平的遗传分化, 同时F1代群体与F2代群体之间存在较小的遗传分化; 基于6个群体276个个体构建的邻接(Neighbor-Joining, NJ)进化树和基于27种单倍型构建的单倍型网络图也得到了相似的结论, 即邗江、九江、吴江3个野生群体和2个选育世代间的亲缘关系较远, 石首群体和2个选育世代两两之间的亲缘关系较近。以上结果表明, 经过2个世代的选择育种, 选育群体的遗传结构已发生了变化, 并且随着选育的进行, 选育世代的遗传多样性下降的较为明显, 这警示着我们在今后的育种工作中应适当改变现有的选育方案, 并实时监测选育群体的遗传多样性, 以便为今后进一步的选育工作打下坚实的基础。     

A NEW MEASURE OF GENETIC IDENTITY BETWEEN POPULATIONS OF SEXUAL AND ASEXUAL SPECIES

We define a new genetic identity measure that is especially well suited for asexual polyploid species as it circumvents errors in the estimation of gene frequencies. It also can be applied to sexuals allowing the study of phylogenetic relationships in species complexes consisting of sexuals and asexuals of different ploidy levels. The measure groups genotypes into classes dependent on homozygosity vs heterozygosity and the number of ancestral allele types vs the number of presumed new mutations. Its value is related to evolutionary time since divergence. The application of the method is illustrated by using electrophoretic data on the species group Solenobia triquetrella (Lepidoptera: Psychidae). A high similarity of estimated relationships among the proposed as well as other genetic identity measures is shown in the case of diploid sexual and asexual races of this species group. The phylogenetic relationships within the group are reanalyzed and monophyletic vs polyphyletic origin of parthenogenesis in this species complex is discussed. The genetic identity values found by the proposed procedure are explained by a polyphyletic origin of parthenogenesis, though a monophyletic origin of parthenogenesis in a broader sense cannot be excluded. The explanation of the phylogenetic relationships is based on the assumption of hybridization between related species and the extinction of one ancestral species. Furthermore, the genetic diversity is compared among sexual and parthenogenetic races of the species.     

MAINTENANCE OF POLYGENIC VARIATION IN SPATIALLY STRUCTURED POPULATIONS: ROLES FOR LOCAL MATING AND GENETIC REDUNDANCY

Although heritable genetic variation is critical to the evolutionary process, we know little about how it is maintained. Obviously, mutation-selection balance must play a role, but there is considerable doubt over whether it can account for heritabilities as high as 0.5, which are commonly found in natural populations. Most models of mutation-selection balance assume panmictic populations. In this paper we use Monte Carlo simulations to examine the effect of isolation by distance on the variation maintained by mutation in a polygenic trait subject to optimizing selection. We show that isolation by distance can substantially increase the total variation maintained in continuous populations over a wide range of dispersal patterns, but only if more than one genotype produces the optimal phenotype (genetic redundancy). Isolation by distance alone has only a slight effect on the variation maintained in the total population for neutral alleles. The combined effect of isolation by distance and genetic redundancy, however, allows the maintenance of substantial variation despite strong stabilizing selection. The mechanism is straightforward. Isolation by distance allows mutation and drift to operate independently in different parts of the population. Because of their independent evolutionary histories, different parts of the population independently draw from the available set of redundant genotypes. Because the genotypes are redundant, selection does not discriminate among them, and they will persist until eliminated by drift. The population as a whole maintains many distinct genotypes. We show that this process allows mutation to maintain high levels of variation, even under strong stabilizing selection, and that over a moderate range of dispersal patterns the amount of variation maintained in the entire population is independent of both the strength of selection and the variance of the dispersal distance. Furthermore, we show that individual heterozygosity is increased in locally mating populations when selection is strong. Finally, our simulations provide a rough picture of how selection and the dispersal pattern influence the spatial distribution of genetic and phenotypic variation.     

中国大陆尼罗罗非鱼引进群体间遗传关系分析

为了从分子水平上评价中国大陆尼罗罗非鱼（Oreochromis niloticus）主要引进群体间遗传关系、遗传分化及基因流状况,研究利用12对多态性微卫星引物,以埃及土著群体为对照组,分析中国大陆尼罗罗非鱼9个代表性引进群体的遗传关系。结果显示:①群体间四种遗传距离[D_A、D_C、D_SW和（δμ）2]同时表明,USA群体和EGY群体间的遗传距离最小[D_A=0.2174,D_C=0.4140,D_SW=0.8769,（δμ）2=22.6904];D_A和D_C表明GD群体和XJF群体间遗传距离最大（D_A=0.5851,D_C=0.6789）;D_SW和（δμ）2表明USA群体与XJF群体间遗传距离最大[D_SW=4.0907,（δμ）2=138.18]。② EGY群体和GD群体间遗传分化最小（F_ST=0.0326,R_ST=0.0337）,XJF群体和LY群体间遗传分化最大（F_ST=0.2098,R_ST=0.2655）。所有成对群体间均存在显著的遗传分化（P < 0.05）。③群体间系统树显示,WY群体、GD群体、EGY群体和USA群体被聚为一类,BL群体、LY群体和EW群体被聚为一类,JNM群体和GLD群体被聚为一类,XJF群体位于独立的分支;贝叶斯聚类分析将10个群体划分为2类,XJF、BL、LY、EW群体被归入第一类,WY、GD、EGY、USA、GLD和JNM群体被归入第二类。分子方差分析和主成分分析支持了系统树和贝叶斯聚类分析的结果。④根据成对F_ST值和R_ST值估算的群体间历史基因流平均值分别为2.4427和2.1983。群体间近期基因流检测结果显示,各群体中发生第一代迁移的个体数在0-7个,占样本数的0-23.3%。总体而言,我国尼罗罗非鱼引进群体间遗传分化显著,群体间存在一定程度的历史基因流和近期基因流。研究结果为开展我国尼罗罗非鱼引进群体的种质资源保护和综合利用提供了科学依据。     

DISPERSAL AND PLANT MATING SYSTEMS: THE EVOLUTION OF SELF-FERTILIZATION IN SUBDIVIDED POPULATIONS

Intermediate rates of self-fertilization can be evolutionarily stable when the progeny of self-fertilization events are less successful migrants than those of outcrossing events, unless self-fertilization reduces an individual's contribution to the pollen pool by an amount equal to the rate at which it self-fertilizes. This result holds regardless of whether pollen or diaspores are more widely dispersed. The differential migration of selfed and outcrossed progeny may be a result of differential establishment with comparable rates of dispersal, or it may be a result of differential dispersal rates. In the first case, detailed predictions concerning the evolutionarily stable selfing rate can be made. In the second case, only qualitative predictions are possible in the absence of specific assumptions about how the migration rate is affected by the average selfing rate in each subpopulation.     

QUANTITATIVE GENETICS OF BRYOZOAN PHENOTYPIC EVOLUTION. III. PHENOTYPIC PLASTICITY AND THE MAINTENANCE OF GENETIC VARIATION

Cheilostome bryozoan species show long-term morphologic stasis, implying stabilizing selection sustained for millions of years, but nevertheless retain significant heritable variation in traits of skeletal morphology. The possible role of within-genotype (within-colony) phenotypic variability in preserving genetic diversity was analyzed using breeding data for two species of Stylopoma from sites along 110 km of the Caribbean coast of Panama. Variation among zooids within colonies accounts for nearly two-thirds of the phenotypic variance on average, increases with environmental heterogeneity, and includes significant genotype-environment interaction. Thus, within-colony variability apparently represents phenotypic plasticity, at least some of which is heritable, rather than random “developmental noise.” Almost all of the among-colonies component of phenotypic variance is accounted for by additive genetic differences in trait means, suggesting that within-colony plasticity includes virtually all of the environmental component of phenotypic variance in these populations of Stylopoma. Thus, heritable within-colony plasticity could play a significant part in maintaining genetic diversity in cheilostomes, but it is also possible that rates of polygenic mutation alone are sufficient to balance the effects of selection.