Linkage Modification with Mixed Random Mating and Selfing: A Numerical Study

Although recombination cannot increase under conditions of random mating or complete selfing in regimes of constant selection, with mixed random mating and selfing, selection for increased recombination can occur. For some fitness regimes there may be selection for reduced recombination with both low and high degrees of selfing but selection for increased recombination with moderate degrees of selfing. With some fitness regimes there is a historical effect: depending on which equilibrium a population starts from, there may be selection for either increased or decreased recombination. In other cases the direction of selection may be determined by the present state of individuals within the population. If recombination is already fairly limited, there may be selection for further reduction. If recombination is already fairly frequent, there may be selection for increased recombination. For certain symmetric viability systems there may be an intermediate value of the recombination fraction between 0 and 0.5 toward which the population will evolve. Although it is not yet possible to classify precisely those fitness matrices that can exhibit selection for increased recombination, it does appear that selection for increased recombination can occur only if at least two of the double homozygotes are less fit than would be expected on the basis of a comparison of the fitnesses of the single and double heterozygotes on an additive scale.     

Hitchhiking of Deleterious Alleles and the Cost of Adaptation in Partially Selfing Species

Self-fertilization is generally seen to be disadvantageous in the long term. It increases genetic drift, which subsequently reduces polymorphism and the efficiency of selection, which also challenges adaptation. However, high selfing rates can increase the fixation probability of recessive beneficial mutations, but existing theory has generally not accounted for the effect of linked sites. Here, we analyze a model for the fixation probability of deleterious mutants that hitchhike with selective sweeps in diploid, partially selfing populations. Approximate analytical solutions show that, conditional on the sweep not being lost by drift, higher inbreeding rates increase the fixation probability of the deleterious allele, due to the resulting reduction in polymorphism and effective recombination. When extending the analysis to consider a distribution of deleterious alleles, as well as the average fitness increase after a sweep, we find that beneficial alleles generally need to be more recessive than the previously assumed dominance threshold (h < 1/2) for selfing to be beneficial from one-locus theory. Our results highlight that recombination aiding the efficiency of selection on multiple loci amplifies the fitness benefits of outcrossing over selfing, compared to results obtained from one-locus theory. This effect additionally increases the parameter range under which obligate outcrossing is beneficial over partial selfing.     

Selection with Partial Selfing. I. Mass Selection

The expected responses to mass selection carried out before or after reproduction in a population whose members all have a fixed probability of self pollination (s) are formulated using covariances of relatives and their component quadratic functions for a model with arbitrary additive and dominance effects. The response measured in the first generation offspring after selection (immediate gain) can differ from that retained when the population has regained equilibrium (permanent gain). The population mean behaves in a predictable manner during the return to equilibrium, and its value at any time can be predicted from earlier generations. The permanent gain from selection after reproduction is always (1 + s)/2 times as large as that from selection before reproduction, but the relationship of the immediate gains depends on the genetic model assumed. Numerical analysis applied to a model with two alleles per locus and varying allele frequencies, dominance ratios and numbers of loci showed that the proportion of the immediate gain retained at equilibrium was reduced with the large inbreeding depression associated with increasing dominance levels and numbers of loci and was generally lower for selection after reproduction than before. In the absence of information as to the magnitude of genetic variances and inbreeding depression in species reproducing by partial selfing, the importance of this phenomenon is unknown.     

On the Theory of Partially Inbreeding Finite Populations. I. Partial Selfing

Some stochastic theory is developed for monoecious populations of size N in which there are probabilities beta and 1 - beta of reproduction by selfing and by random mating. It is assumed that beta much greater than N-1. Expressions are derived for the inbreeding coefficient of one random individual and the coefficient of kinship of two random separate individuals at time t. The mean and between-lines variance of the fraction of copies of a locus that are identical in two random separate individuals in an equilibrium population are obtained under the assumption that there is an infinite number of possible alleles. It is found that the theory for random mating populations holds if the effective population number is Ne = N'/(1 + FIS), where FIS is the inbreeding coefficient at equilibrium when N is infinite and N' is the reciprocal of the probability that two gametes contributing to random separate adults come from the same parent. When there is a binomial distribution of successful gametes emanating from each adult, N' = N. An approximation to the probability that an allele A survives if it is originally present in one AA heterozygote is found to be 2(N'/N)(FISS1 + (1 - FIS)S2), where S1 and S2 are the selective advantages of AA and AA in comparison with AA. In the last section it is shown that if there is partial full sib mating and binomial offspring distributions Ne = N/(1 + 3FIS).     

Effective Size and F-Statistics of Subdivided Populations. I. Monoecious Species with Partial Selfing

Assuming discrete generations and autosomal inheritance involving genes that do not affect viability or reproductive ability, we have derived recurrence equations for the inbreeding coefficient and coancestry between individuals within and among subpopulations for a subdivided monoecious population with arbitrary distributions of male and female gametes per family, variable pollen and seed migration rates, and partial selfing. From the equations, formulas for effective size and expressions for F-statistics are obtained. For the special case of a single unsubdivided population, our equations reduce to the simple expressions derived by previous authors. It is shown that population structure (subdivision and migration) is important in determining the inbreeding coefficient and effective size. Failure to recognize internal structures of populations may lead to considerable bias in predicting effective size. Inbreeding coefficient, coancestry between individuals within and among subpopulations accrue at different and variable rates over initial generations before they converge to the same asymptotic rate of increase. For a given population, the smaller the pollen and seed migration rates, the more generations are required to attain the asymptotic rate and the larger the asymptotic effective size. The equations presented herein can be used for the study of evolutionary biology and conservation genetics.     

Coalescence with Background and Balancing Selection in Systems with Bi- and Uniparental Reproduction: Contrasting Partial Asexuality and Selfing

Uniparental reproduction in diploids, via asexual reproduction or selfing, reduces the independence with which separate loci are transmitted across generations. This is expected to increase the extent to which a neutral marker is affected by selection elsewhere in the genome. Such effects have previously been quantified in coalescent models involving selfing. Here we examine the effects of background selection and balancing selection in diploids capable of both sexual and asexual reproduction (i.e., partial asexuality). We find that the effect of background selection on reducing coalescent time (and effective population size) can be orders of magnitude greater when rates of sex are low than when sex is common. This is because asexuality enhances the effects of background selection through both a recombination effect and a segregation effect. We show that there are several reasons that the strength of background selection differs between systems with partial asexuality and those with comparable levels of uniparental reproduction via selfing. Expectations for reductions in N_e via background selection have been verified using stochastic simulations. In contrast to background selection, balancing selection increases the coalescence time for a linked neutral site. With partial asexuality, the effect of balancing selection is somewhat dependent upon the mode of selection (e.g., heterozygote advantage vs. negative frequency-dependent selection) in a manner that does not apply to selfing. This is because the frequency of heterozygotes, which are required for recombination onto alternative genetic backgrounds, is more dependent on the pattern of selection with partial asexuality than with selfing.     

A Scale-Corrected Comparison of Linkage Disequilibrium Levels between Genic and Non-Genic Regions

The understanding of non-random association between loci, termed linkage disequilibrium (LD), plays a central role in genomic research. Since causal mutations are generally not included in genomic marker data, LD between those and available markers is essential for capturing the effects of causal loci on localizing genes responsible for traits. Thus, the interpretation of association studies requires a detailed knowledge of LD patterns. It is well known that most LD measures depend on minor allele frequencies (MAF) of the considered loci and the magnitude of LD is influenced by the physical distances between loci. In the present study, a procedure to compare the LD structure between genomic regions comprising several markers each is suggested. The approach accounts for different scaling factors, namely the distribution of MAF, the distribution of pair-wise differences in MAF, and the physical extent of compared regions, reflected by the distribution of pair-wise physical distances. In the first step, genomic regions are matched based on similarity in these scaling factors. In the second step, chromosome- and genome-wide significance tests for differences in medians of LD measures in each pair are performed. The proposed framework was applied to test the hypothesis that the average LD is different in genic and non-genic regions. This was tested with a genome-wide approach with data sets for humans (Homo sapiens), a highly selected chicken line (Gallus gallus domesticus) and the model plant Arabidopsis thaliana. In all three data sets we found a significantly higher level of LD in genic regions compared to non-genic regions. About 31% more LD was detected genome-wide in genic compared to non-genic regions in Arabidopsis thaliana, followed by 13.6% in human and 6% chicken. Chromosome-wide comparison discovered significant differences on all 5 chromosomes in Arabidopsis thaliana and on one third of the human and of the chicken chromosomes.     

A Bayesian Approach to Inferring Rates of Selfing and Locus-Specific Mutation

We present a Bayesian method for characterizing the mating system of populations reproducing through a mixture of self-fertilization and random outcrossing. Our method uses patterns of genetic variation across the genome as a basis for inference about reproduction under pure hermaphroditism, gynodioecy, and a model developed to describe the self-fertilizing killifish Kryptolebias marmoratus. We extend the standard coalescence model to accommodate these mating systems, accounting explicitly for multilocus identity disequilibrium, inbreeding depression, and variation in fertility among mating types. We incorporate the Ewens sampling formula (ESF) under the infinite-alleles model of mutation to obtain a novel expression for the likelihood of mating system parameters. Our Markov chain Monte Carlo (MCMC) algorithm assigns locus-specific mutation rates, drawn from a common mutation rate distribution that is itself estimated from the data using a Dirichlet process prior model. Our sampler is designed to accommodate additional information, including observations pertaining to the sex ratio, the intensity of inbreeding depression, and other aspects of reproduction. It can provide joint posterior distributions for the population-wide proportion of uniparental individuals, locus-specific mutation rates, and the number of generations since the most recent outcrossing event for each sampled individual. Further, estimation of all basic parameters of a given model permits estimation of functions of those parameters, including the proportion of the gene pool contributed by each sex and relative effective numbers.     

Hitchhiking the high seas: Global genomics of rafting crabs

Population differentiation and diversification depend in large part on the ability and propensity of organisms to successfully disperse. However, our understanding of these processes in organisms with high dispersal ability is biased by the limited genetic resolution offered by traditional genotypic markers. Many neustonic animals disperse not only as pelagic larvae, but also as juveniles and adults while drifting or rafting at the surface of the open ocean. In theory, the heightened dispersal ability of these animals should limit opportunities for species diversification and population differentiation. To test these predictions, we used next‐generation sequencing of genomewide restriction‐site‐associated DNA tags (RADseq) and traditional mitochondrial DNA sequencing, to investigate the species‐level relationships and global population structure of Planes crabs collected from oceanic flotsam and sea turtles. Our results indicate that species diversity in this clade is low—likely three closely related species—with no evidence of cryptic or undescribed species. Moreover, our results indicate weak population differentiation among widely separated aggregations with genetic indices showing only subtle genetic discontinuities across all oceans of the world (RADseq F_ST = 0.08–0.16). The results of this study provide unprecedented resolution of the systematics and global biogeography of this group and contribute valuable information to our understanding of how theoretical dispersal potential relates to actual population differentiation and diversification among marine organisms. Moreover, these results demonstrate the limitations of single gene analyses and the value of genomic‐level resolution for estimating contemporary population structure in organisms with large, highly connected populations.     

Robust Forward Simulations of Recurrent Hitchhiking

Evolutionary forces shape patterns of genetic diversity within populations and contribute to phenotypic variation. In particular, recurrent positive selection has attracted significant interest in both theoretical and empirical studies. However, most existing theoretical models of recurrent positive selection cannot easily incorporate realistic confounding effects such as interference between selected sites, arbitrary selection schemes, and complicated demographic processes. It is possible to quantify the effects of arbitrarily complex evolutionary models by performing forward population genetic simulations, but forward simulations can be computationally prohibitive for large population sizes (>10⁵). A common approach for overcoming these computational limitations is rescaling of the most computationally expensive parameters, especially population size. Here, we show that ad hoc approaches to parameter rescaling under the recurrent hitchhiking model do not always provide sufficiently accurate dynamics, potentially skewing patterns of diversity in simulated DNA sequences. We derive an extension of the recurrent hitchhiking model that is appropriate for strong selection in small population sizes and use it to develop a method for parameter rescaling that provides the best possible computational performance for a given error tolerance. We perform a detailed theoretical analysis of the robustness of rescaling across the parameter space. Finally, we apply our rescaling algorithms to parameters that were previously inferred for Drosophila and discuss practical considerations such as interference between selected sites.     

自交与异交象牙参属植物的蜜腺结构及其生物学意义

蜜腺是有花植物与传粉昆虫构建互惠关系的关键花部结构,解析不同繁殖特性物种间蜜腺结构的差异可为理解有花植物繁殖特性的演化提供理论依据。以传粉系统高度特化、异交实现有性生殖的早花象牙参（Roscoea cautleoides）和缺乏有效传粉者、主动自交实现有性生殖的无柄象牙参（R. schneideriana）为材料,通过野外测量2个物种蜜腺特性、超景深显微镜观察和石蜡切片染色,探究早花象牙参与无柄象牙参在蜜腺分布位置、外部形态及内部结构的异同。结果表明：2个物种均具有结构蜜腺,从外部形态来看,早花象牙参蜜腺体积较大、分泌糖浓度较高的花蜜,而无柄象牙参蜜腺体积较小、无花蜜分泌;从内部结构来看,早花象牙参蜜腺结构特化、各个组成部分有明显的区分,而无柄象牙参蜜腺出现一定程度的退化。该研究结果为揭示早花象牙参与无柄象牙参在花部特征、传粉机制及繁育系统的差异以及无柄象牙参蜜腺无花蜜分泌的可能机理提供了重要的形态学依据,也为深入地探讨植物与传粉动物间的协同进化关系以及理解蜜腺多样性的起源与维持机制奠定了科学基础。     

Hitchhiking and associative overdominance at a microsatellite locus

The possible effects of a selected locus on a closely linked microsatellite locus are discussed and analyzed in terms of coalescent theory and models of the mutation process. Background selection caused by recurrent deleterious mutations will reduce the variance of allele size at a microsatellite locus. The occasional substitution of advantageous alleles (genetic hitchhiking) will also reduce the variance, but a high mutation rate at a microsatellite locus can restore the variance relatively rapidly. Overdominance at the selected locus will increase the variance at the microsatellite locus and create partitioning of the variation in allele size among gametes carrying one or the other of the overdominant alleles. These results suggest that neutral microsatellite loci can provide indicators of selective processes at closely linked loci.