Effective population size associated with self-fertilization: lessons from temporal changes in allele frequencies in the selfing annual Medicago truncatula

Despite its significance in evolutionary and conservation biology, few estimates of effective population size (N(e)) are available in plant species. Self-fertilization is expected to affect N(e), through both its effect on homozygosity and population dynamics. Here, we estimated N(e) using temporal variation in allele frequencies for two contrasted populations of the selfing annual Medicago truncatula: a large and continuous population and a subdivided population. Estimated N(e) values were around 5-10% of the population census size suggesting that other factors than selfing must contribute to variation in allele frequencies. Further comparisons between monolocus allelic variation and changes in the multilocus genotypic composition of the populations show that the local dynamics of inbred lines can play an important role in the fluctuations of allele frequencies. Finally, comparing N(e) estimates and levels of genetic variation suggest that H(e) is a poor estimator of the contemporaneous variance effective population size.     

Estimating Effective Population Size from Temporally Spaced Samples with a Novel,Efficient Maximum-Likelihood Algorithm

The effective population size N_e is a key parameter in population genetics and evolutionary biology, as it quantifies the expected distribution of changes in allele frequency due to genetic drift. Several methods of estimating N_e have been described, the most direct of which uses allele frequencies measured at two or more time points. A new likelihood-based estimator NB^ for contemporary effective population size using temporal data is developed in this article. The existing likelihood methods are computationally intensive and unable to handle the case when the underlying N_e is large. This article tries to work around this problem by using a hidden Markov algorithm and applying continuous approximations to allele frequencies and transition probabilities. Extensive simulations are run to evaluate the performance of the proposed estimator NB^, and the results show that it is more accurate and has lower variance than previous methods. The new estimator also reduces the computational time by at least 1000-fold and relaxes the upper bound of N_e to several million, hence allowing the estimation of larger N_e. Finally, we demonstrate how this algorithm can cope with nonconstant N_e scenarios and be used as a likelihood-ratio test to test for the equality of N_e throughout the sampling horizon. An R package “NB” is now available for download to implement the method described in this article.     

植物亲缘地理学的研究现状与发展趋势

新生代以来剧烈的地质和气候变化,特别是第四纪冰期和间冰期的反复交错对温带植物类群的地理分布格局、种群结构和物种分化造成了深刻影响。近20年来,随着分子标记技术的发展和分析方法的成熟,植物亲缘地理学利用基因谱系关系和在种群中的时空分布来追溯种群的进化历史,在探讨植物类群对地质气候变迁的响应以及种群分化的历史成因等方面开展了大量工作,取得了一些重要进展。在取得这些成绩的同时,作者也注意到了被研究者所忽略的一些问题。试图对这些问题进行初步的总结,着重于分析方法和几个常用软件的使用,并对今后的发展趋势进行了展望。     

Small effective population sizes in a widespread selfing species, Lymnaea truncatula (Gastropoda: Pulmonata)

We present here a spatial and temporal population genetic survey of a common freshwater snail, also a predominantly selfing species, Lymnaea truncatula. The rate of genetic diversity loss was quantified by estimating the effective size (Ne) of the snail populations, using two different methods. A temporal survey allowed estimation of a variance effective size of the populations, and a spatial survey allowed the estimation of an inbreeding effective size, from two-locus identity disequilibria estimates. Both methods were consistent and provided low Ne values. Drift due to (i) high amounts of selfing and (ii) fluctuations in population sizes because of temporary habitats, and also selection coupled to genome-wide linkage disequilibria, could explain such reductions in Ne. The loss of genetic diversity appears to be counterbalanced only very partially by low apparent rates of gene flow.     

Disentangling the impact of demographic factors on population differentiation of an endangered freshwater crayfish (Austropotamobius pallipes) using population density and microsatellite data

1. Habitat fragmentation of stream ecosystems often results in decreased connectivity between populations and lower population sizes. Hence, understanding how habitat fragmentation affects genetic erosion is important for the preservation of freshwater biodiversity, in particular, as small populations suffer from loss of genetic diversity through genetic drift and loss of fitness because of inbreeding, increasing the risk of extinction. 2. Here, we assess the impact of demographic factors on population differentiation in the endangered freshwater crayfish Austropotamobius pallipes by analysing population genetic structure, estimating effective population sizes and comparing levels of polymorphism at five microsatellite loci with density estimates of 10 populations within a small French catchment that has become progressively confined to headwaters over the last six decades. 3. Levels of expected heterozygosity and allelic richness per population were relatively low (0.214–0.396 and 1.6–2.6, respectively). We found strong genetic differentiation between these geographically close populations (F_ST = 0.283), with weak statistical evidence for a pattern of isolation by distance. Estimates of effective population size were low (<150) in most populations, but potentially reached several thousands in three populations. 4. Population density and allelic richness were strongly positively correlated. A robust relationship between population density and heterozygosity values was also noted, but only after discarding two populations for which significant genetic signatures of a recent bottleneck were found; these two populations displayed high expected heterozygosity compared with a very low density. Populations with the highest densities of individuals had the highest effective population size estimates and vice versa. 5. Our results clearly show the importance of demographic factors and genetic drift on A. pallipes populations. Furthermore, analysis of genetic and population density data is a pragmatic and efficient approach to corroborate inferences from genetic data and can be particularly useful in the identification of populations experiencing a bottleneck and therefore in conservation genetics studies aiming at identifying priority populations for conservation.     

Is drift ‘directional’? Unequal breeding sex ratio revisited

Unequal breeding sex ratio can significantly reduce effective population size, allowing a rare neutral allele to jump to a high frequency through genetic drift. However, this one-way alteration to allele frequency appears inconsistent with the concept that drift is non-directional. Based on binomial sampling distribution, this study developed a method to directly and exhaustively measure drift by calculating the mean deviation of change in allele frequency, then applied it to cases of unequal breeding sex ratio. The result shows that, under those cases, (1) the mean deviation can always be divided into two halves that are equal in size but opposite in direction; (2) each half consists of one or several categories represented by various allele proportions in the rare sex; (3) this proportion is another factor that determines the outcome of drift, in addition to effective population size and allele frequency; (4) drift is non-directional on a global scale, but whether an allele will drift up or down can be predicted based on the above factors. This method enables us to dissect every component of the expected change in allele frequency caused by drift and to find out the combined effect of population size, allele frequency and allele proportion in the rarer sex under neutrality but unequal breeding sex ratio.