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.     

Genetic isolation of fragmented populations is exacerbated by drift and selection

Reduced genetic variation at marker loci in small populations has been well documented, whereas the relationship between quantitative genetic variation and population size has attracted little empirical investigation. Here we demonstrate that both neutral and quantitative genetic variation are reduced in small populations of a fragmented plant metapopulation, and that both drift and selective change are enhanced in small populations. Measures of neutral genetic differentiation (F(ST)) and quantitative genetic differentiation (Q(ST)) in two traits were higher among small demes, and Q(ST) between small populations exceeded that expected from drift alone. This suggests that fragmented populations experience both enhanced genetic drift and divergent selection on phenotypic traits, and that drift affects variation in both neutral markers and quantitative traits. These results highlight the need to integrate natural selection into conservation genetic theory, and suggests that small populations may represent reservoirs of genetic variation adaptive within a wide range of environments.     

Consequences of the founder effect in the genetic structure of introduced island coral reef fish populations

Between 1955 and 1961, the Division of Fish and Game of the State of Hawaii (USA) undertook an introduction program which brought 11 species of families Serranidae and Lutjanidae (Pisces) from French Polynesia to the coral reefs off Oahu and Big Island in Hawaii. Only three— Cephalopholis argus, Lutjanus fulvus and Lutjanus kasmira —for which we have records of locations and number offish released, are known to have become established. Comparison of allozyme distribution of C. argus and L. kasmira between individuals collected in Hawaiian and Polynesian populations provided a unique opportunity to estimate the impact of genetic drift and selection processes caused by a founder event. We used temporal variance of allelic frequencies to estimate and validate effective population size within marine fish populations. Despite the fact that only 571 C. argus and 2435 L. kasmira were released, we did not observe major changes in polymorphism and heterozygosity. Using different models to estimate effective population size from temporal variance in allelic frequencies and the number of generations, we estimate that the effective population size is about 1–5% of the total population size. Such reduced effective population size explains why most of the species introduced in Hawaii (8/11) failed to become established. Our results have implications for conservation biology because they emphasize that in spite of the fact that only a few individuals bequeathed their characteristics to subsequent generations, no significant change in genetic diversity was observed; success of introduced species is therefore limited by the number of fish released.     

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.     

Analysis of genetic diversity for the management of conserved subdivided populations

Recent studies in the literature have appliedphylogenetic methods based on genetic distancesto set priorities for conservation of domesticanimal breeds. While these methods may beappropriate for between-species conservation,they are clearly inappropriate forwithin-species breed conservation, because theyignore within-breed variation. In this paper weshow the basic tools to analyse geneticdiversity in subdivided populations withinspecies, and illustrate the errors incurred byapplying methods based exclusively on geneticdistances. We also show that maximisation ofgenetic diversity (minimisation of coancestryor kinship) is equivalent to maximisation ofeffective population size, as in undividedpopulations, and derive a generalisation ofprevious equations for the prediction ofeffective size. Finally, we discuss thestrategies for conservation in the light of thetheory.     

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.     

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.