Detecting past changes of effective population size

Abstract

Understanding and predicting population abundance is a major challenge confronting scientists. Several genetic models have been developed using microsatellite markers to estimate the present and ancestral effective population sizes. However, to get an overview on the evolution of population requires that past fluctuation of population size be traceable. To address the question, we developed a new model estimating the past changes of effective population size from microsatellite by resolving coalescence theory and using approximate likelihoods in a Monte Carlo Markov Chain approach. The efficiency of the model and its sensitivity to gene flow and to assumptions on the mutational process were checked using simulated data and analysis. The model was found especially useful to provide evidence of transient changes of population size in the past. The times at which some past demographic events cannot be detected because they are too ancient and the risk that gene flow may suggest the false detection of a bottleneck are discussed considering the distribution of coalescence times. The method was applied on real data sets from several Atlantic salmon populations. The method called VarEff (Variation of Effective size) was implemented in the R package VarEff and is made available at https://qgsp.jouy.inra.fr and at http://cran.r-project.org/web/packages/VarEff.

Conservation Genetics of the Cheetah: Genetic History and Implications for Conservation

“…c cal: Reference time point used as calibration; µ: mutation rate given per generation; MYA, million years ago. d 1/µ × G (Nei, 1987); coal, coalescent methods, MSVAR1.3 (Storz and Beaumont, 2002), VarEff (Nikolic and Chevalet, 2013), DIYABC-FDA (Cornuet et al, 2010); DaDi, Diffusion approximation to the allele frequency spectrum (Gutenkunst et al, 2009); fixation 4N e , fixation of a neutral nuclear marker is expected after 4N e generations (Nichols, 2001); PSMC, Pairwise Sequential Markovian Coalescent (Li and Durbin, 2011); SMM, Stepwise Mutation Model (Valdes et al, 1993). e An accelerated decline may be present 10,000 and 13,000 years ago.…”

Historical Processes and Contemporary Anthropogenic Activities Influence Genetic Population Dynamics of Nassau Grouper (Epinephelus striatus) within The Bahamas

“…Temporal changes in N e were analyzed using the VarEff package in R to determine when historical population declines occurred (Nikolic and Chevalet, 2014). The VarEff model uses the coalescent method and approximate likelihoods to derive posterior distributions of N e over a specified past generation time.…”

“…Initially, this analysis was performed assuming a two-phase model, T, with a commonly used microsatellite mutation rate, µ = 5 × 10 −4 (Estoup et al, 2002), and burn-in of 10,000 over the past 1,000 generations. Additional parameters included setting the number batch to 50,000, length and space batch to 10, with an acceptance rate of 0.25 and diagonale of 0.5, following recommendations from Nikolic and Chevalet (2014). The model was also run using mutation rates of 5.57 × 10 −4 (C. carpio), 2.0 × 10 −3 (S. typhle) and 1.5 × 10 −4 (D. rerio) respectively, under the same parameters.…”

Genetics and Conservation of Plant Species of Extremely Narrow Geographic Range

“…Here, the bottleneck effects were not statistically supported for M. albiflora, but this may be related to the fact that we did not have the 20 sampled loci as the software demands [48]. Another explanation is that in M. albiflora an event of bottleneck effectively occurred but, as has been shown for other species [51], if this was very ancient it could not be detected since the mutation-drift equilibrium was already restored. Also, it may be that the bottleneck has been occurring gradually for a long time in a diffuse mode, which causes a relatively low number of alleles with relatively discordant levels of heterozygosity [52], like the results here obtained.…”