fastsimcoal2: demographic inference under complex evolutionary scenarios

Abstract

Motivation fastsimcoal2 extends fastsimcoal, a continuous time coalescent-based genetic simulation program, by enabling the estimation of demographic parameters under very complex scenarios from the site frequency spectrum under a maximum-likelihood framework. Results Other improvements include multi-threading, handling of population inbreeding, extended input file syntax facilitating the description of complex demographic scenarios, and more efficient simulations of sparsely structured populations and of large chromosomes. Availability fastsimcoal2 is freely available on http://cmpg.unibe.ch/software/fastsimcoal2/. It includes console versions for Linux, Windows and MacOS, additional scripts for the analysis and visualization of simulated and estimated scenarios, as well as a detailed documentation and ready-to-use examples.

Demographic history and identification of threats revealed by population genomic analysis provide insights into conservation for an endangered maple

“…First, demographic trajectories of A. yangbiense were inferred from Dataset 5 using stairway plot 2 (Liu & Fu, 2020), a model-free method, with 200 bootstrap iterations. Second, fastsimcoal2 (Excofffier et al, 2021) was used to infer the demographic dynamics of A. yangbiense using Dataset 5. Model comparison was based on the maximum value of the likelihood using the Akaike information criterion (AIC) and Akaike weight of evidence.…”

Rapid and repeatable genome evolution across three hybrid ant populations

“…1D) and low diversity of mitotypes within a population (£ 2) support a model where each hybrid population formed independently from a small number of founders. To elucidate the ancestry of the hybrid populations and date admixture events, we reconstructed their demographic histories using a coalescent approach based on the sitefrequency spectrum [FASTSIMCOAL2, (12)]. Coalescent analyses support balanced admixture proportions between species (i.e., no apparent minor ancestry) and together with field observations suggest recent admixture (< 50 generations, Fig.…”

Strong neutral sweeps occurring during a population contraction

“…In fig. 7 we show a trough generated during a population contraction corresponding to these inferred values, using the software fastsimcoal2 (Excofffier et al 2021). We see that the neutral sweep fit is almost indistinguishable from the selective sweep fit because they not only have the same width, but also practically the same depth.…”