Divergence time estimation using ddRAD data and an isolation-with-migration model applied to water vole populations of Arvicola

Alfonso Balmori-De La Puente,Aitor Somoano,Jacint Ventura,Jody Hey,Jose Castresana,Marcos Miñarro

doi:10.1038/s41598-022-07877-y

Abstract

Molecular dating methods of population splits are crucial in evolutionary biology, but they present important difficulties due to the complexity of the genealogical relationships of genes and past migrations between populations. Using the double digest restriction-site associated DNA (ddRAD) technique and an isolation-with-migration (IM) model, we studied the evolutionary history of water vole populations of the genus Arvicola, a group of complex evolution with fossorial and semi-aquatic ecotypes. To do this, we first estimated mutation rates of ddRAD loci using a phylogenetic approach. An IM model was then used to estimate split times and other relevant demographic parameters. A set of 300 ddRAD loci that included 85 calibrated loci resulted in good mixing and model convergence. The results showed that the two populations of A. scherman present in the Iberian Peninsula split 34 thousand years ago, during the last glaciation. In addition, the much greater divergence from its sister species, A. amphibius, may help to clarify the controversial taxonomy of the genus. We conclude that this approach, based on ddRAD data and an IM model, is highly useful for analyzing the origin of populations and species.

Highlights

Estimating diversification times using genetic data is crucial for analyzing the evolutionary history of species and populations
The genus Arvicola is a group of Eurasian rodents with a rich evolutionary history and several taxonomic aspects currently under debate[22–25], which would greatly benefit from the use of an accurate methodology to estimate population split times and other demographic parameters
Due to the presence of several mountain ranges, it was hypothesized that the Iberian Peninsula was not a single homogeneous refuge during the glaciations and rather that important levels of population structure were generated in different isolated refugia within the p eninsula[34]

Summary

Introduction

Estimating diversification times using genetic data is crucial for analyzing the evolutionary history of species and populations. Among the most powerful methods for estimating population split times and other demographic parameters are isolation-with-migration (IM) models, which consider coalescence and migration while taking into account mutation rates of the sequence markers used[5–7]. Polymorphism (SNP) discovery, but full ddRAD sequences have enormous potential for using them with IM models They have not so far been combined with these methods and it is not yet clear whether, being so short, they can help produce robust estimates, especially between recently diverged populations and species. Due to the presence of several mountain ranges, it was hypothesized that the Iberian Peninsula was not a single homogeneous refuge during the glaciations and rather that important levels of population structure were generated in different isolated refugia within the p eninsula[34] This refugia-within-refugia hypothesis may be especially true for species of low dispersal capacity such as amphibians, reptiles and small mammals. Obtaining accurate population split times such as those between the Cantabrian and Pyrenean populations of A. scherman may be key for testing the refugia-within-refugia hypothesis and understanding whether these populations became isolated due to the effects of glaciations or if their divergence occurred more recently

Results

Discussion

Conclusion