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

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.

Holocene climate change promoted allopatric divergence and disjunct geographic distribution in a bee orchid species

“…The allopatric divergence in the Ophrys aveyronensis we report here is indeed extremely recent compared to other species with disjunct geographic distributions in terrestrial systems (e.g. González-Serna, Cordero & Orego, 2018; Tomasello, Karbstein, Hodač, Paetzold & Hörandl, 2020; Wang et al, 2022; Cao et al, 2022; Balmori-de la Puente et al, 2022). It is likely to have arisen as a result of climate warming, not as a consequence of Quaternary climate fluctuations but as late as following the Last Glacial Maximum, which disrupted an ancestral geographic distribution and subsequently constrained the spatial dynamics of its subranges and does not a priori imply a human- induced biological introduction.…”

“…The allopatric divergence in the Ophrys aveyronensis species complex we report here is extremely recent compared to other species complex harboring disjunct geographic distribution in terrestrial (e.g. González-Serna et al, 2018; Tomasello et al, 2020; Wang et al, 2022; Cao et al, 2022; Balmori-de la Puente et al, 2022) or marine systems (Schmid et al, 2023; Marcionetti et al, 2023). It is likely to have arisen because of climate warming that dissected an ancestral geographic distribution and subsequently constrained the spatial dynamics of its subranges and does not a priori imply a human-induced biological introduction.…”

Evaluating the use of non‐invasive hair sampling and ddRAD to characterize populations of endangered species: Application to a peripheral population of the European mink

“…Since sonication is not used in ddRAD library preparation, this is not an issue with the ddRAD protocol. In fact, in other published ddRAD studies (e.g., Balmori‐de la Puente et al, 2022 ; Escoda et al, 2019 ), samples with an excess of C to A changes are either not found or are very rare and of small magnitude. Rather, the problem in the present work is likely to be related to the preservation of some samples.…”

Do Fossorial Water Voles have a Functional Vomeronasal Organ? A Histological and Immunohistochemical Study

“…The fossorial water vole, Arvicola scherman (former fossorial form of Arvicola terrestris = Arvicola amphibius ; for taxonomic considerations see Balmori-de la Puente et al (2022) and references therein) is a cricetid rodent that lives in extensive burrow systems and preferentially consumes roots, bulbs and tubers of dicotyledons and some Poaceae (Airoldi 1976). This species inhabits grasslands and orchards in the main mountain massifs of Europe, including the northern Iberian Peninsula, the Alps, the mountains of central Europe and the Carpathians, and is considered one of the most important agricultural pests in these areas (Somoano 2020).…”