DOI: 10.5061/dryad.5tb2rbp23
title: Data from: Multiple glacial refugia and contemporary dispersal shape the genetic structure of an endemic amphibian from the Pyrenees

description: Historical factors (colonization scenarios, demographic oscillations) and
 contemporary processes (population connectivity, current population size)
 largely contribute to shaping species’ present-day genetic diversity and
 structure. In this study, we use a combination of mitochondrial and
 nuclear DNA markers to understand the role of Quaternary climatic
 oscillations and present-day gene flow dynamics in determining the genetic
 diversity and structure of the newt Calotriton asper (Al. Dugès, 1852),
 endemic to the Pyrenees. Mitochondrial DNA did not show a clear
 phylogeographic pattern and presented low levels of variation. In
 contrast, microsatellites revealed five major genetic lineages with
 admixture patterns at their boundaries. Approximate Bayesian computation
 analyses and linear models indicated that the five lineages likely
 underwent separate evolutionary histories and can be tracked back to
 distinct glacial refugia. Lineage differentiation started around the Last
 Glacial Maximum at three focal areas (western, central and eastern
 Pyrenees) and extended through the end of the Last Glacial Period in the
 central Pyrenees, where it led to the formation of two more lineages. Our
 data revealed no evidence of recent dispersal between lineages, whereas
 borders likely represent zones of secondary contact following expansion
 from multiple refugia. Finally, we did not find genetic evidence of
 sex-biased dispersal. This work highlights the importance of integrating
 past evolutionary processes and present-day gene flow and dispersal
 dynamics, together with multilocus approaches, to gain insights into what
 shaped the current genetic attributes of amphibians living in montane
 habitats.
description: Sampling was conducted in the period 2004-2017 across the whole
 Pyrenees, encompassing most of the species range. DNA was sampled via
 buccal swab or toe clipping of metamorphosed individuals. Samples were
 preserved in EDTA or absolute ethanol and stored at -20°C until DNA
 extraction. Genomic DNA was extracted using QIAGEN DNeasy Blood and Tissue
 Kit (Qiagen<sup>TM</sup>, Hilden, Germany) according to the
 manufacturer’s protocol, or following the HotSHOT method (Montero‐Pau,
 Gómez, & Muñoz, 2008), in a total volume of 100 µl.
 A fragment of the cytochrome <i>b
 </i>(cyt-<i>b</i>) gene was sequenced from 258
 individuals from 59 sampling sites. We amplified a fragment of 374 bp
 using primers Cytb1EuprF and Cytb2EuprR (Carranza & Amat, 2005).
 Amplification conditions were those described in Carranza, Arnold, Mateo,
 and López-Jurado (2000). Sequences were aligned using the ClustalW
 algorithm in MEGA 7 (Kumar, Stecher, & Tamura, 2016).
 A total of 1,299 individuals from 96 sampling sites were
 genotyped for a set of 17 microsatellite loci combined in three
 multiplexes (Drechsler et al., 2013). Fragments were sized with LIZ-500
 size standard and binned using either GeneMapper v4.0 (Applied Biosystems)
 or Geneious 11.0.5 (Kearse et al., 2012). Only individuals that could be
 scored in a reliable manner for at least 15 loci were included in the
 analyses.