DOI: 10.5061/dryad.n5s02
title: Data from: The impact of Quaternary climate oscillations on divergence times and historical population sizes in Thylamys opossums from the Andes

description: Climate oscillations during the Quaternary altered the distributions of
 terrestrial animals at a global scale. In mountainous regions, temperature
 fluctuations may have led to shifts in range size and population size as
 species tracked their shifting habitats upslope or downslope. This creates
 the potential for both allopatric speciation and population size
 fluctuations, as species are either constrained to smaller patches of
 habitat at higher elevations or able to expand into broader areas at
 higher latitudes. We considered the impact of climate oscillations on
 three pairs of marsupial species from the Andes (Thylamys opossums) by
 inferring divergence times and demographic changes. We compare four
 different divergence dating approaches, using anywhere from one to 26
 loci. Each pair comprises a northern (tropical) lineage and a southern
 (subtropical to temperate) lineage. We predicted that divergences would
 have occurred during the last interglacial (LIG) period approximately 125
 000 years ago and that population sizes for northern and southern lineages
 would either contract or expand, respectively. Our results suggest that
 all three north–south pairs diverged in the late Pleistocene during or
 slightly after the LIG. The three northern lineages showed no signs of
 population expansion, whereas two southern lineages exhibited dramatic,
 recent expansions. We attribute the difference in responses between
 tropical and subtropical lineages to the availability of ‘montane-like’
 habitats at lower elevations in regions at higher latitudes. We conclude
 that climate oscillations of the late Quaternary had a powerful impact on
 the evolutionary history of some of these species, both promoting
 speciation and leading to significant population size shifts.
description: BEAST Divergence Dating
 Tree FilesTree files resulting
 from analysis of (1) CYTB alone in BEAST, (2) 26 genes in BEAST, and (3)
 16 genes in *BEAST.BEAST Divergence Dating
 XML FilesInput XML files for (1)
 CYTB alone in BEAST, (2) 26 genes in BEAST, and (3) 16 genes in
 *BEAST.BEAST EBSP XML
 FilesBEAST Extended Bayesian
 Skyline Plot XML input files for all six Thylamys
 lineages.BEAST PS SS Model
 Comparisons XML FilesBEAST input XML files
 for Path Sampling/Stepping Stone Sampling coalescent model comparisons
 (constant size versus exponential change) for all six Thylamys
 lineages.BPP Input
 FilesAll input files used in
 BPP for the estimation of divergence times between A and B
 lineages.Geographic
 InformationExcel file containing
 specimen museum voucher numbers, detailed locality information, and
 geographic coordinates for individuals sequenced in Giarla et al.
 (2014).16 Nexus Files from
 Giarla et al 2014DNA alignments of 14
 anonymous loci, one X-linked intron, and the mitochondrial gene CYTB.
 Densely sampled among the six focal Andean lineages. Data originally from
 Giarla et al. (2014).26 Nexus Files from
 Giarla and Jansa 2014Alignments of 26 loci
 used to estimate divergence times in BEAST. Loci are sampled across 50
 different marsupial taxa. Originally from Giarla and Jansa
 (2014).