10.5061/DRYAD.BQ68F
Derkarabetian, Shahan
San Diego State University
Burns, Mercedes
San Diego State University
Starrett, James
San Diego State University
Hedin, Marshal
San Diego State University
Data from: Population genomic evidence for multiple Pliocene refugia in a
montane-restricted harvestman (Arachnida, Opiliones, Sclerobunus robustus)
from the southwestern United States
Dryad
dataset
2016
landscape genomics
Sclerobunus robustus
isolation by environment
sky islands
refugial persistence
ddRAD-seq
2016-08-01T14:40:03Z
2016-08-01T14:40:03Z
en
https://doi.org/10.1111/mec.13789
35601436 bytes
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CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
The integration of ecological niche modelling into phylogeographic
analyses has allowed for the identification and testing of potential
refugia under a hypothesis-based framework, where the expected patterns of
higher genetic diversity in refugial populations and evidence of range
expansion of nonrefugial populations are corroborated with empirical data.
In this study, we focus on a montane-restricted cryophilic harvestman,
Sclerobunus robustus, distributed throughout the heterogeneous Southern
Rocky Mountains and Intermontane Plateau of southwestern North America. We
identified hypothetical refugia using ecological niche models (ENMs)
across three time periods, corroborated these refugia with population
genetic methods using double-digest RAD-seq data and conducted
population-level phylogenetic and divergence dating analyses. ENMs
identify two large temporally persistent regions in the mid-latitude
highlands. Genetic patterns support these two hypothesized refugia with
higher genetic diversity within refugial populations and evidence for
range expansion in populations found outside hypothesized refugia.
Phylogenetic analyses identify five to six genetically divergent,
geographically cohesive clades of S. robustus. Divergence dating analyses
suggest that these separate refugia date to the Pliocene and that
divergence between clades pre-dates the late Pleistocene glacial cycles,
while diversification within clades was likely driven by these cycles.
Population genetic analyses reveal effects of both isolation by distance
(IBD) and isolation by environment (IBE), with IBD more important in the
continuous mountainous portion of the distribution, while IBE was stronger
in the populations inhabiting the isolated sky islands of the south. Using
model-based coalescent approaches, we find support for postdivergence
migration between clades from separate refugia.
Environmental distance matrixThe environmental distance matrix used in
assessing isolation by
environment.EnvironmentalDistance.csvm16_ConcatenatedLociConcatenated
matrix of loci from the m16 pyRAD analysism16_PCA_StructureStructure from
the m16 pyRAD analysis file used for PCA.m16_SNPsSNPs file from the m16
pyRAD analysism32_ConcatenatedLociConcatenated matrix of loci from the m32
pyRAD analysism32_PCA_StructureStructure from the m32 pyRAD analysis file
used for PCA.m32_SNPsSNPs file from the m32 pyRAD analysis
Southwestern United States
southwestern United States