DOI: 10.5061/dryad.8jm51
title: Data from: Quantifying the similarity between genes and geography across Alaska's alpine small mammals

description: Aim: Quantitatively evaluate the similarity of genomic variation and
 geography in five different alpine small mammals in Alaska, and use this
 quantitative assessment of concordance as a framework for refining
 hypotheses about the processes structuring population genetic variation in
 either a species-specific or shared manner. Location: Alaska and adjacent
 north-western Canada. Methods: For each taxon we generated 3500–7500
 single-nucleotide polymorphisms and applied a Procrustes analysis to find
 an optimal transformation that maximizes the similarity between principal
 components analysis maps of genetic variation and geographical maps of
 sample locations. We generate stability maps using projected distributions
 from ecological niche models of the Last Glacial Maximum and the present.
 Results: Significant similarity between genes and geography exists across
 taxa. However, the extent to which geography is predictive of patterns of
 genetic variation not only differs among taxa, but the correspondence
 between genes and geography varies over space. Geographical areas where
 genetic structure aligns poorly with the geographical coordinates are of
 particular interest because they indicate regions where processes other
 than isolation by distance (IBD) have influenced genetic variation. The
 clustering of individuals according to their sample location does not
 support suppositions of admixture, despite the presumed high vagility of
 some species (e.g. arctic ground squirrels). Main conclusions: Genomic
 data indicate a more nuanced biogeographical history for the taxa than
 suggested by previous studies based on mtDNA alone. These include
 departures from IBD that are shared among taxa, which suggest some shared
 processes structuring genetic variation, including new potential ancestral
 source populations. In addition, some regions fit expectations of IBD
 where incremental migration and gene flow play a strong role in population
 structure, despite any ecological difference among taxa. Differences in
 dispersal capabilities do not result in different species-specific local
 patterns of population structure, at least at the sampling scale examined
 here. We highlight how the general fit to, as well as departures from,
 expectations for patterns of genetic variation based on the Procrustes
 analyses can be used to generate hypotheses about the underlying
 processes.
description: Ochotona collaris
 distribution pointsDistribution points used
 to generate ENMs for Ochotona collarisocho_rare_rarefied_points.csvMarmota caligata distribution pointsDistribution points used to generate ENMs for Marmota caligatamarm_rare_rarefied_points.csvMicrotus miurus distribution pointsDistribution points used to generate ENMs for Microtus miurusmicro_rare_rarefied_points.csvLemmus trimucronatus distribution pointsDistribution points used to generate ENMs for Lemmus trimucronatuslemm_rare_rarefied_points.csvSpermophilus parryi distribution pointsDistribution points used to generate ENMs for Spermophilus parryisperm_rare_rarefied_points.csvProcessing of Illumina reads with script: deMultiplex_V7This script compare each sequence first n letters to barcode list and assign them to different species, add SpNum/MID number to each sequence, and output statistics of barcode, including errors.deMultiplex_V7.py