Data from: Quantifying the similarity between genes and geography across Alaska's alpine small mammals ...

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...

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Bibliographic Details
Main Authors: Knowles, L. Lacey, Massatti, Rob, He, Qixin, Olson, Link E., Lanier, Hayley C.
Format: Dataset
Language:English
Published: Dryad 2017
Subjects:
Next Generation Sequencing
Microtus miurus
Procrustes analyses
isolation by distance
Lemmus trimucronatus
Spermophilus parryi
mammal
Alaska
Marmota caligata
Holocene
Ochotona collaris
Canada
Online Access:https://dx.doi.org/10.5061/dryad.8jm51
https://datadryad.org/stash/dataset/doi:10.5061/dryad.8jm51
Description
Summary: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 ... : 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 ...

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