Data from: Unlocking the vault: next generation museum population genomics

Natural history museum collections provide unique resources for
understanding how species respond to environmental change, including the
abrupt, anthropogenic climate change of the past century. Ideally,
researchers would conduct genome-scale screening of museum specimens to
explore the evolutionary consequences of environmental changes, but to
date such analyses have been severely limited by the numerous challenges
of working with the highly degraded DNA typical of historic samples. Here
we circumvent these challenges by using custom, multiplexed, exon-capture
to enrich and sequence ~11,000 exons (~4Mb) from early 20th century museum
skins. We used this approach to test for changes in genomic diversity
accompanying a climate-related range retraction in the alpine chipmunks
(Tamias alpinus) in the high Sierra Nevada area of California, USA. We
developed robust bioinformatic pipelines that rigorously detect and
filter-out base misincorporations in DNA derived from skins, most of which
likely resulted from post-mortem damage. Furthermore, to accommodate
genotyping uncertainties associated with low-medium coverage data, we
applied a recently developed probabilistic method to call SNPs and
estimate allele frequencies and the joint site frequency spectrum. Our
results show increased genetic subdivision following range retraction, but
no change in overall genetic diversity at either non-synonymous or
synonymous sites. This case study showcases the advantages of integrating
emerging genomic and statistical tools in museum collection-based
population genomic applications. Such technical advances greatly enhance
the value of museum collections, even where a pre-existing reference is
lacking, and points to a broad range of potential applications in
evolutionary and conservation biology.