Temporal genomic contrasts reveal rapid evolutionary responses in an alpine mammal during recent climate change
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Temporal genomic contrasts reveal rapid evolutionary responses in an alpine mammal during recent climate change. / Bi, Ke; Linderoth, Tyler; Singhal, Sonal; Vanderpool, Dan; Patton, James L.; Nielsen, Rasmus; Moritz, Craig; Good, Jeffrey M.
In: PLOS Genetics, Vol. 15, No. 5, e1008119, 2019.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Temporal genomic contrasts reveal rapid evolutionary responses in an alpine mammal during recent climate change
AU - Bi, Ke
AU - Linderoth, Tyler
AU - Singhal, Sonal
AU - Vanderpool, Dan
AU - Patton, James L.
AU - Nielsen, Rasmus
AU - Moritz, Craig
AU - Good, Jeffrey M.
N1 - Publisher Copyright: © 2019 Bi et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
PY - 2019
Y1 - 2019
N2 - Many species have experienced dramatic changes in their abundance and distribution during recent climate change, but it is often unclear whether such ecological responses are accompanied by evolutionary change. We used targeted exon sequencing of 294 museum specimens (160 historic, 134 modern) to generate independent temporal genomic contrasts spanning a century of climate change (1911–2012) for two co-distributed chipmunk species: an endemic alpine specialist (Tamias alpinus) undergoing severe range contraction and a stable mid-elevation species (T. speciosus). Using a novel analytical approach, we reconstructed the demographic histories of these populations and tested for evidence of recent positive directional selection. Only the retracting species showed substantial population genetic fragmentation through time and this was coupled with positive selection and substantial shifts in allele frequencies at a gene, Alox15, involved in regulation of inflammation and response to hypoxia. However, these rapid population and gene-level responses were not detected in an analogous temporal contrast from another area where T. alpinus has also undergone severe range contraction. Collectively, these results highlight that evolutionary responses may be variable and context dependent across populations, even when they show seemingly synchronous ecological shifts. Our results demonstrate that temporal genomic contrasts can be used to detect very recent evolutionary responses within and among contemporary populations, even in the face of complex demographic changes. Given the wealth of specimens archived in natural history museums, comparative analyses of temporal population genomic data have the potential to improve our understanding of recent and ongoing evolutionary responses to rapidly changing environments.
AB - Many species have experienced dramatic changes in their abundance and distribution during recent climate change, but it is often unclear whether such ecological responses are accompanied by evolutionary change. We used targeted exon sequencing of 294 museum specimens (160 historic, 134 modern) to generate independent temporal genomic contrasts spanning a century of climate change (1911–2012) for two co-distributed chipmunk species: an endemic alpine specialist (Tamias alpinus) undergoing severe range contraction and a stable mid-elevation species (T. speciosus). Using a novel analytical approach, we reconstructed the demographic histories of these populations and tested for evidence of recent positive directional selection. Only the retracting species showed substantial population genetic fragmentation through time and this was coupled with positive selection and substantial shifts in allele frequencies at a gene, Alox15, involved in regulation of inflammation and response to hypoxia. However, these rapid population and gene-level responses were not detected in an analogous temporal contrast from another area where T. alpinus has also undergone severe range contraction. Collectively, these results highlight that evolutionary responses may be variable and context dependent across populations, even when they show seemingly synchronous ecological shifts. Our results demonstrate that temporal genomic contrasts can be used to detect very recent evolutionary responses within and among contemporary populations, even in the face of complex demographic changes. Given the wealth of specimens archived in natural history museums, comparative analyses of temporal population genomic data have the potential to improve our understanding of recent and ongoing evolutionary responses to rapidly changing environments.
U2 - 10.1371/journal.pgen.1008119
DO - 10.1371/journal.pgen.1008119
M3 - Journal article
C2 - 31050681
AN - SCOPUS:85066163845
VL - 15
JO - P L o S Genetics
JF - P L o S Genetics
SN - 1553-7390
IS - 5
M1 - e1008119
ER -
ID: 336600513