Genomic variation in the American pika: signatures of geographic isolation and implications for conservation
Background: Distributional responses by alpine taxa to repeated, glacial-interglacial cycles throughout the last two million years have significantly influenced the spatial genetic structure of populations. These effects have been exacerbated for the American pika (Ochotona princeps), a small alpine lagomorph constrained by thermal sensitivity and a limited dispersal capacity. As a species of conservation concern, long-term lack of gene flow has important consequences for landscape genetic structure and levels of diversity within populations. Here, we use reduced representation sequencing (ddRADseq) to provide a genome-wide perspective on patterns of genetic variation across pika populations representing distinct subspecies. To investigate how landscape and environmental features shape genetic variation, we collected genetic samples from distinct geographic regions as well as across finer spatial scales in two geographically proximate mountain ranges of eastern Nevada.
Results: Our genome-wide analyses corroborate range-wide, mitochondrial subspecific designations and reveal pronounced fine-scale population structure between the Ruby Mountains and East Humboldt Range of eastern Nevada. Populations in Nevada were characterized by low genetic diversity (π=0.0006β0.0009; πW=0.0005β0.0007) relative to populations in California (π=0.0014β0.0019; πW=0.0011β0.0017) and the Rocky Mountains (π=0.0025β0.0027; πW=0.0021β0.0024), indicating substantial genetic drift in these isolated populations. Tajimaβs D was positive for all sites (D=0.240-0.811), consistent with recent contraction in population sizes range-wide.
Conclusions: Substantial influences of geography, elevation and climate variables on genetic differentiation were also detected and may interact with the regional effects of anthropogenic climate change to force the loss of unique genetic lineages through continued population extirpations in the Great Basin and Sierra Nevada.
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Posted 04 Jan, 2021
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Genomic variation in the American pika: signatures of geographic isolation and implications for conservation
Posted 04 Jan, 2021
On 21 Jan, 2021
On 19 Dec, 2020
On 16 Dec, 2020
Received 09 Dec, 2020
Received 16 Nov, 2020
On 15 Nov, 2020
Invitations sent on 13 Nov, 2020
On 13 Nov, 2020
On 11 Nov, 2020
On 11 Nov, 2020
On 11 Nov, 2020
On 12 Oct, 2020
Received 27 Sep, 2020
Received 22 Sep, 2020
On 13 Sep, 2020
On 07 Sep, 2020
On 26 Aug, 2020
Invitations sent on 25 Aug, 2020
On 24 Aug, 2020
On 19 Aug, 2020
On 19 Aug, 2020
On 11 Aug, 2020
Background: Distributional responses by alpine taxa to repeated, glacial-interglacial cycles throughout the last two million years have significantly influenced the spatial genetic structure of populations. These effects have been exacerbated for the American pika (Ochotona princeps), a small alpine lagomorph constrained by thermal sensitivity and a limited dispersal capacity. As a species of conservation concern, long-term lack of gene flow has important consequences for landscape genetic structure and levels of diversity within populations. Here, we use reduced representation sequencing (ddRADseq) to provide a genome-wide perspective on patterns of genetic variation across pika populations representing distinct subspecies. To investigate how landscape and environmental features shape genetic variation, we collected genetic samples from distinct geographic regions as well as across finer spatial scales in two geographically proximate mountain ranges of eastern Nevada.
Results: Our genome-wide analyses corroborate range-wide, mitochondrial subspecific designations and reveal pronounced fine-scale population structure between the Ruby Mountains and East Humboldt Range of eastern Nevada. Populations in Nevada were characterized by low genetic diversity (π=0.0006β0.0009; πW=0.0005β0.0007) relative to populations in California (π=0.0014β0.0019; πW=0.0011β0.0017) and the Rocky Mountains (π=0.0025β0.0027; πW=0.0021β0.0024), indicating substantial genetic drift in these isolated populations. Tajimaβs D was positive for all sites (D=0.240-0.811), consistent with recent contraction in population sizes range-wide.
Conclusions: Substantial influences of geography, elevation and climate variables on genetic differentiation were also detected and may interact with the regional effects of anthropogenic climate change to force the loss of unique genetic lineages through continued population extirpations in the Great Basin and Sierra Nevada.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7