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Genomic variation in the American pika: signatures of geographic isolation and implications for conservation
Mary Peacock
University of Nevada Reno
Corresponding Author
ORCiD: https://orcid.org/0000-0001-9273-8464
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published version at BMC Ecology and Evolution.
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.
Keywords
alpine, climate, conservation, genetic diversity, genotyping-by-sequencing, Great Basin, metapopulation, Ochotona princeps, Rocky Mountains, Sierra Nevada
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CURRENT STATUS: Published
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Posted 04 Jan, 2021
Published
On 21 Jan, 2021
No community comments so far
Submission checks complete
On 19 Dec, 2020
Editorial decision: Accept
On 16 Dec, 2020
No comments provided
Review #1 received
Received 09 Dec, 2020
Review #2 received
Received 16 Nov, 2020
Reviewer #2 agreed
On 15 Nov, 2020
Reviewers invited
Invitations sent on 13 Nov, 2020
Reviewer #1 agreed
On 13 Nov, 2020
Editor assigned
On 11 Nov, 2020
Submission checks complete
On 11 Nov, 2020
Editor invited
On 11 Nov, 2020
No comments provided
Editorial decision: Major revision
On 12 Oct, 2020
Review #2 received
Received 27 Sep, 2020
Review #1 received
Received 22 Sep, 2020
Reviewer #3 agreed
On 13 Sep, 2020
Reviewer #2 agreed
On 07 Sep, 2020
Reviewer #1 agreed
On 26 Aug, 2020
Reviewers invited
Invitations sent on 25 Aug, 2020
Editor assigned
On 24 Aug, 2020
Submission checks complete
On 19 Aug, 2020
Editor invited
On 19 Aug, 2020
First submitted
On 11 Aug, 2020
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This preprint is under consideration at BMC Ecology and Evolution. A preprint is a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research article
Genomic variation in the American pika: signatures of geographic isolation and implications for conservation
Mary Peacock
University of Nevada Reno
Corresponding Author
ORCiD: https://orcid.org/0000-0001-9273-8464
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Published
Version 3
Posted 04 Jan, 2021
Published
On 21 Jan, 2021
No community comments so far
Submission checks complete
On 19 Dec, 2020
Editorial decision: Accept
On 16 Dec, 2020
No comments provided
Review #1 received
Received 09 Dec, 2020
Review #2 received
Received 16 Nov, 2020
Reviewer #2 agreed
On 15 Nov, 2020
Reviewers invited
Invitations sent on 13 Nov, 2020
Reviewer #1 agreed
On 13 Nov, 2020
Editor assigned
On 11 Nov, 2020
Submission checks complete
On 11 Nov, 2020
Editor invited
On 11 Nov, 2020
No comments provided
Editorial decision: Major revision
On 12 Oct, 2020
Review #2 received
Received 27 Sep, 2020
Review #1 received
Received 22 Sep, 2020
Reviewer #3 agreed
On 13 Sep, 2020
Reviewer #2 agreed
On 07 Sep, 2020
Reviewer #1 agreed
On 26 Aug, 2020
Reviewers invited
Invitations sent on 25 Aug, 2020
Editor assigned
On 24 Aug, 2020
Submission checks complete
On 19 Aug, 2020
Editor invited
On 19 Aug, 2020
First submitted
On 11 Aug, 2020
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published version at BMC Ecology and Evolution.
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