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Schmidt DA, Galbreath KE, Russello MA. Phylogenomics of American pika (Ochotona princeps) lineage diversification. Mol Phylogenet Evol 2024; 193:108030. [PMID: 38341008 DOI: 10.1016/j.ympev.2024.108030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 01/31/2024] [Accepted: 02/05/2024] [Indexed: 02/12/2024]
Abstract
Quaternary climate oscillations have profoundly influenced current species distributions. For many montane species, these fluctuations were a prominent driver in species range shifts, often resulting in intraspecific diversification, as has been the case for American pikas (Ochotona princeps). Range shifts and population declines in this thermally-sensitive lagomorph have been linked to historical and contemporary environmental changes across its western North American range, with previous research reconstructing five mitochondrial DNA lineages. Here, we paired genome-wide data (25,244 SNPs) with range-wide sampling to re-examine the number and distribution of intra-specific lineages, and investigate patterns of within- and among-lineage divergence and diversity. Our results provide genomic evidence of O. princeps monophyly, reconstructing six distinct lineages that underwent multiple rounds of divergence (0.809-2.81 mya), including a new Central Rocky Mountain lineage. We further found evidence for population differentiation across multiple spatial scales, and reconstructed levels of standing variation comparable to those found in other small mammals. Overall, our findings demonstrate the influence of past glacial cycles on O. princeps lineage diversification, suggest that current subspecific taxonomy may need to be revisited, and provide an important framework for investigations of American pika adaptive potential in the face of anthropogenic climate change.
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Affiliation(s)
- Danielle A Schmidt
- Department of Biology, The University of British Columbia, Kelowna, BC, Canada
| | - Kurt E Galbreath
- Department of Biology, Northern Michigan University, Marquette, MI, USA
| | - Michael A Russello
- Department of Biology, The University of British Columbia, Kelowna, BC, Canada.
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Kraatz B, Belabbas R, Fostowicz-Frelik Ł, Ge DY, Kuznetsov AN, Lang MM, López-Torres S, Mohammadi Z, Racicot RA, Ravosa MJ, Sharp AC, Sherratt E, Silcox MT, Słowiak J, Winkler AJ, Ruf I. Lagomorpha as a Model Morphological System. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.636402] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Due to their global distribution, invasive history, and unique characteristics, European rabbits are recognizable almost anywhere on our planet. Although they are members of a much larger group of living and extinct mammals [Mammalia, Lagomorpha (rabbits, hares, and pikas)], the group is often characterized by several well-known genera (e.g., Oryctolagus, Sylvilagus, Lepus, and Ochotona). This representation does not capture the extraordinary diversity of behavior and form found throughout the order. Model organisms are commonly used as exemplars for biological research, but there are a limited number of model clades or lineages that have been used to study evolutionary morphology in a more explicitly comparative way. We present this review paper to show that lagomorphs are a strong system in which to study macro- and micro-scale patterns of morphological change within a clade that offers underappreciated levels of diversity. To this end, we offer a summary of the status of relevant aspects of lagomorph biology.
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Klingler KB, Jahner JP, Parchman TL, Ray C, Peacock MM. Genomic variation in the American pika: signatures of geographic isolation and implications for conservation. BMC Ecol Evol 2021; 21:2. [PMID: 33514306 PMCID: PMC7853312 DOI: 10.1186/s12862-020-01739-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 12/17/2020] [Indexed: 01/12/2023] Open
Abstract
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 = 0.0006–0.0009; θW = 0.0005–0.0007) relative to populations in California (π = 0.0014–0.0019; θW = 0.0011–0.0017) and the Rocky Mountains (π = 0.0025–0.0027; θW = 0.0021–0.0024), indicating substantial genetic drift in these isolated populations. Tajima’s 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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Affiliation(s)
| | - Joshua P Jahner
- Department of Biology, University of Nevada, Reno, 89557, USA
| | - Thomas L Parchman
- Department of Biology, University of Nevada, Reno, 89557, USA.,Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV, 89557, USA
| | - Chris Ray
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309-0334, USA
| | - Mary M Peacock
- Department of Biology, University of Nevada, Reno, 89557, USA. .,Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV, 89557, USA.
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Parker LD, Hawkins MTR, Camacho-Sanchez M, Campana MG, West-Roberts JA, Wilbert TR, Lim HC, Rockwood LL, Leonard JA, Maldonado JE. Little genetic structure in a Bornean endemic small mammal across a steep ecological gradient. Mol Ecol 2020; 29:4074-4090. [PMID: 32911576 DOI: 10.1111/mec.15626] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 08/14/2020] [Accepted: 08/20/2020] [Indexed: 01/02/2023]
Abstract
Janzen's influential "mountain passes are higher in the tropics" hypothesis predicts restricted gene flow and genetic isolation among populations spanning elevational gradients in the tropics. Few studies have tested this prediction, and studies that focus on population genetic structure in Southeast Asia are particularly underrepresented in the literature. Here, we test the hypothesis that mountain treeshrews (Tupaia montana) exhibit limited dispersal across their broad elevational range which spans ~2,300 m on two peaks in Kinabalu National Park (KNP) in Borneo: Mt Tambuyukon (MT) and Mt Kinabalu (MK). We sampled 83 individuals across elevations on both peaks and performed population genomics analyses on mitogenomes and single nucleotide polymorphisms from 4,106 ultraconserved element loci. We detected weak genetic structure and infer gene flow both across elevations and between peaks. We found higher genetic differentiation on MT than MK despite its lower elevation and associated environmental variation. This implies that, contrary to our hypothesis, genetic structure in this system is not primarily shaped by elevation. We propose that this pattern may instead be the result of historical processes and limited upslope gene flow on MT. Importantly, our results serve as a foundational estimate of genetic diversity and population structure from which to track potential future effects of climate change on mountain treeshrews in KNP, an important conservation stronghold for the mountain treeshrew and other montane species.
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Affiliation(s)
- Lillian D Parker
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, DC, USA.,School of Systems Biology, George Mason University, Fairfax, VA, USA
| | - Melissa T R Hawkins
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, DC, USA.,Division of Mammals, Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.,Department of Environmental Science and Policy, George Mason University, Fairfax, VA, USA
| | - Miguel Camacho-Sanchez
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
| | - Michael G Campana
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, DC, USA.,School of Systems Biology, George Mason University, Fairfax, VA, USA.,Department of Environmental Science and Policy, George Mason University, Fairfax, VA, USA
| | - Jacob A West-Roberts
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, DC, USA.,Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Tammy R Wilbert
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, DC, USA
| | - Haw Chuan Lim
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, DC, USA.,School of Systems Biology, George Mason University, Fairfax, VA, USA
| | - Larry L Rockwood
- School of Systems Biology, George Mason University, Fairfax, VA, USA
| | - Jennifer A Leonard
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
| | - Jesús E Maldonado
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, DC, USA.,School of Systems Biology, George Mason University, Fairfax, VA, USA.,Department of Environmental Science and Policy, George Mason University, Fairfax, VA, USA
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