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Lang AR, Boveng P, Quakenbush L, Robertson K, Lauf M, Rode KD, Ziel H, Taylor BL. Re-examination of population structure in Arctic ringed seals using DArTseq genotyping. ENDANGER SPECIES RES 2021. [DOI: 10.3354/esr01087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Although Arctic ringed seals Phoca hispida hispida are currently abundant and broadly distributed, their numbers are projected to decline substantially by the year 2100 due to climate warming. While understanding population structure could provide insight into the impact of environmental changes on this subspecies, detecting demographically important levels of exchange can be difficult in taxa with high abundance. We used a next-generation sequencing approach (DArTseq) to genotype ~5700 single nucleotide polymorphisms in 79 seals from 4 Pacific Arctic regions. Comparison of the 2 most geographically separated strata (eastern Bering vs. northeastern Chukchi-Beaufort Seas) revealed a statistically significant level of genetic differentiation (FST = 0.001, p = 0.005) that, while small, was 1 to 2 orders of magnitude greater than expected based on divergence estimated for similarly sized populations connected by low (1% yr-1) dispersal. A relatively high proportion (72 to 88%) of individuals within these strata could be genetically assigned to their stratum of origin. These results indicate that demographically important structure may be present among Arctic ringed seals breeding in different areas, increasing the risk that declines in the number of seals breeding in areas most negatively affected by environmental warming could occur.
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Affiliation(s)
- AR Lang
- Ocean Associates, Inc., Arlington, VA 22207, USA, under contract to the Southwest Fisheries Science Center, NOAA Fisheries, La Jolla, CA 92037, USA
| | - P Boveng
- Marine Mammal Laboratory, Alaska Fisheries Science Center, NOAA Fisheries, Seattle, WA 98115, USA
| | - L Quakenbush
- Arctic Marine Mammal Program, Alaska Department of Fish and Game, Fairbanks, AK 99701, USA
| | - K Robertson
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, NOAA Fisheries, La Jolla, CA 92037, USA
| | - M Lauf
- Ocean Associates, Inc., Arlington, VA 22207, USA, under contract to the Southwest Fisheries Science Center, NOAA Fisheries, La Jolla, CA 92037, USA
| | - KD Rode
- Alaska Science Center, US Geological Survey, Anchorage, AK 99508, USA
| | - H Ziel
- Marine Mammal Laboratory, Alaska Fisheries Science Center, NOAA Fisheries, Seattle, WA 98115, USA
| | - BL Taylor
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, NOAA Fisheries, La Jolla, CA 92037, USA
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Dussex N, Broquet T, Yearsley JM. Contrasting dispersal inference methods for the greater white-toothed shrew. J Wildl Manage 2016. [DOI: 10.1002/jwmg.21075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Nicolas Dussex
- Department of Ecology and Evolution; University of Lausanne; CH-1015 Lausanne Switzerland
- Department of Anatomy; University of Otago; Dunedin 9054 New Zealand
| | - Thomas Broquet
- Department of Ecology and Evolution; University of Lausanne; CH-1015 Lausanne Switzerland
| | - Jon M. Yearsley
- Department of Ecology and Evolution; University of Lausanne; CH-1015 Lausanne Switzerland
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Putman AI, Carbone I. Challenges in analysis and interpretation of microsatellite data for population genetic studies. Ecol Evol 2014; 4:4399-428. [PMID: 25540699 PMCID: PMC4267876 DOI: 10.1002/ece3.1305] [Citation(s) in RCA: 237] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 10/02/2014] [Accepted: 10/03/2014] [Indexed: 12/14/2022] Open
Abstract
Advancing technologies have facilitated the ever-widening application of genetic markers such as microsatellites into new systems and research questions in biology. In light of the data and experience accumulated from several years of using microsatellites, we present here a literature review that synthesizes the limitations of microsatellites in population genetic studies. With a focus on population structure, we review the widely used fixation (F ST) statistics and Bayesian clustering algorithms and find that the former can be confusing and problematic for microsatellites and that the latter may be confounded by complex population models and lack power in certain cases. Clustering, multivariate analyses, and diversity-based statistics are increasingly being applied to infer population structure, but in some instances these methods lack formalization with microsatellites. Migration-specific methods perform well only under narrow constraints. We also examine the use of microsatellites for inferring effective population size, changes in population size, and deeper demographic history, and find that these methods are untested and/or highly context-dependent. Overall, each method possesses important weaknesses for use with microsatellites, and there are significant constraints on inferences commonly made using microsatellite markers in the areas of population structure, admixture, and effective population size. To ameliorate and better understand these constraints, researchers are encouraged to analyze simulated datasets both prior to and following data collection and analysis, the latter of which is formalized within the approximate Bayesian computation framework. We also examine trends in the literature and show that microsatellites continue to be widely used, especially in non-human subject areas. This review assists with study design and molecular marker selection, facilitates sound interpretation of microsatellite data while fostering respect for their practical limitations, and identifies lessons that could be applied toward emerging markers and high-throughput technologies in population genetics.
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Affiliation(s)
- Alexander I Putman
- Department of Plant Pathology, North Carolina State University Raleigh, North Carolina, 27695-7616
| | - Ignazio Carbone
- Department of Plant Pathology, North Carolina State University Raleigh, North Carolina, 27695-7616
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SCASCITELLI M, WHITNEY KD, RANDELL RA, KING MATTHEW, BUERKLE CA, RIESEBERG LH. Genome scan of hybridizing sunflowers from Texas (Helianthus annuusandH. debilis) reveals asymmetric patterns of introgression and small islands of genomic differentiation. Mol Ecol 2010; 19:521-41. [DOI: 10.1111/j.1365-294x.2009.04504.x] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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