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Beatty WS, Lemons PR, Sethi SA, Everett JP, Lewis CJ, Lynn RJ, Cook GM, Garlich-Miller JL, Wenburg JK. Panmixia in a sea ice-associated marine mammal: evaluating genetic structure of the Pacific walrus (Odobenus rosmarus divergens) at multiple spatial scales. J Mammal 2020. [DOI: 10.1093/jmammal/gyaa050] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
AbstractThe kin structure of a species at relatively fine spatial scales impacts broad-scale patterns in genetic structure at the population level. However, kin structure rarely has been elucidated for migratory marine mammals. The Pacific walrus (Odobenus rosmarus divergens) exhibits migratory behavior linked to seasonal patterns in sea ice dynamics. Consequently, information on the spatial genetic structure of the subspecies, including kin structure, could aid wildlife managers in designing future studies to evaluate the impacts of sea ice loss on the subspecies. We sampled 8,303 individual walruses over a 5-year period and used 114 single-nucleotide polymorphisms to examine both broad-scale patterns in genetic structure and fine-scale patterns in relatedness. We did not detect any evidence of genetic structure at broad spatial scales, with low FST values (≤ 0.001) across all pairs of putative aggregations. To evaluate kin structure at fine spatial scales, we defined a walrus group as a cluster of resting individuals that were less than one walrus body length apart. We found weak evidence of kin structure at fine spatial scales, with 3.72% of groups exhibiting mean relatedness values greater than expected by chance, and a significantly higher overall observed mean value of relatedness within groups than expected by chance. Thus, the high spatiotemporal variation in the distribution of resources in the Pacific Arctic environment likely has favored a gregarious social system in Pacific walruses, with unrelated animals forming temporary associations.
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Affiliation(s)
- William S Beatty
- U.S. Fish and Wildlife Service, Marine Mammals Management, Anchorage, AK, USA
| | - Patrick R Lemons
- U.S. Fish and Wildlife Service, Marine Mammals Management, Anchorage, AK, USA
| | - Suresh A Sethi
- U.S. Geological Survey, New York Cooperative Fish and Wildlife Research Unit, Ithaca, NY, USA
| | - Jason P Everett
- U.S. Fish and Wildlife Service, Conservation Genetics Laboratory, Anchorage, AK, USA
| | - Cara J Lewis
- U.S. Fish and Wildlife Service, Conservation Genetics Laboratory, Anchorage, AK, USA
| | - Robert J Lynn
- U.S. Fish and Wildlife Service, Marine Mammals Management, Anchorage, AK, USA
| | - Geoffrey M Cook
- U.S. Fish and Wildlife Service, Conservation Genetics Laboratory, Anchorage, AK, USA
| | | | - John K Wenburg
- U.S. Fish and Wildlife Service, Conservation Genetics Laboratory, Anchorage, AK, USA
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Olsen JB, Brown RJ, Russ OL, Harper K, Wenburg JK. Contemporary factors influencing genetic diversity in the Alaska humpback whitefish Coregonus clupeaformis complex. J Fish Biol 2018; 92:1065-1081. [PMID: 29479698 DOI: 10.1111/jfb.13568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 01/17/2018] [Indexed: 06/08/2023]
Abstract
Thirteen microsatellite loci were used to address three hypotheses regarding genetic diversity in the humpback whitefish Coregonus clupeaformis complex in Alaska. The test results provided further insight into the factors influencing C. clupeaformis complex population structure and level of genetic variation. First, the microsatellite data did not provide evidence of two spatially distinct Beringian and Eurasian refugial groups as revealed in previous phylogeographic analyses of mitochondrial DNA variation. Rather, the population structure inferred from the microsatellite variation appears to reveal the influence of factors on a more recent time scale, including gene flow among the refugial groups and isolation of some anadromous and freshwater resident populations. Second, anadromous C. clupeaformis complex collections exhibited higher intra-population genetic diversity than freshwater resident collections. This outcome is consistent with previous meta analyses suggesting that freshwater resident populations probably have smaller historical effective population sizes and less conspecific gene flow because the habitat tends to be smaller and supports fewer and smaller populations. Finally, the analysis of contemporary immigration rates was consistent with, but did not provide statistical support for, the hypothesis that gene flow among anadromous C. clupeaformis complex populations along coastal Alaska is influenced by the Alaska Coastal Current. Further studies are needed to evaluate gene flow among coastal Alaska C. clupeaformis complex populations.
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Affiliation(s)
- J B Olsen
- Conservation Genetics Laboratory, U.S. Fish and Wildlife Service, 1011 East Tudor Road, Anchorage, Alaska 99503, U.S.A
| | - R J Brown
- Fairbanks Fish and Wildlife Field Office, U.S. Fish and Wildlife Service, 101 12th Ave., Room 222, Fairbanks, Alaska, 99701, U.S.A
| | - O L Russ
- Conservation Genetics Laboratory, U.S. Fish and Wildlife Service, 1011 East Tudor Road, Anchorage, Alaska 99503, U.S.A
| | - K Harper
- Kenai Fish and Wildlife Field Office, U.S. Fish and Wildlife Service, P.O. Box 1670, Kenai, Alaska, 99611, U.S.A
| | - J K Wenburg
- Conservation Genetics Laboratory, U.S. Fish and Wildlife Service, 1011 East Tudor Road, Anchorage, Alaska 99503, U.S.A
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Smith CT, Adams B, Bartron M, Burnham-Curtis MK, Monroe E, Olsen JB, Wilson WD, Williams A, Millard MJ, Webb MAH, Wenburg JK. Comment on Haig et al. (): the conservation genetics juggling act: integrating genetics and ecology, science and policy. Evol Appl 2017; 9:635-637. [PMID: 28435441 PMCID: PMC4869405 DOI: 10.1111/eva.12374] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 02/24/2016] [Indexed: 12/03/2022] Open
Affiliation(s)
- Christian T Smith
- Abernathy Fish Technology Center U.S. Fish and Wildlife Service Longview WA USA
| | - Brice Adams
- Abernathy Fish Technology Center U.S. Fish and Wildlife Service Longview WA USA
| | - Meredith Bartron
- Northeast Fishery Center U.S. Fish and Wildlife Service Lamar PA USA
| | - Mary K Burnham-Curtis
- Clark R. Bavin National Fish and Wildlife Forensic Laboratory U.S. Fish and Wildlife Service Ashland OR USA
| | - Emy Monroe
- Whitney Genetics Laboratory U.S. Fish and Wildlife Service Onalaska WI USA
| | - Jeffrey B Olsen
- Conservation Genetics Laboratory U.S. Fish and Wildlife Service Anchorage AK USA
| | - Wade D Wilson
- Southwestern Native Aquatic Resources and Recovery Center U.S. Fish and Wildlife Service Dexter NM USA
| | - Ashantye' Williams
- Conservation Genetics Laboratory U.S. Fish and Wildlife Service Warm Springs GA USA
| | - Michael J Millard
- Northeast Fishery Center U.S. Fish and Wildlife Service Lamar PA USA
| | - Molly A H Webb
- Bozeman Fish Technology Center U.S. Fish and Wildlife Service Bozeman MT USA
| | - John K Wenburg
- Conservation Genetics Laboratory U.S. Fish and Wildlife Service Anchorage AK USA
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Dunker KJ, Sepulveda AJ, Massengill RL, Olsen JB, Russ OL, Wenburg JK, Antonovich A. Correction: Potential of Environmental DNA to Evaluate Northern Pike (Esox lucius) Eradication Efforts: An Experimental Test and Case Study. PLoS One 2017; 12:e0173837. [PMID: 28273174 PMCID: PMC5342300 DOI: 10.1371/journal.pone.0173837] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Dunker KJ, Sepulveda AJ, Massengill RL, Olsen JB, Russ OL, Wenburg JK, Antonovich A. Potential of Environmental DNA to Evaluate Northern Pike (Esox lucius) Eradication Efforts: An Experimental Test and Case Study. PLoS One 2016; 11:e0162277. [PMID: 27626271 PMCID: PMC5023132 DOI: 10.1371/journal.pone.0162277] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 08/20/2016] [Indexed: 01/21/2023] Open
Abstract
Determining the success of invasive species eradication efforts is challenging because populations at very low abundance are difficult to detect. Environmental DNA (eDNA) sampling has recently emerged as a powerful tool for detecting rare aquatic animals; however, detectable fragments of DNA can persist over time despite absence of the targeted taxa and can therefore complicate eDNA sampling after an eradication event. This complication is a large concern for fish eradication efforts in lakes since killed fish can sink to the bottom and slowly decay. DNA released from these carcasses may remain detectable for long periods. Here, we evaluated the efficacy of eDNA sampling to detect invasive Northern pike (Esox lucius) following piscicide eradication efforts in southcentral Alaskan lakes. We used field observations and experiments to test the sensitivity of our Northern pike eDNA assay and to evaluate the persistence of detectable DNA emitted from Northern pike carcasses. We then used eDNA sampling and traditional sampling (i.e., gillnets) to test for presence of Northern pike in four lakes subjected to a piscicide-treatment designed to eradicate this species. We found that our assay could detect an abundant, free-roaming population of Northern pike and could also detect low-densities of Northern pike held in cages. For these caged Northern pike, probability of detection decreased with distance from the cage. We then stocked three lakes with Northern pike carcasses and collected eDNA samples 7, 35 and 70 days post-stocking. We detected DNA at 7 and 35 days, but not at 70 days. Finally, we collected eDNA samples ~ 230 days after four lakes were subjected to piscicide-treatments and detected Northern pike DNA in 3 of 179 samples, with a single detection at each of three lakes, though we did not catch any Northern pike in gillnets. Taken together, we found that eDNA can help to inform eradication efforts if used in conjunction with multiple lines of inquiry and sampling is delayed long enough to allow full degradation of DNA in the water.
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Affiliation(s)
- Kristine J. Dunker
- Alaska Department of Fish and Game, Sport Fish Division, Anchorage, Alaska, United States of America
| | - Adam J. Sepulveda
- U.S. Geological Survey, Northern Rocky Mountain Science Center, Bozeman, Montana, United States of America
- * E-mail:
| | - Robert L. Massengill
- Alaska Department of Fish and Game, Sport Fish Division, Soldotna, Alaska, United States of America
| | - Jeffrey B. Olsen
- Conservation Genetics Laboratory, U.S. Fish and Wildlife Service, Anchorage, Alaska, United States of America
| | - Ora L. Russ
- Conservation Genetics Laboratory, U.S. Fish and Wildlife Service, Anchorage, Alaska, United States of America
| | - John K. Wenburg
- Conservation Genetics Laboratory, U.S. Fish and Wildlife Service, Anchorage, Alaska, United States of America
| | - Anton Antonovich
- Alaska Department of Fish and Game, Sport Fish Division, Anchorage, Alaska, United States of America
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Olsen JB, Lewis CJ, Massengill RL, Dunker KJ, Wenburg JK. Erratum to: An evaluation of target specificity and sensitivity of three qPCR assay for detecting environmental DNA from Northern Pike (Esox lucius). CONSERV GENET RESOUR 2016. [DOI: 10.1007/s12686-016-0526-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Olsen JB, Lewis CJ, Massengill RL, Dunker KJ, Wenburg JK. An evaluation of target specificity and sensitivity of three qPCR assays for detecting environmental DNA from Northern Pike (Esox lucius). CONSERV GENET RESOUR 2015. [DOI: 10.1007/s12686-015-0459-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Olsen JB, Crane PA, Flannery BG, Dunmall K, Templin WD, Wenburg JK. Comparative landscape genetic analysis of three Pacific salmon species from subarctic North America. CONSERV GENET 2010. [DOI: 10.1007/s10592-010-0135-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Olsen JB, Beacham TD, Wetklo M, Seeb LW, Smith CT, Flannery BG, Wenburg JK. The influence of hydrology and waterway distance on population structure of Chinook salmon Oncorhynchus tshawytscha in a large river. J Fish Biol 2010; 76:1128-1148. [PMID: 20409166 DOI: 10.1111/j.1095-8649.2010.02554.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Adult Chinook salmon Oncorhynchus tshawytscha navigate in river systems using olfactory cues that may be influenced by hydrologic factors such as flow and the number, size and spatial distribution of tributaries. Thus, river hydrology may influence both homing success and the level of straying (gene flow), which in turn influences population structure. In this study, two methods of multivariate analysis were used to examine the extent to which four indicators of hydrology and waterway distance explained population structure of O. tshawytscha in the Yukon River. A partial Mantel test showed that the indicators of hydrology were positively associated with broad-scale (Yukon basin) population structure, when controlling for the influence of waterway distance. Multivariate multiple regression showed that waterway distance, supplemented with the number and flow of major drainage basins, explained more variation in broad-scale population structure than any single indicator. At an intermediate spatial scale, indicators of hydrology did not appear to influence population structure after accounting for waterway distance. These results suggest that habitat changes in the Yukon River, which alter hydrology, may influence the basin-wide pattern of population structure in O. tshawytscha. Further research is warranted on the role of hydrology in concert with waterway distance in influencing population structure in Pacific salmon.
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Affiliation(s)
- J B Olsen
- Conservation Genetics Laboratory, US Fish and Wildlife Service Alaska Region, Anchorage, AK 99503, USA. jeffrey
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Kretschmer EJ, Olsen JB, Wenburg JK. Characterization of eight microsatellite loci in Sea Otter, Enhydra lutris, and cross-species amplification in other Mustelidae. CONSERV GENET 2008. [DOI: 10.1007/s10592-008-9660-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Oleĭnik AG, Skurikhina LA, Brykov VA, Crane PA, Wenburg JK. [Differentiation of Dolly Varden char Salvelinus malma from Asia and North America inferred from PCR-RFLP analysis of mitochondrial DNA]. Genetika 2005; 41:626-34. [PMID: 15977814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Genetic differentiation of Dolly Varden char Salvelinus malma Walbaum from the Asian and North American Pacific coasts was studied. We examined restriction fragment length polymorphism of three mitochondrial DNA (mtDNA) fragments amplified in polymerase chain reaction, which encoded four NADH dehydrogenase subunits, the cytochrome b gene, and a D-loop segment. The mtDNA haplotypes were shown to form three phylogenetic groups, whose geographic distribution corresponded to three Dolly Varden subspecies: S. malma malma, S. malma krascheninnikovi, and S. malma lordi. The nucleotide sequence divergence between S. malma malma and S. malma krascheninnikovi was 3.8%; between S. malma malma and S. malma lordi, 3.1%; and between S. malma krascheninnikovi and S. malma lordi, 2.5%. The northern Dolly Varden S. malma malma from Asia was shown to be genetically identical to that from North America.
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Abstract
The antagonistic pleiotropy theory of senescence postulates genes or traits that have opposite effects on early-life and late-life performances. Because selection is generally weaker late in life, genes or traits that improve early-life performance but impair late-life performance should come to predominate. Variation in the strength of age-specific selection should then generate adaptive variation in senescence. We demonstrate this mechanism by comparing early and late breeders within a population of semelparous capital-breeding sockeye salmon (Oncorhynchus nerka). We show that early breeders (but not late breeders) are under strong selection for a long reproductive lifespan (RLS), which facilitates defence of their nests against disturbance by later females. Accordingly, early females invest less energy in egg production while reserving more for nest defence. Variation along this reproductive trade-off causes delayed or slower senescence in early females (average RLS of 26 days) than in late females (reproductive lifespan of 12 days). We use microsatellites to confirm that gene flow is sufficiently limited between early and late breeders to allow adaptive divergence in response to selection. Because reproductive trade-offs should be almost universal and selection acting on them should typically vary in time and space, the mechanism described herein may explain much of the natural variation in senescence.
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Affiliation(s)
- Andrew P Hendry
- Redpath Museum and Department of Biology, McGill University, Montréal, Québec, Canada.
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Crane PA, Lewis CJ, Kretschmer EJ, Miller SJ, Spearman WJ, DeCicco AL, Lisac MJ, Wenburg JK. Characterization and inheritance of seven microsatellite loci from Dolly Varden, Salvelinus malma, and cross-species amplification in Arctic char, S. alpinus. CONSERV GENET 2004. [DOI: 10.1007/s10592-004-1853-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Abstract
Colonization of new environments should promote rapid speciation as a by-product of adaptation to divergent selective regimes. Although this process of ecological speciation is known to have occurred over millennia or centuries, nothing is known about how quickly reproductive isolation actually evolves when new environments are first colonized. Using DNA microsatellites, population-specific natural tags, and phenotypic variation, we tested for reproductive isolation between two adjacent salmon populations of a common ancestry that colonized divergent reproductive environments (a river and a lake beach). We found evidence for the evolution of reproductive isolation after fewer than 13 generations.
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Affiliation(s)
- A P Hendry
- Organismic and Evolutionary Biology Program, University of Massachusetts, Amherst, MA 01003-5810, USA.
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Olsen JB, Wenburg JK, Bentzen P. Semiautomated multilocus genotyping of Pacific salmon (Oncorhnychus spp.) using microsatellites. Mol Mar Biol Biotechnol 1996; 5:259-72. [PMID: 8983195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We report the development of a semiautomated multilocus genotyping system for Pacific salmon using four-color fluorescent detection of microsatellites. An initial screening of microsatellites was conducted on five species of Pacific salmon (Oncorhynchus spp.) and Atlantic salmon (Salmo salar) using 35 primer pairs developed from six species of salmonid. The number of loci that amplified varied by species from 11 (chum salmon) to 22 (chinook salmon). We then tested co-amplification of microsatellites in chinook, coho, and sockeye salmon and developed six-locus multiplex systems. The species-specific multiplex systems were applied to two populations using a sequencer/gene scanner (Perkin-Elmer Applied Biosystems, Inc. [ABI] 373A). The genetic variability at each locus was calculated to evaluate the utility of this system for genetic studies. Significant differences in allele frequencies were observed between populations in 14 of 18 pair-wise comparisons. Average heterozygosity ranged from 0.47 in Togiak River coho salmon to 0.75 in Dungeness River chinook salmon. Observed heterozygosities ranged from 0 at One mu 1 in Togiak River coho to 0.96 at Ssa85 in Dungeness River chinook. The probability of match (PM) for each six-locus multiplex system was 4.0 x 10(-10), 7.2 x 10(-8), and 3.2 x 10(-7) for chinook, coho, and sockeye, respectively. The average polymorphic information content (PIC) was 0.77, 0.56, and 0.60 for chinook, coho, and sockeye, respectively. The microsatellite loci used here show promise for high-resolution genetic studies of Pacific salmon such as fine-scale population analysis kinship, and parentage studies.
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Affiliation(s)
- J B Olsen
- Marine Molecular Biotechnology Laboratory, University of Washington, Seattle 98105-6715, USA
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