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Fujito NT, Hanna ZR, Levy-Sakin M, Bowie RCK, Kwok PY, Dumbacher JP, Wall JD. Genomic Variation and Recent Population Histories of Spotted (Strix occidentalis) and Barred (Strix varia) Owls. Genome Biol Evol 2021; 13:evab066. [PMID: 33764456 PMCID: PMC8120011 DOI: 10.1093/gbe/evab066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/24/2021] [Indexed: 11/29/2022] Open
Abstract
Spotted owls (SOs, Strix occidentalis) are a flagship species inhabiting old-growth forests in western North America. In recent decades, their populations have declined due to ongoing reductions in suitable habitat caused by logging, wildfires, and competition with the congeneric barred owl (BO, Strix varia). The northern spotted owl (S. o. caurina) has been listed as "threatened" under the Endangered Species Act since 1990. Here, we use an updated SO genome assembly along with 51 high-coverage whole-genome sequences to examine population structure, hybridization, and recent changes in population size in SO and BO. We found that potential hybrids identified from intermediate plumage morphology were a mixture of pure BO, F1 hybrids, and F1 × BO backcrosses. Also, although SO underwent a population bottleneck around the time of the Pleistocene-Holocene transition, their population sizes rebounded and show no evidence of any historical (i.e., 100-10,000 years ago) population decline. This suggests that the current decrease in SO abundance is due to events in the past century. Finally, we estimate that western and eastern BOs have been genetically separated for thousands of years, instead of the previously assumed recent (i.e., <150 years) divergence. Although this result is surprising, it is unclear where the ancestors of western BO lived after the separation. In particular, although BO may have colonized western North America much earlier than the first recorded observations, it is also possible that the estimated divergence time reflects unsampled BO population structure within central or eastern North America.
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Affiliation(s)
- Naoko T Fujito
- Institute for Human Genetics, University of California San Francisco, CA, USA
| | - Zachary R Hanna
- Institute for Human Genetics, University of California San Francisco, CA, USA
- Museum of Vertebrate Zoology, University of California Berkeley, CA, USA
| | - Michal Levy-Sakin
- Cardiovascular Research Institute, University of California San Francisco, CA, USA
| | - Rauri C K Bowie
- Museum of Vertebrate Zoology, University of California Berkeley, CA, USA
- Department of Integrative Biology, University of California Berkeley, CA, USA
| | - Pui-Yan Kwok
- Institute for Human Genetics, University of California San Francisco, CA, USA
- Cardiovascular Research Institute, University of California San Francisco, CA, USA
| | - John P Dumbacher
- Department of Ornithology and Mammology, California Academy of Sciences, San Francisco, CA, USA
| | - Jeffrey D Wall
- Institute for Human Genetics, University of California San Francisco, CA, USA
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Population genomic diversity and structure at the discontinuous southern range of the Great Gray Owl in North America. CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01280-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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3
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Hanna ZR, Henderson JB, Sellas AB, Fuchs J, Bowie RCK, Dumbacher JP. Complete mitochondrial genome sequences of the northern spotted owl ( Strix occidentalis caurina) and the barred owl ( Strix varia; Aves: Strigiformes: Strigidae) confirm the presence of a duplicated control region. PeerJ 2017; 5:e3901. [PMID: 29038757 PMCID: PMC5639871 DOI: 10.7717/peerj.3901] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 09/18/2017] [Indexed: 11/20/2022] Open
Abstract
We report here the successful assembly of the complete mitochondrial genomes of the northern spotted owl (Strix occidentalis caurina) and the barred owl (S. varia). We utilized sequence data from two sequencing methodologies, Illumina paired-end sequence data with insert lengths ranging from approximately 250 nucleotides (nt) to 9,600 nt and read lengths from 100–375 nt and Sanger-derived sequences. We employed multiple assemblers and alignment methods to generate the final assemblies. The circular genomes of S. o. caurina and S. varia are comprised of 19,948 nt and 18,975 nt, respectively. Both code for two rRNAs, twenty-two tRNAs, and thirteen polypeptides. They both have duplicated control region sequences with complex repeat structures. We were not able to assemble the control regions solely using Illumina paired-end sequence data. By fully spanning the control regions, Sanger-derived sequences enabled accurate and complete assembly of these mitochondrial genomes. These are the first complete mitochondrial genome sequences of owls (Aves: Strigiformes) possessing duplicated control regions. We searched the nuclear genome of S. o. caurina for copies of mitochondrial genes and found at least nine separate stretches of nuclear copies of gene sequences originating in the mitochondrial genome (Numts). The Numts ranged from 226–19,522 nt in length and included copies of all mitochondrial genes except tRNAPro, ND6, and tRNAGlu. Strix occidentalis caurina and S. varia exhibited an average of 10.74% (8.68% uncorrected p-distance) divergence across the non-tRNA mitochondrial genes.
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Affiliation(s)
- Zachary R Hanna
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, United States of America.,Department of Integrative Biology, University of California, Berkeley, CA, United States of America.,Department of Ornithology & Mammalogy, California Academy of Sciences, San Francisco, CA, United States of America.,Center for Comparative Genomics, California Academy of Sciences, San Francisco, CA, United States of America
| | - James B Henderson
- Department of Ornithology & Mammalogy, California Academy of Sciences, San Francisco, CA, United States of America.,Center for Comparative Genomics, California Academy of Sciences, San Francisco, CA, United States of America
| | - Anna B Sellas
- Center for Comparative Genomics, California Academy of Sciences, San Francisco, CA, United States of America.,Chan Zuckerberg Biohub, San Francisco, CA, United States of America
| | - Jérôme Fuchs
- Department of Ornithology & Mammalogy, California Academy of Sciences, San Francisco, CA, United States of America.,UMR 7205 Institut de Systématique, Evolution, Biodiversité, CNRS, MNHN, UPMC, EPHE, Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris, France
| | - Rauri C K Bowie
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, United States of America.,Department of Integrative Biology, University of California, Berkeley, CA, United States of America
| | - John P Dumbacher
- Department of Ornithology & Mammalogy, California Academy of Sciences, San Francisco, CA, United States of America.,Center for Comparative Genomics, California Academy of Sciences, San Francisco, CA, United States of America
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Miller MP, Mullins TD, Forsman ED, Haig SM. Genetic differentiation and inferred dynamics of a hybrid zone between Northern Spotted Owls ( Strix occidentalis caurina) and California Spotted Owls ( S. o. occidentalis) in northern California. Ecol Evol 2017; 7:6871-6883. [PMID: 28904767 PMCID: PMC5587499 DOI: 10.1002/ece3.3260] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 06/05/2017] [Accepted: 06/28/2017] [Indexed: 12/04/2022] Open
Abstract
Genetic differentiation among Spotted Owl (Strix occidentalis) subspecies has been established in prior studies. These investigations also provided evidence for introgression and hybridization among taxa but were limited by a lack of samples from geographic regions where subspecies came into close contact. We analyzed new sets of samples from Northern Spotted Owls (NSO: S. o. caurina) and California Spotted Owls (CSO: S. o. occidentalis) in northern California using mitochondrial DNA sequences (mtDNA) and 10 nuclear microsatellite loci to obtain a clearer depiction of genetic differentiation and hybridization in the region. Our analyses revealed that a NSO population close to the northern edge of the CSO range in northern California (the NSO Contact Zone population) is highly differentiated relative to other NSO populations throughout the remainder of their range. Phylogenetic analyses identified a unique lineage of mtDNA in the NSO Contact Zone, and Bayesian clustering analyses of the microsatellite data identified the Contact Zone as a third distinct population that is differentiated from CSO and NSO found in the remainder of the subspecies' range. Hybridization between NSO and CSO was readily detected in the NSO Contact Zone, with over 50% of individuals showing evidence of hybrid ancestry. Hybridization was also identified among 14% of CSO samples, which were dispersed across the subspecies' range in the Sierra Nevada Mountains. The asymmetry of hybridization suggested that the hybrid zone may be dynamic and moving. Although evidence of hybridization existed, we identified no F1 generation hybrid individuals. We instead found evidence for F2 or backcrossed individuals among our samples. The absence of F1 hybrids may indicate that (1) our 10 microsatellites were unable to distinguish hybrid types, (2) primary interactions between subspecies are occurring elsewhere on the landscape, or (3) dispersal between the subspecies' ranges is reduced relative to historical levels, potentially as a consequence of recent regional fires.
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Affiliation(s)
- Mark P Miller
- U.S. Geological Survey Forest and Rangeland Ecosystem Science Center Corvallis OR USA
| | - Thomas D Mullins
- U.S. Geological Survey Forest and Rangeland Ecosystem Science Center Corvallis OR USA
| | - Eric D Forsman
- USDA Forest ServicePacific Northwest Research Station Corvallis OR USA
| | - Susan M Haig
- U.S. Geological Survey Forest and Rangeland Ecosystem Science Center Corvallis OR USA
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Haig SM, Miller MP, Bellinger R, Draheim HM, Mercer DM, Mullins TD. The conservation genetics juggling act: integrating genetics and ecology, science and policy. Evol Appl 2015; 9:181-95. [PMID: 27087847 PMCID: PMC4780381 DOI: 10.1111/eva.12337] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 09/27/2015] [Indexed: 01/08/2023] Open
Abstract
The field of conservation genetics, when properly implemented, is a constant juggling act integrating molecular genetics, ecology, and demography with applied aspects concerning managing declining species or implementing conservation laws and policies. This young field has grown substantially since the 1980s following the development of polymerase chain reaction and now into the genomics era. Our laboratory has ‘grown up’ with the field, having worked on these issues for over three decades. Our multidisciplinary approach entails understanding the behavior and ecology of species as well as the underlying processes that contribute to genetic viability. Taking this holistic approach provides a comprehensive understanding of factors that influence species persistence and evolutionary potential while considering annual challenges that occur throughout their life cycle. As a federal laboratory, we are often addressing the needs of the U.S. Fish and Wildlife Service in their efforts to list, de‐list, or recover species. Nevertheless, there remains an overall communication gap between research geneticists and biologists who are charged with implementing their results. Therefore, we outline the need for a National Center for Small Population Biology to ameliorate this problem and provide organizations charged with making status decisions firmer ground from which to make their critical decisions.
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Affiliation(s)
- Susan M Haig
- U.S. Geological Survey Forest and Rangeland Ecosystem Science Center Corvallis OR USA
| | - Mark P Miller
- U.S. Geological Survey Forest and Rangeland Ecosystem Science Center Corvallis OR USA
| | - Renee Bellinger
- Department of Biology, Tropical Conservation Biology and Environmental Science University of Hawaii Hilo HI USA
| | - Hope M Draheim
- Pacific States Marine Fisheries Commission Eagle Fish Genetics Laboratory Eagle ID USA
| | - Dacey M Mercer
- Hatfield Marine Science Center Oregon State University Newport OR USA
| | - Thomas D Mullins
- U.S. Geological Survey Forest and Rangeland Ecosystem Science Center Corvallis OR USA
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Barn owls (Tyto alba) in western North America: phylogeographic structure, connectivity, and genetic diversity. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0787-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Miller MP, Haig SM, Mullins TD, Ruan L, Casler B, Dondua A, Gates HR, Johnson JM, Kendall S, Tomkovich PS, Tracy D, Valchuk OP, Lanctot RB. Intercontinental genetic structure and gene flow in Dunlin (Calidris alpina), a potential vector of avian influenza. Evol Appl 2015; 8:149-71. [PMID: 25685191 PMCID: PMC4319863 DOI: 10.1111/eva.12239] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 12/04/2014] [Indexed: 12/02/2022] Open
Abstract
Waterfowl (Anseriformes) and shorebirds (Charadriiformes) are the most common wild vectors of influenza A viruses. Due to their migratory behavior, some may transmit disease over long distances. Migratory connectivity studies can link breeding and nonbreeding grounds while illustrating potential interactions among populations that may spread diseases. We investigated Dunlin (Calidris alpina), a shorebird with a subspecies (C. a. arcticola) that migrates from nonbreeding areas endemic to avian influenza in eastern Asia to breeding grounds in northern Alaska. Using microsatellites and mitochondrial DNA, we illustrate genetic structure among six subspecies: C. a. arcticola,C. a. pacifica,C. a. hudsonia,C. a. sakhalina,C. a. kistchinski, and C. a. actites. We demonstrate that mitochondrial DNA can help distinguish C. a. arcticola on the Asian nonbreeding grounds with >70% accuracy depending on their relative abundance, indicating that genetics can help determine whether C. a. arcticola occurs where they may be exposed to highly pathogenic avian influenza (HPAI) during outbreaks. Our data reveal asymmetric intercontinental gene flow, with some C. a. arcticola short-stopping migration to breed with C. a. pacifica in western Alaska. Because C. a. pacifica migrates along the Pacific Coast of North America, interactions between these subspecies and other taxa provide route for transmission of HPAI into other parts of North America.
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Affiliation(s)
- Mark P Miller
- U.S. Geological Survey, Forest and Rangeland Ecosystem Science Center Corvallis, OR, USA
| | - Susan M Haig
- U.S. Geological Survey, Forest and Rangeland Ecosystem Science Center Corvallis, OR, USA
| | - Thomas D Mullins
- U.S. Geological Survey, Forest and Rangeland Ecosystem Science Center Corvallis, OR, USA
| | - Luzhang Ruan
- U.S. Geological Survey, Forest and Rangeland Ecosystem Science Center Corvallis, OR, USA ; School of Life Sciences and Food Engineering, Nanchang University Nanchang, China
| | - Bruce Casler
- Izembek National Wildlife Refuge Cold Bay, AK, USA
| | | | - H River Gates
- U.S. Fish and Wildlife Service, Migratory Bird Management Anchorage, AK, USA
| | - J Matthew Johnson
- U.S. Geological Survey, Forest and Rangeland Ecosystem Science Center Corvallis, OR, USA
| | - Steve Kendall
- U.S. Fish and Wildlife Service, Arctic National Wildlife Refuge Fairbanks, AK, USA
| | | | | | - Olga P Valchuk
- Institute of Biology and Soil Science, Russian Academy of Science Vladivostok, Russia
| | - Richard B Lanctot
- U.S. Fish and Wildlife Service, Migratory Bird Management Anchorage, AK, USA
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Mercer DM, Haig SM, Roby DD. Phylogeography and population genetic structure of double-crested cormorants (Phalacrocorax auritus). CONSERV GENET 2013. [DOI: 10.1007/s10592-013-0477-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Miller MP, Haig SM. Identifying shared genetic structure patterns among Pacific Northwest forest taxa: insights from use of visualization tools and computer simulations. PLoS One 2010; 5:e13683. [PMID: 21060824 PMCID: PMC2966394 DOI: 10.1371/journal.pone.0013683] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Accepted: 10/05/2010] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Identifying causal relationships in phylogeographic and landscape genetic investigations is notoriously difficult, but can be facilitated by use of multispecies comparisons. METHODOLOGY/PRINCIPAL FINDINGS We used data visualizations to identify common spatial patterns within single lineages of four taxa inhabiting Pacific Northwest forests (northern spotted owl: Strix occidentalis caurina; red tree vole: Arborimus longicaudus; southern torrent salamander: Rhyacotriton variegatus; and western white pine: Pinus monticola). Visualizations suggested that, despite occupying the same geographical region and habitats, species responded differently to prevailing historical processes. S. o. caurina and P. monticola demonstrated directional patterns of spatial genetic structure where genetic distances and diversity were greater in southern versus northern locales. A. longicaudus and R. variegatus displayed opposite patterns where genetic distances were greater in northern versus southern regions. Statistical analyses of directional patterns subsequently confirmed observations from visualizations. Based upon regional climatological history, we hypothesized that observed latitudinal patterns may have been produced by range expansions. Subsequent computer simulations confirmed that directional patterns can be produced by expansion events. CONCLUSIONS/SIGNIFICANCE We discuss phylogeographic hypotheses regarding historical processes that may have produced observed patterns. Inferential methods used here may become increasingly powerful as detailed simulations of organisms and historical scenarios become plausible. We further suggest that inter-specific comparisons of historical patterns take place prior to drawing conclusions regarding effects of current anthropogenic change within landscapes.
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Affiliation(s)
- Mark P Miller
- Department of Biology and Center for High Performance Computing, Utah State University, Logan, Utah, United States of America.
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Red- and yellow-footed tortoises, Chelonoidis carbonaria and C. denticulata (Reptilia: Testudines: Testudinidae), in South American savannahs and forests: do their phylogeographies reflect distinct habitats? ORG DIVERS EVOL 2010. [DOI: 10.1007/s13127-010-0016-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Range-wide genetic differentiation among North American great gray owls (Strix nebulosa) reveals a distinct lineage restricted to the Sierra Nevada, California. Mol Phylogenet Evol 2010; 56:212-21. [PMID: 20193768 DOI: 10.1016/j.ympev.2010.02.027] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2009] [Revised: 02/18/2010] [Accepted: 02/23/2010] [Indexed: 11/23/2022]
Abstract
Investigations of regional genetic differentiation are essential for describing phylogeographic patterns and informing management efforts for species of conservation concern. In this context, we investigated genetic diversity and evolutionary relationships among great gray owl (Strix nebulosa) populations in western North America, which includes an allopatric range in the southern Sierra Nevada in California. Based on a total dataset consisting of 30 nuclear microsatellite DNA loci and 1938-base pairs of mitochondrial DNA, we found that Pacific Northwest sampling groups were recovered by frequency and Bayesian analyses of microsatellite data and each population sampled, except for western Canada, showed evidence of recent population bottlenecks and low effective sizes. Bayesian and maximum likelihood phylogenetic analyses of sequence data indicated that the allopatric Sierra Nevada population is also a distinct lineage with respect to the larger species range in North America; we suggest a subspecies designation for this lineage should be considered (Strix nebulosa yosemitensis). Our study underscores the importance of phylogeographic studies for identifying lineages of conservation concern, as well as the important role of Pleistocene glaciation events in driving genetic differentiation of avian fauna.
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Evidence for recent population bottlenecks in northern spotted owls (Strix occidentalis caurina). CONSERV GENET 2009. [DOI: 10.1007/s10592-009-9946-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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13
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Affiliation(s)
- Robert M Zink
- Bell Museum of Natural History, University of Minnesota, St Paul, MN 55108, USA.
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Funk WC, Forsman ED, Mullins TD, Haig SM. Introgression and dispersal among spotted owl (Strix occidentalis) subspecies. Evol Appl 2008; 1:161-71. [PMID: 25567499 PMCID: PMC3352401 DOI: 10.1111/j.1752-4571.2007.00002.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/13/2007] [Indexed: 11/27/2022] Open
Abstract
Population genetics plays an increasingly important role in the conservation and management of declining species, particularly for defining taxonomic units. Subspecies are recognized by several conservation organizations and countries and receive legal protection under the US Endangered Species Act (ESA). Two subspecies of spotted owls, northern (Strix occidentalis caurina) and Mexican (S. o. lucida) spotted owls, are ESA-listed as threatened, but the California (S. o. occidentalis) spotted owl is not listed. Thus, determining the boundaries of these subspecies is critical for effective enforcement of the ESA. We tested the validity of previously recognized spotted owl subspecies by analysing 394 spotted owls at 10 microsatellite loci. We also tested whether northern and California spotted owls hybridize as suggested by previous mitochondrial DNA studies. Our results supported current recognition of three subspecies. We also found bi-directional hybridization and dispersal between northern and California spotted owls centered in southern Oregon and northern California. Surprisingly, we also detected introgression of Mexican spotted owls into the range of northern spotted owls, primarily in the northern part of the subspecies' range in Washington, indicating long-distance dispersal of Mexican spotted owls. We conclude with a discussion of the conservation implications of our study.
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Affiliation(s)
- W Chris Funk
- US Geological Survey, Forest and Rangeland Ecosystem Science Center Corvallis, OR, USA
| | - Eric D Forsman
- USDA Forest Service, Pacific Northwest Research Station Corvallis, OR, USA
| | - Thomas D Mullins
- US Geological Survey, Forest and Rangeland Ecosystem Science Center Corvallis, OR, USA
| | - Susan M Haig
- US Geological Survey, Forest and Rangeland Ecosystem Science Center Corvallis, OR, USA
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Conservation genetics of snowy plovers (Charadrius alexandrinus) in the Western Hemisphere: population genetic structure and delineation of subspecies. CONSERV GENET 2007. [DOI: 10.1007/s10592-006-9278-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Miller MP, Haig SM, Wagner RS. Phylogeography and spatial genetic structure of the Southern torrent salamander: implications for conservation and management. ACTA ACUST UNITED AC 2006; 97:561-70. [PMID: 17135462 DOI: 10.1093/jhered/esl038] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
The Southern torrent salamander (Rhyacotriton variegatus) was recently found not warranted for listing under the US Endangered Species Act due to lack of information regarding population fragmentation and gene flow. Found in small-order streams associated with late-successional coniferous forests of the US Pacific Northwest, threats to their persistence include disturbance related to timber harvest activities. We conducted a study of genetic diversity throughout this species' range to 1) identify major phylogenetic lineages and phylogeographic barriers and 2) elucidate regional patterns of population genetic and spatial phylogeographic structure. Cytochrome b sequence variation was examined for 189 individuals from 72 localities. We identified 3 major lineages corresponding to nonoverlapping geographic regions: a northern California clade, a central Oregon clade, and a northern Oregon clade. The Yaquina River may be a phylogeographic barrier between the northern Oregon and central Oregon clades, whereas the Smith River in northern California appears to correspond to the discontinuity between the central Oregon and northern California clades. Spatial analyses of genetic variation within regions encompassing major clades indicated that the extent of genetic structure is comparable among regions. We discuss our results in the context of conservation efforts for Southern torrent salamanders.
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Affiliation(s)
- Mark P Miller
- Department of Biology, Utah State University, Logan, UT 84322-5305, USA
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