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Barnes TM, Karlin M, vonHoldt BM, Adams JR, Waits LP, Hinton JW, Henderson J, Brzeski KE. Genetic diversity and family groups detected in a coyote population with red wolf ancestry on Galveston Island, Texas. BMC Ecol Evol 2022; 22:134. [PMCID: PMC9664737 DOI: 10.1186/s12862-022-02084-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 10/20/2022] [Indexed: 11/16/2022] Open
Abstract
Abstract
Background
Hybridization can be a conservation concern if genomic introgression leads to the loss of an endangered species’ unique genome, or when hybrid offspring are sterile or less fit than their parental species. Yet hybridization can also be an adaptive management tool if rare populations are inbred and have reduced genetic variation, and there is the opportunity to enhance genetic variation through hybridization. The red wolf (Canis rufus) is a critically endangered wolf endemic to the eastern United States, where all extant red wolves are descended from 14 founders which has led to elevated levels of inbreeding over time. Red wolves were considered extirpated from the wild by 1980, but before they disappeared, they interbred with encroaching coyotes creating a genetically admixed population of canids along coastal Texas and Louisiana. In 2018, a genetic study identified individuals on Galveston Island, Texas with significant amounts of red wolf ancestry. We collected 203 fecal samples from Galveston for a more in-depth analysis of this population to identify the amount of red wolf ancestry present and potential mechanisms that support retention of red wolf ancestry on the landscape.
Results
We identified 24 individual coyotes from Galveston Island and 8 from mainland Texas with greater than 10% red wolf ancestry. Two of those individuals from mainland Texas had greater than 50% red wolf ancestry estimates. Additionally, this population had 5 private alleles that were absent in the North American reference canid populations used in this study, which included 107 southeastern coyotes, 19 captive red wolves, and 38 gray wolves, possibly representing lost red wolf genetic variation. We also identified several individuals on Galveston Island and the mainland of Texas that retained a unique red wolf mitochondrial haplotype present in the red wolf founding population. On Galveston Island, we identified a minimum of four family groups and found coyotes on the island to be highly related, but not genetically depauperate. We did not find clear associations between red wolf ancestry estimates and landscape features, such as open green space or developed areas.
Conclusion
Our results confirm the presence of substantial red wolf ancestry persisting on Galveston Island and adjacent mainland Texas. This population has the potential to benefit future red wolf conservation efforts through novel reproductive techniques and possibly through de-introgression strategies, with the goals of recovering extinct red wolf genetic variation and reducing inbreeding within the species.
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vonHoldt BM, Brzeski KE, Aardema ML, Schell CJ, Rutledge LY, Fain SR, Shutt AC, Linderholm A, Murphy WJ. Persistence and expansion of cryptic endangered red wolf genomic ancestry along the American Gulf coast. Mol Ecol 2022; 31:5440-5454. [PMID: 34585803 DOI: 10.1111/mec.16200] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 09/03/2021] [Accepted: 09/22/2021] [Indexed: 12/24/2022]
Abstract
Admixture and introgression play a critical role in adaptation and genetic rescue that has only recently gained a deeper appreciation. Here, we explored the geographical and genomic landscape of cryptic ancestry of the endangered red wolf that persists within the genome of a ubiquitous sister taxon, the coyote, all while the red wolf has been extinct in the wild since the early 1980s. We assessed admixture across 120,621 single nucleotiode polymorphism (SNP) loci genotyped in 293 canid genomes. We found support for increased red wolf ancestry along a west-to-east gradient across the southern United States associated with historical admixture in the past 100 years. Southwestern Louisiana and southeastern Texas, the geographical zone where the last red wolves were known prior to extinction in the wild, contained the highest and oldest levels of red wolf ancestry. Further, given the paucity of inferences based on chromosome types, we compared patterns of ancestry on the X chromosome and autosomes. We additionally aimed to explore the relationship between admixture timing and recombination rate variation to investigate gene flow events. We found that X-linked regions of low recombination rates were depleted of introgression, relative to the autosomes, consistent with the large X effect and enrichment with loci involved in maintaining reproductive isolation. Recombination rate was positively correlated with red wolf ancestry across coyote genomes, consistent with theoretical predictions. The geographical and genomic extent of cryptic red wolf ancestry can provide novel genomic resources for recovery plans targeting the conservation of the endangered red wolf.
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Affiliation(s)
- Bridgett M vonHoldt
- Ecology & Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
| | - Kristin E Brzeski
- College of Forest Resources and Environment Science, Michigan Technological University, Houghton, Michigan, USA
| | - Matthew L Aardema
- Department of Biology, Montclair State University, Montclair, New Jersey, USA.,Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA
| | - Christopher J Schell
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, California, USA
| | - Linda Y Rutledge
- Biology Department, Trent University, Peterborough, Ontario, Canada
| | - Steven R Fain
- USFWS, Clark R. Bavin National Forensics Laboratory, Ashland, Oregon, USA
| | | | - Anna Linderholm
- Department of Anthropology, Texas A&M University, College Station, Texas, USA
| | - William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, USA
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3
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vonHoldt BM, Hinton JW, Shutt AC, Murphy SM, Karlin ML, Adams JR, Waits LP, Brzeski KE. Reviving ghost alleles: Genetically admixed coyotes along the American Gulf Coast are critical for saving the endangered red wolf. SCIENCE ADVANCES 2022; 8:eabn7731. [PMID: 35767623 PMCID: PMC9242586 DOI: 10.1126/sciadv.abn7731] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
The last known red wolves were captured in southwestern Louisiana and eastern Texas in 1980 to establish a captive breeding population. Before their extirpation, gene flow with coyotes resulted in the persistence of endangered red wolf genetic variation in local coyote populations. We assessed genomic ancestry and morphology of coyotes in southwestern Louisiana. We detected that 38 to 62% of the coyote genomes contained red wolf ancestry acquired in the past 30 years and have an admixture profile similar to that of the canids captured before the extirpation of red wolves. We further documented a positive correlation between ancestry and weight. Our findings highlight the importance of hybrids and admixed genomes as a reservoir of endangered species ancestry for innovative conservation efforts. Together, this work presents an unprecedented system that conservation can leverage to enrich the recovery program of an endangered species.
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Affiliation(s)
- Bridgett M. vonHoldt
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | | | | | - Sean M. Murphy
- Forestry and Natural Resources, University of Kentucky, Lexington, KY, USA
| | - Melissa L. Karlin
- Department of Physics and Environmental Science, St. Mary’s University, San Antonio, TX, USA
| | - Jennifer R. Adams
- Laboratory for Ecological, Evolutionary and Conservation Genetics, Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID, USA
| | - Lisette P. Waits
- Laboratory for Ecological, Evolutionary and Conservation Genetics, Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID, USA
| | - Kristin E. Brzeski
- College of Forest Resources and Environment Science, Michigan Technological University, Houghton, MI, USA
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4
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Cairns KM, Crowther MS, Nesbitt B, Letnic M. The myth of wild dogs in Australia: are there any out there? AUSTRALIAN MAMMALOGY 2022. [DOI: 10.1071/am20055] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Hybridisation between wild and domestic canids is a global conservation and management issue. In Australia, dingoes are a distinct lineage of wild-living canid with a controversial domestication status. They are mainland Australia’s apex terrestrial predator. There is ongoing concern that the identity of dingoes has been threatened from breeding with domestic dogs, and that feral dogs have established populations in rural Australia. We collate the results of microsatellite DNA testing from 5039 wild canids to explore patterns of domestic dog ancestry in dingoes and observations of feral domestic dogs across the continent. Only 31 feral dogs were detected, challenging the perception that feral dogs are widespread in Australia. First generation dingo × dog hybrids were similarly rare, with only 27 individuals identified. Spatial patterns of genetic ancestry across Australia identified that dingo populations in northern, western and central Australia were largely free from domestic dog introgression. Our findings challenge the perception that dingoes are virtually extinct in the wild and that feral dogs are common. A shift in terminology from wild dog to dingo would better reflect the identity of these wild canids and allow more nuanced debate about the balance between conservation and management of dingoes in Australia.
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5
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Gese EM, Terletzky PA. Space use in free-ranging canids: are gonadal hormones required for territory maintenance? CAN J ZOOL 2021. [DOI: 10.1139/cjz-2021-0085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Fertility control among carnivores has been used to reduce depredations on livestock and wild neonates, population control, modify behavior, inhibit genetic introgression, and reduce human–wildlife conflicts. Although there is considerable knowledge on techniques to sterilize carnivores, there is little information concerning how the absence of gonadal hormones influences behavior, space use, and survival of wild canids. We examined territorial fidelity, home-range size and overlap, and survival of 179 surgically sterilized free-ranging canids (124 coyotes (Canis latrans Say, 1823), 55 coyote – red wolf (Canis rufus Audubon and Bachman, 1851) hybrids) with gonadal hormones present (tubal-ligated females (n = 70), vasectomized males (n = 73)) versus absent (spayed females (n = 22), neutered males (n = 14)). The absence of gonadal hormones did not influence annual home-range size and home-range overlap, territory fidelity, and annual survival rates. Additionally, no differences were detected across sexes and hormonal treatments in annual home-range size, percent home-range overlap, annual home-range residency rates, and annual survival rates. Methods of fertility control that do not keep gonadal organs intact may prove useful for management without concern for changes in behavior, mainly territoriality, space use, and survival.
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Affiliation(s)
- Eric M. Gese
- U.S. Department of Agriculture, Wildlife Services, National Wildlife Research Center, Department of Wildland Resources, Utah State University, Logan, UT 84322, USA
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6
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Interface of Human/Wildlife Interactions: An Example of a Bold Coyote (Canis latrans) in Atlanta, GA, USA. DIVERSITY 2021. [DOI: 10.3390/d13080372] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
There is arguably no other North American species that better illustrates the complexities of the human-wildlife interface than the coyote. In this study, a melanistic coyote in metropolitan Atlanta, Georgia was exhibiting unusually bold behaviors that included encounters with humans, domestic dogs, and attempts to enter homes. After tracking this coyote (nicknamed Carmine) across a highly urbanized landscape with participatory science, including at least 80 publicly reported sightings, he was captured and relocated to a wildlife sanctuary. Genome-wide analyses revealed 92.8% coyote ancestry, 1.7% gray wolf ancestry, and 5.5% domestic dog ancestry. The dog alleles in Carmine’s genome were estimated to have been acquired by his ancestors 14–29 years ago. Despite his bold behavior, Carmine did not carry any mutations known to shape hypersociability in canines. He did, however, carry a single copy of the dominant mutation responsible for his melanistic coat color. This detailed study of Carmine dispels common assumptions about the reticent coyote personality and the origins of behavior. His unusual bold behavior created a higher level of human-coyote interaction. He now serves as a public ambassador for human-wildlife coexistence, urging the global community to reconsider mythologies about wildlife and promote coexistence with them in landscapes significantly altered by human activity in our rapidly changing world.
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Santostasi NL, Gimenez O, Caniglia R, Fabbri E, Molinari L, Reggioni W, Ciucci P. Estimating Admixture at the Population Scale: Taking Imperfect Detectability and Uncertainty in Hybrid Classification Seriously. J Wildl Manage 2021. [DOI: 10.1002/jwmg.22038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Nina L. Santostasi
- Department of Biology and Biotechnologies “Charles Darwin” University of Rome La Sapienza Rome Italy
| | - Olivier Gimenez
- CEFE, CNRS University of Montpellier, University Paul Valéry Montpellier 3, EPHE, IRD Montpellier France
| | - Romolo Caniglia
- Italian Institute for Environmental Protection and Research (ISPRA), Unit for Conservation Genetics (BIO–CGE), Ozzano dell'Emilia Italy
| | - Elena Fabbri
- Italian Institute for Environmental Protection and Research (ISPRA), Unit for Conservation Genetics (BIO–CGE), Ozzano dell'Emilia Italy
| | - Luigi Molinari
- Wolf Apennine Center, Appennino Tosco‐Emiliano National Park, Ligonchio Italy
| | - Willy Reggioni
- Wolf Apennine Center, Appennino Tosco‐Emiliano National Park, Ligonchio Italy
| | - Paolo Ciucci
- CEFE, CNRS University of Montpellier, University Paul Valéry Montpellier 3, EPHE, IRD Montpellier France
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8
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Taron UH, Salado I, Escobar-Rodríguez M, Westbury MV, Butschkau S, Paijmans JLA, vonHoldt BM, Hofreiter M, Leonard JA. A sliver of the past: The decimation of the genetic diversity of the Mexican wolf. Mol Ecol 2021; 30:6340-6354. [PMID: 34161633 DOI: 10.1111/mec.16037] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 06/21/2021] [Indexed: 01/07/2023]
Abstract
The endangered Mexican wolf (Canis lupus baileyi) is known to carry exceedingly low levels of genetic diversity. This could be (i) the result of long-term evolutionary patterns as they exist at the southernmost limit of the species distribution at a relatively reduced effective size, or (ii) due to rapid population decline caused by human persecution over the last century. If the former, purifying selection is expected to have minimized the impact of inbreeding. If the latter, rapid and recent declines in genetic diversity may have resulted in severe fitness consequences. To differentiate these hypotheses, we conducted comparative whole-genome analyses of five historical Mexican wolves (1907-1917) and 18 contemporary Mexican and grey wolves from North America and Eurasia. Based on whole-genome data, historical and modern Mexican wolves together form a discrete unit. Moreover, we found that modern Mexican wolves have reduced genetic diversity and increased inbreeding relative to the historical population, which was widespread across the southwestern United States and not restricted to Mexico as previously assumed. Finally, although Mexican wolves have evolved in sympatry with coyotes (C. latrans), we observed lower introgression between historical Mexican wolves and coyotes than with modern Mexican wolves, despite similarities in body size. Taken together, our data show that recent population declines probably caused the reduced level of genetic diversity, but not the observed differentiation of the Mexican wolves from other North American wolves.
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Affiliation(s)
- Ulrike H Taron
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Isabel Salado
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
| | | | - Michael V Westbury
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Susanne Butschkau
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | | | - Bridgett M vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Jennifer A Leonard
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
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9
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vonHoldt BM, Aardema ML. Updating the Bibliography of Interbreeding among Canis in North America. J Hered 2021; 111:249-262. [PMID: 32034410 DOI: 10.1093/jhered/esaa004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 02/05/2020] [Indexed: 01/29/2023] Open
Abstract
This bibliography provides a collection of references that documents the evolution of studies evidencing interbreeding among Canis species in North America. Over the past several decades, advances in biology and genomic technology greatly improved our ability to detect and characterize species interbreeding, which has significance for understanding species in a changing landscape as well as for endangered species management. This bibliography includes a discussion within each category of interbreeding, the timeline of developing evidence, and includes a review of past research conducted on experimental crosses. Research conducted in the early 20th century is rich with detailed records and photographs of hybrid offspring development and behavior. With the progression of molecular methods, studies can estimate historical demographic parameters and detect chromosomal patterns of ancestry. As these methods continue to increase in accessibility, the field will gain a deeper and richer understanding of the evolutionary history of North American Canis.
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Affiliation(s)
- Bridgett M vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ
| | - Matthew L Aardema
- Department of Biology, Montclair State University, Montclair, NJ.,Sackler Institute for Comparative Genomics, American Museum of Natural History, New York City, NY
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10
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Cairns KM, Newman KD, Crowther MS, Letnic M. Pelage variation in dingoes across southeastern Australia: implications for conservation and management. J Zool (1987) 2021. [DOI: 10.1111/jzo.12875] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- K. M. Cairns
- Centre for Ecosystem Science School of Biological, Earth and Environmental Sciences University of New South Wales Sydney NSW Australia
- Evolution and Ecology Research Centre School of Biological, Earth and Environmental Sciences University of New South Wales Sydney NSW Australia
| | - K. D. Newman
- School of Biosciences University of Melbourne Parkville VIC Australia
| | - M. S. Crowther
- School of Life and Environmental Sciences University of Sydney Sydney NSW Australia
| | - M. Letnic
- Centre for Ecosystem Science School of Biological, Earth and Environmental Sciences University of New South Wales Sydney NSW Australia
- Evolution and Ecology Research Centre School of Biological, Earth and Environmental Sciences University of New South Wales Sydney NSW Australia
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11
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Murphy SM, Adams JR, Cox JJ, Waits LP. Substantial red wolf genetic ancestry persists in wild canids of southwestern Louisiana. Conserv Lett 2018. [DOI: 10.1111/conl.12621] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Sean M. Murphy
- Large Carnivore Program Louisiana Department of Wildlife and Fisheries Lafayette Louisiana
- Department of Forestry and Natural Resources University of Kentucky Lexington Kentucky
| | - Jennifer R. Adams
- Laboratory for Ecological, Evolutionary and Conservation Genetics, Department of Fish and Wildlife Sciences University of Idaho Moscow Idaho
| | - John J. Cox
- Department of Forestry and Natural Resources University of Kentucky Lexington Kentucky
| | - Lisette P. Waits
- Laboratory for Ecological, Evolutionary and Conservation Genetics, Department of Fish and Wildlife Sciences University of Idaho Moscow Idaho
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12
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Gese EM, Waddell WT, Terletzky PA, Lucash CF, McLellan SR, Behrns SK. Cross-fostering as a conservation tool to augment endangered carnivore populations. J Mammal 2018. [DOI: 10.1093/jmammal/gyy087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Cross-fostering offspring with nonbiological parents could prove useful to augment populations of endangered carnivores. We used cross-fostering to augment captive-born and wild-born litters for the endangered red wolf (Canis rufus). Between 1987 and 2016, 23 cross-fostering events occurred involving captive-born pups fostered into captive litters (n = 8 events) and captive-born pups fostered into wild recipient litters (n = 15 events). Percentage of pups surviving 3 and 12 months was 91.7% for captive-born pups fostered into captive recipient litters. For pups fostered into wild litters, percentage of pups surviving 5 months was > 94% among fostered pups (pups fostered into a wild red wolf litter or replaced a hybrid litter), pups in recipient litters (wild-born litters receiving fostered pups), and pups in control litters (wild-born litters not in a fostering event) when using pups with known fates. Including pups with unknown fates as deaths, percentage of pups surviving 5 months was > 54% among fostered pups, pups in recipient litters, and pups in control litters. Among wild litters, percentage of pups surviving 12 months was > 82% among fostered pups, pups in recipient litters, and pups in control litters when using pups with known fates. Including pups with unknown fates as deaths, percentage of pups surviving 12 months was > 48% among fostered pups, pups in recipient litters, and pups in control litters. Although survival to 12 months was similar among the groups, average life span was different with pups in control litters living 3.3 years, pups in recipient litters living 4.6 years, and fostered pups living 5.6 years. Of fostered pups surviving > 12 months in the wild, 9 animals whelped or sired 26 litters. Cross-fostering was successful at augmenting litter size for red wolves without any deleterious effects on recipient litters, illustrating fostering as a tool for increasing populations of endangered carnivores.
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Affiliation(s)
- Eric M Gese
- United States Department of Agriculture, Wildlife Services, National Wildlife Research Center, Department of Wildland Resources, Utah State University, Logan, UT, USA
| | | | | | - Chris F Lucash
- United States Fish and Wildlife Service, Manteo, NC, USA
| | - Scott R McLellan
- Maine Department of Inland Fisheries and Wildlife, Greenville, ME, USA
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13
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Heppenheimer E, Cosio DS, Brzeski KE, Caudill D, Van Why K, Chamberlain MJ, Hinton JW, vonHoldt B. Demographic history influences spatial patterns of genetic diversityin recently expanded coyote (Canis latrans) populations. Heredity (Edinb) 2018; 120:183-195. [PMID: 29269931 PMCID: PMC5836586 DOI: 10.1038/s41437-017-0014-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 09/06/2017] [Accepted: 10/03/2017] [Indexed: 11/09/2022] Open
Abstract
Human-mediated range expansions have increased in recent decades and represent unique opportunities to evaluate genetic outcomes of establishing peripheral populations across broad expansion fronts. Over the past century, coyotes (Canis latrans) have undergone a pervasive range expansion and now inhabit every state in the continental United States. Coyote expansion into eastern North America was facilitated by anthropogenic landscape changes and followed two broad expansion fronts. The northern expansion extended through the Great Lakes region and southern Canada, where hybridization with remnant wolf populations was common. The southern and more recent expansion front occurred approximately 40 years later and across territory where gray wolves have been historically absent and remnant red wolves were extirpated in the 1970s. We conducted a genetic survey at 10 microsatellite loci of 482 coyotes originating from 11 eastern U.S. states to address how divergent demographic histories influence geographic patterns of genetic diversity. We found that population structure corresponded to a north-south divide, which is consistent with the two known expansion routes. Additionally, we observed extremely high genetic diversity, which is atypical of recently expanded populations and is likely the result of multiple complex demographic processes, in addition to hybridization with other Canis species. Finally, we considered the transition of allele frequencies across geographic space and suggest the mid-Atlantic states of North Carolina and Virginia as an emerging contact zone between these two distinct coyote expansion fronts.
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Affiliation(s)
- Elizabeth Heppenheimer
- Department of Ecology & Evolutionary Biology, Princeton University, 106 A Guyot Hall, Princeton, NJ, 08544, USA.
| | - Daniela S Cosio
- Department of Ecology & Evolutionary Biology, Princeton University, 106 A Guyot Hall, Princeton, NJ, 08544, USA
| | - Kristin E Brzeski
- Department of Ecology & Evolutionary Biology, Princeton University, 106 A Guyot Hall, Princeton, NJ, 08544, USA
| | - Danny Caudill
- Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute, 1105 SW Williston Road, Gainesville, FL, 32601, USA
- Alaska Department of Fish Game, 1300 College Road, Fairbanks, AK, 99701, USA
| | - Kyle Van Why
- United States Department of Agriculture, Animal Plant Health Inspection Service, Wildlife Services, PO Box 60827, Harrisburg, PA, 17106, USA
| | - Michael J Chamberlain
- Warnell School of Forestry and Natural Resources, University of Georgia, 180 E Green Street, Athens, GA, 30621, USA
| | - Joseph W Hinton
- Warnell School of Forestry and Natural Resources, University of Georgia, 180 E Green Street, Athens, GA, 30621, USA
| | - Bridgett vonHoldt
- Department of Ecology & Evolutionary Biology, Princeton University, 106 A Guyot Hall, Princeton, NJ, 08544, USA
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14
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Hinton JW, Proctor C, Kelly MJ, van Manen FT, Vaughan MR, Chamberlain MJ. Space Use and Habitat Selection by Resident and Transient Red Wolves (Canis rufus). PLoS One 2016; 11:e0167603. [PMID: 28002495 PMCID: PMC5176171 DOI: 10.1371/journal.pone.0167603] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Accepted: 11/16/2016] [Indexed: 11/23/2022] Open
Abstract
Recovery of large carnivores remains a challenge because complex spatial dynamics that facilitate population persistence are poorly understood. In particular, recovery of the critically endangered red wolf (Canis rufus) has been challenging because of its vulnerability to extinction via human-caused mortality and hybridization with coyotes (Canis latrans). Therefore, understanding red wolf space use and habitat selection is important to assist recovery because key aspects of wolf ecology such as interspecific competition, foraging, and habitat selection are well-known to influence population dynamics and persistence. During 2009-2011, we used global positioning system (GPS) radio-telemetry to quantify space use and 3rd-order habitat selection for resident and transient red wolves on the Albemarle Peninsula of eastern North Carolina. The Albemarle Peninsula was a predominantly agricultural landscape in which red wolves maintained spatially stable home ranges that varied between 25 km2 and 190 km2. Conversely, transient red wolves did not maintain home ranges and traversed areas between 122 km2 and 681 km2. Space use by transient red wolves was not spatially stable and exhibited shifting patterns until residency was achieved by individual wolves. Habitat selection was similar between resident and transient red wolves in which agricultural habitats were selected over forested habitats. However, transients showed stronger selection for edges and roads than resident red wolves. Behaviors of transient wolves are rarely reported in studies of space use and habitat selection because of technological limitations to observed extensive space use and because they do not contribute reproductively to populations. Transients in our study comprised displaced red wolves and younger dispersers that competed for limited space and mating opportunities. Therefore, our results suggest that transiency is likely an important life-history strategy for red wolves that facilitates metapopulation dynamics through short- and long-distance movements and eventual replacement of breeding residents lost to mortality.
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Affiliation(s)
- Joseph W. Hinton
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, United States of America
| | - Christine Proctor
- Department of Fish and Wildlife Conservation, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Marcella J. Kelly
- Department of Fish and Wildlife Conservation, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Frank T. van Manen
- U.S. Geological Survey, Northern Rocky Mountain Science Center, Interagency Grizzly Bear Study Team, Bozeman, Montana, United States of America
| | - Michael R. Vaughan
- Department of Fish and Wildlife Conservation, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Michael J. Chamberlain
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, United States of America
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15
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Hinton JW, White GC, Rabon DR, Chamberlain MJ. Survival and population size estimates of the red wolf. J Wildl Manage 2016. [DOI: 10.1002/jwmg.21206] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Joseph W. Hinton
- Warnell School of Forestry and Natural Resources; University of Georgia; 180 E. Green Street Athens GA 30605 USA
| | - Gary C. White
- Department of Fish, Wildlife, and Conservation Biology; Colorado State University; Fort Collins CO 80523 USA
| | - David R. Rabon
- Endangered Wolf Center; P.O. Box 760 Eureka MO 63025 USA
| | - Michael J. Chamberlain
- Warnell School of Forestry and Natural Resources; University of Georgia; 180 E. Green Street Athens GA 30605 USA
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Integrating Genomic Data Sets for Knowledge Discovery: An Informed Approach to Management of Captive Endangered Species. Int J Genomics 2016; 2016:2374610. [PMID: 27376076 PMCID: PMC4916311 DOI: 10.1155/2016/2374610] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 03/19/2016] [Accepted: 03/21/2016] [Indexed: 12/31/2022] Open
Abstract
Many endangered captive populations exhibit reduced genetic diversity resulting in health issues that impact reproductive fitness and quality of life. Numerous cost effective genomic sequencing and genotyping technologies provide unparalleled opportunity for incorporating genomics knowledge in management of endangered species. Genomic data, such as sequence data, transcriptome data, and genotyping data, provide critical information about a captive population that, when leveraged correctly, can be utilized to maximize population genetic variation while simultaneously reducing unintended introduction or propagation of undesirable phenotypes. Current approaches aimed at managing endangered captive populations utilize species survival plans (SSPs) that rely upon mean kinship estimates to maximize genetic diversity while simultaneously avoiding artificial selection in the breeding program. However, as genomic resources increase for each endangered species, the potential knowledge available for management also increases. Unlike model organisms in which considerable scientific resources are used to experimentally validate genotype-phenotype relationships, endangered species typically lack the necessary sample sizes and economic resources required for such studies. Even so, in the absence of experimentally verified genetic discoveries, genomics data still provides value. In fact, bioinformatics and comparative genomics approaches offer mechanisms for translating these raw genomics data sets into integrated knowledge that enable an informed approach to endangered species management.
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Effects of anthropogenic mortality on Critically Endangered red wolf Canis rufus breeding pairs: implications for red wolf recovery. ORYX 2015. [DOI: 10.1017/s0030605315000770] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
AbstractFollowing precipitous population declines as a result of intensive hunting and 20th century predator-control programmes, hybridization of the Critically Endangered red wolf Canis rufus with coyotes Canis latrans posed a significant challenge for red wolf recovery efforts. Anthropogenic mortality and hybridization continue to pose challenges; the increasing number of wolf deaths caused by humans has limited wolf population growth, facilitated the encroachment of coyotes into eastern North Carolina, and affected the formation and disbandment of breeding pairs. We assessed the effects of anthropogenic mortality on Canis breeding units during a 22-year period (1991–2013). Our results show that deaths caused by people accounted for 40.6% of breeding pair disbandment, and gunshots were the primary cause of mortality. Red wolves replaced congeneric breeding pairs > 75% of the time when pairs disbanded under natural conditions or as a result of management actions. Since the mid 2000s anthropogenic mortality has caused annual preservation rates of red wolf breeding pairs to decline by 34%, and replacement of Canis breeders by red wolves to decline by 30%. Our results demonstrate that human-caused mortality, specifically by gunshots, had a strong negative effect on the longevity of red wolf pairs, which may benefit coyotes indirectly by removing their primary competitor. Coyotes are exacerbating the decline of red wolves by pair-bonding with resident wolves whose mates have been killed.
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Murray DL, Bastille-Rousseau G, Adams JR, Waits LP. The Challenges of Red Wolf Conservation and the Fate of an Endangered Species Recovery Program. Conserv Lett 2015. [DOI: 10.1111/conl.12157] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Dennis L. Murray
- Department of Biology, Trent University; Peterborough; Ontario K9J 7B8 Canada
| | | | - Jennifer R. Adams
- Department of Fish and Wildlife Sciences; University of Idaho; Moscow ID 83844 USA
| | - Lisette P. Waits
- Department of Fish and Wildlife Sciences; University of Idaho; Moscow ID 83844 USA
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20
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Brzeski KE, Rabon DR, Chamberlain MJ, Waits LP, Taylor SS. Inbreeding and inbreeding depression in endangered red wolves (Canis rufus). Mol Ecol 2014; 23:4241-55. [PMID: 25060763 DOI: 10.1111/mec.12871] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Revised: 07/18/2014] [Accepted: 07/22/2014] [Indexed: 11/29/2022]
Abstract
In natural populations, the expression and severity of inbreeding depression can vary widely across taxa. Describing processes that influence the extent of inbreeding and inbreeding depression aid in our understanding of the evolutionary history of mating systems such as cooperative breeding and nonrandom mate selection. Such findings also help shape wildlife conservation theory because inbreeding depression reduces the viability of small populations. We evaluated the extent of inbreeding and inbreeding depression in a small, re-introduced population of red wolves (Canis rufus) in North Carolina. Since red wolves were first re-introduced in 1987, pedigree inbreeding coefficients (f) increased considerably and almost every wild born wolf was inbred (average f = 0.154 and max f = 0.383). The large inbreeding coefficients were due to both background relatedness associated with few founders and numerous close relative matings. Inbreeding depression was most evident for adult body size and generally absent for direct fitness measures such as reproductive success and survival; no lethal equivalents (LE = 0.00) were detected in juvenile survival. The lack of strong inbreeding depression in direct measures of fitness could be due to a founder effect or because there were no outbred individuals for comparison. Our results highlight the variable expression of inbreeding depression across traits and the need to measure a number of different traits when evaluating inbreeding depression in a wild population.
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Affiliation(s)
- Kristin E Brzeski
- School of Renewable Natural Resources, Louisiana State University Agricultural Center and Louisiana State University, Baton Rouge, LA, 70803, USA
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21
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Devillard S, Jombart T, Léger F, Pontier D, Say L, Ruette S. How reliable are morphological and anatomical characters to distinguish European wildcats, domestic cats and their hybrids in France? J ZOOL SYST EVOL RES 2013. [DOI: 10.1111/jzs.12049] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sébastien Devillard
- Université de Lyon, F-69000, Lyon; Université Lyon 1; CNRS, UMR5558; Laboratoire de Biométrie et Biologie Evolutive; F-69622; Villeurbanne France
| | - Thibaut Jombart
- MRC Centre for Outbreak Analysis and Modelling; Department of Infectious Disease Epidemiology; Imperial College - School of Public Health; London UK
| | - François Léger
- Office National de la Chasse et de la Faune Sauvage; Montfort Birieux France
| | - Dominique Pontier
- Université de Lyon, F-69000, Lyon; Université Lyon 1; CNRS, UMR5558; Laboratoire de Biométrie et Biologie Evolutive; F-69622; Villeurbanne France
| | - Ludovic Say
- Université de Lyon, F-69000, Lyon; Université Lyon 1; CNRS, UMR5558; Laboratoire de Biométrie et Biologie Evolutive; F-69622; Villeurbanne France
| | - Sandrine Ruette
- Office National de la Chasse et de la Faune Sauvage; Montfort Birieux France
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22
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McVey JM, Cobb DT, Powell RA, Stoskopf MK, Bohling JH, Waits LP, Moorman CE. Diets of sympatric red wolves and coyotes in northeastern North Carolina. J Mammal 2013. [DOI: 10.1644/13-mamm-a-109.1] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Hinton JW, Chamberlain MJ, Rabon DR. Red Wolf (Canis rufus) Recovery: A Review with Suggestions for Future Research. Animals (Basel) 2013; 3:722-44. [PMID: 26479530 PMCID: PMC4494459 DOI: 10.3390/ani3030722] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 08/06/2013] [Accepted: 08/07/2013] [Indexed: 11/16/2022] Open
Abstract
By the 1970s, government-supported eradication campaigns reduced red wolves to a remnant population of less than 100 individuals on the southern border of Texas and Louisiana. Restoration efforts in the region were deemed unpromising because of predator-control programs and hybridization with coyotes. The U.S. Fish and Wildlife Service (USFWS) removed the last remaining red wolves from the wild and placed them in a captive-breeding program. In 1980, the USFWS declared red wolves extinct in the wild. During 1987, the USFWS, through the Red Wolf Recovery Program, reintroduced red wolves into northeastern North Carolina. Although restoration efforts have established a population of approximately 70-80 red wolves in the wild, issues of hybridization with coyotes, inbreeding, and human-caused mortality continue to hamper red wolf recovery. We explore these three challenges and, within each challenge, we illustrate how research can be used to resolve problems associated with red wolf-coyote interactions, effects of inbreeding, and demographic responses to human-caused mortality. We hope this illustrates the utility of research to advance restoration of red wolves.
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Affiliation(s)
- Joseph W Hinton
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA 30602, USA.
| | - Michael J Chamberlain
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA 30602, USA.
| | - David R Rabon
- Red Wolf Recovery Program, United States Fish and Wildlife Service, P.O. Box 1969, Manteo, NC 27954, USA.
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Bohling JH, Adams JR, Waits LP. Evaluating the ability of Bayesian clustering methods to detect hybridization and introgression using an empirical red wolf data set. Mol Ecol 2012; 22:74-86. [DOI: 10.1111/mec.12109] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2011] [Revised: 09/25/2012] [Accepted: 10/03/2012] [Indexed: 11/27/2022]
Affiliation(s)
- Justin H. Bohling
- Department of Ecosystem Science and Management; Penn State University; University Park; PA; 16802; USA
| | - Jennifer R. Adams
- Department of Fish and Wildlife Sciences; University of Idaho; Moscow; ID; 83844-1136; USA
| | - Lisette P. Waits
- Department of Fish and Wildlife Sciences; University of Idaho; Moscow; ID; 83844-1136; USA
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25
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vonHoldt BM, Pollinger JP, Earl DA, Parker HG, Ostrander EA, Wayne RK. Identification of recent hybridization between gray wolves and domesticated dogs by SNP genotyping. Mamm Genome 2012; 24:80-8. [PMID: 23064780 DOI: 10.1007/s00335-012-9432-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 09/10/2012] [Indexed: 02/03/2023]
Abstract
The ability to detect recent hybridization between dogs and wolves is important for conservation and legal actions, which often require accurate and rapid resolution of ancestry. The availability of a genetic test for dog-wolf hybrids would greatly support federal and legal enforcement efforts, particularly when the individual in question lacks prior ancestry information. We have developed a panel of 100 unlinked ancestry-informative SNP markers that can detect mixed ancestry within up to four generations of dog-wolf hybridization based on simulations of seven genealogical classes constructed following the rules of Mendelian inheritance. We establish 95 % confidence regions around the spatial clustering of each genealogical class using a tertiary plot of allele dosage and heterozygosity. The first- and second-backcrossed-generation hybrids were the most distinct from parental populations, with >90 % correctly assigned to genealogical class. In this article we provide a tool kit with population-level statistical quantification that can detect recent dog-wolf hybridization using a panel of dog-wolf ancestry-informative SNPs with divergent allele frequency distributions.
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Affiliation(s)
- Bridgett M vonHoldt
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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26
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Dellinger JA, Ortman BL, Steury TD, Bohling J, Waits LP. Food Habits of Red Wolves during Pup-Rearing Season. SOUTHEAST NAT 2011. [DOI: 10.1656/058.010.0412] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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28
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BOHLING JUSTINH, WAITS LISETTEP. Assessing the prevalence of hybridization between sympatric Canis species surrounding the red wolf (Canis rufus) recovery area in North Carolina. Mol Ecol 2011; 20:2142-56. [DOI: 10.1111/j.1365-294x.2011.05084.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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29
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Trigo TC, Freitas TRO, Kunzler G, Cardoso L, Silva JCR, Johnson WE, O'Brien SJ, Bonatto SL, Eizirik E. Inter-species hybridization among Neotropical cats of the genus Leopardus, and evidence for an introgressive hybrid zone between L. geoffroyi and L. tigrinus in southern Brazil. Mol Ecol 2009; 17:4317-33. [PMID: 18785898 DOI: 10.1111/j.1365-294x.2008.03919.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Natural hybrid zones between distinct species have been reported for many taxa, but so far, few examples involve carnivores or Neotropical mammals in general. In this study, we employed mitochondrial DNA (mtDNA) sequences and nine microsatellite loci to identify and characterize a hybrid zone between two Neotropical felids, Leopardus geoffroyi and L. tigrinus, both of which are well-established species having diverged from each other c. 1 million years ago. These two felids are mostly allopatric throughout their ranges in South America, with a narrow contact zone that includes southern Brazil. We present strong evidence for the occurrence of hybridization between these species and identify at least 14 individuals (most of them originating from the geographical contact zone) exhibiting signs of interspecific genomic introgression. The genetic structure of Brazilian L. tigrinus populations seems to be affected by this introgression process, showing a gradient of differentiation from L. geoffroyi correlated with distance from the contact zone. We also corroborate and extend previous findings of hybridization between L. tigrinus and a third related felid, L. colocolo, leading to an unusual situation for a mammal, in which the former species contains introgressed mtDNA lineages from two distinct taxa in addition to its own.
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Affiliation(s)
- T C Trigo
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.
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30
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Lockyear K, Waddell W, Goodrowe K, MacDonald S. Retrospective investigation of captive red wolf reproductive success in relation to age and inbreeding. Zoo Biol 2009; 28:214-29. [DOI: 10.1002/zoo.20224] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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31
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32
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Elledge AE, Allen LR, Carlsson BL, Wilton AN, Leung LKP. An evaluation of genetic analyses, skull morphology and visual appearance for assessing dingo purity: implications for dingo conservation. WILDLIFE RESEARCH 2008. [DOI: 10.1071/wr07056] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The introgression of domestic dog genes into dingo populations threatens the genetic integrity of ‘pure’ dingoes. However, dingo conservation efforts are hampered by difficulties in distinguishing between dingoes and hybrids in the field. This study evaluates consistency in the status of hybridisation (i.e. dingo, hybrid or dog) assigned by genetic analyses, skull morphology and visual assessments. Of the 56 south-east Queensland animals sampled, 39 (69.6%) were assigned the same status by all three methods, 10 (17.9%) by genetic and skull methods, four (7.1%) by genetic and visual methods; and two (3.6%) by skull and visual methods. Pair-wise comparisons identified a significant relationship between genetic and skull methods, but not between either of these and visual methods. Results from surveying 13 experienced wild dog managers showed that hybrids were more easily identified by visual characters than were dingoes. A more reliable visual assessment can be developed through determining the relationship between (1) genetics and phenotype by sampling wild dog populations and (2) the expression of visual characteristics from different proportions and breeds of domestic dog genes by breeding trials. Culling obvious hybrids based on visual characteristics, such as sable and patchy coat colours, should slow the process of hybridisation.
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33
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HEDRICK PW, FREDRICKSON RJ. Captive breeding and the reintroduction of Mexican and red wolves. Mol Ecol 2008; 17:344-50. [DOI: 10.1111/j.1365-294x.2007.03400.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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35
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Andreakis N, Procaccini G, Maggs C, Kooistra WHCF. Phylogeography of the invasive seaweed Asparagopsis (Bonnemaisoniales, Rhodophyta) reveals cryptic diversity. Mol Ecol 2007; 16:2285-99. [PMID: 17561891 DOI: 10.1111/j.1365-294x.2007.03306.x] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The rhodophyte seaweed Asparagopsis armata Harvey is distributed in the northern and southern temperate zones, and its congener Asparagopsis taxiformis (Delile) Trevisan abounds throughout the tropics and subtropics. Here, we determine intraspecific phylogeographic patterns to compare potential causes of the disjunctions in the distributions of both species. We obtained specimens throughout their ranges and inferred phylogenies from the hypervariable domains D1-D3 of the nuclear rDNA LSU, the plastid spacer between the large and small subunits of RuBisCo and the mitochondrial cox 2-3 intergenic spacer. The cox spacer acquired base changes the fastest and the RuBisCo spacer the slowest. Median-joining networks inferred from the sequences revealed the absence of phylogeographic structure in the introduced range of A. armata, corroborating the species' reported recent introduction. A. taxiformis consisted of three nuclear, three plastid and four mitochondrial genetically distinct, lineages (1-4). Mitochondrial lineage 3 is found in the western Atlantic, the Canary Islands and the eastern Mediterranean. Mitochondrial lineages 1, 2, and 4 occur in the Indo-Pacific, but one of them (lineage 2) is also found in the central Mediterranean and southern Portugal. Phylogeographic results suggest separation of Atlantic and Indo-Pacific lineages resulted from the emergence of the Isthmus of Panama, as well as from dispersal events postdating the closure event, such as the invasion of the Mediterranean Sea by mitochondrial lineages 2 and 3. Molecular clock estimates using the Panama closure event as a calibration for the split of lineages 3 and 4 suggest that A. taxiformis diverged into two main cryptic species (1 + 2 and 3 + 4) about 3.2-5.5 million years ago (Ma), and that the separation of the mitochondrial lineages 1 and 2 occurred 1-2.3 Ma.
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Affiliation(s)
- Nikos Andreakis
- Biochemistry and Molecular Biology Laboratory, Stazione Zoologica A Dohrn, Villa Comunale, 80121 Naples, Italy.
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36
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The conspecific nature of eastern and red wolves: conservation and management implications. CONSERV GENET 2007. [DOI: 10.1007/s10592-007-9380-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Adams JR, Lucash C, Schutte L, Waits LP. Locating hybrid individuals in the red wolf (Canis rufus) experimental population area using a spatially targeted sampling strategy and faecal DNA genotyping. Mol Ecol 2007; 16:1823-34. [PMID: 17444895 DOI: 10.1111/j.1365-294x.2007.03270.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hybridization with coyotes (Canis latrans) continues to threaten the recovery of endangered red wolves (Canis rufus) in North Carolina and requires the development of new strategies to detect and remove coyotes and hybrids. Here, we combine a spatially targeted faecal collection strategy with a previously published reference genotype data filtering method and a genetic test for coyote ancestry to screen portions of the red wolf experimental population area for the presence of nonred wolf canids. We also test the accuracy of our maximum-likelihood assignment test for identifying hybrid individuals using eight microsatellite loci instead of the original 18 loci and compare its performance to the Bayesian approach implemented in newhybrids. We obtained faecal DNA genotypes for 89 samples, 73 of which were matched to 23 known individuals. The performance of two sampling strategies - comprehensive sweep and opportunistic spot-check was evaluated. The opportunistic spot-check sampling strategy required less effort than the comprehensive sweep sampling strategy but identified fewer individuals. Six hybrids or coyotes were detected and five of these individuals were subsequently captured and removed from the population. The accuracy and power of the genetic test for coyote ancestry is decreased when using eight loci; however, nonred wolf canids are identified with high frequency. This combination of molecular and traditional field-based approaches has great potential for addressing the challenge of hybridization in other species and ecosystems.
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Affiliation(s)
- Jennifer R Adams
- Department of Fish and Wildlife, University of Idaho, College of Natural Resources, Moscow, Idaho 83844-1136, USA.
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38
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Schwartz MK, Cushman SA, McKelvey KS, Hayden J, Engkjer C. Detecting genotyping errors and describing American black bear movement in northern Idaho. URSUS 2006. [DOI: 10.2192/1537-6176(2006)17[138:dgeada]2.0.co;2] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Fredrickson RJ, Hedrick PW. Dynamics of hybridization and introgression in red wolves and coyotes. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2006; 20:1272-83. [PMID: 16922243 DOI: 10.1111/j.1523-1739.2006.00401.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Hybridization and introgression are significant causes of endangerment in many taxa and are considered the greatest biological threats to the reintroduced population of red wolves (Canis rufus) in North Carolina (U.S.A.). Little is known, however, about these processes in red wolves and coyotes (C. latrans). We used individual-based simulations to examine the process of hybridization and introgression between these species. Under the range of circumstances we considered, red wolves in colonizing and established populations were quickly extirpated, persisted near the carrying capacity, or had intermediate outcomes. Sensitivity analyses suggested that the probabilities of quasi extinction and persistence of red wolves near the carrying capacity were most affected by the strength of two reproductive barriers: red wolf challenges and assortative mating between red wolves and coyotes. Because model parameters for these barriers may be difficult to estimate, we also sought to identify other predictors of red wolf population fate. The proportion of pure red wolves in the population was a strong predictor of the future probabilities of red wolf quasi extinction and persistence. Finally, we examined whether sterilization can be effective in minimizing introgression while allowing the reintroduced red wolfpopulation to grow. Our results suggest sterilization can be an effective short-term strategy to reduce the likelihood of extirpation in colonizing populations of red wolves. Whether red wolf numbers are increased by sterilization depends on the level of sterilization effort and the acting reproductive barriers. Our results provide an outline of the conditions likely required for successful reestablishment and long-term maintenance of populations of wild red wolves in the presence of coyotes. Our modeling approach may prove generally useful in providing insight into situations involving complex species interactions when data are few.
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Adams JR, Waits LP. An efficient method for screening faecal DNA genotypes and detecting new individuals and hybrids in the red wolf (Canis rufus) experimental population area. CONSERV GENET 2006. [DOI: 10.1007/s10592-006-9154-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Kyle C, Johnson A, Patterson B, Wilson P, Shami K, Grewal S, White B. Genetic nature of eastern wolves: Past, present and future. CONSERV GENET 2006. [DOI: 10.1007/s10592-006-9130-0] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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42
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ELLEDGE AMANDAE, LEUNG LUKEKP, ALLEN LEER, FIRESTONE KAREN, WILTON ALANN. Assessing the taxonomic status of dingoes Canis familiaris dingo for conservation. Mamm Rev 2006. [DOI: 10.1111/j.1365-2907.2006.00086.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Vähä JP, Primmer CR. Efficiency of model-based Bayesian methods for detecting hybrid individuals under different hybridization scenarios and with different numbers of loci. Mol Ecol 2005; 15:63-72. [PMID: 16367830 DOI: 10.1111/j.1365-294x.2005.02773.x] [Citation(s) in RCA: 506] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Accurate detection of offspring resulting from hybridization between individuals of distinct populations has a range of applications in conservation and population genetics. We assessed the hybrid identification efficiency of two methods (implemented in the STRUCTURE and NEWHYBRIDS programs) which are tailored to identifying hybrid individuals but use different approaches. Simulated first- and second-generation hybrids were used to assess the performance of these two methods in detecting recent hybridization under scenarios with different levels of genetic divergence and varying numbers of loci. Despite the different approaches of the methods, the hybrid detection efficiency was generally similar and neither of the two methods outperformed the other in all scenarios assessed. Interestingly, hybrid detection efficiency was only minimally affected by whether reference population allele frequency information was included or not. In terms of genotyping effort, efficient detection of F1 hybrid individuals requires the use of 12 or 24 loci with pairwise F(ST) between hybridizing parental populations of 0.21 or 0.12, respectively. While achievable, these locus numbers are nevertheless higher than the number of loci currently commonly applied in population genetic studies. The method of STRUCTURE seemed to be less sensitive to the proportion of hybrids included in the sample, while NEWHYBRIDS seemed to perform slightly better when individuals from both backcross and F1 hybrid classes were present in the sample. However, separating backcrosses from purebred parental individuals requires a considerable genotyping effort (at least 48 loci), even when divergence between parental populations is high.
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Affiliation(s)
- Juha-Pekka Vähä
- Department of Biological and Environmental Sciences, PO Box 65, FIN-00014, University of Helsinki, Finland
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44
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Halbert ND, Ward TJ, Schnabel RD, Taylor JF, Derr JN. Conservation genomics: disequilibrium mapping of domestic cattle chromosomal segments in North American bison populations. Mol Ecol 2005; 14:2343-62. [PMID: 15969719 DOI: 10.1111/j.1365-294x.2005.02591.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Introgressive hybridization is one of the major threats to species conservation, and is often induced by human influence on the natural habitat of wildlife species. The ability to accurately identify introgression is critical to understanding its importance in evolution and effective conservation management of species. Hybridization between North American bison (Bison bison) and domestic cattle (Bos taurus) as a result of human activities has been recorded for over 100 years, and domestic cattle mitochondrial DNA was previously detected in bison populations. In this study, linked microsatellite markers were used to identify domestic cattle chromosomal segments in 14 genomic regions from 14 bison populations. Cattle nuclear introgression was identified in five populations, with an average frequency per population ranging from 0.56% to 1.80%. This study represents the first use of linked molecular markers to examine introgression between mammalian species and the first demonstration of domestic cattle nuclear introgression in bison. To date, six public bison populations have been identified with no evidence of mitochondrial or nuclear domestic cattle introgression, providing information critical to the future management of bison genetic resources. The ability to identify even low levels of introgression resulting from historic hybridization events suggests that the use of linked molecular markers to identify introgression is a significant development in the study of introgressive hybridization across a broad range of taxa.
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Affiliation(s)
- Natalie D Halbert
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biochemical Sciences, Texas A&M University, College Station, TX 77843, USA
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Abstract
The 'crisis discipline' of conservation biology has voraciously incorporated many technologies to speed up and increase the accuracy of conservation decision-making. Genetic approaches to characterizing endangered species or areas that contain endangered species are prime examples of this. Technical advances in areas such as high-throughput sequencing, microsatellite analysis and non-invasive DNA sampling have led to a much-expanded role for genetics in conservation. Such expansion will allow for more precise conservation decisions to be made and, more importantly, will allow conservation genetics to contribute to area- and landscape-based decision-making processes.
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Affiliation(s)
- Rob DeSalle
- American Museum of Natural History, New York, New York 10024, USA.
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