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Pečnerová P, Lord E, Garcia-Erill G, Hanghøj K, Rasmussen MS, Meisner J, Liu X, van der Valk T, Santander CG, Quinn L, Lin L, Liu S, Carøe C, Dalerum F, Götherström A, Måsviken J, Vartanyan S, Raundrup K, Al-Chaer A, Rasmussen L, Hvilsom C, Heide-Jørgensen MP, Sinding MHS, Aastrup P, Van Coeverden de Groot PJ, Schmidt NM, Albrechtsen A, Dalén L, Heller R, Moltke I, Siegismund HR. Population genomics of the muskox' resilience in the near absence of genetic variation. Mol Ecol 2024; 33:e17205. [PMID: 37971141 DOI: 10.1111/mec.17205] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 10/07/2023] [Accepted: 11/01/2023] [Indexed: 11/19/2023]
Abstract
Genomic studies of species threatened by extinction are providing crucial information about evolutionary mechanisms and genetic consequences of population declines and bottlenecks. However, to understand how species avoid the extinction vortex, insights can be drawn by studying species that thrive despite past declines. Here, we studied the population genomics of the muskox (Ovibos moschatus), an Ice Age relict that was at the brink of extinction for thousands of years at the end of the Pleistocene yet appears to be thriving today. We analysed 108 whole genomes, including present-day individuals representing the current native range of both muskox subspecies, the white-faced and the barren-ground muskox (O. moschatus wardi and O. moschatus moschatus) and a ~21,000-year-old ancient individual from Siberia. We found that the muskox' demographic history was profoundly shaped by past climate changes and post-glacial re-colonizations. In particular, the white-faced muskox has the lowest genome-wide heterozygosity recorded in an ungulate. Yet, there is no evidence of inbreeding depression in native muskox populations. We hypothesize that this can be explained by the effect of long-term gradual population declines that allowed for purging of strongly deleterious mutations. This study provides insights into how species with a history of population bottlenecks, small population sizes and low genetic diversity survive against all odds.
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Affiliation(s)
- Patrícia Pečnerová
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Copenhagen Zoo, Frederiksberg, Denmark
| | - Edana Lord
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Genís Garcia-Erill
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Hanghøj
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Malthe Sebro Rasmussen
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jonas Meisner
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xiaodong Liu
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Tom van der Valk
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Cindy G Santander
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Liam Quinn
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Immunology, Zealand University Hospital, Køge, Denmark
| | - Long Lin
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Shanlin Liu
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Christian Carøe
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Fredrik Dalerum
- Department of Zoology, Stockholm University, Stockholm, Sweden
- Biodiversity Research Institute (CSIC-UO-PA), Mieres, Spain
- Department of Zoology and Entomology, Mammal Research Institute, University of Pretoria, Hatfield, South Africa
| | - Anders Götherström
- Centre for Palaeogenetics, Stockholm, Sweden
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Johannes Måsviken
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Sergey Vartanyan
- North-East Interdisciplinary Scientific Research Institute N.A.N.A. Shilo, Russian Academy of Sciences, Magadan, Russia
| | | | - Amal Al-Chaer
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Linett Rasmussen
- Copenhagen Zoo, Frederiksberg, Denmark
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Mads Peter Heide-Jørgensen
- Greenland Institute of Natural Resources, Nuuk, Greenland
- Greenland Institute of Natural Resources, Copenhagen, Denmark
| | - Mikkel-Holger S Sinding
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Greenland Institute of Natural Resources, Nuuk, Greenland
| | - Peter Aastrup
- Department of Ecoscience, Aarhus University, Roskilde, Denmark
- Arctic Research Centre, Aarhus University, Aarhus, Denmark
| | | | - Niels Martin Schmidt
- Department of Ecoscience, Aarhus University, Roskilde, Denmark
- Arctic Research Centre, Aarhus University, Aarhus, Denmark
| | - Anders Albrechtsen
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Love Dalén
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Rasmus Heller
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ida Moltke
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Hans Redlef Siegismund
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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2
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Mochales-Riaño G, Fontsere C, de Manuel M, Talavera A, Burriel-Carranza B, Tejero-Cicuéndez H, AlGethami RHM, Shobrak M, Marques-Bonet T, Carranza S. Genomics reveals introgression and purging of deleterious mutations in the Arabian leopard ( Panthera pardus nimr). iScience 2023; 26:107481. [PMID: 37601769 PMCID: PMC10432787 DOI: 10.1016/j.isci.2023.107481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/21/2023] [Accepted: 07/24/2023] [Indexed: 08/22/2023] Open
Abstract
In endangered species, low-genetic variation and inbreeding result from recent population declines. Genetic screenings in endangered populations help to assess their vulnerability to extinction and to create informed management actions toward their conservation efforts. The leopard, Panthera pardus, is a highly generalist predator with currently eight different subspecies. Yet, genomic data are still lacking for the Critically Endangered Arabian leopard (P. p. nimr). Here, we sequenced the whole genome of two Arabian leopards and assembled the most complete genomic dataset for leopards to date. Our phylogenomic analyses show that leopards are divided into two deeply divergent clades: the African and the Asian. Conservation genomic analyses indicate a prolonged population decline, which has led to an increase in inbreeding and runs of homozygosity, with consequent purging of deleterious mutations in both Arabian individuals. Our study represents the first attempt to genetically inform captive breeding programmes for this Critically Endangered subspecies.
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Affiliation(s)
| | - Claudia Fontsere
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Øster Farimagsgade 5A, 1352 Copenhagen, Denmark
| | - Marc de Manuel
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Adrián Talavera
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | | | - Héctor Tejero-Cicuéndez
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
- Department of Biodiversity, Ecology and Evolution, Faculty of Biology, Universidad Complutense de Madrid, Madrid, Spain
| | - Raed Hamoud M. AlGethami
- National Center for Wildlife, Prince Saud Al-Faisal for Wildlife Research, P. O Box 1086, Taif, Taif 21944, Saudi Arabia
| | - Mohammed Shobrak
- National Center for Wildlife, Prince Saud Al-Faisal for Wildlife Research, P. O Box 1086, Taif, Taif 21944, Saudi Arabia
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Salvador Carranza
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
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3
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Galla SJ, Brown L, Couch-Lewis Ngāi Tahu Te Hapū O Ngāti Wheke Ngāti Waewae Y, Cubrinovska I, Eason D, Gooley RM, Hamilton JA, Heath JA, Hauser SS, Latch EK, Matocq MD, Richardson A, Wold JR, Hogg CJ, Santure AW, Steeves TE. The relevance of pedigrees in the conservation genomics era. Mol Ecol 2021; 31:41-54. [PMID: 34553796 PMCID: PMC9298073 DOI: 10.1111/mec.16192] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 09/12/2021] [Accepted: 09/17/2021] [Indexed: 01/21/2023]
Abstract
Over the past 50 years conservation genetics has developed a substantive toolbox to inform species management. One of the most long‐standing tools available to manage genetics—the pedigree—has been widely used to characterize diversity and maximize evolutionary potential in threatened populations. Now, with the ability to use high throughput sequencing to estimate relatedness, inbreeding, and genome‐wide functional diversity, some have asked whether it is warranted for conservation biologists to continue collecting and collating pedigrees for species management. In this perspective, we argue that pedigrees remain a relevant tool, and when combined with genomic data, create an invaluable resource for conservation genomic management. Genomic data can address pedigree pitfalls (e.g., founder relatedness, missing data, uncertainty), and in return robust pedigrees allow for more nuanced research design, including well‐informed sampling strategies and quantitative analyses (e.g., heritability, linkage) to better inform genomic inquiry. We further contend that building and maintaining pedigrees provides an opportunity to strengthen trusted relationships among conservation researchers, practitioners, Indigenous Peoples, and Local Communities.
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Affiliation(s)
- Stephanie J Galla
- Department of Biological Sciences, Boise State University, Boise, Idaho, USA.,School of Biological Sciences, University of Canterbury, Christchurch, Canterbury, New Zealand
| | - Liz Brown
- New Zealand Department of Conservation, Twizel, Canterbury, New Zealand
| | | | - Ilina Cubrinovska
- School of Biological Sciences, University of Canterbury, Christchurch, Canterbury, New Zealand
| | - Daryl Eason
- New Zealand Department of Conservation, Invercargill, Southland, New Zealand
| | - Rebecca M Gooley
- Smithsonian-Mason School of Conservation, Front Royal, Maryland, USA.,Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia, USA
| | - Jill A Hamilton
- Department of Biological Sciences, North Dakota State University, Fargo, North Dakota, USA
| | - Julie A Heath
- Department of Biological Sciences, Boise State University, Boise, Idaho, USA
| | - Samantha S Hauser
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Emily K Latch
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Marjorie D Matocq
- Department of Natural Resources and Environmental Science, Program in Ecology, Evolution and Conservation Biology, University of Nevada Reno, Reno, Nevada, USA
| | - Anne Richardson
- The Isaac Conservation and Wildlife Trust, Christchurch, Canterbury, New Zealand
| | - Jana R Wold
- School of Biological Sciences, University of Canterbury, Christchurch, Canterbury, New Zealand
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland, Auckland, New Zealand
| | - Tammy E Steeves
- School of Biological Sciences, University of Canterbury, Christchurch, Canterbury, New Zealand
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4
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Grueber CE, Farquharson KA, Wright BR, Wallis GP, Hogg CJ, Belov K. First evidence of deviation from Mendelian proportions in a conservation programme. Mol Ecol 2021; 30:3703-3715. [PMID: 34051005 DOI: 10.1111/mec.16004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 05/05/2021] [Indexed: 11/29/2022]
Abstract
Classic Mendelian inheritance is the bedrock of population genetics and underpins pedigree-based management of animal populations. However, assumptions of Mendelian inheritance might not be upheld in conservation breeding programmes if early viability selection occurs, even when efforts are made to equalise genetic contributions of breeders. To test this possibility, we investigated deviations from Mendelian proportions in a captive metapopulation of the endangered Tasmanian devil. This marsupial population is ideal for addressing evolutionary questions in conservation due to its large size, range of enclosure types (varying in environmental conditions), good genomic resources (which aid interpretation), and the species' biology. Devil mothers give birth to more offspring than they can nurse in the pouch, providing the potential for intense viability selection amongst embryos. We used data from 140 known sire-dam-offspring triads to isolate within-family selection from population-level mechanisms (such as mate choice or inbreeding), and compared observed offspring genotypes at 123 targeted SNPs to neutral (i.e., Mendelian) expectations. We found lower offspring heterozygosity than expected, and subtle patterns that varied across a gradient of management intensity from zoo-like enclosures to semi-wild environments for some loci. Meiotic drive or maternal-foetal incompatibilities are consistent with our results, although we cannot statistically confirm these mechanisms. We found some evidence that maternal genotype affects annual litter size, suggesting that family-level patterns are driven by differential offspring mortality before birth or during early development. Our results show that deviations from Mendelian inheritance can occur in conservation programmes, despite best-practice management to prevent selection.
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Affiliation(s)
- Catherine E Grueber
- Faculty of Science, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia.,San Diego Zoo Global, San Diego, CA, USA
| | - Katherine A Farquharson
- Faculty of Science, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Belinda R Wright
- Faculty of Science, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Graham P Wallis
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Carolyn J Hogg
- Faculty of Science, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Katherine Belov
- Faculty of Science, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
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5
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Grueber CE, Peel E, Wright B, Hogg CJ, Belov K. A Tasmanian devil breeding program to support wild recovery. Reprod Fertil Dev 2020; 31:1296-1304. [PMID: 32172782 DOI: 10.1071/rd18152] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 10/01/2018] [Indexed: 01/03/2023] Open
Abstract
Tasmanian devils are threatened in the wild by devil facial tumour disease: a transmissible cancer with a high fatality rate. In response, the Save the Tasmanian Devil Program (STDP) established an 'insurance population' to enable the preservation of genetic diversity and natural behaviours of devils. This breeding program includes a range of institutions and facilities, from zoo-based intensive enclosures to larger, more natural environments, and a strategic approach has been required to capture and maintain genetic diversity, natural behaviours and to ensure reproductive success. Laboratory-based research, particularly genetics, in tandem with adaptive management has helped the STDP reach its goals, and has directly contributed to the conservation of the species in the wild. Here we review this work and show that the Tasmanian devil breeding program is a powerful example of how genetic research can be used to understand and improve reproductive success in a threatened species.
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Affiliation(s)
- C E Grueber
- The University of Sydney, School of Life and Environmental Sciences, Faculty of Science, Sydney, NSW 2006, Australia
| | - E Peel
- The University of Sydney, School of Life and Environmental Sciences, Faculty of Science, Sydney, NSW 2006, Australia
| | - B Wright
- The University of Sydney, School of Life and Environmental Sciences, Faculty of Science, Sydney, NSW 2006, Australia
| | - C J Hogg
- The University of Sydney, School of Life and Environmental Sciences, Faculty of Science, Sydney, NSW 2006, Australia
| | - K Belov
- The University of Sydney, School of Life and Environmental Sciences, Faculty of Science, Sydney, NSW 2006, Australia
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6
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Gooley RM, Tamazian G, Castañeda‐Rico S, Murphy KR, Dobrynin P, Ferrie GM, Haefele H, Maldonado JE, Wildt DE, Pukazhenthi BS, Edwards CW, Koepfli K. Comparison of genomic diversity and structure of sable antelope ( Hippotragus niger) in zoos, conservation centers, and private ranches in North America. Evol Appl 2020; 13:2143-2154. [PMID: 32908610 PMCID: PMC7463370 DOI: 10.1111/eva.12976] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 04/01/2020] [Accepted: 04/02/2020] [Indexed: 12/30/2022] Open
Abstract
As we enter the sixth mass extinction, many species that are no longer self-sustaining in their natural habitat will require ex situ management. Zoos have finite resources for ex situ management, and there is a need for holistic conservation programs between the public and private sector. Ex situ populations of sable antelope, Hippotragus niger, have existed in zoos and privately owned ranches in North America since the 1910s. Unknown founder representation and relatedness has made the genetic management of this species challenging within zoos, while populations on privately owned ranches are managed independently and retain minimal-to-no pedigree history. Consequences of such challenges include an increased risk of inbreeding and a loss of genetic diversity. Here, we developed and applied a customized targeted sequence capture panel based on 5,000 genomewide single-nucleotide polymorphisms to investigate the genomic diversity present in these uniquely managed populations. We genotyped 111 sable antelope: 23 from zoos, 43 from a single conservation center, and 45 from ranches. We found significantly higher genetic diversity and significantly lower inbreeding in herds housed in zoos and conservation centers, when compared to those in privately owned ranches, likely due to genetic-based breeding recommendations implemented in the former populations. Genetic clustering was strong among all three populations, possibly as a result of genetic drift. We propose that the North American ex situ population of sable antelope would benefit from a metapopulation management system, to halt genetic drift, reduce the occurrence of inbreeding, and enable sustainable population sizes to be managed ex situ.
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Affiliation(s)
- Rebecca M. Gooley
- Smithsonian‐Mason School of ConservationFront RoyalVAUSA
- Center for Species Survival, Smithsonian Conservation Biology InstituteNational Zoological ParkWashingtonDCUSA
| | - Gaik Tamazian
- Theodosius Dobzhansky Center for Genome BioinformaticsSaint Petersburg State UniversitySt. PetersburgRussian Federation
| | - Susette Castañeda‐Rico
- Smithsonian‐Mason School of ConservationFront RoyalVAUSA
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteNational Zoological ParkWashingtonDCUSA
| | - Katherine R. Murphy
- Laboratories of Analytical BiologyNational Museum of Natural HistorySmithsonian InstitutionWashingtonDCUSA
| | - Pavel Dobrynin
- Computer Technologies LaboratoryITMO UniversitySt. PetersburgRussian Federation
| | - Gina M. Ferrie
- Animals, Science and EnvironmentDisney’s Animal KingdomLake Buena VistaFLUSA
| | | | - Jesús E. Maldonado
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteNational Zoological ParkWashingtonDCUSA
| | - David E. Wildt
- Center for Species Survival, Smithsonian Conservation Biology InstituteNational Zoological ParkWashingtonDCUSA
| | - Budhan S. Pukazhenthi
- Center for Species Survival, Smithsonian Conservation Biology InstituteNational Zoological ParkWashingtonDCUSA
| | - Cody W. Edwards
- Smithsonian‐Mason School of ConservationFront RoyalVAUSA
- Department of BiologyGeorge Mason UniversityFairfaxVAUSA
| | - Klaus‐Peter Koepfli
- Center for Species Survival, Smithsonian Conservation Biology InstituteNational Zoological ParkWashingtonDCUSA
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7
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White LC, Thomson VA, West R, Ruykys L, Ottewell K, Kanowski J, Moseby KE, Byrne M, Donnellan SC, Copley P, Austin JJ. Genetic monitoring of the greater stick-nest rat meta-population for strategic supplementation planning. CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01299-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
AbstractTranslocation is an increasingly common component of species conservation efforts. However, translocated populations often suffer from loss of genetic diversity and increased inbreeding, and thus may require active management to establish gene flow across isolated populations. Assisted gene flow can be laborious and costly, so recipient and source populations should be carefully chosen to maximise genetic diversity outcomes. The greater stick-nest rat (GSNR, Leporillus conditor), a threatened Australian rodent, has been the focus of a translocation program since 1985, resulting in five extant translocated populations (St Peter Island, Reevesby Island, Arid Recovery, Salutation Island and Mt Gibson), all derived from a remnant wild population on the East and West Franklin Islands. We evaluated the genetic diversity in all extant GSNR populations using a large single nucleotide polymorphism dataset with the explicit purpose of informing future translocation planning. Our results show varying levels of genetic divergence, inbreeding and loss of genetic diversity in all translocated populations relative to the remnant source on the Franklin Islands. All translocated populations would benefit from supplementation to increase genetic diversity, but two—Salutation Island and Mt Gibson—are of highest priority. We recommend a targeted admixture approach, in which animals for supplementation are sourced from populations that have low relatedness to the recipient population. Subject to assessment of contemporary genetic diversity, St Peter Island and Arid Recovery are the most appropriate source populations for genetic supplementation. Our study demonstrates an effective use of genetic surveys for data-driven management of threatened species.
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8
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Wright BR, Farquharson KA, McLennan EA, Belov K, Hogg CJ, Grueber CE. A demonstration of conservation genomics for threatened species management. Mol Ecol Resour 2020; 20:1526-1541. [DOI: 10.1111/1755-0998.13211] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 06/02/2020] [Accepted: 06/08/2020] [Indexed: 12/13/2022]
Affiliation(s)
- Belinda R. Wright
- School of Life and Environmental Sciences Faculty of Science The University of Sydney Sydney NSW Australia
| | - Katherine A. Farquharson
- School of Life and Environmental Sciences Faculty of Science The University of Sydney Sydney NSW Australia
| | - Elspeth A. McLennan
- School of Life and Environmental Sciences Faculty of Science The University of Sydney Sydney NSW Australia
| | - Katherine Belov
- School of Life and Environmental Sciences Faculty of Science The University of Sydney Sydney NSW Australia
| | - Carolyn J. Hogg
- School of Life and Environmental Sciences Faculty of Science The University of Sydney Sydney NSW Australia
| | - Catherine E. Grueber
- School of Life and Environmental Sciences Faculty of Science The University of Sydney Sydney NSW Australia
- San Diego Zoo Global San Diego CA USA
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9
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Gooley RM, Hogg CJ, Fox S, Pemberton D, Belov K, Grueber CE. Inbreeding depression in one of the last DFTD-free wild populations of Tasmanian devils. PeerJ 2020; 8:e9220. [PMID: 32587794 PMCID: PMC7304431 DOI: 10.7717/peerj.9220] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 04/28/2020] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Vulnerable species experiencing inbreeding depression are prone to localised extinctions because of their reduced fitness. For Tasmanian devils, the rapid spread of devil facial tumour disease (DFTD) has led to population declines and fragmentation across the species' range. Here we show that one of the few remaining DFTD-free populations of Tasmanian devils is experiencing inbreeding depression. Moreover, this population has experienced a significant reduction in reproductive success over recent years. METHODS We used 32 microsatellite loci to examine changes in genetic diversity and inbreeding in the wild population at Woolnorth, alongside field data on breeding success from females to test for inbreeding depression. RESULTS Wefound that maternal internal relatedness has a negative impact on litter sizes. The results of this study imply that this population may be entering an extinction vortex and that to protect the population genetic rescue should be considered. This study provides conservation managers with useful information for managing wild devils and provides support for the "Wild Devil Recovery Program", which is currently augmenting small, isolated populations.
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Affiliation(s)
- Rebecca M. Gooley
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Carolyn J. Hogg
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Samantha Fox
- Save the Tasmanian Devil Program, Hobart, Tasmania, Australia
- Toledo Zoo, Toledo, OH, United States of America
| | - David Pemberton
- Save the Tasmanian Devil Program, Hobart, Tasmania, Australia
| | - Katherine Belov
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Catherine E. Grueber
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
- San Diego Zoo Global, San Diego, CA, United States of America
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11
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Galla SJ, Moraga R, Brown L, Cleland S, Hoeppner MP, Maloney RF, Richardson A, Slater L, Santure AW, Steeves TE. A comparison of pedigree, genetic and genomic estimates of relatedness for informing pairing decisions in two critically endangered birds: Implications for conservation breeding programmes worldwide. Evol Appl 2020; 13:991-1008. [PMID: 32431748 PMCID: PMC7232769 DOI: 10.1111/eva.12916] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 12/27/2019] [Accepted: 01/02/2020] [Indexed: 12/18/2022] Open
Abstract
Conservation management strategies for many highly threatened species include conservation breeding to prevent extinction and enhance recovery. Pairing decisions for these conservation breeding programmes can be informed by pedigree data to minimize relatedness between individuals in an effort to avoid inbreeding, maximize diversity and maintain evolutionary potential. However, conservation breeding programmes struggle to use this approach when pedigrees are shallow or incomplete. While genetic data (i.e., microsatellites) can be used to estimate relatedness to inform pairing decisions, emerging evidence indicates this approach may lack precision in genetically depauperate species, and more effective estimates will likely be obtained from genomic data (i.e., thousands of genome-wide single nucleotide polymorphisms, or SNPs). Here, we compare relatedness estimates and subsequent pairing decisions using pedigrees, microsatellites and SNPs from whole-genome resequencing approaches in two critically endangered birds endemic to New Zealand: kakī/black stilt (Himantopus novaezelandiae) and kākāriki karaka/orange-fronted parakeet (Cyanoramphus malherbi). Our findings indicate that SNPs provide more precise estimates of relatedness than microsatellites when assessing empirical parent-offspring and full sibling relationships. Further, our results show that relatedness estimates and subsequent pairing recommendations using PMx are most similar between pedigree- and SNP-based approaches. These combined results indicate that in lieu of robust pedigrees, SNPs are an effective tool for informing pairing decisions, which has important implications for many poorly pedigreed conservation breeding programmes worldwide.
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Affiliation(s)
- Stephanie J. Galla
- School of Biological SciencesUniversity of CanterburyChristchurchNew Zealand
| | - Roger Moraga
- Tea Break Bioinformatics, LtdPalmerston NorthNew Zealand
| | - Liz Brown
- New Zealand Department of ConservationTwizelNew Zealand
| | | | - Marc P. Hoeppner
- Institute for Clinical Molecular BiologyChristian‐Albrechts‐University KielKielGermany
| | | | - Anne Richardson
- The Isaac Conservation and Wildlife TrustChristchurchNew Zealand
| | - Lyndon Slater
- New Zealand Department of ConservationRangioraNew Zealand
| | - Anna W. Santure
- School of Biological SciencesUniversity of AucklandAucklandNew Zealand
| | - Tammy E. Steeves
- School of Biological SciencesUniversity of CanterburyChristchurchNew Zealand
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12
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Clendenin HR, Adams JR, Ausband DE, Hayden JA, Hohenlohe PA, Waits LP. Combining Harvest and Genetics to Estimate Reproduction in Wolves. J Wildl Manage 2020. [DOI: 10.1002/jwmg.21820] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Heather R. Clendenin
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary StudiesUniversity of Idaho 875 Perimeter Drive MS3051 Moscow ID 83844‐3051 USA
| | - Jennifer R. Adams
- Department of Fish and Wildlife Sciences, Laboratory for Ecological, Evolutionary and Conservation GeneticsUniversity of Idaho 875 Perimeter Drive MS1136 Moscow ID 83844‐1136 USA
| | | | - James A. Hayden
- Idaho Department of Fish and Game, P.O. Box 25Boise ID 83814 USA
| | - Paul A. Hohenlohe
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary StudiesUniversity of Idaho 875 Perimeter Drive MS3051 Moscow ID 83844‐3051 USA
| | - Lisette P. Waits
- Department of Fish and Wildlife SciencesUniversity of Idaho 875 Perimeter Drive MS1136 Moscow ID 83844‐1136 USA
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13
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Brandies P, Peel E, Hogg CJ, Belov K. The Value of Reference Genomes in the Conservation of Threatened Species. Genes (Basel) 2019; 10:E846. [PMID: 31717707 PMCID: PMC6895880 DOI: 10.3390/genes10110846] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 10/18/2019] [Accepted: 10/23/2019] [Indexed: 12/17/2022] Open
Abstract
Conservation initiatives are now more crucial than ever-over a million plant and animal species are at risk of extinction over the coming decades. The genetic management of threatened species held in insurance programs is recommended; however, few are taking advantage of the full range of genomic technologies available today. Less than 1% of the 13505 species currently listed as threated by the International Union for Conservation of Nature (IUCN) have a published genome. While there has been much discussion in the literature about the importance of genomics for conservation, there are limited examples of how having a reference genome has changed conservation management practice. The Tasmanian devil (Sarcophilus harrisii), is an endangered Australian marsupial, threatened by an infectious clonal cancer devil facial tumor disease (DFTD). Populations have declined by 80% since the disease was first recorded in 1996. A reference genome for this species was published in 2012 and has been crucial for understanding DFTD and the management of the species in the wild. Here we use the Tasmanian devil as an example of how a reference genome has influenced management actions in the conservation of a species.
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Affiliation(s)
| | | | | | - Katherine Belov
- School of Life & Environmental Sciences, The University of Sydney, Sydney 2006, Australia; (P.B.); (E.P.); (C.J.H.)
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14
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Levine BA, Douglas MR, Yackel Adams AA, Lardner B, Reed RN, Savidge JA, Douglas ME. Genomic pedigree reconstruction identifies predictors of mating and reproductive success in an invasive vertebrate. Ecol Evol 2019; 9:11863-11877. [PMID: 31695893 PMCID: PMC6822066 DOI: 10.1002/ece3.5694] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 09/02/2019] [Indexed: 01/16/2023] Open
Abstract
The persistence of an invasive species is influenced by its reproductive ecology, and a successful control program must operate on this premise. However, the reproductive ecology of invasive species may be enigmatic due to factors that also limit their management, such as cryptic coloration and behavior. We explored the mating and reproductive ecology of the invasive Brown Treesnake (BTS: Boiga irregularis) by reconstructing a multigenerational genomic pedigree based on 654 single nucleotide polymorphisms for a geographically closed population established in 2004 on Guam (N = 426). The pedigree allowed annual estimates of individual mating and reproductive success to be inferred for snakes in the study population over a 14-year period. We then employed generalized linear mixed models to gauge how well phenotypic and genomic data could predict sex-specific annual mating and reproductive success. Average snout-vent length (SVL), average body condition index (BCI), and trappability were significantly related to annual mating success for males, with average SVL also related to annual mating success for females. Male and female annual reproductive success was positively affected by SVL, BCI, and trappability. Surprisingly, the degree to which individuals were inbred had no effect on annual mating or reproductive success. When juxtaposed with current control methods, these results indicate that baited traps, a common interdiction tool, may target fecund BTS in some regards but not others. Our study emphasizes the importance of reproductive ecology as a focus for improving BTS control and promotes genomic pedigree reconstruction for such an endeavor in this invasive species and others.
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Affiliation(s)
- Brenna A. Levine
- University of ArkansasFayettevilleArkansas
- Present address:
University of TulsaTulsaOklahoma
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15
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Day J, Gooley RM, Hogg CJ, Belov K, Whittington CM, Grueber CE. MHC-associated mate choice under competitive conditions in captive versus wild Tasmanian devils. Behav Ecol 2019. [DOI: 10.1093/beheco/arz092] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
AbstractMate choice contributes to driving evolutionary processes when animals choose breeding partners that confer genetic advantages to offspring, such as increased immunocompetence. The major histocompatibility complex (MHC) is an important group of immunological molecules, as MHC antigens bind and present foreign peptides to T-cells. Recent studies suggest that mates may be selected based on their MHC profile, leading to an association between an individual’s MHC diversity and their breeding success. In conservation, it may be important to consider mate choice in captive breeding programs, as this mechanism may improve reproductive rates. We investigated the reproductive success of Tasmanian devils in a group housing facility to determine whether increased MHC-based heterozygosity led individuals to secure more mating partners and produce more offspring. We also compared the breeding success of captive females to a wild devil population. MHC diversity was quantified using 12 MHC-linked microsatellite markers, including 11 previously characterized markers and one newly identified marker. Our analyses revealed that there was no relationship between MHC-linked heterozygosity and reproductive success either in captivity or the wild. The results of this study suggest that, for Tasmanian devils, MHC-based heterozygosity does not produce greater breeding success and that no specific changes to current captive management strategies are required with respect to preserving MHC diversity.
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Affiliation(s)
- Jenna Day
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, NSW, Australia
| | - Rebecca M Gooley
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, NSW, Australia
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, NSW, Australia
- Zoo and Aquarium Association Australasia, Mosman, NSW, Australia
| | - Katherine Belov
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, NSW, Australia
| | - Camilla M Whittington
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, NSW, Australia
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, NSW, Australia
| | - Catherine E Grueber
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, NSW, Australia
- San Diego Zoo Global, San Diego, CA, USA
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16
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17
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Russell T, Lane A, Clarke J, Hogg C, Morris K, Keeley T, Madsen T, Ujvari B. Multiple paternity and precocial breeding in wild Tasmanian devils, Sarcophilus harrisii (Marsupialia: Dasyuridae). Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Polyandry, a common reproductive strategy in various animal species, has potential female benefits, which include enhanced offspring fitness. Benefits can be direct, such as reduced risk of male infanticide of offspring, or indirect, such as increased genetic diversity of offspring and the acquisition of ‘good genes’. Multiple paternity of litters has been recorded in numerous marsupial species but has not been reported in Tasmanian devils, Sarcophilus harrisii (Boitard). We investigated whether multiple paternity occurred in litters within a wild population of Tasmanian devils. Using major histocompatibility complex-linked and neutral microsatellite markers, the paternity of nine litters was analysed. We found multiple paternity in four out of nine litters and that yearling (> 1, < 2 years old) male devils were siring offspring. This is the first record of multiple paternity and of male precocial breeding in wild Tasmanian devils. To date, there are no data relating to the subsequent survival of devils from single- vs. multiple-sired litters; therefore, we do not know whether multiple paternity increases offspring survival in the wild. These results have implications for the Tasmanian devil captive insurance programme, because group housing can lead to multiple-sired litters, making the maintenance of genetic diversity over time difficult to manage.
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Affiliation(s)
- Tracey Russell
- School of Life and Environmental Science, The University of Sydney, Sydney, NSW, Australia
| | - Amanda Lane
- School of Life and Environmental Science, The University of Sydney, Sydney, NSW, Australia
| | - Judy Clarke
- Tasmanian Department of Primary Industries, Parks, Water and Environment, Hobart, TAS, Australia
| | - Carolyn Hogg
- School of Life and Environmental Science, The University of Sydney, Sydney, NSW, Australia
| | - Katrina Morris
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, UK
| | - Tamara Keeley
- School of Agriculture and Food Sciences, The University of Queensland, Gatton, QLD, Australia
| | - Thomas Madsen
- School of Biological Sciences, University of Wollongong, Wollongong, NSW, Australia
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC, Australia
| | - Beata Ujvari
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC, Australia
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18
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McLennan EA, Wright BR, Belov K, Hogg CJ, Grueber CE. Too much of a good thing? Finding the most informative genetic data set to answer conservation questions. Mol Ecol Resour 2019; 19:659-671. [DOI: 10.1111/1755-0998.12997] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 01/10/2019] [Accepted: 01/14/2019] [Indexed: 12/18/2022]
Affiliation(s)
- Elspeth A. McLennan
- School of Life and Environmental Sciences University of Sydney Sydney New South Wales Australia
| | - Belinda R. Wright
- School of Life and Environmental Sciences University of Sydney Sydney New South Wales Australia
| | - Katherine Belov
- School of Life and Environmental Sciences University of Sydney Sydney New South Wales Australia
| | - Carolyn J. Hogg
- School of Life and Environmental Sciences University of Sydney Sydney New South Wales Australia
| | - Catherine E. Grueber
- School of Life and Environmental Sciences University of Sydney Sydney New South Wales Australia
- San Diego Zoo Global San Diego California
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19
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Grueber CE, Fox S, McLennan EA, Gooley RM, Pemberton D, Hogg CJ, Belov K. Complex problems need detailed solutions: Harnessing multiple data types to inform genetic management in the wild. Evol Appl 2019; 12:280-291. [PMID: 30697339 PMCID: PMC6346650 DOI: 10.1111/eva.12715] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 08/15/2018] [Accepted: 09/04/2018] [Indexed: 12/18/2022] Open
Abstract
For bottlenecked populations of threatened species, supplementation often leads to improved population metrics (genetic rescue), provided that guidelines can be followed to avoid negative outcomes. In cases where no "ideal" source populations exist, or there are other complicating factors such as prevailing disease, the benefit of supplementation becomes uncertain. Bringing multiple data and analysis types together to plan genetic management activities can help. Here, we consider three populations of Tasmanian devil, Sarcophilus harrisii, as candidates for genetic rescue. Since 1996, devil populations have been severely impacted by devil facial tumour disease (DFTD), causing significant population decline and fragmentation. Like many threatened species, the key threatening process for devils cannot currently be fully mitigated, so species management requires a multifaceted approach. We examined diversity of 31 putatively neutral and 11 MHC-linked microsatellite loci of three remnant wild devil populations (one sampled at two time-points), alongside computational diversity projections, parameterized by field data from DFTD-present and DFTD-absent sites. Results showed that populations had low diversity, connectivity was poor, and diversity has likely decreased over the last decade. Stochastic simulations projected further diversity losses. For a given population size, the effects of DFTD on population demography (including earlier age at death and increased female productivity) did not impact diversity retention, which was largely driven by final population size. Population sizes ≥500 (depending on the number of founders) were necessary for maintaining diversity in otherwise unmanaged populations, even if DFTD is present. Models indicated that smaller populations could maintain diversity with ongoing immigration. Taken together, our results illustrate how multiple analysis types can be combined to address complex population genetic challenges.
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Affiliation(s)
- Catherine E. Grueber
- Faculty of Science, School of Life and Environmental SciencesThe University of SydneySydneyNew South WalesAustralia
- San Diego Zoo GlobalSan DiegoCalifornia
| | - Samantha Fox
- Save the Tasmanian Devil ProgramDPIPWEHobartTasmaniaAustralia
- Toledo ZooToledoOhio
| | - Elspeth A. McLennan
- Faculty of Science, School of Life and Environmental SciencesThe University of SydneySydneyNew South WalesAustralia
| | - Rebecca M. Gooley
- Faculty of Science, School of Life and Environmental SciencesThe University of SydneySydneyNew South WalesAustralia
| | - David Pemberton
- Save the Tasmanian Devil ProgramDPIPWEHobartTasmaniaAustralia
| | - Carolyn J. Hogg
- Faculty of Science, School of Life and Environmental SciencesThe University of SydneySydneyNew South WalesAustralia
- Zoo and Aquarium Association AustralasiaMosmanNew South WalesAustralia
| | - Katherine Belov
- Faculty of Science, School of Life and Environmental SciencesThe University of SydneySydneyNew South WalesAustralia
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20
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Hohenlohe PA, McCallum HI, Jones ME, Lawrance MF, Hamede RK, Storfer A. Conserving adaptive potential: lessons from Tasmanian devils and their transmissible cancer. CONSERV GENET 2019; 20:81-87. [PMID: 31551664 PMCID: PMC6759055 DOI: 10.1007/s10592-019-01157-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 02/09/2019] [Indexed: 11/26/2022]
Abstract
Maintenance of adaptive genetic variation has long been a goal of management of natural populations, but only recently have genomic tools allowed identification of specific loci associated with fitness-related traits in species of conservation concern. This raises the possibility of managing for genetic variation directly relevant to specific threats, such as those due to climate change or emerging infectious disease. Tasmanian devils (Sarcophilus harrisii) face the threat of a transmissible cancer, devil facial tumor disease (DFTD), that has decimated wild populations and led to intensive management efforts. Recent discoveries from genomic and modeling studies reveal how natural devil populations are responding to DFTD, and can inform management of both captive and wild devil populations. Notably, recent studies have documented genetic variation for disease-related traits and rapid evolution in response to DFTD, as well as potential mechanisms for disease resistance such as immune response and tumor regression in wild devils. Recent models predict dynamic persistence of devils with or without DFTD under a variety of modeling scenarios, although at much lower population densities than before DFTD emerged, contrary to previous predictions of extinction. As a result, current management that focuses on captive breeding and release for maintaining genome-wide genetic diversity or demographic supplementation of populations could have negative consequences. Translocations of captive devils into wild populations evolving with DFTD can cause outbreeding depression and/or increases in the force of infection and thereby the severity of the epidemic, and we argue that these risks outweigh any benefits of demographic supplementation in wild populations. We also argue that genetic variation at loci associated with DFTD should be monitored in both captive and wild populations, and that as our understanding of DFTD-related genetic variation improves, considering genetic management approaches to target this variation is warranted in developing conservation strategies for Tasmanian devils.
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Affiliation(s)
- Paul A. Hohenlohe
- Institute for Bioinformatics and Evolutionary Studies, Department of Biological Sciences, University of Idaho, Moscow, ID 83843, USA
| | - Hamish I. McCallum
- Environmental Futures Research Institute, Griffith University, Brisbane, QLD 4111, Australia
| | - Menna E. Jones
- School of Biological Sciences, University of Tasmania, Hobart, TAS 7001, Australia
| | - Matthew F. Lawrance
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Rodrigo K. Hamede
- School of Biological Sciences, University of Tasmania, Hobart, TAS 7001, Australia
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
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21
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Zieger M, Springer S. Thylacine and Tasmanian devil: between hope and reality – a lesson to be learnt from Google Trends search data. AUST J ZOOL 2019. [DOI: 10.1071/zo20073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The two iconic Tasmanian species, the Tasmanian devil (Sarcophilus harrisii) and the thylacine (Thylacinus cynocephalus), are of great interest to the general public and the media. The most likely extinct Tasmanian wolf or tiger, the thylacine, symbolises human responsibility for nature and species conservation and inspired the ‘National Threatened Species Day’, which commemorates the death of the last thylacine at Beaumaris Zoo in Hobart on 7 September 1936 to raise awareness of endangered plants and animals. Since the spread of the Devil Facial Tumour Disease critically endangered the survival of the largest remaining native carnivore (S. harrisii) today, this has generated both scientific interest and the interest of the general public. Google Trends has already been used as a tool for documenting and investigating the information needs and concerns of the population, as has been shown using the example of diseases. In this study, Google Trends data were used to examine the seasonality of the search term ‘thylacine sightings’ and the development of the frequency of different search terms in the period between 2004 and 2020. As a result, relative search intensities for ‘thylacine cloning’ and ‘cloning extinct species’ have shown a decrease over time. While Google Trends cannot clearly determine search motivation, search terms can be selected for the examinations that document more hope or a rational need for information or concern.
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22
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Hogg CJ, Wright B, Morris KM, Lee AV, Ivy JA, Grueber CE, Belov K. Founder relationships and conservation management: empirical kinships reveal the effect on breeding programmes when founders are assumed to be unrelated. Anim Conserv 2018. [DOI: 10.1111/acv.12463] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- C. J. Hogg
- School of Life and Environmental Sciences The University of Sydney Sydney NSW Australia
- Zoo and Aquarium Association Australasia Mosman NSW Australia
| | - B. Wright
- School of Life and Environmental Sciences The University of Sydney Sydney NSW Australia
| | - K. M. Morris
- School of Life and Environmental Sciences The University of Sydney Sydney NSW Australia
| | - A. V. Lee
- Save the Tasmanian Devil Program DPIPWE Hobart TAS Australia
| | - J. A. Ivy
- San Diego Zoo Global San Diego CA USA
| | - C. E. Grueber
- School of Life and Environmental Sciences The University of Sydney Sydney NSW Australia
- San Diego Zoo Global San Diego CA USA
| | - K. Belov
- School of Life and Environmental Sciences The University of Sydney Sydney NSW Australia
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23
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Muñoz-Fuentes V, Cacheiro P, Meehan TF, Aguilar-Pimentel JA, Brown SDM, Flenniken AM, Flicek P, Galli A, Mashhadi HH, Hrabě de Angelis M, Kim JK, Lloyd KCK, McKerlie C, Morgan H, Murray SA, Nutter LMJ, Reilly PT, Seavitt JR, Seong JK, Simon M, Wardle-Jones H, Mallon AM, Smedley D, Parkinson HE. The International Mouse Phenotyping Consortium (IMPC): a functional catalogue of the mammalian genome that informs conservation. CONSERV GENET 2018; 19:995-1005. [PMID: 30100824 PMCID: PMC6061128 DOI: 10.1007/s10592-018-1072-9] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 05/03/2018] [Indexed: 01/08/2023]
Abstract
The International Mouse Phenotyping Consortium (IMPC) is building a catalogue of mammalian gene function by producing and phenotyping a knockout mouse line for every protein-coding gene. To date, the IMPC has generated and characterised 5186 mutant lines. One-third of the lines have been found to be non-viable and over 300 new mouse models of human disease have been identified thus far. While current bioinformatics efforts are focused on translating results to better understand human disease processes, IMPC data also aids understanding genetic function and processes in other species. Here we show, using gorilla genomic data, how genes essential to development in mice can be used to help assess the potentially deleterious impact of gene variants in other species. This type of analyses could be used to select optimal breeders in endangered species to maintain or increase fitness and avoid variants associated to impaired-health phenotypes or loss-of-function mutations in genes of critical importance. We also show, using selected examples from various mammal species, how IMPC data can aid in the identification of candidate genes for studying a condition of interest, deliver information about the mechanisms involved, or support predictions for the function of genes that may play a role in adaptation. With genotyping costs decreasing and the continued improvements of bioinformatics tools, the analyses we demonstrate can be routinely applied.
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Affiliation(s)
- Violeta Muñoz-Fuentes
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - Pilar Cacheiro
- Clinical Pharmacology, William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ UK
| | - Terrence F. Meehan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - Juan Antonio Aguilar-Pimentel
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Steve D. M. Brown
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD UK
| | - Ann M. Flenniken
- The Centre for Phenogenomics, Toronto, ON M5T 3H7 Canada
- Mount Sinai Hospital, Toronto, ON M5G 1X5 Canada
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | | | - Hamed Haseli Mashhadi
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - Martin Hrabě de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
- German Center for Diabetes Research (DZD), Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
- School of Life Science Weihenstephan, Technische Universität München, Alte Akademie 8, 85354 Freising, Germany
| | - Jong Kyoung Kim
- Department of New Biology, DGIST, Daegu, 42988 Republic of Korea
| | - K. C. Kent Lloyd
- Mouse Biology Program, University of California, Davis, CA 95618 USA
| | - Colin McKerlie
- The Centre for Phenogenomics, Toronto, ON M5T 3H7 Canada
- Mount Sinai Hospital, Toronto, ON M5G 1X5 Canada
- The Hospital for Sick Children, Toronto, ON M5G 1X84 Canada
| | - Hugh Morgan
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD UK
| | | | - Lauryl M. J. Nutter
- The Centre for Phenogenomics, Toronto, ON M5T 3H7 Canada
- The Hospital for Sick Children, Toronto, ON M5G 1X84 Canada
| | - Patrick T. Reilly
- PHENOMIN-iCS, 1 Rue Laurent Fries, 67404 Illkirch Cedex, Alsace France
| | - John R. Seavitt
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Je Kyung Seong
- Laboratory of Developmental Biology and Genomics, College of Veterinary Medicine, Interdisciplinary Program for Bioinformatics and Program for Cancer Biology, Seoul National University, Seoul, Republic of Korea
| | - Michelle Simon
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD UK
| | | | - Ann-Marie Mallon
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD UK
| | - Damian Smedley
- Clinical Pharmacology, William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ UK
| | - Helen E. Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - the IMPC consortium
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
- Clinical Pharmacology, William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ UK
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD UK
- The Centre for Phenogenomics, Toronto, ON M5T 3H7 Canada
- Mount Sinai Hospital, Toronto, ON M5G 1X5 Canada
- Wellcome Trust Sanger Institute, Cambridge, CB10 1SA UK
- German Center for Diabetes Research (DZD), Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
- School of Life Science Weihenstephan, Technische Universität München, Alte Akademie 8, 85354 Freising, Germany
- Department of New Biology, DGIST, Daegu, 42988 Republic of Korea
- Mouse Biology Program, University of California, Davis, CA 95618 USA
- The Hospital for Sick Children, Toronto, ON M5G 1X84 Canada
- The Jackson Laboratory, Bar Harbor, ME 04609 USA
- PHENOMIN-iCS, 1 Rue Laurent Fries, 67404 Illkirch Cedex, Alsace France
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Laboratory of Developmental Biology and Genomics, College of Veterinary Medicine, Interdisciplinary Program for Bioinformatics and Program for Cancer Biology, Seoul National University, Seoul, Republic of Korea
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24
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Gooley RM, Hogg CJ, Belov K, Grueber CE. The effects of group versus intensive housing on the retention of genetic diversity in insurance populations. BMC ZOOL 2018. [DOI: 10.1186/s40850-017-0026-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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25
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Goldingay RL. Population monitoring of an urban gliding mammal in eastern Australia. AUSTRALIAN MAMMALOGY 2018. [DOI: 10.1071/am17029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Long-term monitoring is an important element of species conservation. This study describes changes in the size of a squirrel glider (Petaurus norfolcensis) population over a 10-year period. The population occupied a 45-ha forest remnant within the urban area of Brisbane. Gliders were tagged from 25 nights of trapping during 2006–08 and from 16 nights of trapping in 2015. Population modelling was used to estimate adult population size. This suggested the adult population comprised 30–40 individuals at the beginning and end of the 10-year period. It reached a peak of 70 individuals in mid-2007. These data suggest that the study area contains a small population that is prone to interannual variation but there was no evidence of it being in decline. Survival estimates during 2006–08 were equivalent to those estimated for a larger population in Victoria. Population monitoring should be continued to determine how resilient this population is to population decline and to investigate factors that may cause decline. This study provides an example of an approach that could be used to monitor threatened populations of the squirrel glider.
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McLennan EA, Gooley RM, Wise P, Belov K, Hogg CJ, Grueber CE. Pedigree reconstruction using molecular data reveals an early warning sign of gene diversity loss in an island population of Tasmanian devils (Sarcophilus harrisii). CONSERV GENET 2017. [DOI: 10.1007/s10592-017-1017-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Phillips KP, Jorgensen TH, Jolliffe KG, Richardson DS. Evidence of opposing fitness effects of parental heterozygosity and relatedness in a critically endangered marine turtle? J Evol Biol 2017; 30:1953-1965. [PMID: 28787533 DOI: 10.1111/jeb.13152] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 07/27/2017] [Accepted: 07/31/2017] [Indexed: 01/13/2023]
Abstract
How individual genetic variability relates to fitness is important in understanding evolution and the processes affecting populations of conservation concern. Heterozygosity-fitness correlations (HFCs) have been widely used to study this link in wild populations, where key parameters that affect both variability and fitness, such as inbreeding, can be difficult to measure. We used estimates of parental heterozygosity and genetic similarity ('relatedness') derived from 32 microsatellite markers to explore the relationship between genetic variability and fitness in a population of the critically endangered hawksbill turtle, Eretmochelys imbricata. We found no effect of maternal MLH (multilocus heterozygosity) on clutch size or egg success rate, and no single-locus effects. However, we found effects of paternal MLH and parental relatedness on egg success rate that interacted in a way that may result in both positive and negative effects of genetic variability. Multicollinearity in these tests was within safe limits, and null simulations suggested that the effect was not an artefact of using paternal genotypes reconstructed from large samples of offspring. Our results could imply a tension between inbreeding and outbreeding depression in this system, which is biologically feasible in turtles: female-biased natal philopatry may elevate inbreeding risk and local adaptation, and both processes may be disrupted by male-biased dispersal. Although this conclusion should be treated with caution due to a lack of significant identity disequilibrium, our study shows the importance of considering both positive and negative effects when assessing how variation in genetic variability affects fitness in wild systems.
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Affiliation(s)
- K P Phillips
- School of Biological Sciences, Norwich Research Park, University of East Anglia, Norwich, UK.,NERC Biomolecular Analysis Facility (NBAF), Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.,Evolutionary Biology Group, Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - T H Jorgensen
- School of Biological Sciences, Norwich Research Park, University of East Anglia, Norwich, UK.,Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - K G Jolliffe
- Victoria, Mahé, Republic of Seychelles.,Drie Kuilen Private Nature Reserve, Breede River District, South Africa
| | - D S Richardson
- School of Biological Sciences, Norwich Research Park, University of East Anglia, Norwich, UK
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