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Richdon S, Menchaca Rodriguez A, Price E, Wormell D, McCabe G, Jones G. Thirty years of conservation breeding: Assessing the genetic diversity of captive Livingstone's fruit bats. Zoo Biol 2024. [PMID: 38837463 DOI: 10.1002/zoo.21845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/18/2024] [Accepted: 05/21/2024] [Indexed: 06/07/2024]
Abstract
Fruit bats (genus Pteropus) are typically island-endemic species important in seed dispersal and reforestation that are vulnerable to increased extinction risk. An effective method of reducing extinction risk in vulnerable species that cannot be conserved in their native habitat is establishing an ex-situ captive breeding programme. Due to anthropogenic threats and low population numbers, in the early 1990s, a captive breeding programme was established at Jersey Zoo, British Isles, for Critically Endangered Livingstone's fruit bats (Pteropus livingstonii). Here we use six polymorphic microsatellite loci to assess genetic diversity in the captive breeding population of Livingstone's fruit bats (P. livingstonii), 30 years after the programme's establishment, investigating change over generations and comparing our findings with published data from the wild population. We found no significant difference between the genetic diversity in the captive and wild populations of Livingstone's fruit bats (P. livingstonii), in both expected heterozygosity and allelic richness. The captive population has retained a comparable level of genetic diversity to that documented in the wild, and there has been no significant decline in genetic diversity over the last 30 years. We advise that a full pedigree of the paternal lineage is created to improve the management of the captive breeding programme and further reduce the possibility of inbreeding. However, it appears that the captive breeding programme is currently effective at maintaining genetic diversity at levels comparable to those seen in the wild population, which suggests reintroductions could be viable if genetic diversity remains stable in captivity.
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Affiliation(s)
- Sarah Richdon
- School of Biological Sciences, University of Bristol, Bristol, UK
- Bristol Zoological Society, Clifton, Bristol, UK
| | | | - Eluned Price
- Durrell Wildlife Conservation Trust, La Profonde Rue, Jersey, UK
| | - Dominic Wormell
- Durrell Wildlife Conservation Trust, La Profonde Rue, Jersey, UK
| | | | - Gareth Jones
- School of Biological Sciences, University of Bristol, Bristol, UK
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Aliaga-Samanez GG, Bulhões Javarotti N, Orecife G, Chávez-Congrains K, Pissinatti A, Monticelli C, Cristina Marques M, Galbusera P, Galetti PM, Domingues de Freitas P. Genetic diversity in ex situ populations of the endangered Leontopithecus chrysomelas and implications for its conservation. PLoS One 2023; 18:e0288097. [PMID: 37531319 PMCID: PMC10395972 DOI: 10.1371/journal.pone.0288097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 06/19/2023] [Indexed: 08/04/2023] Open
Abstract
Leontopithecus chrysomelas, the Golden-headed Lion Tamarin (GHLT), is an endangered and endemic Neotropical primate from the Atlantic Forest of Brazil that has suffered a reduction of its habitat and population size in the wild. Ex situ populations have been established as a relevant alternative to safeguard the species and retain its genetic diversity and evolutionary potential. This study evaluated the genetic diversity and structure of the two main Brazilian captive populations of GHLT, which have been under human care at the Primatology Center of Rio de Janeiro (CPRJ) and the Zoological Park Foundation of São Paulo (FPZSP). Our results revealed levels of genetic diversity overall comparable to those observed for other Leontopithecus species and for ex situ and in situ populations of GHLT previously studied. Bayesian and principal coordinate analyses showed a moderate differentiation between CPRJ and FPZSP populations. Both populations presented observed heterozygosity values higher than expected heterozygosity values for most of the microsatellites used in this study, suggesting that the management has been efficient in avoiding an increase in homozygosity. However, simulations point to a significant loss of genetic diversity in the next 100 years, mainly in the FPZSP population. Such data are relevant for further decision-making on the metapopulation management of L. chrysomelas in captive conditions and for integrating in situ and ex situ conservation plans.
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Affiliation(s)
| | | | - Gisele Orecife
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Karla Chávez-Congrains
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Alcides Pissinatti
- Centro de Primatologia do Rio de Janeiro, Guapimirim, Rio de Janeiro, Brazil
| | - Cauê Monticelli
- Departamento de Conservação e Pesquisas Aplicadas, Coordenadoria de Fauna Silvestre, Secretaria de Meio Ambiente, Infraestrutura e Logística do Estado de São Paulo, São Paulo, São Paulo, Brazil
| | | | - Peter Galbusera
- Antwerp Zoo Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium
| | - Pedro Manoel Galetti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
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3
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Ex situ versus in situ Eurasian lynx populations: implications for successful breeding and genetic rescue. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01494-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Comparison of the Genetic Diversity of the Captive and Wild Populations of the Tsushima Leopard Cat Using a GRAS-Di Analysis. Animals (Basel) 2022; 12:ani12111464. [PMID: 35681928 PMCID: PMC9179428 DOI: 10.3390/ani12111464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/28/2022] [Accepted: 06/01/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary The Tsushima leopard cat (Prionailurus bengalensis euptilurus) is exclusively found on the Tsushima Island in Japan; however, its population has been declining in recent years and is in danger of extinction. Hence, effort is underway for both in situ and ex situ conservation. Genetic management is also important in the management of captive populations, and various studies are being conducted regarding the same. In our previous study, we developed a reference genome of the Tsushima leopard cat and used GRAS-Di analysis, a genome-wide analysis, to genetically evaluate the wild populations. In this study, we attempted to improve the Tsushima leopard cat reference genome and compared the captive and wild populations by GRAS-di analysis. The results showed that the captive population had almost the same genetic diversity as the wild population and managed to remain in good condition. Abstract The Tsushima leopard cat (Prionailurus bengalensis euptilurus) (TLC) is a regional population of the Amur leopard cat (P. bengalensis euptilurus) that lives only on the Tsushima Island in Japan and is threatened with extinction. Because the TLC population is small, genetic management is important. In this study, we obtained the draft genome of the TLC and identified single-nucleotide polymorphism (SNP) markers using a genotyping by random amplicon sequencing-direct (GRAS-Di) analysis. We genotyped 31 captive individuals and 50 wild individuals, of which 48 were from a previous study. The identified SNPs were used to clarify the genetic diversity and genetic structure of the wild and captive populations of the TLC. The size of the genome was estimated to be about 2.42 Gb. The number of SNP markers developed was 139, and although PID and probability of exclusion obtained using these SNP markers were not as high as those reported in the studies of other wild species, these SNP markers could be used to identify individuals and parentage. Moreover, the genetic diversity indices of the captive population were similar to those of the wild population. These SNP markers will be useful for understanding the ecology of the TLC and planning conservation strategies.
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5
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Rabier R, Erlichman A, Lesobre L, Robert A. The necessity of considering founder kinships in conservation breeding programs. Anim Conserv 2022. [DOI: 10.1111/acv.12779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- R. Rabier
- Reneco International Wildlife Consultants LLC Abu Dhabi United Arab Emirates
- Centre d'Ecologie et des Sciences de la Conservation (CESCO) Muséum national d'Histoire naturelle, Centre National de la Recherche Scientifique, Sorbonne Université Paris France
- Emirates Center for Wildlife Propagation Missour Morocco
| | - A. Erlichman
- Reneco International Wildlife Consultants LLC Abu Dhabi United Arab Emirates
- Centre d'Ecologie et des Sciences de la Conservation (CESCO) Muséum national d'Histoire naturelle, Centre National de la Recherche Scientifique, Sorbonne Université Paris France
| | - L. Lesobre
- Reneco International Wildlife Consultants LLC Abu Dhabi United Arab Emirates
- Emirates Center for Wildlife Propagation Missour Morocco
| | - A. Robert
- Centre d'Ecologie et des Sciences de la Conservation (CESCO) Muséum national d'Histoire naturelle, Centre National de la Recherche Scientifique, Sorbonne Université Paris France
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Davidović S, Marinković S, Kukobat M, Mihajlović M, Tanasić V, Hribšek I, Tanasković M, Stamenković-Radak M. Genetic Diversity Analysis of Mitochondrial Cytb Gene, Phylogeny and Phylogeography of Protected Griffon Vulture (Gyps fulvus) from Serbia. Life (Basel) 2022; 12:life12020164. [PMID: 35207453 PMCID: PMC8880743 DOI: 10.3390/life12020164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/13/2022] [Accepted: 01/19/2022] [Indexed: 11/16/2022] Open
Abstract
Once a widespread and common species across the region of southeast Europe, the Griffon vulture is now confined to small and isolated populations across the Balkan Peninsula. The population from Serbia with 290 couples represents its biggest and most viable population that can serve as an important reservoir of genetic diversity from which the birds can be used for the region’s reintroduction or recolonization programs. To estimate the level of genetic diversity, the mitochondrial Cytb gene from 58 unrelated birds sampled during the marking in the nests was sequenced and compared to the homologous Griffon vulture sequences available in publicly accessible online databases. Phylogeographic analysis based on Cytb sequences showed that the most frequent haplotype is found in all Griffon vulture populations and that each population possesses private haplotypes. Our data suggest that the Griffon vulture population from Serbia should be used as a source population for restocking and reintroduction programs in the region. The observed genetic differentiation between the populations from the Iberian and Balkan Peninsulas suggest that the introduction of foreign birds from remote populations should be avoided and that birds from indigenous or neighboring populations, if available, should be used instead.
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Affiliation(s)
- Slobodan Davidović
- Department of Genetics of Populations and Ecogenotoxicology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia; (M.T.); (M.S.-R.)
- Correspondence:
| | - Saša Marinković
- Department of Ecology, Institute for Biological Research “Siniša Stanković”—National Institute of Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia;
| | - Mila Kukobat
- Faculty of Biology, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia;
| | - Milica Mihajlović
- Center for Forensic and Applied Molecular Genetics, Faculty of Biology, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia; (M.M.); (V.T.)
| | - Vanja Tanasić
- Center for Forensic and Applied Molecular Genetics, Faculty of Biology, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia; (M.M.); (V.T.)
| | - Irena Hribšek
- Birds of Prey Protection Foundation, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia;
| | - Marija Tanasković
- Department of Genetics of Populations and Ecogenotoxicology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia; (M.T.); (M.S.-R.)
| | - Marina Stamenković-Radak
- Department of Genetics of Populations and Ecogenotoxicology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia; (M.T.); (M.S.-R.)
- Faculty of Biology, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia;
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Pirastru M, Mereu P, Manca L, Bebbere D, Naitana S, Leoni GG. Anthropogenic Drivers Leading to Population Decline and Genetic Preservation of the Eurasian Griffon Vulture ( Gyps fulvus). Life (Basel) 2021; 11:life11101038. [PMID: 34685409 PMCID: PMC8540517 DOI: 10.3390/life11101038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 09/27/2021] [Accepted: 09/28/2021] [Indexed: 11/17/2022] Open
Abstract
Human activities are having increasingly devastating effects on the health of marine and terrestrial ecosystems. Studying the adaptive responses of animal species to changes in their habitat can be useful in mitigating this impact. Vultures represent one of the most virtuous examples of adaptation to human-induced environmental changes. Once dependent on wild ungulate populations, these birds have adapted to the epochal change resulting from the birth of agriculture and livestock domestication, maintaining their essential role as ecological scavengers. In this review, we retrace the main splitting events characterising the vultures’ evolution, with particular emphasis on the Eurasian griffon Gyps fulvus. We summarise the main ecological and behavioural traits of this species, highlighting its vulnerability to elements introduced into the habitat by humans. We collected the genetic information available to date, underlining their importance for improving the management of this species, as an essential tool to support restocking practices and to protect the genetic integrity of G. fulvus. Finally, we examine the difficulties in implementing a coordination system that allows genetic information to be effectively transferred into management programs. Until a linking network is established between scientific research and management practices, the risk of losing important wildlife resources remains high.
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Affiliation(s)
- Monica Pirastru
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43b, 07100 Sassari, Italy; (M.P.); (L.M.)
| | - Paolo Mereu
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43b, 07100 Sassari, Italy; (M.P.); (L.M.)
- Correspondence:
| | - Laura Manca
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43b, 07100 Sassari, Italy; (M.P.); (L.M.)
| | - Daniela Bebbere
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100 Sassari, Italy; (D.B.); (S.N.); (G.G.L.)
| | - Salvatore Naitana
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100 Sassari, Italy; (D.B.); (S.N.); (G.G.L.)
| | - Giovanni G. Leoni
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100 Sassari, Italy; (D.B.); (S.N.); (G.G.L.)
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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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Ayala-Burbano PA, Galetti Junior PM, Wormell D, Pissinatti A, Marques MC, de Freitas PD. Studbook and molecular analyses for the endangered black-lion-tamarin; an integrative approach for assessing genetic diversity and driving management in captivity. Sci Rep 2020; 10:6781. [PMID: 32321949 PMCID: PMC7176676 DOI: 10.1038/s41598-020-63542-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 03/10/2020] [Indexed: 11/09/2022] Open
Abstract
Breeding strategies based on molecular markers have been adopted by ex-situ conservation programs to assess alternative parameters for the genetic diversity estimates. In this work we evaluated molecular and studbook data for captive populations of black-lion-tamarin (BLT), an endangered primate endemic to Brazil's Atlantic Forest. Pedigree analyses were performed using BLT studbook information collected from 1973 to 2018. We analyzed the whole captive population since its foundation; the current captive population (CCP); and all extant BLTs in the Brazilian captive population (BCP), separately. Microsatellite analyses were implemented on the BCP individuals from the eighth generation (BCP-F8) only to avoid generation overlap. The expected heterozygosity for BCP-F8, using molecular, data was 0.45, and the initial expected heterozygosity was 0.69. Kinship parameters showed high genetic relationships in both pedigree and molecular analyses. The genealogy-based endogamy evidenced a high inbreeding coefficient, while the molecular analyses suggested a non-inbreeding signature. The Mate Suitability Index showed detrimental values for the majority of potential pairs in the CCP. Nevertheless, some individuals evidenced high individual heterozygosity and allele representation, demonstrating good potential to be used as breeders. Thus, we propose the use of molecular data as a complementary parameter to evaluate mating-pairs and to aid management decision-making.
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Affiliation(s)
| | | | - Dominic Wormell
- Durrell Wildlife Conservation Trust, Trinity, Jersey, England
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10
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Ito H, Inoue-Murayama M. The Tsushima leopard cat exhibits extremely low genetic diversity compared with the Korean Amur leopard cat: Implications for conservation. PeerJ 2019; 7:e7297. [PMID: 31341743 PMCID: PMC6637929 DOI: 10.7717/peerj.7297] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 06/14/2019] [Indexed: 11/20/2022] Open
Abstract
We examined genetic diversity of the wild Tsushima leopard cat-a regional population of the Amur leopard cat-using microsatellite markers. In addition, we compared genetic diversity of the Tsushima leopard cat with that of the Korean population of Amur leopard cat. Although bias should be considered when applying cross-species amplification, the Tsushima leopard cat showed a lower index of molecular genetic diversity than did the Korean population. These results were consistent with those obtained using other genetic markers, such as mitochondrial DNA and Y chromosome sequences. This low genetic diversity of the wild Tsushima leopard cat may be derived from the founding population. Furthermore, our results suggest that the captive populations held in Japanese zoos may show extremely low genetic diversity, leading to difficulties in genetic management of the Tsushima leopard cat. Moreover, the two regional populations were clearly separated using these marker sets. In the present study, we demonstrated that the genetic diversity of the Tsushima leopard cat is extremely low compared with that of the continental regional population. Importantly, the Japanese captive population for ex situ conservation was derived from a founding population with extremely low genetic diversity; hence, we assume that both the captive and wild populations showed extremely low genetic diversities. Our findings emphasize the need to develop carefully considered management strategies for genetic conservation.
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Affiliation(s)
- Hideyuki Ito
- Kyoto City Zoo, Kyoto, Kyoto, Japan.,Wildlife Research Center, Kyoto University, Kyoto, Kyoto, Japan
| | - Miho Inoue-Murayama
- Wildlife Research Center, Kyoto University, Kyoto, Kyoto, Japan.,Wildlife Genome Collaborative Research Group, National Institute for Environmental Studies, Tsukuba, Japan
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11
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Gallardo-Alvárez MI, Lesher-Gordillo JM, Machkour-M’Rabet S, Zenteno-Ruiz CE, Olivera-Gómez LD, Barragán-Vázquez MDR, Ríos-Rodas L, Valdés-Marín A, Vázquez-López HG, Arriaga-Weiss SL. Genetic diversity and population structure of founders from wildlife conservation management units and wild populations of critically endangered Dermatemys mawii. Glob Ecol Conserv 2019. [DOI: 10.1016/j.gecco.2019.e00616] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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12
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Kleinhans C, Willows-Munro S. Low genetic diversity and shallow population structure in the endangered vulture, Gyps coprotheres. Sci Rep 2019; 9:5536. [PMID: 30940898 PMCID: PMC6445149 DOI: 10.1038/s41598-019-41755-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 03/15/2019] [Indexed: 11/08/2022] Open
Abstract
Globally, vulture species are experiencing major population declines. The southern African Cape vulture (Gyps coprotheres) has undergone severe population collapse which has led to a listing of Endangered by the IUCN. Here, a comprehensive genetic survey of G. coprotheres is conducted using microsatellite markers. Analyses revealed an overall reduction in heterozygosity compared to other vulture species that occur in South Africa (Gypaetus barbatus, Necrosyrtes monachus, and Gyps africanus). Bayesian clustering analysis and principal coordinate analysis identified shallow, subtle population structuring across South Africa. This provides some support for regional natal philopatry in this species. Despite recent reductions in population size, a genetic bottleneck was not detected by the genetic data. The G. coprotheres, however, did show a significant deficiency of overall heterozygosity. This, coupled with the elevated levels of inbreeding and reduced effective population size, suggests that G. coprotheres is genetically depauperate. Given that genetic variation is considered a prerequisite for adaptation and population health, the low genetic diversity within G. coprotheres populations is of concern and has implications for the future management and conservation of this species.
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Affiliation(s)
- Courtneë Kleinhans
- School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Sandi Willows-Munro
- School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa.
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13
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Robertson EP, Fletcher RJ, Austin JD. Microsatellite polymorphism in the endangered snail kite reveals a panmictic, low diversity population. CONSERV GENET 2017. [DOI: 10.1007/s10592-017-1003-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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14
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Coetzer WG, Downs CT, Perrin MR, Willows-Munro S. Testing of microsatellite multiplexes for individual identification of Cape Parrots ( Poicephalus robustus): paternity testing and monitoring trade. PeerJ 2017; 5:e2900. [PMID: 28344897 PMCID: PMC5363265 DOI: 10.7717/peerj.2900] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 12/12/2016] [Indexed: 12/04/2022] Open
Abstract
Background Illegal trade in rare wildlife species is a major threat to many parrot species around the world. Wildlife forensics plays an important role in the preservation of endangered or threatened wildlife species. Identification of illegally harvested or traded animals through DNA techniques is one of the many methods used during forensic investigations. Natural populations of the South African endemic Cape Parrot (Poicephalus robustus) are negatively affected by the removal of eggs and chicks for the pet trade. Methods In this study, 16 microsatellite markers specifically designed for the South African endemic Cape Parrot (P. robustus) are assessed for their utility in forensic casework. Using these 16 loci, the genetic diversity of a subset of the captive Cape Parrot population was also assessed and compared to three wild Cape Parrot populations. Results It was determined that the full 16 locus panel has sufficient discriminatory power to be used in parentage analyses and can be used to determine if a bird has been bred in captivity and so can be legally traded or if it has been illegally removed from the wild. In cases where birds have been removed from the wild, this study suggests that a reduced 12 locus microsatellite panel has sufficient power to assign confiscated birds to geographic population of origin. Discussion The level of genetic diversity observed within the captive Cape Parrot population was similar to that observed in the wild populations, which suggests that the captive population is not suffering from decreased levels of genetic diversity. The captive Cape Parrots did however have double the number of private alleles compared to that observed in the most genetically diverse wild population. This is probably due to the presence of rare alleles present in the founder population, which has not been lost due to genetic drift, as many of the individuals tested in this study are F1–F3 wild descendants. The results from this study provide a suit of markers that can be used to aid conservation and law enforcement authorities to better control legal and illegal trade of this South African endemic.
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Affiliation(s)
- Willem G Coetzer
- School of Life Science, University of KwaZulu-Natal , Pietermaritzburg , South Africa
| | - Colleen T Downs
- School of Life Science, University of KwaZulu-Natal , Pietermaritzburg , South Africa
| | - Mike R Perrin
- School of Life Science, University of KwaZulu-Natal , Pietermaritzburg , South Africa
| | - Sandi Willows-Munro
- School of Life Science, University of KwaZulu-Natal , Pietermaritzburg , South Africa
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Ito H, Ogden R, Langenhorst T, Inoue-Murayama M. Contrasting results from molecular and pedigree-based population diversity measures in captive zebra highlight challenges facing genetic management of zoo populations. Zoo Biol 2016; 36:87-94. [PMID: 27981608 DOI: 10.1002/zoo.21342] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 11/14/2016] [Accepted: 11/28/2016] [Indexed: 11/12/2022]
Abstract
Zoo conservation breeding programs manage the retention of population genetic diversity through analysis of pedigree records. The range of demographic and genetic indices determined through pedigree analysis programs allows the conservation of diversity to be monitored relative to the particular founder population for a species. Such approaches are based on a number of well-documented founder assumptions, however without knowledge of actual molecular genetic diversity there is a risk that pedigree-based measures will be misinterpreted and population genetic diversity misunderstood. We examined the genetic diversity of the captive populations of Grevy's zebra, Hartmann's mountain zebra and plains zebra in Japan and the United Kingdom through analysis of mitochondrial DNA sequences. Very low nucleotide variability was observed in Grevy's zebra. The results were evaluated with respect to current and historic diversity in the wild, and indicate that low genetic diversity in the captive population is likely a result of low founder diversity, which in turn suggests relatively low wild genetic diversity prior to recent population declines. Comparison of molecular genetic diversity measures with analogous diversity indices generated from the studbook data for Grevy's zebra and Hartmann's mountain zebra show contrasting patterns, with Grevy's zebra displaying markedly less molecular diversity than mountain zebra, despite studbook analysis indicating that the Grevy's zebra population has substantially more founders, greater effective population size, lower mean kinship, and has suffered less loss of gene diversity. These findings emphasize the need to validate theoretical estimates of genetic diversity in captive breeding programs with empirical molecular genetic data. Zoo Biol. 36:87-94, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Hideyuki Ito
- Wildlife Research Center, Kyoto University, Kyoto, Japan.,Kyoto City Zoo, Kyoto, Japan
| | - Rob Ogden
- Wildlife Research Center, Kyoto University, Kyoto, Japan.,TRACE Wildlife Forensics Network, Edinburgh, United Kingdom
| | | | - Miho Inoue-Murayama
- Wildlife Research Center, Kyoto University, Kyoto, Japan.,Wildlife Genome Collaborative Research Group, National Institute for Environmental Studies, Tsukuba, Japan
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16
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Miller EJ, Eldridge MDB, Morris K, Thomas N, Herbert CA. Captive management and the maintenance of genetic diversity in a vulnerable marsupial, the greater bilby. AUSTRALIAN MAMMALOGY 2015. [DOI: 10.1071/am14009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The endemic Australian greater bilby (Macrotis lagotis) is a vulnerable and iconic species. It has declined significantly due to habitat loss, as well as competition and predation from introduced species. Conservation measures include a National Recovery Plan that incorporates several captive breeding programs. Two of these programs were established within 12 months of one another (1997/98), with the same number and sex ratio of founding individuals, but executed different breeding strategies: (1) unmanipulated mating in semi–free range natural habitat versus (2) minimising mean kinship in large enclosures, with the supplementation of new individuals into both populations. This study evaluates the long-term genetic impact of these programs and examines the congruency between the pedigree studbook estimates of diversity and molecular data. Our data demonstrate that genetic diversity was maintained in both populations, with the supplementation of new individuals contributing to the gene pool. The studbook estimates of diversity and inbreeding are not consistent with the microsatellite data and should not solely be relied upon to evaluate the genetic health of captive populations. Our analyses suggest that captive breeding programs may not require costly and intensive management to effectively maintain long-term genetic diversity in a promiscuous species.
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17
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Rija AA, Goboro EM, Mwamende KA, Said A, Kohi EM, Hassan SN. Activity patterns and fine-scale resource partitioning in the gregarious Kihansi spray toad Nectophrynoides asperginis in captivity. Zoo Biol 2014; 33:411-8. [PMID: 25182839 DOI: 10.1002/zoo.21163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Revised: 07/15/2014] [Accepted: 07/23/2014] [Indexed: 11/08/2022]
Abstract
Understanding the behavior of species threatened with extinction is important for conservation planning and for solving problems facing species in captivity and the wild. We examined diurnal activity budgets and habitat use of the extinct in the wild Kihansi spray toad to provide insights into ongoing conservation initiatives for this species. Observations on eight target behaviors were made each morning and evening for 14 days, in two subpopulations at Kihansi and University of Dar es Salaam captive breeding centers. There were significantly more bouts of resting than calling, amplexing, hunting, walking, climbing, or feeding. There was no difference in mean time spent in each activity between the two subpopulations. The use of habitat was variable between age classes, subpopulations and sampling time. Young toads spent significantly more time resting at the top of vegetation and on walls while adults rested more on logs. Further, adults foraged more on the walls and vegetation in the morning and on the ground in the evening. Contrastingly, young toads foraged more on the ground in the morning and switched to elevated patches during evening. The similarity of the toads' behavior suggests that important biological traits are still maintained in captivity and retained across toad generations. Furthermore, temporal and spatial variations in the use of habitat structures between age groups suggest fine-scale resource partitioning to reduce competition in this gregarious species. These results highlight the importance of maintaining diverse habitat structures in captivity and are useful for planning species reintroduction and future restocking programs.
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Affiliation(s)
- Alfan A Rija
- Department of Wildlife Management, Zoology Laboratory, Sokoine University of Agriculture, Morogoro, Tanzania
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18
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Decreasing genetic diversity in wild and captive populations of endangered Itasenpara bittering (Acheilognathus longipinnis) in the Himi region, central Japan, and recommendations for conservation. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0589-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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García CB, Gil JA, Alcántara M, González J, Cortés MR, Bonafonte JI, Arruga MV. The present Pyrenean population of bearded vulture (Gypaetus barbatus): its genetic characteristics. J Biosci 2013; 37:689-94. [PMID: 22922193 DOI: 10.1007/s12038-012-9229-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The Pyrenean population of the endangered bearded vulture (Gypaetus barbatus) is the largest natural population in Europe. In this study, its current genetic variability was assessed using 110 animals of the recent population in order to know what the present situation. Sex identification by DNA methodology in the 110 bearded vultures, mitochondrial DNA (mtDNA) and eight microsatellite markers in 87 bearded vultures have been analysed. Our results for sex identification present a number of 49 males and 61 females; no significant differences for number of males and females in this population have been observed. mtDNA studies indicate that nucleotide and haplotype diversities and number of variable sites were low. Tajima's D test and Fu and Li's D* and F* tests suggest that mutations are selectively neutral and the population is expanding. A mean number of alleles per locus and a mean observed heterozygosity have been obtained by microsatellite analysis. FIS is not high, and inbreeding depression could be discarded in the near future. The results suggest that the Pyrenean population of bearded vultures have to be controlled in order to avoid the loss of genetic variability. This data should be taken into account when considering conservation plans for the species.
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Affiliation(s)
- C B García
- Laboratory of Cytogenetics and Molecular Genetics, University of Zaragoza, Zaragoza, Spain
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20
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Duong TY, Scribner KT, Forsythe PS, Crossman JA, Baker EA. Interannual variation in effective number of breeders and estimation of effective population size in long-lived iteroparous lake sturgeon (Acipenser fulvescens). Mol Ecol 2013; 22:1282-94. [DOI: 10.1111/mec.12167] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Revised: 11/06/2012] [Accepted: 11/07/2012] [Indexed: 11/26/2022]
Affiliation(s)
- Thuy Yen Duong
- Department of Fisheries and Wildlife; Michigan State University; 13 Natural Resources East Lansing MI 48824 USA
| | - Kim T. Scribner
- Department of Fisheries and Wildlife; Michigan State University; 13 Natural Resources East Lansing MI 48824 USA
- Department of Zoology; Michigan State University; 13 Natural Resources East Lansing MI 48824 USA
| | - Patrick S. Forsythe
- Department of Zoology; Michigan State University; 13 Natural Resources East Lansing MI 48824 USA
| | - James A. Crossman
- Department of Fisheries and Wildlife; Michigan State University; 13 Natural Resources East Lansing MI 48824 USA
| | - Edward A. Baker
- Michigan Department of Natural Resources; 488 Cherry Creek Road Marquette MI 49855 USA
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Johnson JA, Talbot SL, Sage GK, Burnham KK, Brown JW, Maechtle TL, Seegar WS, Yates MA, Anderson B, Mindell DP. The use of genetics for the management of a recovering population: temporal assessment of migratory peregrine falcons in North America. PLoS One 2010; 5:e14042. [PMID: 21124969 PMCID: PMC2987794 DOI: 10.1371/journal.pone.0014042] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Accepted: 10/26/2010] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Our ability to monitor populations or species that were once threatened or endangered and in the process of recovery is enhanced by using genetic methods to assess overall population stability and size over time. This can be accomplished most directly by obtaining genetic measures from temporally-spaced samples that reflect the overall stability of the population as given by changes in genetic diversity levels (allelic richness and heterozygosity), degree of population differentiation (F(ST) and D(EST)), and effective population size (N(e)). The primary goal of any recovery effort is to produce a long-term self-sustaining population, and these genetic measures provide a metric by which we can gauge our progress and help make important management decisions. METHODOLOGY/PRINCIPAL FINDINGS The peregrine falcon in North America (Falco peregrinus tundrius and anatum) was delisted in 1994 and 1999, respectively, and its abundance will be monitored by the species Recovery Team every three years until 2015. Although the United States Fish and Wildlife Service makes a distinction between tundrius and anatum subspecies, our genetic results based on eleven microsatellite loci suggest limited differentiation that can be attributed to an isolation by distance relationship and warrant no delineation of these two subspecies in its northern latitudinal distribution from Alaska through Canada into Greenland. Using temporal samples collected at Padre Island, Texas during migration (seven temporal time periods between 1985-2007), no significant differences in genetic diversity or significant population differentiation in allele frequencies between time periods were observed and were indistinguishable from those obtained from tundrius/anatum breeding locations throughout their northern distribution. Estimates of harmonic mean N(e) were variable and imprecise, but always greater than 500 when employing multiple temporal genetic methods. CONCLUSIONS/SIGNIFICANCE These results, including those from simulations to assess the power of each method to estimate N(e), suggest a stable or growing population, which is consistent with ongoing field-based monitoring surveys. Therefore, historic and continuing efforts to prevent the extinction of the peregrine falcon in North America appear successful with no indication of recent decline, at least from the northern latitude range-wide perspective. The results also further highlight the importance of archiving samples and their use for continual assessment of population recovery and long-term viability.
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Affiliation(s)
- Jeff A Johnson
- Department of Biological Sciences, Institute of Applied Sciences, University of North Texas, Denton, Texas, USA.
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Captive breeding and reintroduction of the lesser kestrel Falco naumanni: a genetic analysis using microsatellites. CONSERV GENET 2009. [DOI: 10.1007/s10592-009-9810-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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23
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Genetic diversity and genetic structure of Northern Goshawk (Accipiter gentilis) populations in eastern Japan and Central Asia. CONSERV GENET 2008. [DOI: 10.1007/s10592-008-9567-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Identification of conservation units in the European Mergus merganser based on nuclear and mitochondrial DNA markers. CONSERV GENET 2008. [DOI: 10.1007/s10592-008-9528-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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25
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Quantifying and managing the loss of genetic variation in a free-ranging population of takahe through the use of pedigrees. CONSERV GENET 2007. [DOI: 10.1007/s10592-007-9390-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Le Gouar P, Rigal F, Boisselier-Dubayle MC, Sarrazin F, Arthur C, Choisy JP, Hatzofe O, Henriquet S, Lécuyer P, Tessier C, Susic G, Samadi S. Genetic variation in a network of natural and reintroduced populations of Griffon vulture (Gyps fulvus) in Europe. CONSERV GENET 2007. [DOI: 10.1007/s10592-007-9347-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Araki H, Waples RS, Ardren WR, Cooper B, Blouin MS. Effective population size of steelhead trout: influence of variance in reproductive success, hatchery programs, and genetic compensation between life-history forms. Mol Ecol 2007; 16:953-66. [PMID: 17305853 DOI: 10.1111/j.1365-294x.2006.03206.x] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The effective population size is influenced by many biological factors in natural populations. To evaluate their relative importance, we estimated the effective number of breeders per year (Nb) and effective population size per generation (Ne) in anadromous steelhead trout (Oncorhynchus mykiss) in the Hood River, Oregon (USA). Using demographic data and genetic parentage analysis on an almost complete sample of all adults that returned to the river over 15 years (>15,000 individuals), we estimated Nb for 13 run years and Ne for three entire generations. The results are as follows: (i) the ratio of Ne to the estimated census population size (N) was 0.17-0.40, with large variance in reproductive success among individuals being the primary cause of the reduction in Ne/N; (ii) fish from a traditional hatchery program (Htrad: nonlocal, multiple generations in a hatchery) had negative effects on Nb, not only by reducing mean reproductive success but also by increasing variance in reproductive success among breeding parents, whereas no sign of such effects was found in fish from supplementation hatchery programs (Hsupp: local, single generation in a hatchery); and (iii) Nb was relatively stable among run years, despite the widely fluctuating annual run sizes of anadromous adults. We found high levels of reproductive contribution of nonanadromous parents to anadromous offspring when anadromous run size is small, suggesting a genetic compensation between life-history forms (anadromous and nonanadromous). This is the first study showing that reproductive interaction between different life-history forms can buffer the genetic impact of fluctuating census size on Ne.
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Affiliation(s)
- Hitoshi Araki
- Department of Zoology, Oregon State University, 3029 Cordley Hall, Corvallis, Oregon 97331, USA.
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