1
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Hogg CJ. Translating genomic advances into biodiversity conservation. Nat Rev Genet 2024; 25:362-373. [PMID: 38012268 DOI: 10.1038/s41576-023-00671-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2023] [Indexed: 11/29/2023]
Abstract
A key action of the new Global Biodiversity Framework is the maintenance of genetic diversity in all species to safeguard their adaptive potential. To achieve this goal, a translational mindset, which aims to convert results of basic research into direct practical benefits, needs to be applied to biodiversity conservation. Despite much discussion on the value of genomics to conservation, a disconnect between those generating genomic resources and those applying it to biodiversity management remains. As global efforts to generate reference genomes for non-model species increase, investment into practical biodiversity applications is critically important. Applications such as understanding population and multispecies diversity and longitudinal monitoring need support alongside education for policymakers on integrating the data into evidence-based decisions. Without such investment, the opportunity to revolutionize global biodiversity conservation using genomics will not be fully realized.
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Affiliation(s)
- Carolyn J Hogg
- School of Life & Environmental Sciences, The University of Sydney, Sydney, NSW, Australia.
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2
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Lawson DJ, Howard-McCombe J, Beaumont M, Senn H. How admixed captive breeding populations could be rescued using local ancestry information. Mol Ecol 2024:e17349. [PMID: 38634332 DOI: 10.1111/mec.17349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 12/21/2023] [Accepted: 02/26/2024] [Indexed: 04/19/2024]
Abstract
This paper asks the question: can genomic information be used to recover a species that is already on the pathway to extinction due to genetic swamping from a related and more numerous population? We show that a breeding strategy in a captive breeding program can use whole genome sequencing to identify and remove segments of DNA introgressed through hybridisation. The proposed policy uses a generalized measure of kinship or heterozygosity accounting for local ancestry, that is, whether a specific genetic location was inherited from the target of conservation. We then show that optimizing these measures would minimize undesired ancestry while also controlling kinship and/or heterozygosity, in a simulated breeding population. The process is applied to real data representing the hybridized Scottish wildcat breeding population, with the result that it should be possible to breed out domestic cat ancestry. The ability to reverse introgression is a powerful tool brought about through the combination of sequencing with computational advances in ancestry estimation. Since it works best when applied early in the process, important decisions need to be made about which genetically distinct populations should benefit from it and which should be left to reform into a single population.
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Affiliation(s)
- Daniel J Lawson
- Institute of Statistical Sciences, School of Mathematics, University of Bristol, Bristol, UK
| | - Jo Howard-McCombe
- RZSS WildGenes Laboratory, Conservation Department, Royal Zoological Society of Scotland, Edinburgh, UK
| | - Mark Beaumont
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Helen Senn
- RZSS WildGenes Laboratory, Conservation Department, Royal Zoological Society of Scotland, Edinburgh, UK
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3
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Cetkovská E, Brandlová K, Ogden R, Černá Bolfíková B. Evaluation of the Impact of Population Management on the Genetic Parameters of Selected Spiral-Horned Antelopes. BIOLOGY 2024; 13:104. [PMID: 38392322 PMCID: PMC10886411 DOI: 10.3390/biology13020104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 01/25/2024] [Accepted: 01/30/2024] [Indexed: 02/24/2024]
Abstract
The rapid loss of biodiversity and the associated reduction and fragmentation of habitats means that ex situ populations have become an important part of species conservation. These populations, which are often established from a small number of founders, require careful management to avoid the negative effects of genetic drift and inbreeding. Although the inclusion of molecular data is recommended, their availability for captive breeding management remains limited. The aim of this study was to evaluate the relationship between the levels of genetic diversity in six spiral-horned antelope taxa bred under human care and their respective management strategies, conservation status, demography, and geographic origin, using 10 nuclear DNA microsatellite loci and mitochondrial control region DNA sequences. Our findings include associations between genetic diversity and management intensity but also with the diversity and contribution of wild populations to captive founders, with some populations apparently composed of animals from divergent wild lineages elevating captive genetic diversity. When population sizes are large, the potential advantages of maximizing genetic diversity in widely outcrossed populations may need careful consideration with respect to the potential disruption of adaptive diversity. Genetic data serve as a robust tool for managing captive populations, yet their interpretation necessitates a comprehensive understanding of species biology and history.
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Affiliation(s)
- Ema Cetkovská
- Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamycka 129, 16500 Prague, Czech Republic
| | - Karolína Brandlová
- Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamycka 129, 16500 Prague, Czech Republic
| | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Midlothian EH25 9RG, UK
| | - Barbora Černá Bolfíková
- Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamycka 129, 16500 Prague, Czech Republic
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4
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Smith KJ, Evans MJ, Gordon IJ, Pierson JC, Newport J, Manning AD. Analyzing captive breeding outcomes to inform reintroduction practice: lessons from the pookila ( Pseudomys novaehollandiae). J Mammal 2023; 104:1047-1061. [PMID: 37800101 PMCID: PMC10550247 DOI: 10.1093/jmammal/gyad056] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 05/04/2023] [Indexed: 10/07/2023] Open
Abstract
Captive breeding is often used to produce individuals for reintroduction programs in order to reestablish a species in an area where it has become locally extinct. To maximize the likelihood of establishing a self-sustaining population in the wild, an analysis of data from captive breeding programs is commonly undertaken to (1) increase the quantity of individuals and rate at which they can be released, and (2) maintain or improve the genetic and phenotypic quality of individuals. Here we demonstrate how the knowledge gained from these analyses can also be applied to decision-making during the design of subsequent reintroductions to further advance a reintroduction program toward success. We conducted an analysis of data from a captive breeding program for the threatened pookila (Pseudomys novaehollandiae, New Holland mouse) spanning 6 years. We found evidence for relationships between the reproductive output of pookila and behavioral, demographic, experiential, health, and physiological predictors. Based on a biological interpretation of these results, and with reference to a checklist of all known translocation tactics, we recommend 11 specific design elements to maximize the probability of pookila reproduction postrelease (thereby improving the likelihood of reintroduction success). These recommendations should be interpreted as hypotheses to be evaluated and refined in future reintroduction trials for the pookila. The uncertainty around the postrelease survival and reproduction of a species that is common in reintroduction practice warrants the creative use of existing data to inform adaptive management. Indeed, there is a wealth information in well-kept captive breeding records that is currently underused by reintroduction practitioners. The direct integration of knowledge derived from captive breeding (where available) with decision-making for reintroductions, as described here, will help navigate these uncertainties, which would benefit the conservation of both understudied and well-known species around the world.
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Affiliation(s)
- Kiarrah J Smith
- Fenner School of Environment and Society, The Australian National University, Acton, Australian Capital Territory 2601, Australia
| | - Maldwyn J Evans
- Fenner School of Environment and Society, The Australian National University, Acton, Australian Capital Territory 2601, Australia
- Department of Ecosystem Studies, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Iain J Gordon
- Fenner School of Environment and Society, The Australian National University, Acton, Australian Capital Territory 2601, Australia
- The James Hutton Institute, Dundee DD2 5DA, United Kingdom
- Central Queensland University, Townsville, Queensland 4810, Australia
- Land and Water, CSIRO, Townsville, Queensland 4810, Australia
- Lead, Protected Places Mission, National Environmental Science Program, Reef and Rainforest Research Centre, Cairns, Queensland 4870, Australia
| | - Jennifer C Pierson
- Fenner School of Environment and Society, The Australian National University, Acton, Australian Capital Territory 2601, Australia
- Australian Wildlife Conservancy, Subiaco East, Western Australia 6008, Australia
- Centre for Conservation Ecology and Genomics, Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory 2617, Australia
| | - Jenny Newport
- Fenner School of Environment and Society, The Australian National University, Acton, Australian Capital Territory 2601, Australia
| | - Adrian D Manning
- Fenner School of Environment and Society, The Australian National University, Acton, Australian Capital Territory 2601, Australia
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5
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Dodge TO, Farquharson KA, Ford C, Cavanagh L, Schubert K, Schumer M, Belov K, Hogg CJ. Genomes of two Extinct-in-the-Wild reptiles from Christmas Island reveal distinct evolutionary histories and conservation insights. Mol Ecol Resour 2023. [PMID: 36872490 DOI: 10.1111/1755-0998.13780] [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: 11/22/2022] [Revised: 02/16/2023] [Accepted: 03/02/2023] [Indexed: 03/07/2023]
Abstract
Genomics can play important roles in biodiversity conservation, especially for Extinct-in-the-Wild species where genetic factors greatly influence risk of total extinction and probability of successful reintroductions. The Christmas Island blue-tailed skink (Cryptoblepharus egeriae) and Lister's gecko (Lepidodactylus listeri) are two endemic reptile species that went extinct in the wild shortly after the introduction of a predatory snake. After a decade of management, captive populations have expanded from 66 skinks and 43 geckos to several thousand individuals; however, little is known about patterns of genetic variation in these species. Here, we use PacBio HiFi long-read and Hi-C sequencing to generate highly contiguous reference genomes for both reptiles, including the XY chromosome pair in the skink. We then analyse patterns of genetic diversity to infer ancient demography and more recent histories of inbreeding. We observe high genome-wide heterozygosity in the skink (0.007 heterozygous sites per base-pair) and gecko (0.005), consistent with large historical population sizes. However, nearly 10% of the blue-tailed skink reference genome falls within long (>1 Mb) runs of homozygosity (ROH), resulting in homozygosity at all major histocompatibility complex (MHC) loci. In contrast, we detect a single ROH in Lister's gecko. We infer from the ROH lengths that related skinks may have established the captive populations. Despite a shared recent extinction in the wild, our results suggest important differences in these species' histories and implications for management. We show how reference genomes can contribute evolutionary and conservation insights, and we provide resources for future population-level and comparative genomic studies in reptiles.
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Affiliation(s)
- Tristram O Dodge
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
- Department of Biology, Stanford University, Stanford, California, USA
- Australian-American Fulbright Commission, Deakin, Australian Capital Territory, Australia
| | - Katherine A Farquharson
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Claire Ford
- Taronga Conservation Society Australia, Mosman, New South Wales, Australia
| | - Lisa Cavanagh
- Taronga Conservation Society Australia, Mosman, New South Wales, Australia
| | | | - Molly Schumer
- Department of Biology, Stanford University, Stanford, California, USA
| | - Katherine Belov
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
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6
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Hogg CJ, Silver L, McLennan EA, Belov K. Koala Genome Survey: An Open Data Resource to Improve Conservation Planning. Genes (Basel) 2023; 14:genes14030546. [PMID: 36980819 PMCID: PMC10048327 DOI: 10.3390/genes14030546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/15/2023] [Accepted: 02/20/2023] [Indexed: 02/24/2023] Open
Abstract
Genome sequencing is a powerful tool that can inform the management of threatened species. Koalas (Phascolarctos cinereus) are a globally recognized species that captured the hearts and minds of the world during the 2019/2020 Australian megafires. In 2022, koalas were listed as ‘Endangered’ in Queensland, New South Wales, and the Australian Capital Territory. Populations have declined because of various threats such as land clearing, habitat fragmentation, and disease, all of which are exacerbated by climate change. Here, we present the Koala Genome Survey, an open data resource that was developed after the Australian megafires. A systematic review conducted in 2020 demonstrated that our understanding of genomic diversity within koala populations was scant, with only a handful of SNP studies conducted. Interrogating data showed that only 6 of 49 New South Wales areas of regional koala significance had meaningful genome-wide data, with only 7 locations in Queensland with SNP data and 4 locations in Victoria. In 2021, we launched the Koala Genome Survey to generate resequenced genomes across the Australian east coast. We have publicly released 430 koala genomes (average coverage: 32.25X, range: 11.3–66.8X) on the Amazon Web Services Open Data platform to accelerate research that can inform current and future conservation planning.
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7
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Stojanovic D, McLennan E, Olah G, Cobden M, Heinsohn R, Manning AD, Alves F, Hogg C, Rayner L. Reproductive skew in a Vulnerable bird favors breeders that monopolize nest cavities. Anim Conserv 2023. [DOI: 10.1111/acv.12855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- D. Stojanovic
- Fenner School of Environment and Society Australian National University Canberra Australia
| | - E. McLennan
- School of Life & Environmental Sciences The University of Sydney Sydney New South Wales Australia
| | - G. Olah
- Fenner School of Environment and Society Australian National University Canberra Australia
| | - M. Cobden
- Fenner School of Environment and Society Australian National University Canberra Australia
| | - R. Heinsohn
- Fenner School of Environment and Society Australian National University Canberra Australia
| | - A. D. Manning
- Fenner School of Environment and Society Australian National University Canberra Australia
| | - F. Alves
- Fenner School of Environment and Society Australian National University Canberra Australia
| | - C. Hogg
- School of Life & Environmental Sciences The University of Sydney Sydney New South Wales Australia
| | - L. Rayner
- ACT Parks and Conservation Service, Australian Capital Territory Government Canberra Australia
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8
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Davidović S, Marinković S, Hribšek I, Patenković A, Stamenković-Radak M, Tanasković M. Sex ratio and relatedness in the Griffon vulture ( Gyps fulvus) population of Serbia. PeerJ 2022; 10:e14477. [PMID: 36523455 PMCID: PMC9745909 DOI: 10.7717/peerj.14477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 11/07/2022] [Indexed: 12/12/2022] Open
Abstract
Background Once a widespread 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 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 programmes. The available genetic data for this valuable population are scarce and as a protected species that belongs to the highly endangered vulture group, it needs to be well described so that it can be properly managed and used as a restocking population. Considering the serious recent bottleneck event that the Griffon vulture population from Serbia experienced we estimated the overall relatedness among the birds from this population. Sex ratio, another important parameter that shows the vitality and strength of the population was evaluated as well. Methods During the annual monitoring that was performed in the period from 2013-2021, we collected blood samples from individual birds that were marked in the nests. In total, 169 samples were collected and each was used for molecular sexing while 58 presumably unrelated birds from different nests were used for inbreeding and relatedness analyses. The relatedness was estimated using both biparentally (10 microsatellite loci) and uniparentally (Cytb and D-loop I of mitochondrial DNA) inherited markers. Results The level of inbreeding was relatively high and on average it was 8.3% while the mean number of relatives for each bird was close to three. The sex ratio was close to 1:1 and for the analysed period of 9 years, it didn't demonstrate a statistically significant deviation from the expected ratio of 1:1, suggesting that this is a stable and healthy population. Our data suggest that, even though a relatively high level of inbreeding can be detected among the individual birds, the Griffon vulture population from Serbia can be used as a source population for restocking and reintroduction programmes in the region. These data combined with previously observed genetic differentiation between the populations from the Iberian and Balkan Peninsulas suggest that the introduction of foreign birds should be avoided and that local birds 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, Belgrade, Serbia,Birds of Prey Protection Foundation, Belgrade, Serbia
| | - Saša Marinković
- Birds of Prey Protection Foundation, Belgrade, Serbia,Department of Ecology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Irena Hribšek
- Birds of Prey Protection Foundation, Belgrade, Serbia,Natural History Museum Belgrade, Belgrade, Serbia
| | - Aleksandra Patenković
- Department of Genetics of Populations and Ecogenotoxicology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - 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, Belgrade, Serbia,Faculty of Biology, University of Belgrade, 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, Belgrade, Serbia
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Hauser S, Galla SJ, Putnam AS, Steeves TE, Latch EK. Comparing genome-based estimates of relatedness for use in pedigree-based conservation management. Mol Ecol Resour 2022; 22:2546-2558. [PMID: 35510790 DOI: 10.1111/1755-0998.13630] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 02/28/2022] [Accepted: 03/30/2022] [Indexed: 12/01/2022]
Abstract
Researchers have long debated which estimator of relatedness best captures the degree of relationship between two individuals. In the genomics era, this debate continues, with relatedness estimates being sensitive to the methods used to generate markers, marker quality, and levels of diversity in sampled individuals. Here, we compare six commonly used genome-based relatedness estimators (kinship genetic distance (KGD), Wang Maximum Likelihood (TrioML), Queller and Goodnight (Rxy ), Kinship INference for Genome-wide association studies (KING-robust), and Pairwise Relatedness (RAB ), allele-sharing co-ancestry (AS)) across five species bred in captivity-including three birds and two mammals-with varying degrees of reliable pedigree data, using reduced-representation and whole genome resequencing data. Genome-based relatedness estimates varied widely across estimators, sequencing methods, and species, yet the most consistent results for known first order relationships were found using Rxy , RAB , and AS. However, AS was found to be less consistently correlated with known pedigree relatedness than either Rxy or RAB . Our combined results indicate there is not a single genome-based estimator that is ideal across different species and data types. To determine the most appropriate genome-based relatedness estimator for each new dataset, we recommend assessing the relative: (1) correlation of candidate estimators with known relationships in the pedigree and (2) precision of candidate estimators with known first-order relationships. These recommendations are broadly applicable to conservation breeding programs, particularly where genome-based estimates of relatedness can complement and complete poorly pedigreed populations. Given a growing interest in the application of wild pedigrees, our results are also applicable to in-situ wildlife management.
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Affiliation(s)
- Samantha Hauser
- Department of Biological Sciences, University of Wisconsin, Milwaukee, Wisconsin, USA.,Embark Veterinary, Inc., Boston, Massachusetts, United States of America
| | - Stephanie J Galla
- School of Biological Sciences, University of Canterbury, New Zealand.,Department of Biological Sciences, Boise State University, Boise, Idaho, USA
| | - Andrea S Putnam
- Department of Exhibit-Curators, San Diego Zoo Wildlife Alliance, San Diego, California, USA
| | - Tammy E Steeves
- School of Biological Sciences, University of Canterbury, New Zealand
| | - Emily K Latch
- Department of Biological Sciences, University of Wisconsin, Milwaukee, Wisconsin, USA
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10
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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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11
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Barrett KG, Amaral G, Elphinstone M, McAdie ML, Davis CS, Janes JK, Carnio J, Moehrenschlager A, Gorrell JC. Genetic management on the brink of extinction: sequencing microsatellites does not improve estimates of inbreeding in wild and captive Vancouver Island marmots (Marmota vancouverensis). CONSERV GENET 2022; 23:417-428. [PMID: 35401067 PMCID: PMC8948115 DOI: 10.1007/s10592-022-01429-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 01/04/2022] [Indexed: 11/27/2022]
Abstract
Captive breeding is often a last resort management option in the conservation of endangered species which can in turn lead to increased risk of inbreeding depression and loss of genetic diversity. Thus, recording breeding events via studbook for the purpose of estimating relatedness, and facilitating mating pair selection to minimize inbreeding, is common practice. However, as founder relatedness is often unknown, loss of genetic variation and inbreeding cannot be entirely avoided. Molecular genotyping is slowly being adopted in captive breeding programs, however achieving sufficient resolution can be challenging in small, low diversity, populations. Here, we evaluate the success of the Vancouver Island marmot (Marmota vancouverensis; VIM; among the worlds most endangered mammals) captive breeding program in preventing inbreeding and maintaining genetic diversity. We explored the use of high-throughput amplicon sequencing of microsatellite regions to assay greater genetic variation in both captive and wild populations than traditional length-based fragment analysis. Contrary to other studies, this method did not considerably increase diversity estimates, suggesting: (1) that the technique does not universally improve resolution, and (2) VIM have exceedingly low diversity. Studbook estimates of pairwise relatedness and inbreeding in the current population were weakly, but positively, correlated to molecular estimates. Thus, current studbooks are moderately effective at predicting genetic similarity when founder relatedness is known. Finally, we found that captive and wild populations did not differ in allelic frequencies, and conservation efforts to maintain diversity have been successful with no significant decrease in diversity over the last three generations.
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Affiliation(s)
- Kimberley G. Barrett
- Biology Department, Vancouver Island University, Nanaimo, BC V9R 5S5 Canada
- Present Address: Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2R3 Canada
| | - Geneviève Amaral
- Biology Department, Vancouver Island University, Nanaimo, BC V9R 5S5 Canada
- Present Address: Island Medical Program, University of Victoria, 3800 Finnerty Road, Victoria, BC V8P 5C2 Canada
| | | | | | - Corey S. Davis
- Present Address: Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2R3 Canada
| | - Jasmine K. Janes
- Biology Department, Vancouver Island University, Nanaimo, BC V9R 5S5 Canada
- School of Environmental and Rural Science, University of New England, Armidale, NSW 2351 Australia
| | - John Carnio
- Marmot Recovery Foundation, Nanaimo, BC V9R 6X9 Canada
| | - Axel Moehrenschlager
- Wilder Institute Calgary Zoo, Calgary, AB T2E 7V6 Canada
- IUCN Species Survival Commission, Conservation Translocation Specialist Group, Calgary, AB Canada
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12
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Gooley RM, Dicks KL, Ferrie GM, Lacy RC, Ballou JD, Callicrate T, Senn H, Koepfli KP, Edwards CW, Pukazhenthi BS. Applying genomics to metapopulation management in North American insurance populations of southern sable antelope (Hippotragus niger niger) and addra gazelle (Nanger dama ruficollis). Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2021.e01969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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13
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Alvarez‐Estape M, Fontsere C, Serres‐Armero A, Kuderna LF, Dobrynin P, Guidara H, Pukazhenthi BS, Koepfli K, Marques‐Bonet T, Moreno E, Lizano E. Insights from the rescue and breeding management of Cuvier’s gazelle (
Gazella cuvieri
) through whole genome sequencing. Evol Appl 2021; 15:351-364. [PMID: 35386395 PMCID: PMC8965372 DOI: 10.1111/eva.13336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 12/03/2021] [Indexed: 11/29/2022] Open
Affiliation(s)
- Marina Alvarez‐Estape
- Institute of Evolutionary Biology UPF‐CSIC PRBB, Dr. Aiguader 88 08003 Barcelona Spain
| | - Claudia Fontsere
- Institute of Evolutionary Biology UPF‐CSIC PRBB, Dr. Aiguader 88 08003 Barcelona Spain
| | - Aitor Serres‐Armero
- Institute of Evolutionary Biology UPF‐CSIC PRBB, Dr. Aiguader 88 08003 Barcelona Spain
| | - Lukas F.K. Kuderna
- Institute of Evolutionary Biology UPF‐CSIC PRBB, Dr. Aiguader 88 08003 Barcelona Spain
| | - Pavel Dobrynin
- ITMO University Computer Technologies Laboratory St. Petersburg Russian Federation
- Smithsonian Conservation Biology Institute Center for Species Survival National Zoological Park Front Royal, VA and Washington DC USA
| | - Héla Guidara
- Direction Générale des Forêts 30 rue Alain Savary 1002 Tunis Tunisia
| | - Budhan S. Pukazhenthi
- Smithsonian Conservation Biology Institute Center for Species Survival National Zoological Park Front Royal, VA and Washington DC USA
| | - Klaus‐Peter Koepfli
- ITMO University Computer Technologies Laboratory St. Petersburg Russian Federation
- Smithsonian Conservation Biology Institute Center for Species Survival National Zoological Park Front Royal, VA and Washington DC USA
- Smithsonian‐Mason School of Conservation Front Royal VA USA
| | - Tomas Marques‐Bonet
- Institute of Evolutionary Biology UPF‐CSIC PRBB, Dr. Aiguader 88 08003 Barcelona Spain
- CNAG‐CRG Centre for Genomic Regulation (CRG) Barcelona Institute of Science and Technology (BIST) Baldiri I Reixac 408028 Barcelona Spain
- Institut Català de Paleontologia Miquel Crusafont Universitat Autònoma de Barcelona (UAB) Edifici ICTA‐ICP, c/ Columnes s/n Cerdanyola del Vallès 08193 Barcelona Spain
- Catalan Institution of Research and Advanced Studies (ICREA) Passeig de Lluís Companys 23 08010 Barcelona Spain
| | - Eulalia Moreno
- Dept Ecología Funcional y Evolutiva Estación Experimental de Zonas Áridas‐CSIC E‐04120 La Cañada de San Urbano Almería Spain
| | - Esther Lizano
- Institute of Evolutionary Biology UPF‐CSIC PRBB, Dr. Aiguader 88 08003 Barcelona Spain
- Institut Català de Paleontologia Miquel Crusafont Universitat Autònoma de Barcelona (UAB) Edifici ICTA‐ICP, c/ Columnes s/n Cerdanyola del Vallès 08193 Barcelona Spain
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14
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New developments in the field of genomic technologies and their relevance to conservation management. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01415-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
AbstractRecent technological advances in the field of genomics offer conservation managers and practitioners new tools to explore for conservation applications. Many of these tools are well developed and used by other life science fields, while others are still in development. Considering these technological possibilities, choosing the right tool(s) from the toolbox is crucial and can pose a challenging task. With this in mind, we strive to inspire, inform and illuminate managers and practitioners on how conservation efforts can benefit from the current genomic and biotechnological revolution. With inspirational case studies we show how new technologies can help resolve some of the main conservation challenges, while also informing how implementable the different technologies are. We here focus specifically on small population management, highlight the potential for genetic rescue, and discuss the opportunities in the field of gene editing to help with adaptation to changing environments. In addition, we delineate potential applications of gene drives for controlling invasive species. We illuminate that the genomic toolbox offers added benefit to conservation efforts, but also comes with limitations for the use of these novel emerging techniques.
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15
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IUCN captive management guidelines support ex situ conservation of the Bengal florican Houbaropsis bengalensis blandini. ORYX 2021. [DOI: 10.1017/s0030605319001510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
AbstractEx situ conservation of species is risky and expensive, but it can prevent extinction when in situ conservation fails. We used the IUCN Guidelines on the Use of Ex Situ Management for Species Conservation to evaluate whether to begin ex situ conservation for the South-east Asian subspecies of Bengal florican Houbaropsis bengalensis blandini, which is predicted to be extinct in the wild within 5 years. To inform our decision, we developed a decision tree, and used a demographic model to evaluate the probability of establishing a captive population under a range of husbandry scenarios and egg harvest regimes, and compared this with the probability of the wild population persisting. The model showed that if ex situ conservation draws on international best practice in bustard husbandry there is a high probability of establishing a captive population, but the wild population is unlikely to persist. We identified and evaluated the practical risks associated with ex situ conservation, and documented our plans to mitigate them. Modelling shows that it is unlikely that birds could be released within 20–30 years, by which time genetic, morphological and behavioural changes in the captive population, combined with habitat loss and extinction of the wild population, make it unlikely that Bengal florican could be released into a situation approximating their current wild state. We considered the philosophical and practical implications through a decision tree so that our decision to begin ex situ management is not held back by our preconceived notions of what it means to be wild.
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16
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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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17
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Dickel L, Arcese P, Nietlisbach P, Keller LF, Jensen H, Reid JM. Are immigrants outbred and unrelated? Testing standard assumptions in a wild metapopulation. Mol Ecol 2021; 30:5674-5686. [PMID: 34516687 DOI: 10.1111/mec.16173] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/19/2021] [Accepted: 08/23/2021] [Indexed: 11/30/2022]
Abstract
Immigration into small recipient populations is expected to alleviate inbreeding and increase genetic variation, and hence facilitate population persistence through genetic and/or evolutionary rescue. Such expectations depend on three standard assumptions: that immigrants are outbred, unrelated to existing natives at arrival, and unrelated to each other. These assumptions are rarely explicitly verified, including in key field systems in evolutionary ecology. Yet, they could be violated due to non-random or repeated immigration from adjacent small populations. We combined molecular genetic marker data for 150-160 microsatellite loci with comprehensive pedigree data to test the three assumptions for a song sparrow (Melospiza melodia) population that is a model system for quantifying effects of inbreeding and immigration in the wild. Immigrants were less homozygous than existing natives on average, with mean homozygosity that closely resembled outbred natives. Immigrants can therefore be considered outbred on the focal population scale. Comparisons of homozygosity of real or hypothetical offspring of immigrant-native, native-native and immigrant-immigrant pairings implied that immigrants were typically unrelated to existing natives and to each other. Indeed, immigrants' offspring would be even less homozygous than outbred individuals on the focal population scale. The three standard assumptions of population genetic and evolutionary theory were consequently largely validated. Yet, our analyses revealed some deviations that should be accounted for in future analyses of heterosis and inbreeding depression, implying that the three assumptions should be verified in other systems to probe patterns of non-random or repeated dispersal and facilitate precise and unbiased estimation of key evolutionary parameters.
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Affiliation(s)
- Lisa Dickel
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - Peter Arcese
- Department of Forest & Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Pirmin Nietlisbach
- School of Biological Sciences, Illinois State University, Normal, Illinois, USA
| | - Lukas F Keller
- Department of Evolutionary Biology & Environmental Studies, University of Zurich, Zurich, Switzerland.,Zoological Museum, University of Zurich, Zurich, Switzerland
| | - Henrik Jensen
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - Jane M Reid
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway.,School of Biological Sciences, University of Aberdeen, Aberdeen, UK
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18
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Flanagan AM, Masuda B, Grueber CE, Sutton JT. Moving from trends to benchmarks by using regression tree analysis to find inbreeding thresholds in a critically endangered bird. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2021; 35:1278-1287. [PMID: 33025666 DOI: 10.1111/cobi.13650] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 09/03/2020] [Accepted: 10/02/2020] [Indexed: 06/11/2023]
Abstract
Understanding how inbreeding affects endangered species in conservation breeding programs is essential for their recovery. The Hawaiian Crow ('Alalā) (Corvus hawaiiensis) is one of the world's most endangered birds. It went extinct in the wild in 2002, and, until recent release efforts starting in 2016, nearly all of the population remained under human care for conservation breeding. Using pedigree inbreeding coefficients (F), we evaluated the effects of inbreeding on Hawaiian Crow offspring survival and reproductive success. We used regression tree analysis to identify the level of inbreeding (i.e., inbreeding threshold) that explains a substantial decrease in 'Alalā offspring survival to recruitment. Similar to a previous study of inbreeding in 'Alalā, we found that inbreeding had a negative impact on offspring survival but that parental (vs. artificial) egg incubation improved offspring survival to recruitment. Furthermore, we found that inbreeding did not substantially affect offspring reproductive success, based on the assumption that offspring that survive to adulthood breed with distantly related mates. Our novel application of regression tree analysis showed that offspring with inbreeding levels exceeding F = 0.098 were 69% less likely to survive to recruitment than more outbred offspring, providing a specific threshold value for ongoing population management. Our results emphasize the importance of assessing inbreeding depression across all life history stages, confirm the importance of prioritizing parental over artificial egg incubation in avian conservation breeding programs, and demonstrate the utility of regression tree analysis as a tool for identifying inbreeding thresholds, if present, in any pedigree-managed population.
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Affiliation(s)
- Alison M Flanagan
- Hawaii Endangered Bird Conservation Program, Institute for Conservation Research, San Diego Zoo Global, P.O. Box 39, Volcano, HI, 96785, U.S.A
| | - Bryce Masuda
- Hawaii Endangered Bird Conservation Program, Institute for Conservation Research, San Diego Zoo Global, P.O. Box 39, Volcano, HI, 96785, U.S.A
| | - Catherine E Grueber
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Jolene T Sutton
- Department of Biology, University of Hawaii at Hilo, Hilo, HI, 96720, U.S.A
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19
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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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20
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Farquharson KA, Hogg CJ, Grueber CE. Offspring survival changes over generations of captive breeding. Nat Commun 2021; 12:3045. [PMID: 34031378 PMCID: PMC8144597 DOI: 10.1038/s41467-021-22631-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 03/11/2021] [Indexed: 11/28/2022] Open
Abstract
Conservation breeding programs such as zoos play a major role in preventing extinction, but their sustainability may be impeded by neutral and adaptive population genetic change. These changes are difficult to detect for a single species or context, and impact global conservation efforts. We analyse pedigree data from 15 vertebrate species – over 30,000 individuals – to examine offspring survival over generations of captive breeding. Even accounting for inbreeding, we find that the impacts of increasing generations in captivity are highly variable across species, with some showing substantial increases or decreases in offspring survival over generations. We find further differences between dam and sire effects in first- versus multi-generational analysis. Crucially, our multispecies analysis reveals that responses to captivity could not be predicted from species’ evolutionary (phylogenetic) relationships. Even under best-practice captive management, generational fitness changes that cannot be explained by known processes (such as inbreeding depression), are occurring. Captive breeding could prevent species extinctions, but selection for captivity may decrease fitness. Here the authors analyse pedigree data on 15 long-running vertebrate breeding programs and find generational fitness changes that processes such as inbreeding depression cannot explain.
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Affiliation(s)
- Katherine A Farquharson
- The University of Sydney, School of Life and Environmental Sciences, Faculty of Science, Sydney, NSW, Australia
| | - Carolyn J Hogg
- The University of Sydney, School of Life and Environmental Sciences, Faculty of Science, Sydney, NSW, Australia
| | - Catherine E Grueber
- The University of Sydney, School of Life and Environmental Sciences, Faculty of Science, Sydney, NSW, Australia.
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21
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Petty LE, Phillippi-Falkenstein K, Kubisch HM, Raveendran M, Harris RA, Vallender EJ, Huff CD, Bohm RP, Rogers J, Below JE. Pedigree reconstruction and distant pairwise relatedness estimation from genome sequence data: A demonstration in a population of rhesus macaques (Macaca mulatta). Mol Ecol Resour 2021; 21:1333-1346. [PMID: 33386679 PMCID: PMC8247968 DOI: 10.1111/1755-0998.13317] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 11/13/2020] [Accepted: 12/07/2020] [Indexed: 12/30/2022]
Abstract
A primary challenge in the analysis of free‐ranging animal populations is the accurate estimation of relatedness among individuals. Many aspects of population analysis rely on knowledge of relatedness patterns, including socioecology, demography, heritability and gene mapping analyses, wildlife conservation and the management of breeding colonies. Methods for determining relatedness using genome‐wide data have improved our ability to determine kinship and reconstruct pedigrees in humans. However, methods for reconstructing complex pedigree structures and estimating distant relatedness (beyond third‐degree) have not been widely applied to other species. We sequenced the genomes of 150 male rhesus macaques from the Tulane National Primate Research Center colony to estimate pairwise relatedness, reconstruct closely related pedigrees, estimate more distant relationships and augment colony records. Methods for determining relatedness developed for human genetic data were applied and evaluated in the analysis of nonhuman primates, including identity‐by‐descent‐based methods for pedigree reconstruction and shared segment‐based inference of more distant relatedness. We compared the genotype‐based pedigrees and estimated relationships to available colony pedigree records and found high concordance (95.5% agreement) between expected and identified relationships for close relatives. In addition, we detected distant relationships not captured in colony records, including some as distant as twelfth‐degree. Furthermore, while deep sequence coverage is preferable, we show that this approach can also provide valuable information when only low‐coverage (5×) sequence data is available. Our findings demonstrate the value of these methods for determination of relatedness in various animal populations, with diverse applications to conservation biology, evolutionary and ecological research and biomedical studies.
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Affiliation(s)
- Lauren E Petty
- Vanderbilt Genetics Institute and Department of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - H Michael Kubisch
- Division of Veterinary Medicine, Tulane National Primate Research Center, Covington, LA, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - R Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Eric J Vallender
- Division of Veterinary Medicine, Tulane National Primate Research Center, Covington, LA, USA.,Department of Psychiatry and Human Behavior, University of Mississippi Medical Center, Jackson, MS, USA
| | - Chad D Huff
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rudolf P Bohm
- Division of Veterinary Medicine, Tulane National Primate Research Center, Covington, LA, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer E Below
- Vanderbilt Genetics Institute and Department of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
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22
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Iglesias Pastrana C, Navas González FJ, Ruiz Aguilera MJ, Dávila García JA, Delgado Bermejo JV, Abelló MT. White-naped mangabeys' viable insurance population within European Zoo Network. Sci Rep 2021; 11:674. [PMID: 33436901 PMCID: PMC7804940 DOI: 10.1038/s41598-020-80281-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 12/18/2020] [Indexed: 01/29/2023] Open
Abstract
The success and viability of an ex-situ conservation program lie in the establishment and potential maintenance of a demographically and genetically viable insurance population. Such population reserve may support reintroduction and reinforcement activities of wild populations. White-naped mangabeys are endangered restricted-range African primates which have experienced a dramatic population decrease in their natural habitats over the last few decades. Since 2001, some European zoos singularly monitor an ex-situ population aiming to seek the recovery of the current wild population. The aim of the present paper is to evaluate the genetic status and population demographics of European zoo-captive white-naped mangabeys based on pedigree data. The captive population is gradually growing and preserves specific reproductive and demographic parameters linked to the species. The intensive management program that is implemented has brought about the minimization of inbreeding and average relatedness levels, thus maintaining high levels of genetic diversity despite the existence of fragmented populations. This finding suggests white-naped mangabey ex-situ preservation actions may be a good example of multifaceted conservation throughout studbook management which could be used as a model for other ex-situ live-animal populations.
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Affiliation(s)
| | | | | | | | | | - María Teresa Abelló
- White-naped mangabey EEP Coordination (EAZA: European Association of Zoos & Aquariums), Parc Zoològic de Barcelona, Barcelona, Spain
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23
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Wood J, Ballou JD, Callicrate T, Fant JB, Griffith MP, Kramer AT, Lacy RC, Meyer A, Sullivan S, Traylor‐Holzer K, Walsh SK, Havens K. Applying the zoo model to conservation of threatened exceptional plant species. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2020; 34:1416-1425. [PMID: 32233087 PMCID: PMC7754355 DOI: 10.1111/cobi.13503] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 03/14/2020] [Accepted: 03/18/2020] [Indexed: 05/30/2023]
Abstract
Maintaining a living plant collection is the most common method of ex situ conservation for plant species that cannot be seed banked (i.e., exceptional species). Viability of living collections, and their value for future conservation efforts, can be limited without coordinated efforts to track and manage individuals across institutions. Using a pedigree-focused approach, the zoological community has established an inter-institutional infrastructure to support long-term viability of captive animal populations. We assessed the ability of this coordinated metacollection infrastructure to support the conservation of 4 plant species curated in living collections at multiple botanic gardens around the world. Limitations in current practices include the inability to compile, share, and analyze plant collections data at the individual level, as well as difficulty in tracking original provenance of ex situ material. The coordinated metacollection framework used by zoos can be adopted by the botanical community to improve conservation outcomes by minimizing the loss of genetic diversity in collections. We suggest actions to improve ex situ conservation of exceptional plant species, including developing a central database to aggregate data and track unique individuals of priority threatened species among institutions and adapting a pedigree-based population management tool that incorporates life-history aspects unique to plants. If approached collaboratively across regional, national, and global scales, these actions could transform ex situ conservation of threatened plant species.
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Affiliation(s)
- Jordan Wood
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden1000 Lake Cook RoadGlencoeIL60022U.S.A.
| | - Jonathan D. Ballou
- Smithsonian Conservation Biology Institute3001 Connecticut AvenueNW WashingtonD.C.20008U.S.A.
| | - Taylor Callicrate
- Species Conservation Toolkit InitiativeChicago Zoological Society3300 Golf RoadBrookfieldIL60513U.S.A.
| | - Jeremie B. Fant
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden1000 Lake Cook RoadGlencoeIL60022U.S.A.
| | | | - Andrea T. Kramer
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden1000 Lake Cook RoadGlencoeIL60022U.S.A.
| | - Robert C. Lacy
- Species Conservation Toolkit InitiativeChicago Zoological Society3300 Golf RoadBrookfieldIL60513U.S.A.
| | - Abby Meyer
- Botanic Gardens Conservation International, U.S. at The Huntington Library, Art Museum & Botanical Gardens1151 Oxford RoadSan MarinoCA91108U.S.A.
| | - Sara Sullivan
- Species Conservation Toolkit InitiativeChicago Zoological Society3300 Golf RoadBrookfieldIL60513U.S.A.
| | - Kathy Traylor‐Holzer
- IUCN SSC Conservation Planning Specialist Group12101 Johnny Cake Ridge RoadApple ValleyMN55124U.S.A.
| | - Seana K. Walsh
- Department of Science and ConservationNational Tropical Botanical Garden3530 Papalina RoadKalāheoHI96741U.S.A.
| | - Kayri Havens
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden1000 Lake Cook RoadGlencoeIL60022U.S.A.
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24
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Rabier R, Robert A, Lacroix F, Lesobre L. Genetic assessment of a conservation breeding program of the houbara bustard (Chlamydotis undulata undulata) in Morocco, based on pedigree and molecular analyses. Zoo Biol 2020; 39:422-435. [PMID: 32956518 DOI: 10.1002/zoo.21569] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 08/20/2020] [Accepted: 09/04/2020] [Indexed: 12/29/2022]
Abstract
Protection and restoration of species in the wild may require conservation breeding programs under genetic management to minimize deleterious effects of genetic changes that occur in captivity, while preserving populations' genetic diversity and evolutionary resilience. Here, through interannual pedigree analyses, we first assessed the efficiency of a 21-year genetic management, including minimization of mean kinship, inbreeding avoidance, and regular addition of founders, of a conservation breeding program targeting on Houbara bustard (Chlamydotis undulata undulata) in Morocco. Secondly, we compared pedigree analyses, the classical way of assessing and managing genetic diversity in captivity, to molecular analyses based on seven microsatellites. Pedigree-based results indicated an efficient maintenance of the genetic diversity (99% of the initial genetic diversity retained) while molecular-based results indicated an increase in allelic richness and an increase in unbiased expected heterozygosity across time. The pedigree-based average inbreeding coefficient F remained low (between 0.0004 and 0.003 in 2017) while the proportion of highly inbred individuals (F > .1) decreased over time and reached 0.2% in 2017. Furthermore, pedigree-based F and molecular-based individual multilocus heterozygosity were weakly negatively correlated, (Pearson's r = -.061 when considering all genotyped individuals), suggesting that they cannot be considered as alternatives, but rather as complementary sources of information. These findings suggest that a strict genetic monitoring and management, based on both pedigree and molecular tools can help mitigate genetic changes and allow to preserve genetic diversity and evolutionary resilience in conservation breeding programs.
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Affiliation(s)
- Robin Rabier
- Reneco International Wildlife Consultant 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
| | - Alexandre 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
| | - Frédéric Lacroix
- Reneco International Wildlife Consultant LLC, Abu Dhabi, United Arab Emirates.,Emirates Center for Wildlife Propagation, Missour, Morocco
| | - Loïc Lesobre
- Reneco International Wildlife Consultant LLC, Abu Dhabi, United Arab Emirates.,Emirates Center for Wildlife Propagation, Missour, Morocco
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25
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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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26
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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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27
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McLennan EA, Grueber CE, Wise P, Belov K, Hogg CJ. Mixing genetically differentiated populations successfully boosts diversity of an endangered carnivore. Anim Conserv 2020. [DOI: 10.1111/acv.12589] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- E. A. McLennan
- School of Life and Environmental Sciences University of Sydney Sydney NSW Australia
| | - C. E. Grueber
- School of Life and Environmental Sciences University of Sydney Sydney NSW Australia
- San Diego Zoo Global San Diego CA USA
| | - P. Wise
- Save the Tasmanian Devil Program, DPIPWE Hobart Tas Australia
| | - K. Belov
- School of Life and Environmental Sciences University of Sydney Sydney NSW Australia
| | - C. J. Hogg
- School of Life and Environmental Sciences University of Sydney Sydney NSW Australia
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28
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Jensen EL, McClenaghan B, Ford B, Lentini A, Kerr KCR, Russello MA. Genotyping on the ark: A synthesis of genetic resources available for species in zoos. Zoo Biol 2020; 39:257-262. [DOI: 10.1002/zoo.21539] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 11/21/2019] [Accepted: 03/09/2020] [Indexed: 01/23/2023]
Affiliation(s)
- Evelyn L. Jensen
- Department of BiologyUniversity of British Columbia Okanagan Kelowna Canada
- Department of Ecology and Evolutionary BiologyYale University New Haven
| | - Beverly McClenaghan
- Wildlife and Science DivisionToronto Zoo Toronto
- Centre for Environmental Genomics ApplicationseDNAtec Inc. St. John's Canada
| | - Brett Ford
- Department of BiologyUniversity of British Columbia Okanagan Kelowna Canada
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29
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Lott MJ, Wright BR, Kemp LF, Johnson RN, Hogg CJ. Genetic Management of Captive and Reintroduced Bilby Populations. J Wildl Manage 2019. [DOI: 10.1002/jwmg.21777] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Matthew J. Lott
- Australian Museum Research InstituteAustralian Museum 1 William Street Sydney New South Wales 2010 Australia
| | - Belinda R. Wright
- School of Life and Environmental SciencesThe University of Sydney Camperdown 2006 New South Wales Australia
| | - Leah F. Kemp
- Australian Wildlife Conservancy 5/280 Hay Street Subiaco 6008 Western Australia Australia
| | - Rebecca N. Johnson
- Australian Museum Research InstituteAustralian Museum 1 William Street Sydney New South Wales 2010 Australia
| | - Carolyn J. Hogg
- School of Life and Environmental SciencesThe University of Sydney Camperdown 2006 New South Wales Australia
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30
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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: 53] [Impact Index Per Article: 10.6] [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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31
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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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