1
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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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2
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Carroll RA, Rice ES, Murphy WJ, Lyons LA, Thibaud-Nissen F, Coghill LM, Swanson WF, Terio KA, Boyd T, Warren WC. A chromosome-scale fishing cat reference genome for the evaluation of potential germline risk variants. Sci Rep 2024; 14:8073. [PMID: 38580653 PMCID: PMC10997796 DOI: 10.1038/s41598-024-56003-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 02/29/2024] [Indexed: 04/07/2024] Open
Abstract
The fishing cat, Prionailurus viverrinus, faces a population decline, increasing the importance of maintaining healthy zoo populations. Unfortunately, zoo-managed individuals currently face a high prevalence of transitional cell carcinoma (TCC), a form of bladder cancer. To investigate the genetics of inherited diseases among captive fishing cats, we present a chromosome-scale assembly, generate the pedigree of the zoo-managed population, reaffirm the close genetic relationship with the Asian leopard cat (Prionailurus bengalensis), and identify 7.4 million single nucleotide variants (SNVs) and 23,432 structural variants (SVs) from whole genome sequencing (WGS) data of healthy and TCC cats. Only BRCA2 was found to have a high recurrent number of missense mutations in fishing cats diagnosed with TCC when compared to inherited human cancer risk variants. These new fishing cat genomic resources will aid conservation efforts to improve their genetic fitness and enhance the comparative study of feline genomes.
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Affiliation(s)
- Rachel A Carroll
- Bond Life Sciences Center, University of Missouri, 1201 Rollins St., Columbia, MO, 65211, USA
| | - Edward S Rice
- Bond Life Sciences Center, University of Missouri, 1201 Rollins St., Columbia, MO, 65211, USA
| | - William J Murphy
- Department of Veterinary Integrative Biosciences, Texas A and M University, College Station, TX, 77843-4458, USA
| | - Leslie A Lyons
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA
| | - Francoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Lyndon M Coghill
- Bioinformatics and Analytics Core, University of Missouri, 1201 Rollins St., Columbia, MO, 65211, USA
| | - William F Swanson
- Center for Conservation and Research of Endangered Wildlife, Cincinnati Zoo and Botanical Garden, 3400 Vine St., Cincinnati, OH, 45220, USA
| | - Karen A Terio
- Zoological Pathology Program, University of Illinois, 3300 Golf Rd, Brookfield, IL, 60513, USA
| | - Tyler Boyd
- Oklahoma City Zoo and Botanical Garden, 2000 Remington Pl., Oklahoma, OK, 73111, USA
| | - Wesley C Warren
- Bond Life Sciences Center, University of Missouri, 1201 Rollins St., Columbia, MO, 65211, USA.
- Department of Surgery, Bond Life Sciences Center, Institute of Data Science and Informatics, University of Missouri, 1201 Rollins St., Columbia, MO, 65211, USA.
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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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Coleman JL, Wyffels JT, Penfold LM, Richardson D, Maddox JD. Development of genetic markers for reproductive management of toucans. Zoo Biol 2023; 42:825-833. [PMID: 37338091 DOI: 10.1002/zoo.21792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 04/26/2023] [Accepted: 06/08/2023] [Indexed: 06/21/2023]
Abstract
Retention of genetic diversity in successive generations is key to successful ex situ programs and will become increasingly important to restore wild populations of threatened animals. When animal genealogy is partly unknown or gaps exist in studbook records, the application of molecular resources facilitates informed breeding. Here, we apply molecular resources to an ex situ breeding population of toucans (Ramphastidae), a bird family zoos commonly maintain. Toucans face population declines from illegal poaching and habitat degradation. We developed novel microsatellite markers using blood samples from 15 Keel-billed Toucans (Ramphastos sulfuratus Lesson 1830). Parentage of two individuals was known a priori, but possible sibship among 13 putative founders-including the parents-was unknown. We compared available avian heterologous and novel microsatellite markers to recover known relationships and reconstruct sibship. Eight of 61 heterologous markers amplified consistently and were polymorphic, but less so than the 18 novel markers. Known sibship (and three sibling pairs whose relatedness was unknown a priori) and paternity-though not maternity except in one case-were well-recovered using both likelihood and pairwise relatedness methods, when incorporating novel but not heterologous markers. Zoo researchers seeking microsatellite primer sets for their breeding toucan populations will likely benefit from our heterologous markers, which can be leveraged both to assess relatedness and select breeding pairs. We recommend that zoo biologists rely on species-specific primers and not optimize heterologous primers for toucan species without molecular resources. We conclude with a brief discussion of modern genotyping methods of interest to zoo researchers.
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Affiliation(s)
- Jeffrey L Coleman
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois, USA
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA
| | - Jennifer T Wyffels
- Center for Bioinformatics & Computational Biology, University of Delaware, Newark, Delaware, USA
- Ripley's Aquariums, Orlando, Florida, USA
| | - Linda M Penfold
- South-East Zoo Alliance for Reproduction & Conservation, Yulee, Florida, USA
| | | | - J Dylan Maddox
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois, USA
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5
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Hrabina P, Pernerová L, Suchomel J, Robovský J. Utility of cytochrome c oxidase I for the deciphering of unstable phylogeny and taxonomy of gorals, genus Nemorhaedus Hamilton Smith, 1827 (Bovidae, Ovibovina). Zookeys 2023; 1181:81-110. [PMID: 38313159 PMCID: PMC10838175 DOI: 10.3897/zookeys.1181.108019] [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: 06/14/2023] [Accepted: 09/04/2023] [Indexed: 02/06/2024] Open
Abstract
Gorals represent ungulate mammals of the Palearctic and Indo-Malayan realms that face habitat destruction and intense hunting pressure. Their classification has been the subject of various (mainly genetic) assessments in the last decade, but some results are conflicting, hampering some conservation-based decisions. Genetic sampling of gorals has increased considerably in recent years, at least for mitochondrial (mt) DNA. Results based on two mt genes (cytochrome b and the D-loop) are currently available. Still, the utility of cytochrome oxidase subunit I remains unanalysed, even though it belongs among the gene markers that enable a correct species identification in mammals. This study examines phylogenetic relationships and species delimitation in gorals using all currently available cytochrome oxidase subunit I sequences, including the not yet analysed goral population from Pakistan. Our results of various phylogenetic approaches, such as maximum parsimony, likelihood and Bayesian inference, and exploration of species boundaries via species delimitation support the validity of six species of goral, namely N.baileyi, N.caudatus, N.cranbrooki, N.evansi, N.goral, and N.griseus. This result accords well with results based on other mt genes, especially the cytochrome b from the highly exhaustive data sampling. Our study also summarises common sources of errors in the assessment of goral phylogeny and taxonomy and highlights future priorities in understanding goral diversification.
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Affiliation(s)
- Petr Hrabina
- Department of Zoology, Fisheries, Hydrobiology and Apiculture, Mendel University in Brno, Zemědělská 1, Brno, 61300, Czech Republic Mendel University in Brno Brno Czech Republic
| | - Ludmila Pernerová
- Department of Zoology, Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice, 37005, Czech Republic University of South Bohemia České Budějovice Czech Republic
| | - Josef Suchomel
- Department of Zoology, Fisheries, Hydrobiology and Apiculture, Mendel University in Brno, Zemědělská 1, Brno, 61300, Czech Republic Mendel University in Brno Brno Czech Republic
| | - Jan Robovský
- Department of Zoology, Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice, 37005, Czech Republic University of South Bohemia České Budějovice Czech Republic
- Liberec Zoo, Lidové sady 425/1, Liberec, 46001, Czech Republic Liberec Zoo Liberec Czech Republic
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6
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Powell DM. Losing the forest for the tree? On the wisdom of subpopulation management. Zoo Biol 2023; 42:591-604. [PMID: 37218348 DOI: 10.1002/zoo.21776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 03/24/2023] [Accepted: 04/26/2023] [Indexed: 05/24/2023]
Abstract
Animal habitats are changing around the world in many ways, presenting challenges to the survival of species. Zoo animal populations are also challenged by small population sizes and limited genetic diversity. Some ex situ populations are managed as subpopulations based on presumed subspecies or geographic locality and related concerns over genetic purity or taxonomic integrity. However, these decisions can accelerate the loss of genetic diversity and increase the likelihood of population extinction. Here I challenge the wisdom of subpopulation management, pointing out significant concerns in the literature with delineation of species, subspecies, and evolutionarily significant units. I also review literature demonstrating the value of gene flow for preserving adaptive potential, the often-misunderstood role of hybridization in evolution, and the likely overstated concerns about outbreeding depression, and preservation of local adaptations. I argue that the most effective way to manage animal populations for the long term be they in human care, in the wild, or if a captive population is being managed for reintroduction, is to manage for maximum genetic diversity rather than managing subpopulations focusing on taxonomic integrity, genetic purity, or geographic locale because selection in the future, rather than the past, will determine what genotypes and phenotypes are the most fit. Several case studies are presented to challenge the wisdom of subpopulation management and stimulate thinking about the preservation of genomes rather than species, subspecies, or lineages because those units evolved in habitats that are likely very different from those habitats today and in the future.
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Affiliation(s)
- David M Powell
- Department of Reproductive & Behavioral Sciences, Saint Louis Zoo, Saint Louis, Missouri, USA
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7
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Clark FE, Greggor AL, Montgomery SH, Plotnik JM. The endangered brain: actively preserving ex-situ animal behaviour and cognition will benefit in-situ conservation. ROYAL SOCIETY OPEN SCIENCE 2023; 10:230707. [PMID: 37650055 PMCID: PMC10465207 DOI: 10.1098/rsos.230707] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 08/15/2023] [Indexed: 09/01/2023]
Abstract
Endangered species have small, unsustainable population sizes that are geographically or genetically restricted. Ex-situ conservation programmes are therefore faced with the challenge of breeding sufficiently sized, genetically diverse populations earmarked for reintroduction that have the behavioural skills to survive and breed in the wild. Yet, maintaining historically beneficial behaviours may be insufficient, as research continues to suggest that certain cognitive-behavioural skills and flexibility are necessary to cope with human-induced rapid environmental change (HIREC). This paper begins by reviewing interdisciplinary studies on the 'captivity effect' in laboratory, farmed, domesticated and feral vertebrates and finds that captivity imposes rapid yet often reversible changes to the brain, cognition and behaviour. However, research on this effect in ex-situ conservation sites is lacking. This paper reveals an apparent mismatch between ex-situ enrichment aims and the cognitive-behavioural skills possessed by animals currently coping with HIREC. After synthesizing literature across neuroscience, behavioural biology, comparative cognition and field conservation, it seems that ex-situ endangered species deemed for reintroduction may have better chances of coping with HIREC if their natural cognition and behavioural repertoires are actively preserved. Evaluating the effects of environmental challenges rather than captivity per se is recommended, in addition to using targeted cognitive enrichment.
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Affiliation(s)
- Fay E. Clark
- School of Psychological Science, University of Bristol, Bristol, UK
| | | | | | - Joshua M. Plotnik
- Department of Psychology, Hunter College, City University of New York, New York, NY, USA
- Department of Psychology, The Graduate Center, City University of New York, New York, NY, USA
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8
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By Bits and Pieces: The Contributions of Zoos and Aquariums to Science and Society via Biomaterials. JOURNAL OF ZOOLOGICAL AND BOTANICAL GARDENS 2023. [DOI: 10.3390/jzbg4010023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023] Open
Abstract
Scientific research has long been recognized as one of the four pillars of the zoo or aquarium mission, alongside recreation, conservation, and education. This study sought to quantify a sample of zoos’ participation in scientific research via the provision of biomaterials from animals to outside scientists and the associated training of undergraduate and graduate students that resulted from these projects. A convenience sample of zoos provided data on their participation in biomaterials-related projects and a focused analysis of biomaterials-related research facilitated by the Saint Louis Zoo was conducted. In addition, the Association of Zoos & Aquariums’ conservation & science database was queried to uncover what research projects AZA members engaged in over the last five years that likely involved biomaterials research and training of students. Results demonstrate that zoos are making significant contributions to science by agreeing to participate in large numbers of biomaterials-related projects across different areas of focus involving a variety of animal species annually, with results applicable to human and non-human animals. Support of such research often involves student thesis projects, thus contributing to the education of future scientists.
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9
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Gray R, Fusco N, Miller JM, Tapia W, Mariani C, Caccone A, Jensen EL. Temporal Monitoring of the Floreana Island Galapagos Giant Tortoise Captive Breeding Program. Integr Comp Biol 2022; 62:1864-1871. [PMID: 35906184 DOI: 10.1093/icb/icac129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/22/2022] [Accepted: 07/22/2022] [Indexed: 01/05/2023] Open
Abstract
Captive breeding programs benefit from genetic analyses that identify relatedness between individuals, assign parentage to offspring, and track levels of genetic diversity. Monitoring these parameters across breeding cycles is critical to the success of a captive breeding program as it allows conservation managers to iteratively evaluate and adjust program structure. However, in practice, genetic tracking of breeding outcomes is rarely conducted. Here, we examined the first three offspring cohorts (2017-2020) of the genetically informed captive breeding program for the Floreana Island Galapagos giant tortoise, Chelonoidis niger. This captive breeding program is unique as the Floreana tortoise has been extinct since the 1800s, but its genome persists, in part, in the form of living hybrids with the extant Volcano Wolf tortoise, C. becki. Breeding over the study period took place at the Galapagos National Park Directorate breeding facility in four corrals, each containing three females and two males. Using 17 microsatellite markers, we were able to assign parentage to 94 of the 98 offspring produced over the study period. We observe that despite the addition of more founders since the pilot breeding program, the effective population size remains low, and changes to the arrangements of breeding corrals may be necessary to encourage more equal reproductive output from the males. This study demonstrates the value of hybrids for species restoration and the importance of continually reassessing the outcomes of captive breeding.
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Affiliation(s)
- Rachel Gray
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Nicole Fusco
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
| | - Joshua M Miller
- Department of Biological Sciences, MacEwan University, Edmonton, AB T5J 4S2, Canada
| | - Washington Tapia
- Galapagos Conservancy, Fairfax, VA 22030, USA.,University of Málaga, Campus Teatinos, Apdo. 59. 29080 Málaga, Spain
| | - Carol Mariani
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
| | - Evelyn L Jensen
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
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10
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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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11
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Aoki Y, Zaitsu Y, Kurita M, Phillips RA, Tadano R. Genetic diversity and structure of captive gentoo penguin populations in Japan. Zoo Biol 2021; 41:218-225. [PMID: 34970775 DOI: 10.1002/zoo.21666] [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: 11/12/2020] [Revised: 11/29/2021] [Accepted: 12/08/2021] [Indexed: 11/08/2022]
Abstract
Until the last decade, gentoo penguins were usually split into two subspecies, northern gentoo penguins (Pygoscelis papua papua) breeding in the Falkland Islands, South Georgia, and other subantarctic islands and southern gentoo penguins (P. papua ellsworthi) breeding in the South Sandwich, South Orkney and South Shetland islands, and Antarctic Peninsula. Recent genetics research, however, suggests that the population at South Georgia is much more closely related to those further south and should be included in P. papua ellsworthi. In Japanese zoos and aquariums, captive breeding of gentoo penguins is conducted separately in three populations: "Captive-South Georgia," originating from South Georgia, "Captive-South Shetlands," originating from South Shetlands, and "Captive-Unknown," originating from at least one founder of unknown subspecies. The aims of the present study were to investigate the genetic diversity and differentiation of these captive populations using microsatellite analysis. Genetic diversity in each captive population was similar to that found in the wild, although they had much lower contemporary effective population sizes. Pairwise genetic differentiation indexes (FST ) among the three captive populations were as follows: 0.0309 ("Captive-South Georgia" and "Captive-Unknown"), 0.1094 ("Captive-South Georgia" and "Captive-South Shetlands"), and 0.1214 ("Captive-South Shetlands" and "Captive-Unknown"). Using Bayesian clustering, there was relatively high genetic differentiation between the "Captive-South Shetlands" group, which formed a distinct cluster, and individuals of the "Captive-Unknown" group, which were assigned to clusters in common with "Captive-South Georgia." The results from the present study are useful for future management of captive gentoo penguin populations in Japan.
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Affiliation(s)
- Yuna Aoki
- Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan
| | | | | | - Richard A Phillips
- British Antarctic Survey, Natural Environment Research Council, Cambridge, UK
| | - Ryo Tadano
- Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan
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12
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Leeflang HL, Van Dongen S, Helsen P. Mother’s curse on conservation: assessing the role of mtDNA in sex‐specific survival differences in ex‐situ breeding programs. Anim Conserv 2021. [DOI: 10.1111/acv.12740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- H. L. Leeflang
- Centre for Research and Conservation Royal Zoological Society of Antwerp Antwerp Belgium
| | - S. Van Dongen
- Department of Biology Evolutionary Ecology Group University of Antwerp Wilrijk Belgium
| | - P. Helsen
- Centre for Research and Conservation Royal Zoological Society of Antwerp Antwerp Belgium
- Department of Biology Evolutionary Ecology Group University of Antwerp Wilrijk Belgium
- Department of Biology Ghent University Ghent Belgium
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13
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Gonçalves M, Siegismund HR, Jansen van Vuuren B, Koepfli KP, Ferrand N, Godinho R. De novo whole-genome assembly and resequencing resources for the roan (Hippotragus equinus), an iconic African antelope. G3-GENES GENOMES GENETICS 2021; 11:6114458. [PMID: 33604669 PMCID: PMC8022987 DOI: 10.1093/g3journal/jkab002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 12/17/2021] [Indexed: 11/22/2022]
Abstract
Roan antelope (Hippotragus equinus) is the second-largest member of the Hippotraginae (Bovidae), and is widely distributed across sub-Saharan mesic woodlands. Despite being listed as "Least Concern" across its African range, population numbers are decreasing with many regional Red List statuses varying between Endangered and Locally Extinct. Although the roan antelope has become an economically-important game species in Southern Africa, the vast majority of wild populations are found only in fragmented protected areas, which is of conservation concern. Genomic information is crucial in devising optimal management plans. To this end, we report here the first de novo assembly and annotation of the whole-genome sequence of a male roan antelope from a captive-breeding program. Additionally, we uncover single-nucleotide variants (SNVs) through re-sequencing of five wild individuals representing five of the six described subspecies. We used 10X Genomics Chromium chemistry to produce a draft genome of 2.56 Gb consisting of 16,880 scaffolds with N50 = 8.42 Mb and a BUSCO completeness of 91.2%. The draft roan genome includes 1.1 Gbp (42.2%) repetitive sequences. De novo annotation identified 20,518 protein-coding genes. Genome synteny to the domestic cow showed an average identity of 92.7%. Re-sequencing of five wild individuals to an average sequencing depth of 9.8x resulted in the identification of a filtered set of 3.4x106 bi-allelic SNVs. The proportion of alternative homozygous SNVs for the individuals representing different subspecies, as well as differentiation as measured by PCA, were consistent with expected divergence from the reference genome and among samples. The roan antelope genome is a valuable resource for evolutionary and population genomic questions, as well as management and conservation actions.
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Affiliation(s)
- Margarida Gonçalves
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus de Vairão, 4485-661 Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
| | - Hans R Siegismund
- Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Bettine Jansen van Vuuren
- Department of Zoology, Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, 2006 Johannesburg, South Africa
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, Front Royal, VA 22630, USA.,Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Washington, DC 20008, USA
| | - Nuno Ferrand
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus de Vairão, 4485-661 Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal.,Department of Zoology, Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, 2006 Johannesburg, South Africa
| | - Raquel Godinho
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus de Vairão, 4485-661 Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal.,Department of Zoology, Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, 2006 Johannesburg, South Africa
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14
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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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15
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Trede F, Kil N, Stranks J, Connell AJ, Fischer J, Ostner J, Schülke O, Zinner D, Roos C. A refined panel of 42 microsatellite loci to universally genotype catarrhine primates. Ecol Evol 2021; 11:498-505. [PMID: 33437445 PMCID: PMC7790618 DOI: 10.1002/ece3.7069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/28/2020] [Accepted: 11/03/2020] [Indexed: 11/30/2022] Open
Abstract
Microsatellite genotyping is an important genetic method for a number of research questions in biology. Given that the traditional fragment length analysis using polyacrylamide gel or capillary electrophoresis has several drawbacks, microsatellite genotyping-by-sequencing (GBS) has arisen as a promising alternative. Although GBS mitigates many of the problems of fragment length analysis, issues with allelic dropout and null alleles often remain due to mismatches in primer binding sites and unnecessarily long PCR products. This is also true for GBS in catarrhine primates where cross-species amplification of loci (often human derived) is common.We therefore redesigned primers for 45 microsatellite loci based on 17 available catarrhine reference genomes. Next, we tested them in singleplex and different multiplex settings in a panel of species representing all major lineages of Catarrhini and further validated them in wild Guinea baboons (Papio papio) using fecal samples.The final panel of 42 microsatellite loci can efficiently be amplified with primers distributed into three amplification pools.With our microsatellite panel, we provide a tool to universally genotype catarrhine primates via GBS from different sample sources in a cost- and time-efficient way, with higher resolution, and comparability among laboratories and species.
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Affiliation(s)
- Franziska Trede
- Cognitive Ethology LaboratoryGerman Primate CenterLeibniz Institute for Primate ResearchGöttingenGermany
- Primate Genetics LaboratoryGerman Primate CenterLeibniz Institute for Primate ResearchGöttingenGermany
| | - Niels Kil
- Primate Genetics LaboratoryGerman Primate CenterLeibniz Institute for Primate ResearchGöttingenGermany
- Department of Behavioral EcologyUniversity of GöttingenGöttingenGermany
- Leibniz ScienceCampus Primate CognitionGöttingenGermany
- Research Group Primate Social EvolutionGerman Primate CenterLeibniz Institute for Primate ResearchGöttingenGermany
| | - James Stranks
- Primate Genetics LaboratoryGerman Primate CenterLeibniz Institute for Primate ResearchGöttingenGermany
- Department of Behavioral EcologyUniversity of GöttingenGöttingenGermany
- Leibniz ScienceCampus Primate CognitionGöttingenGermany
- Research Group Primate Social EvolutionGerman Primate CenterLeibniz Institute for Primate ResearchGöttingenGermany
| | - Andrew Jesse Connell
- Department of MicrobiologyPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Julia Fischer
- Cognitive Ethology LaboratoryGerman Primate CenterLeibniz Institute for Primate ResearchGöttingenGermany
- Leibniz ScienceCampus Primate CognitionGöttingenGermany
- Department of Primate CognitionGeorg‐August‐UniversityGöttingenGermany
| | - Julia Ostner
- Department of Behavioral EcologyUniversity of GöttingenGöttingenGermany
- Leibniz ScienceCampus Primate CognitionGöttingenGermany
- Research Group Primate Social EvolutionGerman Primate CenterLeibniz Institute for Primate ResearchGöttingenGermany
| | - Oliver Schülke
- Department of Behavioral EcologyUniversity of GöttingenGöttingenGermany
- Leibniz ScienceCampus Primate CognitionGöttingenGermany
- Research Group Primate Social EvolutionGerman Primate CenterLeibniz Institute for Primate ResearchGöttingenGermany
| | - Dietmar Zinner
- Cognitive Ethology LaboratoryGerman Primate CenterLeibniz Institute for Primate ResearchGöttingenGermany
- Leibniz ScienceCampus Primate CognitionGöttingenGermany
- Department of Primate CognitionGeorg‐August‐UniversityGöttingenGermany
| | - Christian Roos
- Primate Genetics LaboratoryGerman Primate CenterLeibniz Institute for Primate ResearchGöttingenGermany
- Gene Bank of PrimatesGerman Primate CenterLeibniz Institute for Primate ResearchGöttingenGermany
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16
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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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17
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Farquharson KA, Hogg CJ, Belov K, Grueber CE. Deciphering genetic mate choice: Not so simple in group-housed conservation breeding programs. Evol Appl 2020; 13:2179-2189. [PMID: 33005217 PMCID: PMC7513713 DOI: 10.1111/eva.12981] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 02/19/2020] [Accepted: 03/30/2020] [Indexed: 11/28/2022] Open
Abstract
Incorporating mate choice into conservation breeding programs can improve reproduction and the retention of natural behaviors. However, different types of genetic-based mate choice can have varied consequences for genetic diversity management. As a result, it is important to examine mechanisms of mate choice in captivity to assess its costs and benefits. Most research in this area has focused on experimental pairing trials; however, this resource-intensive approach is not always feasible in captive settings and can interfere with other management constraints. We used generalized linear mixed models and permutation approaches to investigate overall breeding success in group-housed Tasmanian devils at three nonmutually exclusive mate choice hypotheses: (a) advantage of heterozygous individuals, (b) advantage of dissimilar mates, and (c) optimum genetic distance, using both 1,948 genome-wide SNPs and 12 MHC-linked microsatellites. The managed devil insurance population is the largest such breeding program in Australia and is known to have high variance in reproductive success. We found that nongenetic factors such as age were the best predictors of breeding success in a competitive breeding scenario, with younger females and older males being more successful. We found no evidence of mate choice under the hypotheses tested. Mate choice varies among species and across environments, so we advocate for more studies in realistic captive management contexts as experimental or wild studies may not apply. Conservation managers must weigh up the need to wait for adequate sample sizes to detect mate choice with the risk that genetic changes may occur during this time in captivity. Our study shows that examining and integrating mate choice into the captive management of species housed in realistic, semi-natural group-based contexts may be more difficult than previously considered.
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Affiliation(s)
- Katherine A Farquharson
- School of Life and Environmental Sciences Faculty of Science The University of Sydney Sydney Australia
| | - Carolyn J Hogg
- School of Life and Environmental Sciences Faculty of Science The University of Sydney Sydney Australia
| | - Katherine Belov
- School of Life and Environmental Sciences Faculty of Science The University of Sydney Sydney Australia
| | - Catherine E Grueber
- School of Life and Environmental Sciences Faculty of Science The University of Sydney Sydney Australia
- San Diego Zoo Global San Diego USA
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18
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19
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Frandsen P, Fontsere C, Nielsen SV, Hanghøj K, Castejon-Fernandez N, Lizano E, Hughes D, Hernandez-Rodriguez J, Korneliussen TS, Carlsen F, Siegismund HR, Mailund T, Marques-Bonet T, Hvilsom C. Targeted conservation genetics of the endangered chimpanzee. Heredity (Edinb) 2020; 125:15-27. [PMID: 32346130 DOI: 10.1038/s41437-020-0313-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 03/31/2020] [Accepted: 03/31/2020] [Indexed: 11/09/2022] Open
Abstract
Populations of the common chimpanzee (Pan troglodytes) are in an impending risk of going extinct in the wild as a consequence of damaging anthropogenic impact on their natural habitat and illegal pet and bushmeat trade. Conservation management programmes for the chimpanzee have been established outside their natural range (ex situ), and chimpanzees from these programmes could potentially be used to supplement future conservation initiatives in the wild (in situ). However, these programmes have often suffered from inadequate information about the geographical origin and subspecies ancestry of the founders. Here, we present a newly designed capture array with ~60,000 ancestry informative markers used to infer ancestry of individual chimpanzees in ex situ populations and determine geographical origin of confiscated sanctuary individuals. From a test panel of 167 chimpanzees with unknown origins or subspecies labels, we identify 90 suitable non-admixed individuals in the European Association of Zoos and Aquaria (EAZA) Ex situ Programme (EEP). Equally important, another 46 individuals have been identified with admixed subspecies ancestries, which therefore over time, should be naturally phased out of the breeding populations. With potential for future re-introduction to the wild, we determine the geographical origin of 31 individuals that were confiscated from the illegal trade and demonstrate the promises of using non-invasive sampling in future conservation action plans. Collectively, our genomic approach provides an exemplar for ex situ management of endangered species and offers an efficient tool in future in situ efforts to combat the illegal wildlife trade.
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Affiliation(s)
- Peter Frandsen
- Research and Conservation, Copenhagen Zoo, Roskildevej 38, 2000, Frederiksberg, Denmark. .,Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark.
| | - Claudia Fontsere
- Institute of Evolutionary Biology, (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003, Barcelona, Spain.
| | - Svend Vendelbo Nielsen
- Bioinformatics Research Center, Department of Mathematics, Aarhus University, C. F. Møllers Allé 8, 8000, Aarhus C, Denmark
| | - Kristian Hanghøj
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark
| | - Natalia Castejon-Fernandez
- Bioinformatics Research Center, Department of Mathematics, Aarhus University, C. F. Møllers Allé 8, 8000, Aarhus C, Denmark
| | - Esther Lizano
- Institute of Evolutionary Biology, (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003, Barcelona, Spain.,Institut Català de Paleontologia Miquel Crusafant, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, Cerdanyala del Vallès, 08193, Barcelona, Spain
| | - David Hughes
- MRC Integrative Epidemiology Unit at University of Bristol, Bristol, BS8 2BN, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
| | | | - Thorfinn Sand Korneliussen
- GLOBE, Section for Geogenetics, Øster Voldgade 5-7, 1350, Copenhagen, Denmark.,National Research University, Higher School of Economics, 20 Myasnitskaya Ulitsa, 101000, Moscow, Russia
| | - Frands Carlsen
- Research and Conservation, Copenhagen Zoo, Roskildevej 38, 2000, Frederiksberg, Denmark
| | - Hans Redlef Siegismund
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark
| | - Thomas Mailund
- Bioinformatics Research Center, Department of Mathematics, Aarhus University, C. F. Møllers Allé 8, 8000, Aarhus C, Denmark
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology, (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003, Barcelona, Spain.,Institut Català de Paleontologia Miquel Crusafant, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, Cerdanyala del Vallès, 08193, Barcelona, Spain.,Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys 23, 08010, Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri I Reixac, 408028, Barcelona, Spain
| | - Christina Hvilsom
- Research and Conservation, Copenhagen Zoo, Roskildevej 38, 2000, Frederiksberg, Denmark
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20
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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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21
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Putnam AS, Nguyen TN, Mott A, Korody ML, Ryder OA. Assessing possible hybridization among managed Nubian ibex in North America. Zoo Biol 2019; 39:121-128. [PMID: 31833594 DOI: 10.1002/zoo.21527] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 10/21/2019] [Accepted: 11/07/2019] [Indexed: 11/06/2022]
Abstract
Hybridization among closely related species is a concern in zoo and aquarium populations where unpedigreed animals are frequently exchanged with the private sector. In this study, we examine possible hybridization in a group of Nubian ibex (Capra nubiana) imported into the Association of Zoos and Aquariums' (AZA) Species Survival Program (SSP) from a private institution. These individuals appeared smaller in stature than adult SSP Nubian ibex and were excluded from breeding recommendations over the concern that they were hybrids. Twenty-six microsatellites were used to rule out recent hybridization with domestic goats, Siberian ibex (Capra sibirica), and Alpine ibex (Capra ibex). We argue that natural phenotypic variation across the large geographic range of Nubian ibex may account for the small stature of the imported ibex, as private institutions may have historically acquired individuals from locations that differed from the SSP founders. However, the imported Nubian ibex appeared genetically differentiated from the SSP Nubian ibex and may represent a source of genetic variation for the managed population.
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Affiliation(s)
- Andrea S Putnam
- Department of Life Sciences, San Diego Zoo Global, San Diego, California
| | - Tram N Nguyen
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York
| | | | - Marisa L Korody
- Institute for Conservation Research, San Diego Zoo Global, San Diego, California
| | - Oliver A Ryder
- Institute for Conservation Research, San Diego Zoo Global, San Diego, California
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23
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Genetic evaluation of the Iberian lynx ex situ conservation programme. Heredity (Edinb) 2019; 123:647-661. [PMID: 30952964 DOI: 10.1038/s41437-019-0217-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 03/08/2019] [Accepted: 03/11/2019] [Indexed: 11/09/2022] Open
Abstract
Ex situ programmes have become critical for improving the conservation of many threatened species, as they establish backup populations and provide individuals for reintroduction and reinforcement of wild populations. The Iberian lynx was considered the most threatened felid species in the world in the wake of a dramatic decline during the second half of the 20th century that reduced its numbers to around only 100 individuals. An ex situ conservation programme was established in 2003 with individuals from the two well-differentiated, remnant populations, with great success from a demographic point of view. Here, we evaluate the genetic status of the Iberian lynx captive population based on molecular data from 36 microsatellites, including patterns of relatedness and representativeness of the two remnant genetic backgrounds among founders, the evolution of diversity and inbreeding over the years, and genetic differentiation among breeding facilities. In general terms, the ex situ population harbours most of the genetic variability found in the two wild populations and has been able to maintain reasonably low levels of inbreeding and high diversity, thus validating the applied management measures and potentially representing a model for other species in need of conservation.
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