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Femerling G, van Oosterhout C, Feng S, Bristol RM, Zhang G, Groombridge J, P Gilbert MT, Morales HE. Genetic Load and Adaptive Potential of a Recovered Avian Species that Narrowly Avoided Extinction. Mol Biol Evol 2023; 40:msad256. [PMID: 37995319 DOI: 10.1093/molbev/msad256] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 10/26/2023] [Accepted: 11/16/2023] [Indexed: 11/25/2023] Open
Abstract
High genetic diversity is a good predictor of long-term population viability, yet some species persevere despite having low genetic diversity. Here we study the genomic erosion of the Seychelles paradise flycatcher (Terpsiphone corvina), a species that narrowly avoided extinction after having declined to 28 individuals in the 1960s. The species recovered unassisted to over 250 individuals in the 1990s and was downlisted from Critically Endangered to Vulnerable in the International Union for the Conservation of Nature Red List in 2020. By comparing historical, prebottleneck (130+ years old) and modern genomes, we uncovered a 10-fold loss of genetic diversity. Highly deleterious mutations were partly purged during the bottleneck, but mildly deleterious mutations accumulated. The genome shows signs of historical inbreeding during the bottleneck in the 1960s, but low levels of recent inbreeding after demographic recovery. Computer simulations suggest that the species long-term small Ne reduced the masked genetic load and made the species more resilient to inbreeding and extinction. However, the reduction in genetic diversity due to the chronically small Ne and the severe bottleneck is likely to have reduced the species adaptive potential to face environmental change, which together with a higher load, compromises its long-term population viability. Thus, small ancestral Ne offers short-term bottleneck resilience but hampers long-term adaptability to environmental shifts. In light of rapid global rates of population decline, our work shows that species can continue to suffer the effect of their decline even after recovery, highlighting the importance of considering genomic erosion and computer modeling in conservation assessments.
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Affiliation(s)
- Georgette Femerling
- Section for Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | | | - Shaohong Feng
- Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, China
| | - Rachel M Bristol
- Mahe, Seychelles
- Division of Human and Social Sciences, Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury, Kent, CT2 7NR, UK
| | - Guojie Zhang
- Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, China
| | - Jim Groombridge
- Division of Human and Social Sciences, Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury, Kent, CT2 7NR, UK
| | - M Thomas P Gilbert
- Section for Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, NTNU, Trondheim, Norway
| | - Hernán E Morales
- Section for Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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Kim KR, Kwak YH, Sung MS, Cho SJ, Bang IC. Population structure and genetic diversity of the endangered fish black shinner Pseudopungtungia nigra (Cyprinidae) in Korea: a wild and restoration population. Sci Rep 2023; 13:9692. [PMID: 37322262 PMCID: PMC10272174 DOI: 10.1038/s41598-023-36569-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 06/06/2023] [Indexed: 06/17/2023] Open
Abstract
The black shinner Pseudopungtungia nigra Mori, 1935 is an endangered fish endemic to Korea. It lives in the narrow basin of the Geumgang River, Mangyeonggang River, and Ungcheoncheon Stream, which flow into the West Sea of Korea. One population of P. nigra in Ungcheoncheon Stream has been locally exterminated once; it is now inhabiting the upper reaches of the dam through a restoration program. Efforts to identify and understand the genetic structure of these populations are important for conservation planning. Here, we analyzed genetic diversity using 21 microsatellite markers for 9 populations. The mean number of alleles ranged from 4.4 to 8.1, mean allelic richness ranged from 4.6 to 7.8, mean observed heterozygosity ranged from 0.519 to 0.702, and mean expected heterozygosity ranged from 0.540 to 0.763. All groups had recent and historical bottlenecks (P < 0.05, M-ratio < 0.68). Three groups [YD (2019), OC and UC] had significant inbreeding index values, suggesting that they were engaged in inbreeding. We observed a moderate level of genetic differentiation between MG and the rest of the population (FST = 0.135 to 0.168, P < 0.05). The genetic structure exhibited a fitting constant K = 2, along with separation between MG and the remaining populations. With respect to genetic flow, YD (2019), OC, CG, and ND shifted to the UC population (0.263 to 0.278). The genetic flow of each population was transferred only within the population; there was no gene flow among populations, except for the Ungcheoncheon Stream population. This study shows that the Ungcheoncheon Stream population needs conservation efforts to increase its genetic diversity, and the Geumgang River populations needs a conservation plan that considers the possibility of conservation and evolution through gene exchange among the populations.
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Affiliation(s)
- Kang-Rae Kim
- Department of Life Science & Biotechnology, Soonchunhyang University, Asan, 31538, Republic of Korea
| | - Yeong-Ho Kwak
- Department of Life Science & Biotechnology, Soonchunhyang University, Asan, 31538, Republic of Korea
| | - Mu-Sung Sung
- Department of Life Science & Biotechnology, Soonchunhyang University, Asan, 31538, Republic of Korea
| | | | - In-Chul Bang
- Department of Life Science & Biotechnology, Soonchunhyang University, Asan, 31538, Republic of Korea.
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Rare long-distance dispersal of the Island Night Lizard, Xantusia riversiana, maintains high diversity in a fragmented environment. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1055-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Genetic diversity through time and space: diversity and demographic history from natural history specimens and serially sampled contemporary populations of the threatened Gouldian finch (Erythrura gouldiae). CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1051-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Villanova VL, Hughes PT, Hoffman EA. Combining genetic structure and demographic analyses to estimate persistence in endangered Key deer (Odocoileus virginianus clavium). CONSERV GENET 2017. [DOI: 10.1007/s10592-017-0958-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Temporal genetic dynamics of reintroduced and translocated populations of the endangered golden lion tamarin (Leontopithecus rosalia). CONSERV GENET 2017. [DOI: 10.1007/s10592-017-0948-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Slow motion extinction: inbreeding, introgression, and loss in the critically endangered mangrove finch (Camarhynchus heliobates). CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0890-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Bryant JV, Gottelli D, Zeng X, Hong X, Chan BPL, Fellowes JR, Zhang Y, Luo J, Durrant C, Geissmann T, Chatterjee HJ, Turvey ST. Assessing current genetic status of the Hainan gibbon using historical and demographic baselines: implications for conservation management of species of extreme rarity. Mol Ecol 2016; 25:3540-56. [PMID: 27273107 DOI: 10.1111/mec.13716] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 05/13/2016] [Accepted: 05/31/2016] [Indexed: 12/30/2022]
Abstract
Evidence-based conservation planning is crucial for informing management decisions for species of extreme rarity, but collection of robust data on genetic status or other parameters can be extremely challenging for such species. The Hainan gibbon, possibly the world's rarest mammal, consists of a single population of ~25 individuals restricted to one protected area on Hainan Island, China, and has persisted for over 30 years at exceptionally low population size. Analysis of genotypes at 11 microsatellite loci from faecal samples for 36% of the current global population and tissue samples from 62% of existing historical museum specimens demonstrates limited current genetic diversity (Na = 2.27, Ar = 2.24, He = 0.43); diversity has declined since the 19th century and even further within the last 30 years, representing declines of ~30% from historical levels (Na = 3.36, Ar = 3.29, He = 0.63). Significant differentiation is seen between current and historical samples (FST = 0.156, P = 0.0315), and the current population exhibits extremely small Ne (current Ne = 2.16). There is evidence for both a recent population bottleneck and an earlier bottleneck, with population size already reasonably low by the late 19th century (historical Ne = 1162.96). Individuals in the current population are related at the level of half- to full-siblings between social groups, and full-siblings or parent-offspring within a social group, suggesting that inbreeding is likely to increase in the future. The species' current reduced genetic diversity must be considered during conservation planning, particularly for expectations of likely population recovery, indicating that intensive, carefully planned management is essential.
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Affiliation(s)
- J V Bryant
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK.,Department of Genetics, Evolution & Environment, University College London, Gower Street, London, WC1E 6BT, UK
| | - D Gottelli
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
| | - X Zeng
- Bawangling National Nature Reserve Management Office, Changjiang Lizu Autonomous County, Hainan, 572722, China
| | - X Hong
- Bawangling National Nature Reserve Management Office, Changjiang Lizu Autonomous County, Hainan, 572722, China
| | - B P L Chan
- Kadoorie Conservation China, Kadoorie Farm and Botanic Garden, Lam Kam Road, Tai Po, New Territories, Hong Kong
| | - J R Fellowes
- The Kadoorie Institute, University of Hong Kong, Pokfulam Road, Hong Kong
| | - Y Zhang
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,College of Life Sciences, Yunnan University, Kunming, 650091, China
| | - J Luo
- College of Life Sciences, Yunnan University, Kunming, 650091, China
| | - C Durrant
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
| | - T Geissmann
- Anthropological Institute, University Zurich-Irchel, Winterthurerstrasse 190, Zurich, CH-8057, Switzerland
| | - H J Chatterjee
- Department of Genetics, Evolution & Environment, University College London, Gower Street, London, WC1E 6BT, UK
| | - S T Turvey
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
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Wright DJ, Spurgin LG, Collar NJ, Komdeur J, Burke T, Richardson DS. The impact of translocations on neutral and functional genetic diversity within and among populations of the Seychelles warbler. Mol Ecol 2014; 23:2165-77. [PMID: 24689851 PMCID: PMC4237152 DOI: 10.1111/mec.12740] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 03/06/2014] [Accepted: 03/07/2014] [Indexed: 01/10/2023]
Abstract
Translocations are an increasingly common tool in conservation. The maintenance of genetic diversity through translocation is critical for both the short- and long-term persistence of populations and species. However, the relative spatio-temporal impacts of translocations on neutral and functional genetic diversity, and how this affects genetic structure among the conserved populations overall, have received little investigation. We compared the impact of translocating different numbers of founders on both microsatellite and major histocompatibility complex (MHC) class I diversity over a 23-year period in the Seychelles warbler (Acrocephalus sechellensis). We found low and stable microsatellite and MHC diversity in the source population and evidence for only a limited loss of either type of diversity in the four new populations. However, we found evidence of significant, but low to moderate, genetic differentiation between populations, with those populations established with fewer founders clustering separately. Stochastic genetic capture (as opposed to subsequent drift) was the main determinant of translocated population diversity. Furthermore, a strong correlation between microsatellite and MHC differentiation suggested that neutral processes outweighed selection in shaping MHC diversity in the new populations. These data provide important insights into how to optimize the use of translocation as a conservation tool.
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Affiliation(s)
- David J Wright
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK; NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
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