1
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Silver LW, Farquharson KA, Peel E, Gilbert MTP, Belov K, Morales HE, Hogg CJ. Temporal Loss of Genome-Wide and Immunogenetic Diversity in a Near-Extinct Parrot. Mol Ecol 2025; 34:e17746. [PMID: 40130423 PMCID: PMC12010471 DOI: 10.1111/mec.17746] [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: 12/09/2024] [Revised: 02/14/2025] [Accepted: 03/13/2025] [Indexed: 03/26/2025]
Abstract
Loss of genetic diversity threatens a species' adaptive potential and long-term resilience. Predicted to be extinct by 2038, the orange-bellied parrot (Neophema chrysogaster) is a critically endangered migratory bird threatened by numerous viral, bacterial and fungal diseases. The species has undergone multiple population crashes, reaching a low of three wild-born females and 13 males in 2016, and is now represented by only a single wild population and individuals in the captive breeding program. Here we used our high-quality long-read reference genome, and contemporary (N = 19) and historical (N = 16) resequenced genomes from as early as 1829, to track the long-term genomic erosion and immunogenetic diversity decline in this species. 62% of genomic diversity was lost between historical (mean autosomal heterozygosity = 0.00149 ± 0.000699 SD) and contemporary (0.00057 ± 0.000026) parrots. A greater number and length of runs of homozygosity in contemporary samples were also observed. A temporal reduction in the number of alleles at Toll-like receptor genes was found (historical average alleles = 5.78 ± 2.73; contemporary = 3.89 ± 2.10), potentially exacerbating disease susceptibility in the contemporary population. Of particular concern is the new threat of avian influenza strain (HPAI) to Australia. We discuss the conservation implications of our findings and propose that hybridisation and synthetic biology may be required to address the catastrophic loss of genetic diversity that has occurred in this species in order to prevent extinction.
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Affiliation(s)
- Luke W. Silver
- School of Life and Environmental SciencesThe University of SydneySydneyNew South WalesAustralia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein ScienceSydneyNew South WalesAustralia
| | - Katherine A. Farquharson
- School of Life and Environmental SciencesThe University of SydneySydneyNew South WalesAustralia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein ScienceSydneyNew South WalesAustralia
| | - Emma Peel
- School of Life and Environmental SciencesThe University of SydneySydneyNew South WalesAustralia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein ScienceSydneyNew South WalesAustralia
| | - M. Thomas P. Gilbert
- Centre for Evolutionary Hologenomics, The GLOBE InstituteUniversity of CopenhagenCopenhagenDenmark
- University Museum, NTNUTrondheimNorway
| | - Katherine Belov
- School of Life and Environmental SciencesThe University of SydneySydneyNew South WalesAustralia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein ScienceSydneyNew South WalesAustralia
| | - Hernán E. Morales
- Centre for Evolutionary Hologenomics, The GLOBE InstituteUniversity of CopenhagenCopenhagenDenmark
- Department of BiologyLund UniversityLundSweden
| | - Carolyn J. Hogg
- School of Life and Environmental SciencesThe University of SydneySydneyNew South WalesAustralia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein ScienceSydneyNew South WalesAustralia
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2
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De Cahsan B, Sandoval Velasco M, Westbury MV, Duchêne DA, Strander Sinding MH, Morales HE, Kalthoff DC, Barnes I, Brace S, Portela Miguez R, Roca AL, Greenwood AD, Johnson RN, Lott MJ, Gilbert MTP. Road to Extinction? Past and Present Population Structure and Genomic Diversity in the Koala. Mol Biol Evol 2025; 42:msaf057. [PMID: 40129172 PMCID: PMC12014528 DOI: 10.1093/molbev/msaf057] [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: 07/07/2024] [Revised: 01/28/2025] [Accepted: 02/24/2025] [Indexed: 03/26/2025] Open
Abstract
Koalas are arboreal herbivorous marsupials, endemic to Australia. During the late 1800s and early 1900s, the number of koalas declined dramatically due to hunting for their furs. In addition, anthropogenic activities have further decimated their available habitat, and decreased population numbers. Here, we utilize 37 historic and 25 modern genomes sampled from across their historic and present geographic range, to gain insights into how their population structure and genetic diversity have changed across time; assess the genetic consequences of the period of intense hunting, and the current genetic status of this iconic Australian species. Our analyses reveal how genome-wide heterozygosity has decreased through time and unveil previously uncharacterized mitochondrial haplotypes and nuclear genotypes in the historic dataset, which are absent from today's koala populations.
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Affiliation(s)
- Binia De Cahsan
- Globe Institute, University of Copenhagen, 1350 Copenhagen K, Denmark
| | - Marcela Sandoval Velasco
- Globe Institute, University of Copenhagen, 1350 Copenhagen K, Denmark
- Center for Genome Sciences (CCG), National Autonomous University of Mexico (UNAM), Cuernavaca, Mexico
| | | | - David A Duchêne
- Globe Institute, University of Copenhagen, 1350 Copenhagen K, Denmark
| | | | - Hernán E Morales
- Globe Institute, University of Copenhagen, 1350 Copenhagen K, Denmark
| | - Daniela C Kalthoff
- Department of Zoology, Swedish Museum of Natural History, SE-104 05 Stockholm, Sweden
| | - Ian Barnes
- Department of Earth Sciences, Natural History Museum, London SW7 5BD, England, UK
| | - Selina Brace
- Department of Earth Sciences, Natural History Museum, London SW7 5BD, England, UK
| | | | - Alfred L Roca
- Department of Animal Sciences, University of Illinois, Urbana, IL 61801, USA
| | - Alex D Greenwood
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, 10315 Berlin, Germany
- Department of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany
| | - Rebecca N Johnson
- Smithsonian National Museum of Natural History, Washington, D.C. 20560, USA
| | - Matthew J Lott
- Australian Centre for Wildlife Genomics, Australian Museum, Sydney, NSW 2010, Australia
| | - M Thomas P Gilbert
- Globe Institute, University of Copenhagen, 1350 Copenhagen K, Denmark
- Norwegian University of Science and Technology, University Museum, 7491 Trondheim, Norway
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3
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Potapova K, Whitford H, Hodge JA, Price E. Optimal Weight Loss of Pink Pigeon (Nesoenas mayeri) Eggs During Incubation. Zoo Biol 2025. [PMID: 40077923 DOI: 10.1002/zoo.21898] [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: 05/20/2024] [Revised: 02/21/2025] [Accepted: 02/27/2025] [Indexed: 03/14/2025]
Abstract
Incubation of pink pigeon (Nesoenas mayeri) eggs under foster doves is an important element of the captive breeding program for this threatened species, and determining optimal species-specific incubation conditions could help to maximize hatchability. We analyzed 7 years of records (n = 104 eggs) from a captive collection to investigate whether the existing guideline for optimal total weight loss of 15% is appropriate for the pink pigeon. Successfully hatched eggs lost on average 14% of their initial mass during incubation, while a weight loss of 15.5% was associated with embryo mortality, and successful eggs lost slightly less weight per day, both as raw weight and as percentage of fresh weight. Eggs weighing at least 14 g at laying were significantly more likely to hatch than lighter eggs, indicating that low fresh weight may be the most useful predictor of embryo death in pink pigeons.
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Affiliation(s)
- Ksenia Potapova
- Department of Life Sciences, Imperial College London, London, United Kingdom
- Durrell Wildlife Conservation Trust, Trinity, Jersey, United Kingdom
| | - Harriet Whitford
- Durrell Wildlife Conservation Trust, Trinity, Jersey, United Kingdom
| | - Josh A Hodge
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Eluned Price
- Durrell Wildlife Conservation Trust, Trinity, Jersey, United Kingdom
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4
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Liu X, Milesi E, Fontsere C, Owens HL, Heinsohn R, Gilbert MTP, Crates R, Nogués-Bravo D, Morales HE. Time-lagged genomic erosion and future environmental risks in a bird on the brink of extinction. Proc Biol Sci 2025; 292:20242480. [PMID: 40132633 PMCID: PMC11936686 DOI: 10.1098/rspb.2024.2480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2024] [Revised: 01/30/2025] [Accepted: 03/04/2025] [Indexed: 03/27/2025] Open
Abstract
Global biodiversity is rapidly declining due to habitat degradation and genomic erosion, highlighting the urgent need to monitor endangered species and their genetic health. Temporal genomics and ecological modelling offer finer resolution than single-time-point measurements, providing a comprehensive view of species' recent and future trajectories. We investigated genomic erosion and environmental suitability in the critically endangered regent honeyeater (Anthochaera phrygia) by sequencing whole genomes of historical and modern specimens and building multi-temporal species distribution models (SDMs) across the last century. The species has declined from hundreds of thousands of individuals to fewer than 300 over the past 100 years. SDMs correctly predicted known patterns of local extinction in southeast Australia. Our demographic reconstructions revealed a gradual population decline from 2000 to 2500 years ago, sharply accelerating in the last 500 years due to climate variability and habitat loss. Despite this substantial demographic collapse, the regent honeyeater has lost only 9% of its genetic diversity, with no evidence of inbreeding or connectivity loss. Also, it exhibits higher diversity than many other threatened bird species. Forward-in-time genomic simulations indicate that this time lag between population decline and genetic diversity loss conceals the risk of ongoing genomic erosion into a future of rapidly degrading environmental suitability. Our work underscores the need for targeted conservation efforts and continuous genetic monitoring to prevent species extinction.
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Affiliation(s)
- Xufen Liu
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ester Milesi
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Hannah L. Owens
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Informatics Department, University of Florida, Gainesville, FL, USA
| | - Robert Heinsohn
- Fenner School of Environment and Society, Australian National University, Canberra, Australia
| | - M. Thomas P. Gilbert
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, Norwegian University of Science and Technology, Trondheim, Trøndelag, Norway
| | - Ross Crates
- Fenner School of Environment and Society, Australian National University, Canberra, Australia
| | | | - Hernán E. Morales
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Biology, Lund University, Lund, Sweden
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5
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Gargiulo R, Budde KB, Heuertz M. Mind the lag: understanding genetic extinction debt for conservation. Trends Ecol Evol 2025; 40:228-237. [PMID: 39572352 DOI: 10.1016/j.tree.2024.10.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 10/20/2024] [Accepted: 10/21/2024] [Indexed: 03/08/2025]
Abstract
The delay between disturbance events and genetic responses within populations is a common but surprisingly overlooked phenomenon in ecology and evolutionary and conservation genetics. If not accounted for when interpreting genetic data, this time lag problem can lead to erroneous conservation assessments. We (i) identify life-history traits related to longevity and reproductive strategies as the main determinants of time lags, (ii) evaluate potential confounding factors affecting genetic parameters during time lags, and (iii) propose approaches that allow controlling for time lags. Considering the current unprecedented rate of loss of genetic diversity and adaptive potential, we expect our novel interpretive and methodological framework for time lags to stimulate further research and discussion on the most appropriate approaches to analyse genetic diversity for conservation.
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Affiliation(s)
| | - Katharina B Budde
- Northwest German Forest Research Institute, Professor-Olekers-Strasse 6, 34346 Hann. Münden, Germany
| | - Myriam Heuertz
- Univ. Bordeaux, INRAE, Biogeco, 69 route d'Arcachon, 33610 Cestas, France
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6
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Martin EJ, Speak SA, Urban L, Morales HE, van Oosterhout C. Sonification of Genomic Data to Represent Genetic Load in Zoo Populations. Zoo Biol 2024; 43:513-519. [PMID: 39228291 PMCID: PMC11624621 DOI: 10.1002/zoo.21859] [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: 12/22/2023] [Revised: 06/13/2024] [Accepted: 08/14/2024] [Indexed: 09/05/2024]
Abstract
Maintaining a diverse gene pool is important in the captive management of zoo populations, especially in endangered species such as the pink pigeon (Nesoenas mayeri). However, due to the limited number of breeding individuals and relaxed natural selection, the loss of variation and accumulation of harmful variants is inevitable. Inbreeding results in a loss of fitness (i.e., inbreeding depression), principally because related parents are more likely to transmit a copy of the same recessive deleterious genetic variant to their offspring. Genomics-informed captive breeding can manage harmful variants by artificial selection, reducing the genetic load by avoiding the inheritance of two copies of the same harmful variant. To explain this concept in an interactive way to zoo visitors, we developed a sonification game to represent the fitness impacts of harmful variants by detuning notes in a familiar musical melody (i.e., Beethoven's Für Elise). Conceptually, zoo visitors play a game aiming to create the most optimal pink pigeon offspring in terms of inbreeding depression. They select virtual crosses between pink pigeon individuals and listen for the detuning of the melody, which represents the realised load of the resultant offspring. Here we present the sonification algorithm and the results of an online survey to see whether participants could identify the most and least optimal offspring from three potential pink pigeon offspring. Of our 98 respondents, 85 (86.7%) correctly identified the least optimal offspring, 73 (74.5%) correctly identified the most optimal, and 62 (63.3%) identified both the most and least optimal offspring using only the sonification.
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Affiliation(s)
- Edward J. Martin
- Institute of Ecology and Evolution, School of Biological SciencesUniversity of EdinburghEdinburghUK
| | - Samuel A. Speak
- School of Environmental SciencesUniversity of East Anglia, Norwich Research ParkNorwichUK
- Natural History MuseumLondonUK
- North of England Zoological SocietyChester ZooChesterUK
| | - Lara Urban
- Helmholtz AIHelmholtz Zentrum MuenchenNeuherbergGermany
- Helmholtz Pioneer CampusHelmholtz Zentrum MuenchenMunichGermany
- School of Life SciencesTechnical University of MunichFreisingGermany
| | - Hernán E. Morales
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Cock van Oosterhout
- School of Environmental SciencesUniversity of East Anglia, Norwich Research ParkNorwichUK
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7
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Zhang L, Leonard N, Passaro R, Luan MS, Van Tuyen P, Han LTN, Cam NH, Vogelnest L, Lynch M, Fine AE, Nga NTT, Van Long N, Rawson BM, Behie A, Van Nguyen T, Le MD, Nadler T, Walter L, Marques-Bonet T, Hofreiter M, Li M, Liu Z, Roos C. Genomic adaptation to small population size and saltwater consumption in the critically endangered Cat Ba langur. Nat Commun 2024; 15:8531. [PMID: 39358348 PMCID: PMC11447269 DOI: 10.1038/s41467-024-52811-7] [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: 04/26/2023] [Accepted: 09/23/2024] [Indexed: 10/04/2024] Open
Abstract
Many mammal species have declining populations, but the consequences of small population size on the genomic makeup of species remain largely unknown. We investigated the evolutionary history, genetic load and adaptive potential of the Cat Ba langur (Trachypithecus poliocephalus), a primate species endemic to Vietnam's famous Ha Long Bay and with less than 100 living individuals one of the most threatened primates in the world. Using high-coverage whole genome data of four wild individuals, we revealed the Cat Ba langur as sister species to its conspecifics of the northern limestone langur clade and found no evidence for extensive secondary gene flow after their initial separation. Compared to other primates and mammals, the Cat Ba langur showed low levels of genetic diversity, long runs of homozygosity, high levels of inbreeding and an excess of deleterious mutations in homozygous state. On the other hand, genetic diversity has been maintained in protein-coding genes and on the gene-rich human chromosome 19 ortholog, suggesting that the Cat Ba langur retained most of its adaptive potential. The Cat Ba langur also exhibits several unique non-synonymous variants that are related to calcium and sodium metabolism, which may have improved adaptation to high calcium intake and saltwater consumption.
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Affiliation(s)
- Liye Zhang
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany.
- International Max Planck Research School for Genome Science (IMPRS-GS), University of Göttingen, Göttingen, Germany.
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
| | - Neahga Leonard
- Cat Ba Langur Conservation Project (CBLCP), Cat Ba National Park, Cat Ba Island, Cat Hai District, Hai Phong Province, Vietnam
| | - Rick Passaro
- Cat Ba Langur Conservation Project (CBLCP), Cat Ba National Park, Cat Ba Island, Cat Hai District, Hai Phong Province, Vietnam
| | - Mai Sy Luan
- Cat Ba Langur Conservation Project (CBLCP), Cat Ba National Park, Cat Ba Island, Cat Hai District, Hai Phong Province, Vietnam
| | - Pham Van Tuyen
- Cat Ba Langur Conservation Project (CBLCP), Cat Ba National Park, Cat Ba Island, Cat Hai District, Hai Phong Province, Vietnam
| | - Le Thi Ngoc Han
- Cat Ba Langur Conservation Project (CBLCP), Cat Ba National Park, Cat Ba Island, Cat Hai District, Hai Phong Province, Vietnam
| | - Nguyen Huy Cam
- Cat Ba Langur Conservation Project (CBLCP), Cat Ba National Park, Cat Ba Island, Cat Hai District, Hai Phong Province, Vietnam
| | - Larry Vogelnest
- Taronga Conservation Society Australia, Mosman, NSW, Australia
| | - Michael Lynch
- Melbourne Zoo, Zoos Victoria, Parkville, VIC, Australia
| | - Amanda E Fine
- Wildlife Conservation Society (WCS), Health Program, New York, NY, USA
| | | | - Nguyen Van Long
- Wildlife Conservation Society (WCS), Vietnam Country Program, Hanoi, Vietnam
| | - Benjamin M Rawson
- World Wildlife Fund for Nature (WWF) International, Gland, Switzerland
| | - Alison Behie
- School of Archaeology and Anthropology, The Australian National University, Canberra, ACT, Australia
| | - Truong Van Nguyen
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, Department of Science, University of Potsdam, Potsdam, Germany
- Central Institute for Natural Resources and Environmental Studies, Vietnam National University, Hanoi, Vietnam
| | - Minh D Le
- Central Institute for Natural Resources and Environmental Studies, Vietnam National University, Hanoi, Vietnam
- Faculty of Environmental Sciences, University of Science, Vietnam National University, Hanoi, Vietnam
| | - Tilo Nadler
- Three Monkeys Wildlife Conservancy, Nho Quan District, Ninh Binh Province, Ninh Binh, Vietnam
| | - Lutz Walter
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, Cerdanyola del Vallès, Spain
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, Department of Science, University of Potsdam, Potsdam, Germany.
| | - Ming Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
| | - Zhijin Liu
- College of Life Sciences, Capital Normal University, Beijing, China.
| | - Christian Roos
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany.
- Gene Bank of Primates, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany.
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8
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Li X, Hou H, Shen X, Zhao W, Chen Y, Yao J, Yang C. Research Note: Study on the in-situ preservation of pigeons based on the level of endangerment of genetic resources. Poult Sci 2024; 103:104091. [PMID: 39146920 PMCID: PMC11374970 DOI: 10.1016/j.psj.2024.104091] [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: 02/16/2024] [Revised: 06/14/2024] [Accepted: 07/07/2024] [Indexed: 08/17/2024] Open
Abstract
The large-scale and intensive development of the meat pigeon breeding industry have resulted in the replacement of a large number of low-performance local breeds by a few breeds with excellent production performance. However, due to the characteristics of pigeon species that are monogamous, for which the W chromosome cannot be recovered and for which semen cannot be cryopreserved, the preservation of pigeon species is still mainly based on in-situ preservation. In this study, pigeons were classified into 6 classes of endangerment based on the criteria of the 100-year inbreeding coefficient of poultry populations in the "Assessment of Endangered Poultry Genetic Resources" (NY/T 2996-2016). The results show that when the generation interval was 1.5 yr, the number of ideal populations with the same gene frequency variance or the same heterozygosity decay rate of pigeons in class 1 to 5 was ≤149, 150 to 204, 205 to 316, 317 to 649 and ≥650. In random-reserved breeding, when the generation interval was 1.5 yr, the number of male (female) pigeons corresponding to class 1 to 5 was ≤74, 75 to 102, 103 to 157, 158 to 324 and ≥325. In family-equal-reserved breeding, when the generation interval was 1.5 yr, the number of male (female) pigeons corresponding to class 1 to 5 was ≤36, 37 to 50, 51 to 78, 79 to 162 and ≥163. When the generation interval was 1.5 yr, the inbreeding increments corresponding to class 1 to 5 were ≥0.00335, 0.00244 to 0.00334, 0.00159 to 0.00243, 0.00078 to 0.00158 and ≤0.00077; with the same population size, the inbreeding coefficient and inbreeding increment decreased with the increase of generation interval; the population effective content, inbreeding coefficient and inbreeding increment of family-equal-reserved pigeons were lower than those of random-reserved pigeons. The results of this study have certain reference value for analyzing the status quo of local and endangered species, constructing live gene banks and breeding farms of poultry genetic resources, and rescuing endangered species.
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Affiliation(s)
- Xin Li
- Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; National Poultry Engineering Technology Research Center, Shanghai 201106, China
| | - Haobin Hou
- Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; National Poultry Engineering Technology Research Center, Shanghai 201106, China
| | - Xiaohui Shen
- Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Weimin Zhao
- Shanghai Golden Royal Pigeon Industry Co. LTD, Shanghai 201508, China
| | - Yansen Chen
- Shanghai Pigeon Industrial Co. LTD, Shanghai 202152, China
| | - Junfeng Yao
- Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; National Poultry Engineering Technology Research Center, Shanghai 201106, China.
| | - Changsuo Yang
- Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; National Poultry Engineering Technology Research Center, Shanghai 201106, China
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9
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Speak SA, Birley T, Bortoluzzi C, Clark MD, Percival-Alwyn L, Morales HE, van Oosterhout C. Genomics-informed captive breeding can reduce inbreeding depression and the genetic load in zoo populations. Mol Ecol Resour 2024; 24:e13967. [PMID: 38727721 DOI: 10.1111/1755-0998.13967] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 02/10/2024] [Accepted: 04/12/2024] [Indexed: 10/10/2024]
Abstract
Zoo populations of threatened species are a valuable resource for the restoration of wild populations. However, their small effective population size poses a risk to long-term viability, especially in species with high genetic load. Recent bioinformatic developments can identify harmful genetic variants in genome data. Here, we advance this approach, analysing the genetic load in the threatened pink pigeon (Nesoenas mayeri). We lifted the mutation-impact scores that had been calculated for the chicken (Gallus gallus) to estimate the genetic load in six pink pigeons. Additionally, we perform in silico crossings to predict the genetic load and realized load of potential offspring. We thus identify the optimal mate pairs that are theoretically expected to produce offspring with the least inbreeding depression. We use computer simulations to show how genomics-informed conservation can reduce the genetic load whilst reducing the loss of genome-wide diversity. Genomics-informed management is likely to become instrumental in maintaining the long-term viability of zoo populations.
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Affiliation(s)
- Samuel A Speak
- School of Environmental Sciences, University of East Anglia, Norwich, UK
- Natural History Museum, London, UK
- North of England Zoological Society, Chester Zoo, Chester, UK
| | - Thomas Birley
- School of Environmental Sciences, University of East Anglia, Norwich, UK
| | - Chiara Bortoluzzi
- University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, UK
| | - Matthew D Clark
- Natural History Museum, London, UK
- Earlham Institute, Norwich, UK
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10
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Kyriazis CC, Lohmueller KE. Constraining models of dominance for nonsynonymous mutations in the human genome. PLoS Genet 2024; 20:e1011198. [PMID: 39302992 PMCID: PMC11446423 DOI: 10.1371/journal.pgen.1011198] [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: 02/25/2024] [Revised: 10/02/2024] [Accepted: 09/04/2024] [Indexed: 09/22/2024] Open
Abstract
Dominance is a fundamental parameter in genetics, determining the dynamics of natural selection on deleterious and beneficial mutations, the patterns of genetic variation in natural populations, and the severity of inbreeding depression in a population. Despite this importance, dominance parameters remain poorly known, particularly in humans or other non-model organisms. A key reason for this lack of information about dominance is that it is extremely challenging to disentangle the selection coefficient (s) of a mutation from its dominance coefficient (h). Here, we explore dominance and selection parameters in humans by fitting models to the site frequency spectrum (SFS) for nonsynonymous mutations. When assuming a single dominance coefficient for all nonsynonymous mutations, we find that numerous h values can fit the data, so long as h is greater than ~0.15. Moreover, we also observe that theoretically-predicted models with a negative relationship between h and s can also fit the data well, including models with h = 0.05 for strongly deleterious mutations. Finally, we use our estimated dominance and selection parameters to inform simulations revisiting the question of whether the out-of-Africa bottleneck has led to differences in genetic load between African and non-African human populations. These simulations suggest that the relative burden of genetic load in non-African populations depends on the dominance model assumed, with slight increases for more weakly recessive models and slight decreases shown for more strongly recessive models. Moreover, these results also demonstrate that models of partially recessive nonsynonymous mutations can explain the observed severity of inbreeding depression in humans, bridging the gap between molecular population genetics and direct measures of fitness in humans. Our work represents a comprehensive assessment of dominance and deleterious variation in humans, with implications for parameterizing models of deleterious variation in humans and other mammalian species.
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Affiliation(s)
- Christopher C. Kyriazis
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, United States of America
| | - Kirk E. Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, United States of America
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, California, United States of America
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
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11
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Jeon JY, Black AN, Heenkenda EJ, Mularo AJ, Lamka GF, Janjua S, Brüniche-Olsen A, Bickham JW, Willoughby JR, DeWoody JA. Genomic Diversity as a Key Conservation Criterion: Proof-of-Concept From Mammalian Whole-Genome Resequencing Data. Evol Appl 2024; 17:e70000. [PMID: 39257570 PMCID: PMC11386325 DOI: 10.1111/eva.70000] [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: 03/30/2024] [Revised: 06/25/2024] [Accepted: 07/25/2024] [Indexed: 09/12/2024] Open
Abstract
Many international, national, state, and local organizations prioritize the ranking of threatened and endangered species to help direct conservation efforts. For example, the International Union for Conservation of Nature (IUCN) assesses the Green Status of species and publishes the influential Red List of threatened species. Unfortunately, such conservation yardsticks do not explicitly consider genetic or genomic diversity (GD), even though GD is positively associated with contemporary evolutionary fitness, individual viability, and with future evolutionary potential. To test whether populations of genome sequences could help improve conservation assessments, we estimated GD metrics from 82 publicly available mammalian datasets and examined their statistical association with attributes related to conservation. We also considered intrinsic biological factors, including trophic level and body mass, that could impact GD and quantified their relative influences. Our results identify key population GD metrics that are both reflective and predictive of IUCN conservation categories. Specifically, our analyses revealed that Watterson's theta (the population mutation rate) and autozygosity (a product of inbreeding) are associated with the current Red List categorization, likely because demographic declines that lead to "listing" decisions also reduce levels of standing genetic variation. We argue that by virtue of this relationship, conservation organizations like IUCN could leverage emerging genome sequence data to help categorize Red List threat rankings (especially in otherwise data-deficient species) and/or enhance Green Status assessments to establish a baseline for future population monitoring. Thus, our paper (1) outlines the theoretical and empirical justification for a new GD-based assessment criterion, (2) provides a bioinformatic pipeline for estimating GD from population genomic data, and (3) suggests an analytical framework that can be used to measure baseline GD while providing quantitative GD context for consideration by conservation authorities.
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Affiliation(s)
- Jong Yoon Jeon
- Department of Forestry and Natural Resources Purdue University West Lafayette Indiana USA
| | - Andrew N Black
- Department of Forestry and Natural Resources Purdue University West Lafayette Indiana USA
- Western Association of Fish and Wildlife Agencies Boise Idaho USA
| | - Erangi J Heenkenda
- Department of Forestry and Natural Resources Purdue University West Lafayette Indiana USA
| | - Andrew J Mularo
- Department of Biological Sciences Purdue University West Lafayette Indiana USA
| | - Gina F Lamka
- College of Forestry, Wildlife, and Environment Auburn University Auburn Alabama USA
| | - Safia Janjua
- Department of Forestry and Natural Resources Purdue University West Lafayette Indiana USA
| | - Anna Brüniche-Olsen
- Center for Macroecology, Evolution and Climate, Globe Institute University of Copenhagen Copenhagen Denmark
| | - John W Bickham
- Department of Ecology and Conservation Biology Texas A&M University College Station Texas USA
| | - Janna R Willoughby
- College of Forestry, Wildlife, and Environment Auburn University Auburn Alabama USA
| | - J Andrew DeWoody
- Department of Forestry and Natural Resources Purdue University West Lafayette Indiana USA
- Western Association of Fish and Wildlife Agencies Boise Idaho USA
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12
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Cádiz MI, Tengstedt ANB, Sørensen IH, Pedersen ES, Fox AD, Hansen MM. Demographic History and Inbreeding in Two Declining Sea Duck Species Inferred From Whole-Genome Sequence Data. Evol Appl 2024; 17:e70008. [PMID: 39257569 PMCID: PMC11386304 DOI: 10.1111/eva.70008] [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: 05/11/2024] [Revised: 08/16/2024] [Accepted: 08/19/2024] [Indexed: 09/12/2024] Open
Abstract
Anthropogenic impact has transitioned from threatening already rare species to causing significant declines in once numerous organisms. Long-tailed duck (Clangula hyemalis) and velvet scoter (Melanitta fusca) were once important quarry sea duck species in NW Europe, but recent declines resulted in their reclassification as vulnerable on the IUCN Red List. We sequenced and assembled genomes for both species and resequenced 15 individuals of each. Using analyses based on site frequency spectra and sequential Markovian coalescence, we found C. hyemalis to show more historical demographic stability, whereas M. fusca was affected particularly by the Last (Weichselian) Glaciation. This likely reflects C. hyemalis breeding continuously across the Arctic, with cycles of glaciation primarily shifting breeding areas south or north without major population declines, whereas the more restricted southern range of M. fusca would lead to significant range contraction during glaciations. Both species showed evidence of declines over the past thousands of years, potentially reflecting anthropogenic pressures with the recent decline indicating an accelerated process. Analysis of runs of homozygosity (ROH) showed low but nontrivial inbreeding, with F ROH from 0.012 to 0.063 in C. hyemalis and ranging from 0 to 0.047 in M. fusca. Lengths of ROH suggested that this was due to ongoing background inbreeding rather than recent declines. Overall, despite demographically important declines, this has not yet led to strong inbreeding and genetic erosion, and the most pressing conservation concern may be the risk of density-dependent (Allee) effects. We recommend monitoring of inbreeding using ROH analysis as a cost-efficient method to track future developments to support effective conservation of these species.
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Affiliation(s)
- María I Cádiz
- Department of Biology Aarhus University Aarhus Denmark
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13
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Turvey ST, Lau EYX, Duncan C, Ma H, Liu H. Assessing the information-content of messy data to reconstruct population recovery dynamics for the world's rarest primate. Ecol Evol 2024; 14:e70089. [PMID: 39114163 PMCID: PMC11303811 DOI: 10.1002/ece3.70089] [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: 02/06/2024] [Revised: 06/20/2024] [Accepted: 07/16/2024] [Indexed: 08/10/2024] Open
Abstract
Understanding the dynamics of population recovery in threatened species requires robust longitudinal monitoring datasets. However, evidence-based decision-making is often impeded by variable data collection approaches, necessitating critical evaluation of restricted available baselines. The Hainan gibbon, the world's rarest primate, had possibly declined to only seven or eight individuals in 1978 at Bawangling National Nature Reserve but has experienced subsequent population growth. Past population estimates lack detailed reporting of survey effort, and multiple conflicting estimates are available, hindering assessment of gibbon recovery. We investigated all reported estimates of Bawangling gibbon population size from 1978 to 2022, to evaluate the biological signal of population trends and the extent to which noise associated with varying survey effort, reporting and estimation may mask or misrepresent any underlying signal. This longitudinal dataset demonstrates that the Bawangling population experienced a series of bottlenecks and recoveries, with three successive periods of growth interspersed by population crashes (1978-1989, 1989-2000 and 2000-2022). The rate of gibbon population recovery was progressively slower over time in each successive period of growth, and this potential decline in recovery rate following serial bottlenecks suggests that additional management strategies may be required alongside "nature-based solutions" for this species. However, population viability analysis suggests the 1978 founder population is unlikely to have been as low as seven individuals, raising concerns for interpreting reported historical population counts and understanding the dynamics of the species' recovery. We caution against overinterpreting potential signals within "messy" conservation datasets, and we emphasise the crucial importance of standardised replicable survey methods and transparent reporting of data and effort in all future surveys of Hainan gibbons and other highly threatened species.
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Affiliation(s)
| | | | - Clare Duncan
- Institute of ZoologyZoological Society of LondonLondonUK
- Centre for Ecology & Conservation, Biosciences, College of Life and Environmental SciencesUniversity of ExeterCornwallUK
| | - Heidi Ma
- Institute of ZoologyZoological Society of LondonLondonUK
| | - Hui Liu
- School of Tropical Agriculture and ForestryHainan UniversityHaikouChina
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14
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Cavill EL, Morales HE, Sun X, Westbury MV, van Oosterhout C, Accouche W, Zora A, Schulze MJ, Shah N, Adam P, Brooke MDL, Sweet P, Gopalakrishnan S, Gilbert MTP. When birds of a feather flock together: Severe genomic erosion and the implications for genetic rescue in an endangered island passerine. Evol Appl 2024; 17:e13739. [PMID: 38948538 PMCID: PMC11212007 DOI: 10.1111/eva.13739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 05/22/2024] [Accepted: 06/04/2024] [Indexed: 07/02/2024] Open
Abstract
The Seychelles magpie-robin's (SMR) five island populations exhibit some of the lowest recorded levels of genetic diversity among endangered birds, and high levels of inbreeding. These populations collapsed during the 20th century, and the species was listed as Critically Endangered in the IUCN Red List in 1994. An assisted translocation-for-recovery program initiated in the 1990s increased the number of mature individuals, resulting in its downlisting to Endangered in 2005. Here, we explore the temporal genomic erosion of the SMR based on a dataset of 201 re-sequenced whole genomes that span the past ~150 years. Our sample set includes individuals that predate the bottleneck by up to 100 years, as well as individuals from contemporary populations established during the species recovery program. Despite the SMR's recent demographic recovery, our data reveal a marked increase in both the genetic load and realized load in the extant populations when compared to the historical samples. Conservation management may have reduced the intensity of selection by increasing juvenile survival and relaxing intraspecific competition between individuals, resulting in the accumulation of loss-of-function mutations (i.e. severely deleterious variants) in the rapidly recovering population. In addition, we found a 3-fold decrease in genetic diversity between temporal samples. While the low genetic diversity in modern populations may limit the species' adaptability to future environmental changes, future conservation efforts (including IUCN assessments) may also need to assess the threats posed by their high genetic load. Our computer simulations highlight the value of translocations for genetic rescue and show how this could halt genomic erosion in threatened species such as the SMR.
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Affiliation(s)
- Emily L. Cavill
- The Globe Institute, University of CopenhagenCopenhagenDenmark
| | | | - Xin Sun
- The Globe Institute, University of CopenhagenCopenhagenDenmark
| | | | - Cock van Oosterhout
- School of Environmental SciencesUniversity of East Anglia, Norwich Research ParkNorwichUK
| | | | - Anna Zora
- Fregate Island Sanctuary LtdVictoriaSeychelles
| | | | | | | | | | - Paul Sweet
- American Museum of Natural HistoryNew YorkUSA
| | | | - M. Thomas P. Gilbert
- The Globe Institute, University of CopenhagenCopenhagenDenmark
- University Museum, Norwegian University of Science and TechnologyTrondheimNorway
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15
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Al Hikmani H, van Oosterhout C, Birley T, Labisko J, Jackson HA, Spalton A, Tollington S, Groombridge JJ. Can genetic rescue help save Arabia's last big cat? Evol Appl 2024; 17:e13701. [PMID: 38784837 PMCID: PMC11113348 DOI: 10.1111/eva.13701] [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: 12/08/2023] [Revised: 04/01/2024] [Accepted: 04/10/2024] [Indexed: 05/25/2024] Open
Abstract
Genetic diversity underpins evolutionary potential that is essential for the long-term viability of wildlife populations. Captive populations harbor genetic diversity potentially lost in the wild, which could be valuable for release programs and genetic rescue. The Critically Endangered Arabian leopard (Panthera pardus nimr) has disappeared from most of its former range across the Arabian Peninsula, with fewer than 120 individuals left in the wild, and an additional 64 leopards in captivity. We (i) examine genetic diversity in the wild and captive populations to identify global patterns of genetic diversity and structure; (ii) estimate the size of the remaining leopard population across the Dhofar mountains of Oman using spatially explicit capture-recapture models on DNA and camera trap data, and (iii) explore the impact of genetic rescue using three complementary computer modeling approaches. We estimated a population size of 51 (95% CI 32-79) in the Dhofar mountains and found that 8 out of 25 microsatellite alleles present in eight loci in captive leopards were undetected in the wild. This includes two alleles present only in captive founders known to have been wild-sourced from Yemen, which suggests that this captive population represents an important source for genetic rescue. We then assessed the benefits of reintroducing novel genetic diversity into the wild population as well as the risks of elevating the genetic load through the release of captive-bred individuals. Simulations indicate that genetic rescue can improve the long-term viability of the wild population by reducing its genetic load and realized load. The model also suggests that the genetic load has been partly purged in the captive population, potentially making it a valuable source population for genetic rescue. However, the greater loss of its genetic diversity could exacerbate genomic erosion of the wild population during a rescue program, and these risks and benefits should be carefully evaluated. An important next step in the recovery of the Arabian leopard is to empirically validate these conclusions, implement and monitor a genomics-informed management plan, and optimize a strategy for genetic rescue as a tool to recover Arabia's last big cat.
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Affiliation(s)
- Hadi Al Hikmani
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, Division of Human and Social SciencesUniversity of KentCanterburyKentUK
- Office for Conservation of the EnvironmentDiwan of Royal CourtMuscatOman
- The Royal Commission for AlUlaAlUlaSaudi Arabia
| | - Cock van Oosterhout
- School of Environmental SciencesUniversity of East Anglia, Norwich Research ParkNorwichUK
| | - Thomas Birley
- School of Environmental SciencesUniversity of East Anglia, Norwich Research ParkNorwichUK
| | - Jim Labisko
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, Division of Human and Social SciencesUniversity of KentCanterburyKentUK
- Centre for Biodiversity and Environment Research, Research Department of Genetics, Evolution and EnvironmentUniversity College LondonLondonUK
- Island Biodiversity and Conservation CentreUniversity of SeychellesVictoriaSeychelles
- Department of Life SciencesThe Natural History MuseumLondonUK
| | - Hazel A. Jackson
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, Division of Human and Social SciencesUniversity of KentCanterburyKentUK
| | | | - Simon Tollington
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, Division of Human and Social SciencesUniversity of KentCanterburyKentUK
- School of Animal Rural and Environmental SciencesNottingham Trent UniversityNottinghamUK
| | - Jim J. Groombridge
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, Division of Human and Social SciencesUniversity of KentCanterburyKentUK
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16
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Bourgeois Y, Warren BH, Augiron S. The burden of anthropogenic changes and mutation load in a critically endangered harrier from the Reunion biodiversity hotspot, Circus maillardi. Mol Ecol 2024; 33:e17300. [PMID: 38372440 DOI: 10.1111/mec.17300] [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: 08/09/2022] [Revised: 01/18/2024] [Accepted: 01/30/2024] [Indexed: 02/20/2024]
Abstract
Anthropogenic impact is causing the decline of a large proportion of species worldwide and reduces their genetic diversity. Island species typically have smaller ranges than continental species. As a consequence, island species are particularly liable to undergo population bottlenecks, giving rise to conservation challenges such as inbreeding and unmasking of deleterious genetic load. Such challenges call for more detailed assessments of the genetic make-up of threatened island populations. The Mascarene islands (Indian Ocean) present many prime examples, being unusual in having been pristine until first human arrival ~400 years ago, following which anthropogenic pressure was unusually intense. A threatened harrier (Circus maillardi) endemic to the westernmost island of the archipelago is a good example of the challenges faced by species that have declined to small population size following intense anthropogenic pressure. In this study, we use an extensive set of population genomic tools to quantify variation at near-neutral and coding loci, in order to test the historical impact of human activity on this species, and evaluate the species' (mal)adaptive potential. We observed low but significant genetic differentiation between populations on the West and North-East sides of the island, echoing observations in other endemic species. Inbreeding was significant, with a substantial fraction of samples being first or second-degree relatives. Historical effective population sizes have declined from ~3000 to 300 individuals in the past 1000 years, with a more recent drop ~100 years ago consistent with human activity. Based on our simulations and comparisons with a close relative (Circus melanoleucos), this demographic history may have allowed purging of the most deleterious variants but is unlikely to have allowed the purging of mildly deleterious variants. Our study shows how using relatively affordable methods can reveal the massive impact that human activity may have on the genetic diversity and adaptive potential of island populations, and calls for urgent action to closely monitor the reproductive success of such endemic populations, in association with genetic studies.
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Affiliation(s)
- Yann Bourgeois
- DIADE, University of Montpellier, CIRAD, IRD, Montpellier, France
- School of Biological Sciences, University of Portsmouth, Portsmouth, UK
| | - Ben H Warren
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, UA, Paris, France
| | - Steve Augiron
- Société d'Études Ornithologiques de La Réunion, Saint-André, France
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17
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van Oosterhout C. AI-informed conservation genomics. Heredity (Edinb) 2024; 132:1-4. [PMID: 38151537 PMCID: PMC10798949 DOI: 10.1038/s41437-023-00666-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/09/2023] [Accepted: 12/11/2023] [Indexed: 12/29/2023] Open
Affiliation(s)
- Cock van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
- Conservation Genetics Specialist Group, International Union for Conservation of Nature (IUCN), Gland, Switzerland.
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18
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Peters C, Geary M, Hosie C, Nelson H, Rusk B, Muir A. Non-invasive sampling reveals low mitochondrial genetic diversity for an island endemic species: The critically endangered Grenada Dove Leptotila wellsi. Ecol Evol 2023; 13:e10767. [PMID: 38020693 PMCID: PMC10667608 DOI: 10.1002/ece3.10767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/30/2023] [Accepted: 11/07/2023] [Indexed: 12/01/2023] Open
Abstract
As an island endemic with a decreasing population, the critically endangered Grenada Dove Leptotila wellsi is threatened by accelerated loss of genetic diversity resulting from ongoing habitat fragmentation. Small, threatened populations are difficult to sample directly but advances in molecular methods mean that non-invasive samples can be used. We performed the first assessment of genetic diversity of populations of Grenada Dove by (a) assessing mtDNA genetic diversity in the only two areas of occupancy on Grenada, (b) defining the number of haplotypes present at each site and (c) evaluating evidence of isolation between sites. We used non-invasively collected samples from two locations: Mt Hartman (n = 18) and Perseverance (n = 12). DNA extraction and PCR were used to amplify 1751 bps of mtDNA from two mitochondrial markers: NADH dehydrogenase 2 (ND2) and Cytochrome b (Cyt b). Haplotype diversity (h) of 0.4, a nucleotide diversity (π) of 0.00023 and two unique haplotypes were identified within the ND2 sequences; a single haplotype was identified within the Cyt b sequences. Of the two haplotypes identified, the most common haplotype (haplotype A = 73.9%) was observed at both sites and the other (haplotype B = 26.1%) was unique to Perseverance. Our results show low mitochondrial genetic diversity and clear evidence for genetically isolated populations. The Grenada Dove needs urgent conservation action, including habitat protection and potentially augmentation of gene flow by translocation in order to increase genetic resilience and diversity with the ultimate aim of securing the long-term survival of this critically endangered species.
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Affiliation(s)
- Catherine Peters
- Conservation Biology Research Group, Department of Biological SciencesUniversity of ChesterChesterUK
| | - Matthew Geary
- Conservation Biology Research Group, Department of Biological SciencesUniversity of ChesterChesterUK
| | - Charlotte Hosie
- Conservation Biology Research Group, Department of Biological SciencesUniversity of ChesterChesterUK
| | | | - Bonnie Rusk
- Grenada Dove Conservation ProgrammeSt GeorgesGrenada
| | - Anna Muir
- Conservation Biology Research Group, Department of Biological SciencesUniversity of ChesterChesterUK
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19
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Dussex N, Morales HE, Grossen C, Dalén L, van Oosterhout C. Purging and accumulation of genetic load in conservation. Trends Ecol Evol 2023; 38:961-969. [PMID: 37344276 DOI: 10.1016/j.tree.2023.05.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 06/23/2023]
Abstract
Our ability to assess the threat posed by the genetic load to small and declining populations has been greatly improved by advances in genome sequencing and computational approaches. Yet, considerable confusion remains around the definitions of the genetic load and its dynamics, and how they impact individual fitness and population viability. We illustrate how both selective purging and drift affect the distribution of deleterious mutations during population size decline and recovery. We show how this impacts the composition of the genetic load, and how this affects the extinction risk and recovery potential of populations. We propose a framework to examine load dynamics and advocate for the introduction of load estimates in the management of endangered populations.
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Affiliation(s)
- Nicolas Dussex
- Department of Natural History, NTNU University Museum, Erling Skakkes Gate 47A, 7012 Trondheim, Norway.
| | - Hernán E Morales
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Christine Grossen
- WSL Swiss Federal Research Institute, CH-8903 Birmensdorf, Switzerland
| | - Love Dalén
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, SE-106 91 Stockholm, Sweden
| | - Cock van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, NR4 7TJ Norwich, UK
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20
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Urban L, Perlas A, Francino O, Martí‐Carreras J, Muga BA, Mwangi JW, Boykin Okalebo L, Stanton JL, Black A, Waipara N, Fontsere C, Eccles D, Urel H, Reska T, Morales HE, Palmada‐Flores M, Marques‐Bonet T, Watsa M, Libke Z, Erkenswick G, van Oosterhout C. Real-time genomics for One Health. Mol Syst Biol 2023; 19:e11686. [PMID: 37325891 PMCID: PMC10407731 DOI: 10.15252/msb.202311686] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/31/2023] [Accepted: 06/02/2023] [Indexed: 06/17/2023] Open
Abstract
The ongoing degradation of natural systems and other environmental changes has put our society at a crossroad with respect to our future relationship with our planet. While the concept of One Health describes how human health is inextricably linked with environmental health, many of these complex interdependencies are still not well-understood. Here, we describe how the advent of real-time genomic analyses can benefit One Health and how it can enable timely, in-depth ecosystem health assessments. We introduce nanopore sequencing as the only disruptive technology that currently allows for real-time genomic analyses and that is already being used worldwide to improve the accessibility and versatility of genomic sequencing. We showcase real-time genomic studies on zoonotic disease, food security, environmental microbiome, emerging pathogens, and their antimicrobial resistances, and on environmental health itself - from genomic resource creation for wildlife conservation to the monitoring of biodiversity, invasive species, and wildlife trafficking. We stress why equitable access to real-time genomics in the context of One Health will be paramount and discuss related practical, legal, and ethical limitations.
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Affiliation(s)
- Lara Urban
- Helmholtz AI, Helmholtz Zentrum MuenchenNeuherbergGermany
- Helmholtz Pioneer Campus, Helmholtz Zentrum MuenchenNeuherbergGermany
- School of Life Sciences, Technical University of MunichFreisingGermany
| | - Albert Perlas
- Helmholtz AI, Helmholtz Zentrum MuenchenNeuherbergGermany
- Helmholtz Pioneer Campus, Helmholtz Zentrum MuenchenNeuherbergGermany
| | - Olga Francino
- Nano1Health SL, Parc de Recerca UABCampus Universitat Autònoma de BarcelonaBarcelonaSpain
| | - Joan Martí‐Carreras
- Nano1Health SL, Parc de Recerca UABCampus Universitat Autònoma de BarcelonaBarcelonaSpain
| | - Brenda A Muga
- Department of AnatomyUniversity of OtagoDunedinNew Zealand
| | | | | | | | - Amanda Black
- Bioprotection AotearoaLincoln UniversityLincolnNew Zealand
| | | | - Claudia Fontsere
- Center for Evolutionary HologenomicsThe Globe Institute, University of CopenhagenCopenhagenDenmark
| | - David Eccles
- Hugh Green Cytometry CentreMalaghan Institute of Medical ResearchWellingtonNew Zealand
| | - Harika Urel
- Helmholtz AI, Helmholtz Zentrum MuenchenNeuherbergGermany
- Helmholtz Pioneer Campus, Helmholtz Zentrum MuenchenNeuherbergGermany
- School of Life Sciences, Technical University of MunichFreisingGermany
| | - Tim Reska
- Helmholtz AI, Helmholtz Zentrum MuenchenNeuherbergGermany
- Helmholtz Pioneer Campus, Helmholtz Zentrum MuenchenNeuherbergGermany
- School of Life Sciences, Technical University of MunichFreisingGermany
| | - Hernán E Morales
- Center for Evolutionary HologenomicsThe Globe Institute, University of CopenhagenCopenhagenDenmark
- Department of Biology, Ecology BuildingLund UniversityLundSweden
| | - Marc Palmada‐Flores
- Institute of Evolutionary BiologyUniversitat Pompeu Fabra‐CSIC, PRBBBarcelonaSpain
| | - Tomas Marques‐Bonet
- Institute of Evolutionary BiologyUniversitat Pompeu Fabra‐CSIC, PRBBBarcelonaSpain
- Catalan Institution of Research and Advanced Studies (ICREA)BarcelonaSpain
- CNAGCentre of Genomic AnalysisBarcelonaSpain
- Institut Català de Paleontologia Miquel CrusafontUniversitat Autònoma de BarcelonaBarcelonaSpain
| | | | - Zane Libke
- Instituto Nacional de BiodiversidadQuitoEcuador
- Fundación Sumak Kawsay In SituCantón MeraEcuador
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21
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Dicks KL, Ball AD, Banfield L, Barrios V, Boufaroua M, Chetoui A, Chuven J, Craig M, Faqeer MYA, Garba HHM, Guedara H, Harouna A, Ivy J, Najjar C, Petretto M, Pusey R, Rabeil T, Riordan P, Senn HV, Taghouti E, Wacher T, Woodfine T, Gilbert T. Genetic diversity in global populations of the critically endangered addax ( Addax nasomaculatus) and its implications for conservation. Evol Appl 2023; 16:111-125. [PMID: 36699120 PMCID: PMC9850015 DOI: 10.1111/eva.13515] [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: 07/20/2022] [Revised: 10/10/2022] [Accepted: 11/04/2022] [Indexed: 12/24/2022] Open
Abstract
Threatened species are frequently patchily distributed across small wild populations, ex situ populations managed with varying levels of intensity and reintroduced populations. Best practice advocates for integrated management across in situ and ex situ populations. Wild addax (Addax nasomaculatus) now number fewer than 100 individuals, yet 1000 of addax remain in ex situ populations, which can provide addax for reintroductions, as has been the case in Tunisia since the mid-1980s. However, integrated management requires genetic data to ascertain the relationships between wild and ex situ populations that have incomplete knowledge of founder origins, management histories, and pedigrees. We undertook a global assessment of genetic diversity across wild, ex situ and reintroduced populations in Tunisia to assist conservation planning for this Critically Endangered species. We show that the remnant wild populations retain more mitochondrial haplotypes that are more diverse than the entirety of the ex situ populations across Europe, North America and the United Arab Emirates, and the reintroduced Tunisian population. Additionally, 1704 SNPs revealed that whilst population structure within the ex situ population is minimal, each population carries unique diversity. Finally, we show that careful selection of founders and subsequent genetic management is vital to ensure genetic diversity is provided to, and minimize drift and inbreeding within reintroductions. Our results highlight a vital need to conserve the last remaining wild addax population, and we provide a genetic foundation for determining integrated conservation strategies to prevent extinction and optimize future reintroductions.
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Affiliation(s)
- Kara L. Dicks
- RZSS WildGenes, Royal Zoological Society of ScotlandEdinburghUK
| | - Alex D. Ball
- RZSS WildGenes, Royal Zoological Society of ScotlandEdinburghUK
| | - Lisa Banfield
- Life Sciences DepartmentAl Ain ZooAl AinUnited Arab Emirates
| | | | | | | | - Justin Chuven
- Terrestrial & Marine Biodiversity Management Sector, Environment Agency – Abu DhabiAbu DhabiUnited Arab Emirates
| | - Mark Craig
- Life Sciences DepartmentAl Ain ZooAl AinUnited Arab Emirates
| | | | | | | | - Abdoulaye Harouna
- SaharaConservationSaint Maur des FossésFrance
- Noé au NigerRéserve Naturelle Nationale de Termit et Tin‐ToummaNiger
| | - Jamie Ivy
- San Diego Zoo Wildlife AllianceSan DiegoCaliforniaUSA
| | - Chawki Najjar
- Conservation Biology, Marwell WildlifeWinchesterUK
- Association Tunisienne de la Vie SauvageTunisTunisia
| | | | - Ricardo Pusey
- Terrestrial & Marine Biodiversity Management Sector, Environment Agency – Abu DhabiAbu DhabiUnited Arab Emirates
| | | | - Philip Riordan
- Conservation Biology, Marwell WildlifeWinchesterUK
- School of Biological Sciences, Faculty of Environmental and Life SciencesUniversity of SouthamptonSouthamptonUK
| | - Helen V. Senn
- RZSS WildGenes, Royal Zoological Society of ScotlandEdinburghUK
| | | | - Tim Wacher
- Conservation & Policy, Zoological Society of LondonLondonUK
| | - Tim Woodfine
- Conservation Biology, Marwell WildlifeWinchesterUK
- School of Biological Sciences, Faculty of Environmental and Life SciencesUniversity of SouthamptonSouthamptonUK
| | - Tania Gilbert
- Conservation Biology, Marwell WildlifeWinchesterUK
- School of Biological Sciences, Faculty of Environmental and Life SciencesUniversity of SouthamptonSouthamptonUK
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