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Das A, Suvo MSH, Shaha M, Gupta MD. Genome sequencing of captive white tigers from Bangladesh. BMC Genom Data 2024; 25:52. [PMID: 38844863 PMCID: PMC11155014 DOI: 10.1186/s12863-024-01239-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Accepted: 05/30/2024] [Indexed: 06/09/2024] Open
Abstract
OBJECTIVES The Bengal tiger Panthera tigris tigris, is an emblematic animal for Bangladesh. Despite being the apex predator in the wild, their number is decreasing due to anthropogenic activities such as hunting, urbanization, expansion of agriculture and deforestation. By contrast, captive tigers are flourishing due to practical conservation efforts. Breeding within the small captive population can produce inbreeding depression and genetic bottlenecks, which may limit the success of conservation efforts. Despite past decades of research, a comprehensive database on genetic variation in the captive and wild Bengal tigers in Bangladesh still needs to be included. Therefore, this research aimed to investigate the White Bengal tiger genome to create a resource for future studies to understand variation underlying important functional traits. DATA DESCRIPTION Blood samples from Chattogram Zoo were collected for three white Bengal tigers. Genomic DNA for all collected samples were extracted using a commercial DNA extraction kit. Whole genome sequencing was performed using a DNBseq platform. We generated 77 Gb of whole-genome sequencing (WGS) data for three white Bengal tigers (Average 11X coverage/sample). The data we generated will establish a paradigm for tiger research in Bangladesh by providing a genomic resource for future functional studies on the Bengal white tiger.
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Affiliation(s)
- Ashutosh Das
- Department of Genetics and Animal Breeding, Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Khulshi, Chattogram-4225, Bangladesh.
| | | | - Mishuk Shaha
- Department of Genetics and Animal Breeding, Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Khulshi, Chattogram-4225, Bangladesh
| | - Mukta Das Gupta
- Department of Microbiology and Veterinary Public Health, Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Khulshi, Chattogram-4225, Bangladesh
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Zhang W, Lin K, Fu W, Xie J, Fan X, Zhang M, Luo H, Yin Y, Guo Q, Huang H, Chen T, Lin X, Yuan Y, Huang C, Du S. Insights for the Captive Management of South China Tigers Based on a Large-Scale Genetic Survey. Genes (Basel) 2024; 15:398. [PMID: 38674333 PMCID: PMC11049310 DOI: 10.3390/genes15040398] [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: 02/17/2024] [Revised: 03/17/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
There is an urgent need to find a way to improve the genetic diversity of captive South China tiger (SCT, Panthera tigris amoyensis), the most critically endangered taxon of living tigers, facing inbreeding depression. The genomes showed that 13 hybrid SCTs from Meihuashan were divided into two groups; one group included three individuals who had a closer relationship with pureblood SCTs than another group. The three individuals shared more that 40% of their genome with pureblood SCTs and might be potential individuals for genetic rescuing in SCTs. A large-scale genetic survey based on 319 pureblood SCTs showed that the mean microsatellite inbreeding coefficient of pureblood SCTs decreased significantly from 0.1789 to 0.0600 (p = 0.000009) and the ratio of heterozygous loci increased significantly from 38.5% to 43.2% (p = 0.02) after one individual of the Chongqing line joined the Suzhou line and began to breed in the mid-1980s, which is a reason why the current SCTs keep a moderate level of microsatellite heterozygosity and nucleotide diversity. However, it is important to establish a back-up population based on the three individuals through introducing one pureblood SCT into the back-up population every year. The back-up population should be an important reserve in case the pureblood SCTs are in danger in the future.
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Affiliation(s)
- Wenping Zhang
- Key Laboratory of Monitoring Biological Diversity in Minshan Mountain of National Park of Giant Pandas, College of Life Science & Biotechnology, Mianyang Normal University, Mianyang 621000, China; (W.Z.)
| | - Kaixiong Lin
- Fujian Meihuashan Institute of South China Tiger Breeding, Longyan 364201, China; (K.L.); (H.L.)
| | - Wenyuan Fu
- Longyan Geopark Protection and Development Center, Longyan 364201, China
| | - Junjin Xie
- Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China
| | - Xueyang Fan
- Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China
| | - Mingchun Zhang
- China Conservation and Research Center for the Giant Panda, Chengdu 611830, China;
| | - Hongxing Luo
- Fujian Meihuashan Institute of South China Tiger Breeding, Longyan 364201, China; (K.L.); (H.L.)
| | | | - Qiang Guo
- Key Laboratory of Monitoring Biological Diversity in Minshan Mountain of National Park of Giant Pandas, College of Life Science & Biotechnology, Mianyang Normal University, Mianyang 621000, China; (W.Z.)
| | - He Huang
- Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China
| | - Tengteng Chen
- Fujian Meihuashan Institute of South China Tiger Breeding, Longyan 364201, China; (K.L.); (H.L.)
| | - Xipan Lin
- Fujian Meihuashan Institute of South China Tiger Breeding, Longyan 364201, China; (K.L.); (H.L.)
| | | | - Cheng Huang
- Fujian Meihuashan Institute of South China Tiger Breeding, Longyan 364201, China; (K.L.); (H.L.)
| | - Shizhang Du
- Key Laboratory of Monitoring Biological Diversity in Minshan Mountain of National Park of Giant Pandas, College of Life Science & Biotechnology, Mianyang Normal University, Mianyang 621000, China; (W.Z.)
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3
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Wang D, Smith JLD, Accatino F, Ge J, Wang T. Addressing the impact of canine distemper spreading on an isolated tiger population in northeast Asia. Integr Zool 2023; 18:994-1008. [PMID: 36881515 DOI: 10.1111/1749-4877.12712] [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] [Indexed: 03/08/2023]
Abstract
The continuation of the isolated Amur tiger (Panthera tigris altaica) population living along the China-Russia border is facing serious challenges due to factors such as its small size (including 38 individuals) and canine distemper virus (CDV). We use a population viability analysis metamodel, which consists of a traditional individual-based demographic model linked to an epidemiological model, to assess options for controlling the impact of negative factors through domestic dog management in protected areas, increasing connectivity to the neighboring large population (including more than 400 individuals), and habitat expansion. Without intervention, under inbreeding depression of 3.14, 6.29, and 12.26 lethal equivalents, our metamodel predicted the extinction within 100 years is 64.4%, 90.6%, and 99.8%, respectively. In addition, the simulation results showed that dog management or habitat expansion independently will not ensure tiger population viability for the next 100 years, and connectivity to the neighboring population would only keep the population size from rapidly declining. However, when the above three conservation scenarios are combined, even at the highest level of 12.26 lethal equivalents inbreeding depression, population size will not decline and the probability of extinction will be <5.8%. Our findings highlight that protecting the Amur tiger necessitates a multifaceted synergistic effort. Our key management recommendations for this population underline the importance of reducing CDV threats and expanding tiger occupancy to its former range in China, but re-establishing habitat connectivity to the neighboring population is an important long-term objective.
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Affiliation(s)
- Dawei Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Engineering, NFGA Key Laboratory for Conservation Ecology of Northeast Tiger and Leopard & College of Life Sciences, Beijing Normal University, Beijing, China
| | - James L D Smith
- Department of Fisheries, Wildlife and Conservation Biology, University of Minnesota, St. Paul, MN, USA
| | - Francesco Accatino
- UMR SADAPT, INRAE, AgroParisTech, Université Paris-Saclay, PALAISEAU Cedex, France
| | - Jianping Ge
- Ministry of Education Key Laboratory for Biodiversity Science and Engineering, NFGA Key Laboratory for Conservation Ecology of Northeast Tiger and Leopard & College of Life Sciences, Beijing Normal University, Beijing, China
| | - Tianming Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Engineering, NFGA Key Laboratory for Conservation Ecology of Northeast Tiger and Leopard & College of Life Sciences, Beijing Normal University, Beijing, China
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4
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Sun X, Liu YC, Tiunov MP, Gimranov DO, Zhuang Y, Han Y, Driscoll CA, Pang Y, Li C, Pan Y, Velasco MS, Gopalakrishnan S, Yang RZ, Li BG, Jin K, Xu X, Uphyrkina O, Huang Y, Wu XH, Gilbert MTP, O'Brien SJ, Yamaguchi N, Luo SJ. Ancient DNA reveals genetic admixture in China during tiger evolution. Nat Ecol Evol 2023; 7:1914-1929. [PMID: 37652999 DOI: 10.1038/s41559-023-02185-8] [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: 09/14/2022] [Accepted: 08/02/2023] [Indexed: 09/02/2023]
Abstract
The tiger (Panthera tigris) is a charismatic megafauna species that originated and diversified in Asia and probably experienced population contraction and expansion during the Pleistocene, resulting in low genetic diversity of modern tigers. However, little is known about patterns of genomic diversity in ancient populations. Here we generated whole-genome sequences from ancient or historical (100-10,000 yr old) specimens collected across mainland Asia, including a 10,600-yr-old Russian Far East specimen (RUSA21, 8× coverage) plus six ancient mitogenomes, 14 South China tigers (0.1-12×) and three Caspian tigers (4-8×). Admixture analysis showed that RUSA21 clustered within modern Northeast Asian phylogroups and partially derived from an extinct Late Pleistocene lineage. While some of the 8,000-10,000-yr-old Russian Far East mitogenomes are basal to all tigers, one 2,000-yr-old specimen resembles present Amur tigers. Phylogenomic analyses suggested that the Caspian tiger probably dispersed from an ancestral Northeast Asian population and experienced gene flow from southern Bengal tigers. Lastly, genome-wide monophyly supported the South China tiger as a distinct subspecies, albeit with mitochondrial paraphyly, hence resolving its longstanding taxonomic controversy. The distribution of mitochondrial haplogroups corroborated by biogeographical modelling suggested that Southwest China was a Late Pleistocene refugium for a relic basal lineage. As suitable habitat returned, admixture between divergent lineages of South China tigers took place in Eastern China, promoting the evolution of other northern subspecies. Altogether, our analysis of ancient genomes sheds light on the evolutionary history of tigers and supports the existence of nine modern subspecies.
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Affiliation(s)
- Xin Sun
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Yue-Chen Liu
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Mikhail P Tiunov
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia
| | - Dmitry O Gimranov
- Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, Yekaterinburg, Russia
- Ural Federal University, Yekaterinburg, Russia
| | - Yan Zhuang
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Yu Han
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Carlos A Driscoll
- Section of Comparative Behavioral Genomics, National Institute on Alcohol Abuse and Alcoholism, NIH, Rockville, MD, USA
| | - Yuhong Pang
- Beijing Advanced Innovation Center for Genomics (ICG), Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
| | - Chunmei Li
- Beijing Advanced Innovation Center for Genomics (ICG), Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
| | - Yan Pan
- School of Archaeology and Museology, Peking University, Beijing, China
| | - Marcela Sandoval Velasco
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Shyam Gopalakrishnan
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Rui-Zheng Yang
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Bao-Guo Li
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Kun Jin
- Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China
| | - Xiao Xu
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Olga Uphyrkina
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia
| | - Yanyi Huang
- Beijing Advanced Innovation Center for Genomics (ICG), Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
- Institute for Cell Analysis, Shenzhen Bay Laboratory, Guangdong, China
| | - Xiao-Hong Wu
- School of Archaeology and Museology, Peking University, Beijing, China
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Stephen J O'Brien
- Guy Harvey Oceanographic Center, Halmos College of Arts and Sciences, Nova Southeastern University, Fort Lauderdale, FL, USA.
| | - Nobuyuki Yamaguchi
- Institute of Tropical Biodiversity and Sustainable Development, University of Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia.
| | - Shu-Jin Luo
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
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Yuan J, Wang G, Zhao L, Kitchener AC, Sun T, Chen W, Huang C, Wang C, Xu X, Wang J, Lu H, Xu L, Jiangzuo Q, Murphy WJ, Wu D, Li G. How genomic insights into the evolutionary history of clouded leopards inform their conservation. SCIENCE ADVANCES 2023; 9:eadh9143. [PMID: 37801506 PMCID: PMC10558132 DOI: 10.1126/sciadv.adh9143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 09/06/2023] [Indexed: 10/08/2023]
Abstract
Clouded leopards (Neofelis spp.), a morphologically and ecologically distinct lineage of big cats, are severely threatened by habitat loss and fragmentation, targeted hunting, and other human activities. The long-held poor understanding of their genetics and evolution has undermined the effectiveness of conservation actions. Here, we report a comprehensive investigation of the whole genomes, population genetics, and adaptive evolution of Neofelis. Our results indicate the genus Neofelis arose during the Pleistocene, coinciding with glacial-induced climate changes to the distributions of savannas and rainforests, and signatures of natural selection associated with genes functioning in tooth, pigmentation, and tail development, associated with clouded leopards' unique adaptations. Our study highlights high-altitude adaptation as the main factor driving nontaxonomic population differentiation in Neofelis nebulosa. Population declines and inbreeding have led to reduced genetic diversity and the accumulation of deleterious variation that likely affect reproduction of clouded leopards, highlighting the urgent need for effective conservation efforts.
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Affiliation(s)
- Jiaqing Yuan
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Guiqiang Wang
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Le Zhao
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
- QinLing-Bashan Mountains Bioresources Comprehensive Development C. I. C., School of Bioscience and Engineering, Shaanxi University of Technology, Hanzhong, China
| | - Andrew C. Kitchener
- Department of Natural Sciences, National Museums Scotland, Chambers Street, Edinburgh EH1 1JF, UK
- School of Geosciences, University of Edinburgh, Drummond Street, Edinburgh EH9 3PX, UK
| | - Ting Sun
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Wu Chen
- Guangzhou Zoo, Guangzhou Wildlife Research Center, Guangzhou, China
| | - Chen Huang
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Chen Wang
- Guangzhou Zoo, Guangzhou Wildlife Research Center, Guangzhou, China
| | - Xiao Xu
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Jinhong Wang
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Huimeng Lu
- School of Life Sciences, Northwestern Polytechnical University, Xi’an, China
| | - Lulu Xu
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Qigao Jiangzuo
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | - William J. Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Gang Li
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
- Guangzhou Zoo, Guangzhou Wildlife Research Center, Guangzhou, China
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Deka JR, Ali SZ, Ahamad M, Borah P, Gopi GV, Badola R, Sharma R, Hussain SA. Can Bengal Tiger ( Panthera tigris tigris) endure the future climate and land use change scenario in the East Himalayan Region? Perspective from a multiple model framework. Ecol Evol 2023; 13:e10340. [PMID: 37554398 PMCID: PMC10404654 DOI: 10.1002/ece3.10340] [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: 04/07/2023] [Revised: 07/07/2023] [Accepted: 07/10/2023] [Indexed: 08/10/2023] Open
Abstract
Large mammals are susceptible to land use and climate change, unless they are safeguarded within large, protected areas. It is crucial to comprehend the effects of these changes on mammals to develop a conservation plan. We identified ecological hotspots that can sustain an ecosystem for the endangered Bengal tiger (Panthera tigris tigris), an umbrella species. We developed three distinct ensemble species distribution models (SDMs) for the Bengal tiger in the Indian East Himalayan Region (IEHR). The first model served as the baseline and considered habitat type, climate, land cover, and anthropogenic threats. The second model focused on climate, land use, and anthropogenic threats, the third model focused on climate variables. We projected the second and third models onto two future climate scenarios: RCP 4.5 and RCP 8.5. We evaluated the threats possess to protected areas within eco-sensitive zone based on the potential tiger habitat. Finally, we compared the potential habitat with the IUCN tiger range. Our study revealed that the Brahmaputra valley will serve as the primary habitat for tigers in the future. However, considering the projected severe climate scenarios, it is anticipated that tigers will undergo a range shift towards the north and east, especially in high-altitude regions. Very high conservation priority areas, which make up 3.4% of the total area, are predominantly located in the riverine corridor of Assam. High conservation priority areas, which make up 5.5% of total area are located in Assam and Arunachal Pradesh. It is important to note that conservation priority areas outside of protected areas pose a greater threat to tigers. We recommend reassessing the IUCN Red List's assigned range map for tigers in the IEHR, as it is over-predicted. Our study has led us to conclude both land use and climate change possess threats to the future habitat of tigers. The outcomes of our study will provide crucial information on identifying habitat hotspots and facilitate appropriate conservation planning efforts.
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Affiliation(s)
| | | | | | | | | | - Ruchi Badola
- Wildlife Institute of IndiaDehradunUttarakhandIndia
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7
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Wang C, Wu DD, Yuan YH, Yao MC, Han JL, Wu YJ, Shan F, Li WP, Zhai JQ, Huang M, Peng SM, Cai QH, Yu JY, Liu QX, Liu ZY, Li LX, Teng MS, Huang W, Zhou JY, Zhang C, Chen W, Tu XL. Population genomic analysis provides evidence of the past success and future potential of South China tiger captive conservation. BMC Biol 2023; 21:64. [PMID: 37069598 PMCID: PMC10111772 DOI: 10.1186/s12915-023-01552-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 02/21/2023] [Indexed: 04/19/2023] Open
Abstract
BACKGROUND Among six extant tiger subspecies, the South China tiger (Panthera tigris amoyensis) once was widely distributed but is now the rarest one and extinct in the wild. All living South China tigers are descendants of only two male and four female wild-caught tigers and they survive solely in zoos after 60 years of effective conservation efforts. Inbreeding depression and hybridization with other tiger subspecies were believed to have occurred within the small, captive South China tiger population. It is therefore urgently needed to examine the genomic landscape of existing genetic variation among the South China tigers. RESULTS In this study, we assembled a high-quality chromosome-level genome using long-read sequences and re-sequenced 29 high-depth genomes of the South China tigers. By combining and comparing our data with the other 40 genomes of six tiger subspecies, we identified two significantly differentiated genomic lineages among the South China tigers, which harbored some rare genetic variants introgressed from other tiger subspecies and thus maintained a moderate genetic diversity. We noticed that the South China tiger had higher FROH values for longer runs of homozygosity (ROH > 1 Mb), an indication of recent inbreeding/founder events. We also observed that the South China tiger had the least frequent homozygous genotypes of both high- and moderate-impact deleterious mutations, and lower mutation loads than both Amur and Sumatran tigers. Altogether, our analyses indicated an effective genetic purging of deleterious mutations in homozygous states from the South China tiger, following its population contraction with a controlled increase in inbreeding based on its pedigree records. CONCLUSIONS The identification of two unique founder/genomic lineages coupled with active genetic purging of deleterious mutations in homozygous states and the genomic resources generated in our study pave the way for a genomics-informed conservation, following the real-time monitoring and rational exchange of reproductive South China tigers among zoos.
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Affiliation(s)
- Chen Wang
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, 510070, China
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
- Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, 650204, China
| | | | - Meng-Cheng Yao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
- Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, 650204, China
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
- International Livestock Research Institute (ILRI), Nairobi, 00100, Kenya
| | - Ya-Jiang Wu
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, 510070, China
| | - Fen Shan
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, 510070, China
| | - Wan-Ping Li
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, 510070, China
| | - Jun-Qiong Zhai
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, 510070, China
| | - Mian Huang
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, 510070, China
| | - Shi-Ming Peng
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, 510070, China
| | - Qin-Hui Cai
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, 510070, China
| | | | | | | | - Lin-Xiang Li
- Suzhou Shangfangshan Forest Zoo, Suzhou, 215009, China
| | | | - Wei Huang
- Nanchang Zoo, Nanchang, 330025, China
| | - Jun-Ying Zhou
- Chinese Association of Zoological Gardens, Beijing, 100037, China
| | - Chi Zhang
- Qinghai Province Key Laboratory of Crop Molecular Breeding, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, Qinghai, China
| | - Wu Chen
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, 510070, China.
| | - Xiao-Long Tu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China.
- Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, 650204, China.
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8
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Arden R, Abdellaoui A, Li Q, Zheng Y, Wang D, Su Y. Majestic tigers: personality structure in the great Amur cat. ROYAL SOCIETY OPEN SCIENCE 2023; 10:220957. [PMID: 37035292 PMCID: PMC10073900 DOI: 10.1098/rsos.220957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 03/14/2023] [Indexed: 06/19/2023]
Abstract
We explore individual differences in tiger personality. We first asked-is there evidence of personality dimensions (analogous to the Big Five in human personality research) in the Amur tiger? We then asked, are any discoverable personality dimensions associated with measured outcomes, including group status, health and mating frequency? 152 of our participating tigers live in the world's largest semi-wild tiger sanctuary in North Eastern China. Our second sample of 96 tigers also lives in a sanctuary. Having two samples allowed us to assess the replicability of the personality dimensions or factors reported in our first sample. We found that two factors (explaining 21% and 17% of the variance among items) which we call, for descriptive ease, Majesty and Steadiness, provide the best fit to the data. Tigers that score higher on Majesty are healthier, eat more live prey, have higher group status (among other tigers as assessed by human raters) and mate more often. We provide some ethological context to put flesh on the quantitative bones of our findings concerning these magnificent and charismatic animals.
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Affiliation(s)
- Rosalind Arden
- Centre for the Philosophy of the Natural and Social Sciences, London School of Economics, London, UK
| | - Abdel Abdellaoui
- Department of Psychiatry, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Qian Li
- School of Psychological and Cognitive Sciences and Beijing Key Laboratory of Behaviour and Mental Health, Peking University, Beijing, People's Republic of China
| | - Yao Zheng
- Department of Psychology, University of Alberta, Edmonton, Alberta, Canada
| | - Dengfeng Wang
- School of Psychological and Cognitive Sciences and Beijing Key Laboratory of Behaviour and Mental Health, Peking University, Beijing, People's Republic of China
| | - Yanjie Su
- School of Psychological and Cognitive Sciences and Beijing Key Laboratory of Behaviour and Mental Health, Peking University, Beijing, People's Republic of China
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Khan A. The year of the tiger and the year of tiger genomes! Mol Ecol Resour 2023; 23:327-329. [PMID: 36307962 PMCID: PMC10098588 DOI: 10.1111/1755-0998.13726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/06/2022] [Accepted: 10/19/2022] [Indexed: 01/04/2023]
Abstract
Tigers are endangered apex predators. They typify endangered species because they are elusive, rare, and face numerous threats across their range. Tigers also symbolize conservation. However, it is very difficult to study tigers because of their stated nature. Also, tiger conservation is a geopolitically sensitive topic, making it difficult to use the studies to propose evidence-based management that allows their recovery, especially in the context of conservation genetics. Zhang et al. (Mol. Ecol. Resour., 2022) have created very valuable and rare resources to aid the community in conserving tigers. First, they present chromosome level genome assemblies of a South China tiger and an Amur tiger. Second, they present whole genome sequences of 16 captive South China tigers. Additionally, by using the assemblies they model the demographic history of these populations, estimate inbreeding and the potential threats they face in captivity. This approach is particularly important because genetic management is now the only remaining option for South China tigers, because they are extinct in the wild. In other words, captive individuals are our only hope for some day restoring the wild populations of South China tigers.
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Affiliation(s)
- Anubhab Khan
- SBOHVM, University of Glasgow, Glasgow, UK.,Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA.,National Centre for Biological Sciences, TIFR, Bangalore, India
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10
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Zhang L, Lan T, Lin C, Fu W, Yuan Y, Lin K, Li H, Sahu SK, Liu Z, Chen D, Liu Q, Wang A, Wang X, Ma Y, Li S, Zhu Y, Wang X, Ren X, Lu H, Huang Y, Yu J, Liu B, Wang Q, Zhang S, Xu X, Yang H, Liu D, Liu H, Xu Y. Chromosome-scale genomes reveal genomic consequences of inbreeding in the South China tiger: A comparative study with the Amur tiger. Mol Ecol Resour 2023; 23:330-347. [PMID: 35723950 PMCID: PMC10084155 DOI: 10.1111/1755-0998.13669] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 05/29/2022] [Accepted: 06/10/2022] [Indexed: 01/09/2023]
Abstract
The South China tiger (Panthera tigris amoyensis, SCT) is the most critically endangered subspecies of tiger due to functional extinction in the wild. Inbreeding depression is observed among the captive population descended from six wild ancestors, resulting in high juvenile mortality and low reproduction. We assembled and characterized the first SCT genome and an improved Amur tiger (P. t. altaica, AT) genome named AmyTig1.0 and PanTig2.0. The two genomes are the most continuous and comprehensive among any tiger genomes yet reported at the chromosomal level. By using the two genomes and resequencing data of 15 SCT and 13 AT individuals, we investigated the genomic signature of inbreeding depression of the SCT. The results indicated that the effective population size of SCT experienced three phases of decline, ~5.0-1.0 thousand years ago, 100 years ago, and since captive breeding in 1963. We found 43 long runs of homozygosity fragments that were shared by all individuals in the SCT population and covered a total length of 20.63% in the SCT genome. We also detected a large proportion of identical-by-descent segments across the genome in the SCT population, especially on ChrB4. Deleterious nonsynonymous single nucleotide polymorphic sites and loss-of-function mutations were found across genomes with extensive potential influences, despite a proportion of these loads having been purged by inbreeding depression. Our research provides an invaluable resource for the formulation of genetic management policies for the South China tiger such as developing genome-based breeding and genetic rescue strategy.
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Affiliation(s)
- Le Zhang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Tianming Lan
- State Key Laboratory of Agricultural Genomics, Shenzhen, China.,BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, China
| | - Chuyu Lin
- Shenzhen Zhong Nong Jing Yue Biotech Company Limited, Shenzhen, China
| | - Wenyuan Fu
- Longyan Geopark Protection and Development Center, Longyan, China.,Fujian Meihuashan Institute of South China Tiger Breeding, Longyan, China
| | | | - Kaixiong Lin
- Fujian Meihuashan Institute of South China Tiger Breeding, Longyan, China
| | - Haimeng Li
- State Key Laboratory of Agricultural Genomics, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | | | | | - Daqing Chen
- Suzhou Shangfangshan Forest Zoo, Suzhou, China
| | - Qunxiu Liu
- Shanghai Zoological Park, Shanghai, China
| | | | | | - Yue Ma
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Shizhou Li
- Shaoguan Research Base of South China Tiger, Shaoguan, China
| | - Yixin Zhu
- State Key Laboratory of Agricultural Genomics, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | | | - Xiaotong Ren
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Haorong Lu
- China National GeneBank, Shenzhen, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, China
| | | | - Jieyao Yu
- China National GeneBank, Shenzhen, China
| | - Boyang Liu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Qing Wang
- State Key Laboratory of Agricultural Genomics, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | | | - Xun Xu
- Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, China
| | - Huanming Yang
- Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, Shenzhen, China.,James D. Watson Institute of Genome Sciences, Hangzhou, China
| | - Dan Liu
- Heilongjiang Siberian Tiger Park, Harbin, China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, Shenzhen, China.,BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, China
| | - Yanchun Xu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China.,National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization, Harbin, China
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11
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Shukla H, Suryamohan K, Khan A, Mohan K, Perumal RC, Mathew OK, Menon R, Dixon MD, Muraleedharan M, Kuriakose B, Michael S, Krishnankutty SP, Zachariah A, Seshagiri S, Ramakrishnan U. Near-chromosomal de novo assembly of Bengal tiger genome reveals genetic hallmarks of apex predation. Gigascience 2022; 12:6963323. [PMID: 36576130 PMCID: PMC9795480 DOI: 10.1093/gigascience/giac112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/17/2022] [Accepted: 10/20/2022] [Indexed: 12/29/2022] Open
Abstract
The tiger, a poster child for conservation, remains an endangered apex predator. Continued survival and recovery will require a comprehensive understanding of genetic diversity and the use of such information for population management. A high-quality tiger genome assembly will be an important tool for conservation genetics, especially for the Indian tiger, the most abundant subspecies in the wild. Here, we present high-quality near-chromosomal genome assemblies of a female and a male wild Indian tiger (Panthera tigris tigris). Our assemblies had a scaffold N50 of >140 Mb, with 19 scaffolds corresponding to the 19 numbered chromosomes, containing 95% of the genome. Our assemblies also enabled detection of longer stretches of runs of homozygosity compared to previous assemblies, which will help improve estimates of genomic inbreeding. Comprehensive genome annotation identified 26,068 protein-coding genes, including several gene families involved in key morphological features such as the teeth, claws, vision, olfaction, taste, and body stripes. We also identified 301 microRNAs, 365 small nucleolar RNAs, 632 transfer RNAs, and other noncoding RNA elements, several of which are predicted to regulate key biological pathways that likely contribute to the tiger's apex predatory traits. We identify signatures of positive selection in the tiger genome that are consistent with the Panthera lineage. Our high-quality genome will enable use of noninvasive samples for comprehensive assessment of genetic diversity, thus supporting effective conservation and management of wild tiger populations.
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Affiliation(s)
| | | | | | - Krishna Mohan
- Department of Research and Development, AgriGenome Labs Private Ltd, Kochi, Kerala 682030, India
| | - Rajadurai C Perumal
- Department of Research and Development, AgriGenome Labs Private Ltd, Kochi, Kerala 682030, India
| | - Oommen K Mathew
- Department of Research and Development, AgriGenome Labs Private Ltd, Kochi, Kerala 682030, India
| | - Ramesh Menon
- MedGenome Labs Ltd., Narayana Health City, Bangalore, Karnataka 560099, India
| | - Mandumpala Davis Dixon
- Department of Research and Development, AgriGenome Labs Private Ltd, Kochi, Kerala 682030, India
| | - Megha Muraleedharan
- Department of Research and Development, AgriGenome Labs Private Ltd, Kochi, Kerala 682030, India
| | - Boney Kuriakose
- Department of Research and Development, AgriGenome Labs Private Ltd, Kochi, Kerala 682030, India
| | - Saju Michael
- Department of Research and Development, AgriGenome Labs Private Ltd, Kochi, Kerala 682030, India
| | - Sajesh P Krishnankutty
- Department of Research and Development, AgriGenome Labs Private Ltd, Kochi, Kerala 682030, India
| | - Arun Zachariah
- SciGenom Research Foundation, Narayana Health City, Bangalore, Karnataka 560099, India,Wayanad Wildlife Sanctuary, Sultan Bathery, Kerala 673592, India
| | - Somasekar Seshagiri
- Correspondence address. Somasekar Seshagiri, Department of Research and Development SciGenom Research Foundation 3rd Floor, Narayana Nethralaya Building, Narayana Health City, #258/A, Bommasandra, Hosur Road, Bangalore 560099, India. E-mail:
| | - Uma Ramakrishnan
- Correspondence address. Uma Ramakrishnan, National Centre for Biological Sciences, TIFR Bellary Road, Bangalore 560065, India. E-mail:
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12
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Genomes of endangered great hammerhead and shortfin mako sharks reveal historic population declines and high levels of inbreeding in great hammerhead. iScience 2022; 26:105815. [PMID: 36632067 PMCID: PMC9826928 DOI: 10.1016/j.isci.2022.105815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 11/23/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Despite increasing threats of extinction to Elasmobranchii (sharks and rays), whole genome-based conservation insights are lacking. Here, we present chromosome-level genome assemblies for the Critically Endangered great hammerhead (Sphyrna mokarran) and the Endangered shortfin mako (Isurus oxyrinchus) sharks, with genetic diversity and historical demographic comparisons to other shark species. The great hammerhead exhibited low genetic variation, with 8.7% of the 2.77 Gbp genome in runs of homozygosity (ROH) > 1 Mbp and 74.4% in ROH >100 kbp. The 4.98 Gbp shortfin mako genome had considerably greater diversity and <1% in ROH > 1 Mbp. Both these sharks experienced precipitous declines in effective population size (Ne) over the last 250 thousand years. While shortfin mako exhibited a large historical Ne that may have enabled the retention of higher genetic variation, the genomic data suggest a possibly more concerning picture for the great hammerhead, and a need for evaluation with additional individuals.
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13
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Armstrong EE, Campana MG, Solari KA, Morgan SR, Ryder OA, Naude VN, Samelius G, Sharma K, Hadly EA, Petrov DA. Genome report: chromosome-level draft assemblies of the snow leopard, African leopard, and tiger (Panthera uncia, Panthera pardus pardus, and Panthera tigris). G3 (BETHESDA, MD.) 2022; 12:jkac277. [PMID: 36250809 PMCID: PMC9713438 DOI: 10.1093/g3journal/jkac277] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 09/14/2022] [Indexed: 04/07/2024]
Abstract
The big cats (genus Panthera) represent some of the most popular and charismatic species on the planet. Although some reference genomes are available for this clade, few are at the chromosome level, inhibiting high-resolution genomic studies. We assembled genomes from 3 members of the genus, the tiger (Panthera tigris), the snow leopard (Panthera uncia), and the African leopard (Panthera pardus pardus), at chromosome or near-chromosome level. We used a combination of short- and long-read technologies, as well as proximity ligation data from Hi-C technology, to achieve high continuity and contiguity for each individual. We hope that these genomes will aid in further evolutionary and conservation research of this iconic group of mammals.
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Affiliation(s)
- Ellie E Armstrong
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Department of Biology, Washington State University, Pullman, WA 99164, USA
| | - Michael G Campana
- Center for Conservation Genomics, Smithsonian’s National Zoological Park and Conservation Biology Institute, Washington, DC 20008, USA
| | | | - Simon R Morgan
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Wildlife ACT Fund Trust, Cape Town 8001, South Africa
| | - Oliver A Ryder
- San Diego Zoo Wildlife Alliance, Beckman Center for Conservation Research, San Diego, CA 92027, USA
| | - Vincent N Naude
- Department of Conservation Ecology and Entomology, University of Stellenbosch, Stellenbosch, 7602, South Africa
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg 2000, South Africa
| | | | - Koustubh Sharma
- Snow Leopard Trust, Seattle, WA 98103, USA
- Nature Conservation Foundation, Mysore 570 017, India
| | | | - Dmitri A Petrov
- Department of Biology, Stanford University, Stanford, CA 94305, USA
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14
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Cooper DM, Yamaguchi N, Macdonald DW, Nanova OG, Yudin VG, Dugmore AJ, Kitchener AC. Phenotypic plasticity determines differences between the skulls of tigers from mainland Asia. ROYAL SOCIETY OPEN SCIENCE 2022; 9:220697. [PMID: 36465684 PMCID: PMC9709513 DOI: 10.1098/rsos.220697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 11/11/2022] [Indexed: 06/17/2023]
Abstract
Tiger subspecific taxonomy is controversial because of morphological and genetic variation found between now fragmented populations, yet the extent to which phenotypic plasticity or genetic variation affects phenotypes of putative tiger subspecies has not been explicitly addressed. In order to assess the role of phenotypic plasticity in determining skull variation, we compared skull morphology among continental tigers from zoos and the wild. In turn, we examine continental tiger skulls from across their wild range, to evaluate how the different environmental conditions experienced by individuals in the wild can influence morphological variation. Fifty-seven measurements from 172 specimens were used to analyse size and shape differences among wild and captive continental tiger skulls. Captive specimens have broader skulls, and shorter rostral depths and mandible heights than wild specimens. In addition, sagittal crest size is larger in wild Amur tigers compared with those from captivity, and it is larger in wild Amur tigers compared with other wild continental tigers. The degree of phenotypic plasticity shown by the sagittal crest, skull width and rostral height suggests that the distinctive shape of Amur tiger skulls compared with that of other continental tigers is mostly a phenotypically plastic response to differences in their environments.
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Affiliation(s)
- David M. Cooper
- Department of Natural Sciences, National Museums Scotland, Edinburgh EH1 1JF, UK
- Institute of Geography, School of Geosciences, University of Edinburgh, Edinburgh EH8 9YL, UK
| | - Nobuyuki Yamaguchi
- Institute of Tropical Biodiversity and Sustainable Development, University Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
| | - David W. Macdonald
- Wildlife Conservation Research Unit, Department of Zoology, University of Oxford, The Recanti-Kaplan Centre, Tubney House, Abingdon Road, Abingdon, Oxfordshire OX13 5QL, UK
| | - Olga G. Nanova
- Zoological Museum, M.V. Lomonosov Moscow State University, Bolshaya Nikitskaya 2, Moscow 119991, Russia
| | - Viktor G. Yudin
- Federal Scientific Centre for the Biodiversity of Terrestrial Biota of East Asia, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Primorskij kraj, Russia
| | - Andrew J. Dugmore
- Institute of Geography, School of Geosciences, University of Edinburgh, Edinburgh EH8 9YL, UK
- Human Ecodynamics Research Centerand Doctoral Program in Anthropology, City University of New York (CUNY), NY 10017, USA
| | - Andrew C. Kitchener
- Department of Natural Sciences, National Museums Scotland, Edinburgh EH1 1JF, UK
- Institute of Geography, School of Geosciences, University of Edinburgh, Edinburgh EH8 9YL, UK
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15
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Meiring C, Schurz H, van Helden P, Hoal E, Tromp G, Kinnear C, Kleynhans L, Glanzmann B, van Schalkwyk L, Miller M, Möller M. African wild dogs (Lycaon pictus) from the Kruger National Park, South Africa are currently not inbred but have low genomic diversity. Sci Rep 2022; 12:14979. [PMID: 36056068 PMCID: PMC9440078 DOI: 10.1038/s41598-022-19025-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 08/23/2022] [Indexed: 12/24/2022] Open
Abstract
African wild dogs (Lycaon pictus) have undergone severe population reductions and are listed as endangered on the International Union for Conservation of Nature Red List. Small, isolated populations have the potential to suffer from threats to their genetic diversity that may impact species viability and future survival. This study provides the first set of population-wide genomic data to address conservation concerns for this endangered species. Whole genome sequencing data were generated for 71 free-ranging African wild dogs from the Kruger National Park (KNP), South Africa, and used to estimate important population genomic parameters. Genomic diversity metrics revealed that variation levels were low; however, this African wild dog population showed low levels of inbreeding. Very few first- and second-order relationships were observed in this cohort, with most relationships falling into the third-order or distant category. Patterns of homozygosity could have resulted from historical inbreeding or a loss in genome variation due to a population bottleneck. Although the results suggest that this stronghold African wild dog population maintains low levels of inbreeding, likely due to their cooperative breeding system, it may lead to a continuous population decline when a reduced number of suitable mates are available. Consequently, the low genomic variation may influence species viability over time. This study highlights the importance of assessing population genomic parameters to set conservation priorities. Future studies should include the investigation of the potential of this endangered species to adapt to environmental changes considering the low genomic diversity in this population.
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Affiliation(s)
- Christina Meiring
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town, 7500, South Africa.
| | - Haiko Schurz
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town, 7500, South Africa
| | - Paul van Helden
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town, 7500, South Africa
| | - Eileen Hoal
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town, 7500, South Africa
| | - Gerard Tromp
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town, 7500, South Africa
- South African Tuberculosis Bioinformatics Initiative (SATBBI), Faculty of Medicine and Health Sciences, Stellenbosch University, Francie van Zijl Drive, PO Box 241, Cape Town, 7500, South Africa
| | - Craig Kinnear
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town, 7500, South Africa
- Genomics Centre, South African Medical Research Council, Francie van Zijl Drive, PO Box 19070, Cape Town, 7500, South Africa
| | - Léanie Kleynhans
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town, 7500, South Africa
| | - Brigitte Glanzmann
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town, 7500, South Africa
- Genomics Centre, South African Medical Research Council, Francie van Zijl Drive, PO Box 19070, Cape Town, 7500, South Africa
| | - Louis van Schalkwyk
- Department of Agriculture, Land Reform and Rural Development, PO Box 12, Skukuza, 1350, South Africa
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, Soutpan Road, Pretoria, 0110, South Africa
- Department of Migration, Max Planck Institute of Animal Behavior, Am Obstberg 1, 78315, Radolfzell, Germany
| | - Michele Miller
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town, 7500, South Africa
| | - Marlo Möller
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town, 7500, South Africa
- Centre for Bioinformatics and Computational Biology, Stellenbosch University, Private bag X1, Merriman Avenue, Stellenbosch, 7600, South Africa
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16
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Whole-genome resequencing of Chinese pangolins reveals a population structure and provides insights into their conservation. Commun Biol 2022; 5:821. [PMID: 36008681 PMCID: PMC9411537 DOI: 10.1038/s42003-022-03757-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 07/22/2022] [Indexed: 11/18/2022] Open
Abstract
Poaching and trafficking have a substantial negative impact on the population growth and range expansion of the Chinese pangolin (Manis pentadactyla). However, recently reported activities of Chinese pangolins in several sites of Guangdong province in China indicate a promising sign for the recovery of this threatened species. Here, we re-sequence genomes of 15 individuals and perform comprehensive population genomics analyses with previously published 22 individuals. These Chinese pangolins are found to be divided into three distinct populations. Multiple lines of evidence indicate the existence of a newly discovered population (CPA) comprises entirely of individuals from Guangdong province. The other two populations (CPB and CPC) have previously been documented. The genetic differentiation of the CPA and CPC is extremely large (FST = 0.541), which is larger than many subspecies-level differentiations. Even for the closer CPA and CPB, their differentiation (FST = 0.101) is still comparable with the population-level differentiation of many endangered species. Further analysis reveals that the CPA and CPB populations separate 2.5–4.0 thousand years ago (kya), and on the other hand, CPA and CPC diverge around 25–40 kya. The CPA population harbors more runs of homozygosity (ROHs) than the CPB and CPC populations, indicating that inbreeding is more prevalent in the CPA population. Although the CPC population has less mutational load than CPA and CPB populations, we predict that several Loss of Function (LoF) mutations will be translocated into the CPA or CPB populations by using the CPC as a donor population for genetic rescue. Our findings imply that the conservation of Chinese pangolins is challenging, and implementing genetic rescue among the three groups should be done with extreme caution. Whole-genome resequencing of Chinese pangolins reveals a new population CPA that is genetically distinct from and harbor more homozygosity than CPB and CPC populations, indicating prevalence in inbreeding and implying challenges in conservation.
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17
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Wilder AP, Dudchenko O, Curry C, Korody M, Turbek SP, Daly M, Misuraca A, Gaojianyong WANG, Khan R, Weisz D, Fronczek J, Aiden EL, Houck ML, Shier DM, Ryder OA, Steiner CC. A chromosome-length reference genome for the endangered Pacific pocket mouse reveals recent inbreeding in a historically large population. Genome Biol Evol 2022; 14:6650481. [PMID: 35894178 PMCID: PMC9348616 DOI: 10.1093/gbe/evac122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/21/2022] [Indexed: 11/16/2022] Open
Abstract
High-quality reference genomes are fundamental tools for understanding population history, and can provide estimates of genetic and demographic parameters relevant to the conservation of biodiversity. The federally endangered Pacific pocket mouse (PPM), which persists in three small, isolated populations in southern California, is a promising model for studying how demographic history shapes genetic diversity, and how diversity in turn may influence extinction risk. To facilitate these studies in PPM, we combined PacBio HiFi long reads with Omni-C and Hi-C data to generate a de novo genome assembly, and annotated the genome using RNAseq. The assembly comprised 28 chromosome-length scaffolds (N50 = 72.6 MB) and the complete mitochondrial genome, and included a long heterochromatic region on chromosome 18 not represented in the previously available short-read assembly. Heterozygosity was highly variable across the genome of the reference individual, with 18% of windows falling in runs of homozygosity (ROH) >1 MB, and nearly 9% in tracts spanning >5 MB. Yet outside of ROH, heterozygosity was relatively high (0.0027), and historical Ne estimates were large. These patterns of genetic variation suggest recent inbreeding in a formerly large population. Currently the most contiguous assembly for a heteromyid rodent, this reference genome provides insight into the past and recent demographic history of the population, and will be a critical tool for management and future studies of outbreeding depression, inbreeding depression, and genetic load.
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Affiliation(s)
- Aryn P Wilder
- Conservation Science Wildlife Health, San Diego Zoo Wildlife Alliance, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, USA.,Center for Theoretical Biological Physics and Department of Computer Science, Rice University, USA
| | - Caitlin Curry
- Conservation Science Wildlife Health, San Diego Zoo Wildlife Alliance, USA
| | - Marisa Korody
- Conservation Science Wildlife Health, San Diego Zoo Wildlife Alliance, USA
| | - Sheela P Turbek
- Conservation Science Wildlife Health, San Diego Zoo Wildlife Alliance, USA.,Ecology and Evolutionary Biology, University of Colorado, Boulder, USA
| | | | - Ann Misuraca
- Conservation Science Wildlife Health, San Diego Zoo Wildlife Alliance, USA
| | - W A N G Gaojianyong
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Ruqayya Khan
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, USA
| | - David Weisz
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, USA
| | - Julie Fronczek
- Conservation Science Wildlife Health, San Diego Zoo Wildlife Alliance, USA
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, USA.,Center for Theoretical Biological Physics and Department of Computer Science, Rice University, USA.,UWA School of Agriculture and Environment, The University of Western Australia, Australia.,Broad Institute of MIT and Harvard, USA.,Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech, China
| | - Marlys L Houck
- Conservation Science Wildlife Health, San Diego Zoo Wildlife Alliance, USA
| | - Debra M Shier
- Conservation Science Wildlife Health, San Diego Zoo Wildlife Alliance, USA.,Department of Ecology & Evolutionary Biology, University of California Los Angeles, USA
| | - Oliver A Ryder
- Conservation Science Wildlife Health, San Diego Zoo Wildlife Alliance, USA
| | - Cynthia C Steiner
- Conservation Science Wildlife Health, San Diego Zoo Wildlife Alliance, USA
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Hu J, Westbury MV, Yuan J, Wang C, Xiao B, Chen S, Song S, Wang L, Lin H, Lai X, Sheng G. An extinct and deeply divergent tiger lineage from northeastern China recognized through palaeogenomics. Proc Biol Sci 2022; 289:20220617. [PMID: 35892215 PMCID: PMC9326283 DOI: 10.1098/rspb.2022.0617] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Tigers (Panthera tigris) are flagship big cats and attract extensive public attention due to their charismatic features and endangered status. Despite this, little is known about their prehistoric lineages and detailed evolutionary histories. Through palaeogenomic analyses, we identified a Pleistocene tiger from northeastern China, dated to beyond the limits of radiocarbon dating (greater than 43 500 years ago). We used a simulated dataset and different reads processing pipelines to test the validity of our results and confirmed that, in both mitochondrial and nuclear phylogenies, this ancient individual belongs to a previously unknown lineage that diverged prior to modern tiger diversification. Based on the mitochondrial genome, the divergence time of this ancient lineage was estimated to be approximately 268 ka (95% CI: 187-353 ka), doubling the known age of tigers' maternal ancestor to around 125 ka (95% CI: 88-168 ka). Furthermore, by combining our findings with putative mechanisms underlying the discordant mito-nuclear phylogenetic placement for the South China tigers, we proposed a more complex scenario of tiger evolution that would otherwise be missed using data from modern tigers only. Our study provides the first glimpses of the genetic antiquity of tigers and demonstrates the utility of aDNA-based investigation for further understanding tiger evolution.
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Affiliation(s)
- Jiaming Hu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430078, People's Republic of China,School of Earth Sciences, China University of Geosciences, Wuhan 430074, People's Republic of China
| | - Michael V. Westbury
- Globe Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | - Junxia Yuan
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430078, People's Republic of China
| | - Chunxue Wang
- School of Archaeology, Jilin University, Changchun 130012, People's Republic of China
| | - Bo Xiao
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430078, People's Republic of China,School of Earth Sciences, China University of Geosciences, Wuhan 430074, People's Republic of China
| | - Shungang Chen
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430078, People's Republic of China
| | - Shiwen Song
- School of Environmental Studies, China University of Geosciences, Wuhan 430078, People's Republic of China
| | - Linying Wang
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430078, People's Republic of China
| | - Haifeng Lin
- School of Environmental Studies, China University of Geosciences, Wuhan 430078, People's Republic of China
| | - Xulong Lai
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430078, People's Republic of China,School of Earth Sciences, China University of Geosciences, Wuhan 430074, People's Republic of China
| | - Guilian Sheng
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430078, People's Republic of China,School of Environmental Studies, China University of Geosciences, Wuhan 430078, People's Republic of China
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19
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Du H, Yu J, Li Q, Zhang M. New Evidence of Tiger Subspecies Differentiation and Environmental Adaptation: Comparison of the Whole Genomes of the Amur Tiger and the South China Tiger. Animals (Basel) 2022; 12:ani12141817. [PMID: 35883364 PMCID: PMC9312029 DOI: 10.3390/ani12141817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 06/29/2022] [Accepted: 07/11/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Tigers are top predators and umbrella protectors, vital to the stability of ecosystems. The South China tiger has been declared extinct in the wild and only exists in captivity. The Chinese government is actively promoting the reintroduction of the South China tiger into the wild. The future of the wild population of the Amur tiger in China is not optimistic, and the recovery of the population is an essential task for the conservation of the Amur tiger. The recovery of the population is not only a macroscopic problem but also a significant study of molecular ecology. We used high-throughput sequencing technology to study the differences in adaptive selection between Amur tigers and South China tigers. Significant genetic differences were found between the Amur tiger and the South China tiger based on a principal component analysis and phylogenetic tree. We identified functional genes and regulatory pathways related to reproduction, disease, predation, and metabolism and characterized functional genes related to survival in the wild, such as smell, vision, muscle, and predatory ability. The data also provide new evidence for the adaptation of Amur tigers to cold environments. PRKG1 is involved in temperature regulation in a cold climate. FOXO1 and TPM4 regulate body temperature to keep it constant. The research also provides a molecular basis for future tiger conservation. Abstract Panthera tigris is a top predator that maintains the integrity of forest ecosystems and is an integral part of biodiversity. No more than 400 Amur tigers (P. t. altaica) are left in the wild, whereas the South China tiger (P. t. amoyensis) is thought to be extinct in the wild, and molecular biology has been widely used in conservation and management. In this study, the genetic information of Amur tigers and South China tigers was studied by whole-genome sequencing (WGS). A total of 647 Gb of high-quality clean data was obtained. There were 6.3 million high-quality single-nucleotide polymorphisms (SNPs), among which most (66.3%) were located in intergenic regions, with an average of 31.72% located in coding sequences. There were 1.73 million insertion-deletions (InDels), among which there were 2438 InDels (0.10%) in the coding region, and 270 thousand copy number variations (CNVs). Significant genetic differences were found between the Amur tiger and the South China tiger based on a principal component analysis and phylogenetic tree. The linkage disequilibrium analysis showed that the linkage disequilibrium attenuation distance of the South China tiger and the Amur tiger was almost the same, whereas the r2 of the South China tiger was 0.6, and the r2 of the Amur tiger was 0.4. We identified functional genes and regulatory pathways related to reproduction, disease, predation, and metabolism and characterized functional genes related to survival in the wild, such as smell, vision, muscle, and predatory ability. The data also provide new evidence for the adaptation of Amur tigers to cold environments. PRKG1 is involved in temperature regulation in a cold climate. FOXO1 and TPM4 regulate body temperature to keep it constant. Our results can provide genetic support for precise interspecies conservation and management planning in the future.
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Affiliation(s)
- Hairong Du
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (H.D.); (J.Y.)
| | - Jingjing Yu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (H.D.); (J.Y.)
- Resources & Environment College, Tibet Agricultural and Animal Husbandry University, Nyingchi 860000, China
| | - Qian Li
- College of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, China
- Correspondence: (Q.L.); (M.Z.)
| | - Minghai Zhang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (H.D.); (J.Y.)
- Correspondence: (Q.L.); (M.Z.)
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20
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Aylward M, Sagar V, Natesh M, Ramakrishnan U. How methodological changes have influenced our understanding of population structure in threatened species: insights from tiger populations across India. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200418. [PMID: 35430878 PMCID: PMC9014192 DOI: 10.1098/rstb.2020.0418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Unprecedented advances in sequencing technology in the past decade allow a better understanding of genetic variation and its partitioning in natural populations. Such inference is critical to conservation: to understand species biology and identify isolated populations. We review empirical population genetics studies of Endangered Bengal tigers within India, where 60–70% of wild tigers live. We assess how changes in marker type and sampling strategy have impacted inferences by reviewing past studies, and presenting three novel analyses including a single-nucleotide polymorphism (SNP) panel, genome-wide SNP markers, and a whole-mitochondrial genome network. At a broad spatial scale, less than 100 SNPs revealed the same patterns of population clustering as whole genomes (with the exception of one additional population sampled only in the SNP panel). Mitochondrial DNA indicates a strong structure between the northeast and other regions. Two studies with more populations sampled revealed further substructure within Central India. Overall, the comparison of studies with varied marker types and sample sets allows more rigorous inference of population structure. Yet sampling of some populations is limited across all studies, and these should be the focus of future sampling efforts. We discuss challenges in our understanding of population structure, and how to further address relevant questions in conservation genetics.
This article is part of the theme issue ‘Celebrating 50 years since Lewontin's apportionment of human diversity’.
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Affiliation(s)
- Megan Aylward
- National Centre for Biological Sciences, TIFR, Bangalore, India, 560065
| | - Vinay Sagar
- National Centre for Biological Sciences, TIFR, Bangalore, India, 560065
| | - Meghana Natesh
- Indian Institute of Science Education and Research, Tirupati, India, 517507
| | - Uma Ramakrishnan
- National Centre for Biological Sciences, TIFR, Bangalore, India, 560065
- Senior Fellow, DBT Wellcome Trust India Alliance, Hyderabad, Telangana, India, 500034
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21
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Recapitulating whole genome based population genetic structure for Indian wild tigers through an ancestry informative marker panel. Heredity (Edinb) 2022; 128:88-96. [PMID: 34857925 PMCID: PMC8813985 DOI: 10.1038/s41437-021-00477-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 09/30/2021] [Accepted: 10/01/2021] [Indexed: 02/03/2023] Open
Abstract
Identification of genetic structure within wildlife populations have implications in their conservation and management. Accurately inferring population genetic structure requires whole-genome data across the geographical range of the species, which can be resource-intensive. A cheaper strategy is to employ a subset of markers that can efficiently recapitulate the population genetic structure inferred by the whole genome data. Such ancestry informative markers (AIMs), have rarely been developed for endangered species such as tigers utilizing single nucleotide polymorphisms (SNPs). Here, we first identify the population structure of the Indian tiger using whole-genome sequences and then develop an AIMs panel with a minimum number of SNPs that can recapitulate this structure. We identified four population clusters of Indian tigers with North-East, North-West, and South Indian tigers forming three separate groups, and Terai and Central Indian tigers forming a single cluster. To evaluate the robustness of our AIMs, we applied it to a separate dataset of tigers from across India. Out of 92 SNPs present in our AIMs panel, 49 were present in the new dataset. These 49 SNPs were sufficient to recapitulate the population genetic structure obtained from the whole genome data. To the best of our knowledge, this is the first-ever SNP-based AIMs panel for big cats, which can be used as a cost-effective alternative to whole-genome sequencing for detecting the biogeographical origin of Indian tigers. Our study can be used as a guideline for developing an AIMs panel for the management of other endangered species where obtaining whole genome sequences are difficult.
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22
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Gustafson KD, Gagne RB, Buchalski MR, Vickers TW, Riley SP, Sikich JA, Rudd JL, Dellinger JA, LaCava ME, Ernest HB. Multi‐population puma connectivity could restore genomic diversity to at‐risk coastal populations in California. Evol Appl 2021; 15:286-299. [PMID: 35233248 PMCID: PMC8867711 DOI: 10.1111/eva.13341] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 12/25/2021] [Indexed: 12/01/2022] Open
Abstract
Urbanization is decreasing wildlife habitat and connectivity worldwide, including for apex predators, such as the puma (Puma concolor). Puma populations along California's central and southern coastal habitats have experienced rapid fragmentation from development, leading to calls for demographic and genetic management. To address urgent conservation genomic concerns, we used double‐digest restriction‐site associated DNA (ddRAD) sequencing to analyze 16,285 genome‐wide single‐nucleotide polymorphisms (SNPs) from 401 pumas sampled broadly across the state. Our analyses indicated support for 4–10 geographically nested, broad‐ to fine‐scale genetic clusters. At the broadest scale, the four genetic clusters had high genetic diversity and exhibited low linkage disequilibrium, indicating that pumas have retained genomic diversity statewide. However, multiple lines of evidence indicated substructure, including 10 finer‐scale genetic clusters, some of which exhibited fixed alleles and linkage disequilibrium. Fragmented populations along the Southern Coast and Central Coast had particularly low genetic diversity and strong linkage disequilibrium, indicating genetic drift and close inbreeding. Our results demonstrate that genetically at risk populations are typically nested within a broader‐scale group of interconnected populations that collectively retain high genetic diversity and heterogenous fixations. Thus, extant variation at the broader scale has potential to restore diversity to local populations if management actions can enhance vital gene flow and recombine locally sequestered genetic diversity. These state‐ and genome‐wide results are critically important for science‐based conservation and management practices. Our nested population genomic analysis highlights the information that can be gained from population genomic studies aiming to provide guidance for the conservation of fragmented populations.
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Affiliation(s)
- Kyle D. Gustafson
- Arkansas State University Department of Biological Sciences Jonesboro 72401
| | - Roderick B. Gagne
- University of Pennsylvania School of Veterinary Medicine Department of Pathobiology Kennett Square Wildlife Futures Program PA USA
| | | | - T. Winston Vickers
- University of California ‐ Davis School of Veterinary Medicine Karen C. Drayer Wildlife Health Center Davis 95616
| | - Seth P.D. Riley
- National Park Service Santa Monica Mountains National Recreation Area 401 W. Hillcrest Dr Thousand Oaks 91360
| | - Jeff A. Sikich
- National Park Service Santa Monica Mountains National Recreation Area 401 W. Hillcrest Dr Thousand Oaks 91360
| | - Jaime L. Rudd
- California Department of Fish and Wildlife Rancho Cordova 95670
| | | | - Melanie E.F. LaCava
- Wildlife Genomics and Disease Ecology Laboratory Department of Veterinary Sciences University of Wyoming Laramie 82071
| | - Holly B. Ernest
- Wildlife Genomics and Disease Ecology Laboratory Department of Veterinary Sciences University of Wyoming Laramie 82071
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23
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Khan A, Patel K, Shukla H, Viswanathan A, van der Valk T, Borthakur U, Nigam P, Zachariah A, Jhala YV, Kardos M, Ramakrishnan U. Genomic evidence for inbreeding depression and purging of deleterious genetic variation in Indian tigers. Proc Natl Acad Sci U S A 2021; 118:e2023018118. [PMID: 34848534 PMCID: PMC8670471 DOI: 10.1073/pnas.2023018118] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/11/2021] [Indexed: 01/03/2023] Open
Abstract
Increasing habitat fragmentation leads to wild populations becoming small, isolated, and threatened by inbreeding depression. However, small populations may be able to purge recessive deleterious alleles as they become expressed in homozygotes, thus reducing inbreeding depression and increasing population viability. We used whole-genome sequences from 57 tigers to estimate individual inbreeding and mutation load in a small-isolated and two large-connected populations in India. As expected, the small-isolated population had substantially higher average genomic inbreeding (FROH = 0.57) than the large-connected (FROH = 0.35 and FROH = 0.46) populations. The small-isolated population had the lowest loss-of-function mutation load, likely due to purging of highly deleterious recessive mutations. The large populations had lower missense mutation loads than the small-isolated population, but were not identical, possibly due to different demographic histories. While the number of the loss-of-function alleles in the small-isolated population was lower, these alleles were at higher frequencies and homozygosity than in the large populations. Together, our data and analyses provide evidence of 1) high mutation load, 2) purging, and 3) the highest predicted inbreeding depression, despite purging, in the small-isolated population. Frequency distributions of damaging and neutral alleles uncover genomic evidence that purifying selection has removed part of the mutation load across Indian tiger populations. These results provide genomic evidence for purifying selection in both small and large populations, but also suggest that the remaining deleterious alleles may have inbreeding-associated fitness costs. We suggest that genetic rescue from sources selected based on genome-wide differentiation could offset any possible impacts of inbreeding depression.
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Affiliation(s)
- Anubhab Khan
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India;
| | - Kaushalkumar Patel
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Harsh Shukla
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Ashwin Viswanathan
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
- Nature Conservation Foundation, Mysore 570017, India
| | | | | | - Parag Nigam
- Wildlife Institute of India, Dehradun 248001, India
| | | | | | - Marty Kardos
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA 98112;
| | - Uma Ramakrishnan
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India;
- Department of Biotechnology-Wellcome Trust India Alliance, Hyderabad 500034, India
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24
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Using Keeper Questionnaires to Capture Zoo-Housed Tiger (Panthera tigris) Personality: Considerations for Animal Management. JOURNAL OF ZOOLOGICAL AND BOTANICAL GARDENS 2021. [DOI: 10.3390/jzbg2040047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Individual personalities affect animal experiences of zoo environments, impact on an animal’s coping ability and have potential implications for welfare. Keeper assessments have been identified as a quick and reliable way of capturing data on personality in a range of species and have practical application in improving animal welfare on an individual level. Despite widespread recognition of the importance of animal personality within a zoo environment, there is a paucity of research into tiger personality and the potential impact of this on tiger experiences within zoos. This research investigated the personality of 34 tigers (19 Amur and 15 Sumatran) across 14 facilities in the UK using keeper ratings and identified changes keepers made in animal husbandry to support tiger welfare. Reliability across keepers (n = 49) was established for nine adjectives and a principal component analysis identified three personality components: ‘anxious’, ‘quiet’ and ‘sociable’. When subspecies were combined, there was no relationship between tiger scores on the personality components and age or sex of tigers (p > 0.05). Subspecies of tiger was not related to scores on the ‘quiet’ or ‘sociable’ components (p > 0.05). Sumatran tigers scored more highly than Amur tigers on the ‘anxious’ component (mean ± SD, Sumatran: 3.0 ± 1.7, Amur: 1.8 ± 0.6, p < 0.05). Analysis within subspecies found that male Amur tigers were more sociable than females (mean ± SD, males: 5.5 ± 0.707; females: 4.15 ± 0.55). Amur tiger age was also negatively correlated with scores on the sociable personality component (R = −0.742, p < 0.05). No significant differences were seen in Sumatran tigers. Keepers reported a number of changes to husbandry routines based on their perceptions of their tigers’ personality/needs. However, there was no significant relationship between these changes and tiger personality scores (p > 0.05). Despite significant evolutionary differences between Amur and Sumatran tigers, there are no subspecies specific guidelines for zoo tigers. This research has highlighted the potential for these two subspecies to display personality differences and we advocate further research into this area. Specifically, we highlight a need to validate the relationship between tiger personality, management protocols and behavioural and physiological metrics of welfare. This will enable a fuller understanding of the impact of personality on zoo tiger experiences and will enable identification of evidence-based best practice guidelines.
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25
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Sagar V, Kaelin CB, Natesh M, Reddy PA, Mohapatra RK, Chhattani H, Thatte P, Vaidyanathan S, Biswas S, Bhatt S, Paul S, Jhala YV, Verma MM, Pandav B, Mondol S, Barsh GS, Swain D, Ramakrishnan U. High frequency of an otherwise rare phenotype in a small and isolated tiger population. Proc Natl Acad Sci U S A 2021; 118:e2025273118. [PMID: 34518374 PMCID: PMC8488692 DOI: 10.1073/pnas.2025273118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/09/2021] [Indexed: 11/18/2022] Open
Abstract
Most endangered species exist today in small populations, many of which are isolated. Evolution in such populations is largely governed by genetic drift. Empirical evidence for drift affecting striking phenotypes based on substantial genetic data are rare. Approximately 37% of tigers (Panthera tigris) in the Similipal Tiger Reserve (in eastern India) are pseudomelanistic, characterized by wide, merged stripes. Camera trap data across the tiger range revealed the presence of pseudomelanistic tigers only in Similipal. We investigated the genetic basis for pseudomelanism and examined the role of drift in driving this phenotype's frequency. Whole-genome data and pedigree-based association analyses from captive tigers revealed that pseudomelanism cosegregates with a conserved and functionally important coding alteration in Transmembrane Aminopeptidase Q (Taqpep), a gene responsible for similar traits in other felid species. Noninvasive sampling of tigers revealed a high frequency of the Taqpep p.H454Y mutation in Similipal (12 individuals, allele frequency = 0.58) and absence from all other tiger populations (395 individuals). Population genetic analyses confirmed few (minimal number) tigers in Similipal, and its genetic isolation, with poor geneflow. Pairwise FST (0.33) at the mutation site was high but not an outlier. Similipal tigers had low diversity at 81 single nucleotide polymorphisms (mean heterozygosity = 0.28, SD = 0.27). Simulations were consistent with founding events and drift as possible drivers for the observed stark difference of allele frequency. Our results highlight the role of stochastic processes in the evolution of rare phenotypes. We highlight an unusual evolutionary trajectory in a small and isolated population of an endangered species.
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Affiliation(s)
- Vinay Sagar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India;
| | - Christopher B Kaelin
- Department of Genetics, Stanford University, Palo Alto, CA 94309
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806
| | - Meghana Natesh
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
- Biology Department, Indian Institute of Science Education and Research, Tirupati 411008, India
| | - P Anuradha Reddy
- Laboratory for Conservation of Endangered Species, Center for Cellular & Molecular Biology, Hyderabad 500048, India
| | | | - Himanshu Chhattani
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Prachi Thatte
- World Wide Fund for Nature - India, New Delhi 110003 India
| | - Srinivas Vaidyanathan
- Foundation for Ecological Research, Advocacy and Learning, Auroville Post, Tamil Nadu 605101 India
| | | | | | - Shashi Paul
- Odisha Forest Department, Bhubaneswar 751023, India
| | - Yadavendradev V Jhala
- Wildlife Institute of India, Dehradun 248001, India
- National Tiger Conservation Authority, Wildlife Institute of India Tiger Cell, Wildlife Institute of India, Dehradun 248001, India
| | | | | | | | - Gregory S Barsh
- Department of Genetics, Stanford University, Palo Alto, CA 94309
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806
| | - Debabrata Swain
- Former Member Secretary, National Tiger Conservation Authority, New Delhi 110003, India
- Former Principal Chief Conservator of Forest and Head of Forest Force, Indian Forest Service, Bhubaneswar 751023, India
| | - Uma Ramakrishnan
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India;
- DBT - Wellcome Trust India Alliance, Hyderabad 500034, India
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26
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Considerations for Initiating a Wildlife Genomics Research Project in South and South-East Asia. J Indian Inst Sci 2021. [DOI: 10.1007/s41745-021-00243-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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27
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Excofffier L, Marchi N, Marques DA, Matthey-Doret R, Gouy A, Sousa VC. fastsimcoal2: demographic inference under complex evolutionary scenarios. Bioinformatics 2021; 37:4882-4885. [PMID: 34164653 PMCID: PMC8665742 DOI: 10.1093/bioinformatics/btab468] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/11/2021] [Accepted: 06/22/2021] [Indexed: 01/25/2023] Open
Abstract
Motivation fastsimcoal2 extends fastsimcoal, a continuous time coalescent-based genetic simulation program, by enabling the estimation of demographic parameters under very complex scenarios from the site frequency spectrum under a maximum-likelihood framework. Results Other improvements include multi-threading, handling of population inbreeding, extended input file syntax facilitating the description of complex demographic scenarios, and more efficient simulations of sparsely structured populations and of large chromosomes. Availability and implementation fastsimcoal2 is freely available on http://cmpg.unibe.ch/software/fastsimcoal2/. It includes console versions for Linux, Windows and MacOS, additional scripts for the analysis and visualization of simulated and estimated scenarios, as well as a detailed documentation and ready-to-use examples.
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Affiliation(s)
- Laurent Excofffier
- Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.,Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Nina Marchi
- Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.,Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - David Alexander Marques
- Life Science Division, Natural History Museum Basel, 4051 Basel, Switzerland.,Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.,Department of Fish Ecology and Evolution, EAWAG swiss Federal institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland
| | - Remi Matthey-Doret
- Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.,Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Alexandre Gouy
- Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.,Gouy Data Consulting, 1026 Denges, Switzerland
| | - Vitor C Sousa
- Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.,cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências da Universidade de Lisboa, University of Lisbon, Campo Grande, 1749-016, Lisbon, Portugal
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