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Hu Y, Hu Y, Zhou W, Wei F. Conservation Genomics and Metagenomics of Giant and Red Pandas in the Wild. Annu Rev Anim Biosci 2024; 12:69-89. [PMID: 37863091 DOI: 10.1146/annurev-animal-021022-054730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2023]
Abstract
Giant pandas and red pandas are endangered species with similar specialized bamboo diet and partial sympatric distribution in China. Over the last two decades, the rapid development of genomics and metagenomics research on these species has enriched our knowledge of their biology, ecology, physiology, genetics, and evolution, which is crucial and useful for their conservation. We describe the evolutionary history, endangerment processes, genetic diversity, and population structure of wild giant pandas and two species of red pandas (Chinese and Himalayan red pandas). In addition, we explore how genomics and metagenomics studies have provided insight into the convergent adaptation of pandas to the specialized bamboo diet. Finally, we discuss how these findings are applied to effective conservation management of giant and red pandas in the wild and in captivity to promote the long-term persistence of these species.
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Affiliation(s)
- Yisi Hu
- College of Forestry, Jiangxi Agricultural University, Nanchang, China;
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yibo Hu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Wenliang Zhou
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Fuwen Wei
- College of Forestry, Jiangxi Agricultural University, Nanchang, China;
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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2
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Yang J, Zeng Y, Li C, Liu S, Meng W, Zhang W, He M, Wang L, Zuo Z, Yue C, Li D, Peng G. Occurrence and Molecular Characteristics of Microsporidia in Captive Red Pandas ( Ailurus fulgens) in China. Animals (Basel) 2023; 13:1864. [PMID: 37889781 PMCID: PMC10251819 DOI: 10.3390/ani13111864] [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: 04/17/2023] [Revised: 05/07/2023] [Accepted: 05/26/2023] [Indexed: 10/29/2023] Open
Abstract
Enterocytozoon bieneusi and Encephalitozoon spp. are microsporidian pathogens with zoonotic potential that pose significant public health concerns. To ascertain the occurrence and genotypes of E. bieneusi and Encephalitozoon spp., we used nested PCR to amplify the internal transcribed spacer (ITS) gene and DNA sequencing to analyze 198 fecal samples from red pandas from 6 zoos in China. The total rate of microsporidial infection was 15.7% (31/198), with 12.1% (24/198), 1.0% (2/198), 2.0% (4/198) and 1.0% (2/198) for infection rate of E. bieneusi, Encephalitozoon cuniculi, Encephalitozoon intestinalis and Encephalitozoon hellem, respectively. One red panda was detected positive for a mixed infection (E. bieneusi and E. intestinalis). Red pandas living in semi-free conditions are more likely to be infected with microsporidia (χ2 = 6.212, df = 1, p < 0.05). Three known (SC02, D, and PL2) and one novel (SCR1) genotypes of E. bieneusi were found. Three genotypes of E. bieneusi (SC02, D, SCR1) were grouped into group 1 with public health importance, while genotype PL2 formed a separate clade associated with group 2. These findings suggest that red pandas may serve as a host reservoir for zoonotic microsporidia, potentially allowing transmission from red pandas to humans and other animals.
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Affiliation(s)
- Jinpeng Yang
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China; (J.Y.)
| | - Yangyang Zeng
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China; (J.Y.)
| | - Caiwu Li
- China Conservation and Research Center for the Giant Panda, Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in the Giant Panda National Park, Chengdu 610083, China
| | - Songrui Liu
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Sichuan Academy of Giant Panda, Chengdu 610081, China
| | - Wanyu Meng
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China; (J.Y.)
| | - Wenqing Zhang
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China; (J.Y.)
| | - Ming He
- China Conservation and Research Center for the Giant Panda, Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in the Giant Panda National Park, Chengdu 610083, China
| | | | | | - Chanjuan Yue
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Sichuan Academy of Giant Panda, Chengdu 610081, China
| | - Desheng Li
- China Conservation and Research Center for the Giant Panda, Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in the Giant Panda National Park, Chengdu 610083, China
| | - Guangneng Peng
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China; (J.Y.)
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3
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Sun C, Yang F, Huang Q, Zeng X, Zhang Y, Li S, Yu J, Zhang Q. Genetic population structure and demographic history of the endemic fish
Paralichthys olivaceus
of the Northwest Pacific Ocean. Ecol Evol 2022; 12:e9506. [DOI: 10.1002/ece3.9506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 10/18/2022] [Accepted: 10/24/2022] [Indexed: 11/17/2022] Open
Affiliation(s)
- Cheng‐He Sun
- Department of Ecology and Institute of Hydrobiology Jinan University Guangzhou China
| | - Fan Yang
- Department of Ecology and Institute of Hydrobiology Jinan University Guangzhou China
| | - Qi Huang
- Department of Ecology and Institute of Hydrobiology Jinan University Guangzhou China
| | - Xiao‐Shu Zeng
- Department of Ecology and Institute of Hydrobiology Jinan University Guangzhou China
| | - Ya‐Nan Zhang
- Department of Ecology and Institute of Hydrobiology Jinan University Guangzhou China
| | - Sha Li
- Chinese Sturgeon Research Institute China Three Gorges Corporation Yichang Hubei China
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes Yichang Hubei China
| | - Jian‐Feng Yu
- Department of Ecology and Institute of Hydrobiology Jinan University Guangzhou China
| | - Qun Zhang
- Department of Ecology and Institute of Hydrobiology Jinan University Guangzhou China
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4
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Ku JE, Choi SG. Population Structure of Finless Porpoise (Neophocaena phocaenoides) Discovered off Coastal Waters, Republic of Korea. Genes (Basel) 2022; 13:genes13101701. [PMID: 36292586 PMCID: PMC9602366 DOI: 10.3390/genes13101701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/08/2022] [Accepted: 09/19/2022] [Indexed: 11/16/2022] Open
Abstract
The finless porpoise (Neophocaena phocaenoides Cuvier, 1829) is distributed in the coastal waters of Asia, throughout Indonesia to the east, and as far north as the Taiwan Strait. The finless porpoise has been declared critically endangered by the WWF (World Wide Fund for Nature), and in 2017 was rated vulnerable on the IUCN Red Threatened Species List. Since this species is distributed near the coast and has many interactions with humans, effective conservation of the species requires further studies into their genetic diversity and population. In this study, 45 samples were obtained from bycatch or stranded individuals in the East, South, and West Seas, where Korean porpoises were mainly distributed from 2017–2021. We compared 473 bp mtDNA sequences from the control region. Pairwise fixation indices (FST) revealed that the two populations differed significantly (FST = 0.4557, p = 0.000). In contrast to high levels of genetic differentiation, gene flow was identified as medium levels (Nm of 0.04–0.71). Our data suggest that finless porpoises may have undergone a historic differentiation event, and that finless porpoises in the three regions could be divided into two populations: West and East/South.
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5
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Dueck LA, Steffens EA. Historical genetic diversity and population structure of wild red pandas (Ailurus fulgens) in Nepal. Mamm Biol 2022. [DOI: 10.1007/s42991-022-00272-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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6
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Karki S, Maraseni T, Mackey B, Bista D, Lama ST, Gautam AP, Sherpa AP, Koju U, Shrestha A, Cadman T. Reaching over the gap: A review of trends in and status of red panda research over 193 years (1827-2020). THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 781:146659. [PMID: 33794452 DOI: 10.1016/j.scitotenv.2021.146659] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/15/2021] [Accepted: 03/17/2021] [Indexed: 06/12/2023]
Abstract
The red panda is a unique species taxonomically known for its peculiar biological and ecological characteristics, and extreme attractiveness. Despite being highly significant from conservation, scientific and economic perspectives, this species has experienced a declining population in the wild. Thus, to direct further research priorities and conservation actions and assess gaps in the current research trend of this species, a systematic literature review was conducted covering 175 journal articles published in English over 193 years (1827-2020). This review revealed that (1) the biological aspect was highly studied compared to other thematic areas of red panda (2) captive-based studies are relatively higher than the studies based in wild populations (3) China is leading the red panda studies amongst all red panda range (4) The universities were found contributing more to red panda studies than other institutions. Surprisingly, we found that the researchers from the non-range country were leading red panda study than those from range countries. Our review highlighted the need of prioritising studies in underrepresented locations and understudied thematic areas focusing on the assessment of climate change impact, bamboo distribution status, ecosystem services of red panda habitat, behavior and movement ecology, population estimation, and metapopulation dynamics. We urge landscape-level studies and long-term population monitoring. Besides, we also suggest the documentation and evaluation of the effectiveness of ongoing red panda-focused conservation programs. We also stress the need for strengthening the capacity of institutions and people from range countries.
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Affiliation(s)
- Sikha Karki
- Cities Research Institute, Griffith University, Australia.
| | | | - Brendan Mackey
- Griffith Climate Action Beacon, Griffith University, Australia
| | - Damber Bista
- School of Agriculture and Food Sciences, The University of Queensland, Australia
| | | | | | | | - Upama Koju
- Kathmandu Forestry College, Kathmandu, Nepal
| | | | - Tim Cadman
- Institute for Ethics, Governance and Law, Griffith University, Australia
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Ghorbanzadeh A, Ghasemnezhad A, Sarmast MK, Ebrahimi SN. An analysis of variations in morphological characteristics, essential oil content, and genetic sequencing among and within major Iranian Juniper (Juniperus spp.) populations. PHYTOCHEMISTRY 2021; 186:112737. [PMID: 33740576 DOI: 10.1016/j.phytochem.2021.112737] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 03/08/2021] [Accepted: 03/09/2021] [Indexed: 06/12/2023]
Abstract
Junipers (Juniperus spp.) are important pharmaceutical plants, and they are commonly grown in the northern hemisphere because of the various medicinal properties attributed to the Juniperus genus. However, despite their pharmaceutical and also industrial importance, and despite plant diversity being a common topic of research among professional breeding programs, there is a relatively small body of work which focuses on diversity in juniper, and this is especially true of juniper species that are native to Iran. Thus, the present study set out to investigate juniper diversity via identifying any morphological, phytochemical, and genetic differences among and within three important species of Iranian junipers. The data revealed the terpenoid profiles of the investigated species to be distinct from one another, with α-pinene, β-pinene, myrcene, sabinene, and limonene being the predominant terpenoids detected. Intriguingly, high levels of myrtenyl acetate were detected in the J. sabina tissue collected from the Ramsar site, and this terpenoid was not found in either of the other studied species, nor has it been noted in any other studies that focus on juniper. The genetic variation of Juniperus was analyzed using five ISSR markers and the molecular variance was computed using the GenAlEx software. The results revealed there to be a high degree of genetic diversity both among and within the studied populations. A dendrogram of the genetic data using the UPGMA method with the Dice coefficient divided the genotypes into two main groups. J. communis and J. excelsa were grouped together, while J. sabina was separated into its own group. In general, morphologically speaking, the leaf and cone types were found to be chiefly influential vis-à-vis separating the populations into their respective groups. Ultimately, it is our hope that the biochemical, genetic, and morphological diversity data collected from these species will contribute to the success of future juniper breeding and restoration programs.
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Affiliation(s)
- Amir Ghorbanzadeh
- Department of Horticulture, Faculty of Plant Production, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran
| | - Azim Ghasemnezhad
- Department of Horticulture, Faculty of Plant Production, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran.
| | - Mostafa Khoshhal Sarmast
- Department of Horticulture, Faculty of Plant Production, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran
| | - Samad Nejad Ebrahimi
- Department of Phytochemistry, Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, Tehran, Iran
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8
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Dueck LA. Genetic assessment of captive red pandas (Ailurus fulgens) in American zoos to address management separation by putative subspecies. Zoo Biol 2021; 40:238-251. [PMID: 33689172 DOI: 10.1002/zoo.21597] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 12/18/2020] [Accepted: 02/23/2021] [Indexed: 11/10/2022]
Abstract
Red pandas (Ailurus fulgens) are small charismatic mammals native across montane southern Asia, now endangered by human impacts. They are considered "living fossils" as the sole member of a distinct family, warranting higher conservation priority. Therefore, ex situ breeding programs were initiated to prevent extinction and act as genetic reservoirs for reintroduction, although complicated by apparent taxonomic subdivision. This study investigated whether the separation of captive red pandas in the North American Species Survival Plan® by putative subspecies was justified. A 383-bp segment of mitochondrial DNA control region was therefore sequenced from 67 members representing matriarchal lineages of both groups. A network analysis placed the 11 haplotypes found into separate but closely connected clusters, with one group more strongly related than the other. Statistical analyses and diversity indices corroborated differentiation between the two management units. Phylogenetic analyses employing multiple outgroups confirmed, although not robustly, reciprocal monophyly of the four- and seven-haplotype clades representing putative subspecies Ailurus fulgens fulgens and Ailurus fulgens styani, respectively. These empirical results are adequate to justify continued independent management of these zoo subpopulations, but cannot be definitive for taxonomic classification due to limited sampling from their native range. They will, however, be useful in evaluating long-term genetic diversity changes, focusing management efforts on newly revealed evolutionary limitations, and comparing with an assessment of wild red pandas to determine how representative zoo populations are for reintroduction purposes. Maintaining genetic diversity and population structure of endangered species is essential to protect evolutionary potential and adaptations for long-term sustainability.
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Affiliation(s)
- Lucy A Dueck
- Savannah River Ecology Laboratory, Aiken, South Carolina, USA
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9
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Joshi BD, Dalui S, Singh SK, Mukherjee T, Chandra K, Sharma LK, Thakur M. Siang river in Arunachal Pradesh splits red panda into two phylogenetic species. Mamm Biol 2021. [DOI: 10.1007/s42991-020-00094-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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10
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Dalui S, Singh SK, Joshi BD, Ghosh A, Basu S, Khatri H, Sharma LK, Chandra K, Thakur M. Geological and Pleistocene glaciations explain the demography and disjunct distribution of red panda (A. fulgens) in eastern Himalayas. Sci Rep 2021; 11:65. [PMID: 33420314 PMCID: PMC7794540 DOI: 10.1038/s41598-020-80586-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 12/23/2020] [Indexed: 01/29/2023] Open
Abstract
Pleistocene glaciations facilitated climatic oscillations that caused for enormous heterogeneity in landscapes, and consequently affected demography and distribution patterns of the mountain endemic species. In this context, we investigated demographic history and population genetic structure of red panda, distributed along the geographical proximity in the southern edge of the Qinghai-Tibetan Plateau. Bayesian based phylogeny demonstrated that red panda diverged about 0.30 million years ago (CI 0.23-0.39) into two phylogenetic (sub) species, that correspond to the middle-late Pleistocene transition. The observed intraspecific clades with respect to Himalayan and Chinese red panda indicated restricted gene flow resulting from the Pleistocene glaciations in the eastern and southern Tibetan Plateau. We found Himalayan red panda population at least in KL-India declined abruptly in last 5-10 thousand years after being under demographic equilibrium. We suggest revisiting the ongoing conservation activities through cross border collaboration by developing multi-nationals, and multi-lateral species-oriented conservation action plans to support the red panda populations in transboundary landscapes.
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Affiliation(s)
- Supriyo Dalui
- grid.473833.80000 0001 2291 2164Zoological Survey of India, New Alipore, Kolkata, West Bengal 700053 India ,grid.59056.3f0000 0001 0664 9773Department of Zoology, University of Calcutta, Kolkata, West Bengal 700019 India
| | - Sujeet Kumar Singh
- grid.473833.80000 0001 2291 2164Zoological Survey of India, New Alipore, Kolkata, West Bengal 700053 India
| | - Bheem Dutt Joshi
- grid.473833.80000 0001 2291 2164Zoological Survey of India, New Alipore, Kolkata, West Bengal 700053 India
| | - Avijit Ghosh
- grid.473833.80000 0001 2291 2164Zoological Survey of India, New Alipore, Kolkata, West Bengal 700053 India ,grid.59056.3f0000 0001 0664 9773Department of Zoology, University of Calcutta, Kolkata, West Bengal 700019 India
| | - Shambadeb Basu
- grid.473833.80000 0001 2291 2164Zoological Survey of India, New Alipore, Kolkata, West Bengal 700053 India
| | - Hiren Khatri
- grid.473833.80000 0001 2291 2164Zoological Survey of India, New Alipore, Kolkata, West Bengal 700053 India
| | - Lalit Kumar Sharma
- grid.473833.80000 0001 2291 2164Zoological Survey of India, New Alipore, Kolkata, West Bengal 700053 India
| | - Kailash Chandra
- grid.473833.80000 0001 2291 2164Zoological Survey of India, New Alipore, Kolkata, West Bengal 700053 India
| | - Mukesh Thakur
- grid.473833.80000 0001 2291 2164Zoological Survey of India, New Alipore, Kolkata, West Bengal 700053 India
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11
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The Genetic Diversity and Population Genetic Structure of the Red Panda, Ailurus fulgens, in Zoos in China. Animals (Basel) 2020; 10:ani10061008. [PMID: 32526877 PMCID: PMC7341189 DOI: 10.3390/ani10061008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 06/01/2020] [Accepted: 06/07/2020] [Indexed: 11/17/2022] Open
Abstract
In China, red pandas (Ailurus fulgens) have been raised in zoos for 60 years. It is very important to understand the genetic diversity and population genetic structure of the captive red pandas. Based on 19 microsatellite loci, we investigated genetic diversity and population genetic structure of 116 captive red pandas, with samples taken from 11 captive populations in China. Our results revealed a high genetic diversity among the populations, with mean allelic richness varying from 3.505 (Beijing) to 4.026 (Mianning), and expected heterozygosities varying from 0.631 (Huangshan) to 0.782 (Wenling). In particular, significant deviation from Hardy-Weinberg equilibrium was found in populations of Fuzhou and Jiangsu. The genetic differentiation index across all populations was 0.055, indicating a significant genetic differentiation among the 11 populations. These populations could be divided into three genetic clusters using a microsatellite-based Bayesian clustering analysis, which were consistent with the clustering results of wild populations. We conclude that the genetic diversity among captive red pandas is as high as that of the wild population. More attention should be paid to develop a proper and scientifically-based management program to avoid inbreeding and maintain a high genetic diversity in captive red pandas.
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12
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Hu Y, Thapa A, Fan H, Ma T, Wu Q, Ma S, Zhang D, Wang B, Li M, Yan L, Wei F. Genomic evidence for two phylogenetic species and long-term population bottlenecks in red pandas. SCIENCE ADVANCES 2020; 6:eaax5751. [PMID: 32133395 PMCID: PMC7043915 DOI: 10.1126/sciadv.aax5751] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 12/04/2019] [Indexed: 05/09/2023]
Abstract
The red panda (Ailurus fulgens), an endangered Himalaya-endemic mammal, has been classified as two subspecies or even two species - the Himalayan red panda (A. fulgens) and the Chinese red panda (Ailurus styani) - based on differences in morphology and biogeography. However, this classification has remained controversial largely due to lack of genetic evidence, directly impairing scientific conservation management. Data from 65 whole genomes, 49 Y-chromosomes, and 49 mitochondrial genomes provide the first comprehensive genetic evidence for species divergence in red pandas, demonstrating substantial inter-species genetic divergence for all three markers and correcting species-distribution boundaries. Combined with morphological evidence, these data thus clearly define two phylogenetic species in red pandas. We also demonstrate different demographic trajectories in the two species: A. styani has experienced two population bottlenecks and one large population expansion over time, whereas A. fulgens has experienced three bottlenecks and one very small expansion, resulting in very low genetic diversity, high linkage disequilibrium, and high genetic load.
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Affiliation(s)
- Yibo Hu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Arjun Thapa
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Huizhong Fan
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tianxiao Ma
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Qi Wu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Shuai Ma
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Dongling Zhang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Bing Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Min Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Li Yan
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Fuwen Wei
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
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13
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HEMATOLOGY AND SERUM BIOCHEMISTRY VALUES OF THE RED PANDA SUBSPECIES ( AILURUS FULGENS STYANI). J Zoo Wildl Med 2018; 49:384-395. [PMID: 29900763 DOI: 10.1638/2017-0104.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Health evaluations were conducted on individuals ( n = 62, age < 1 to 11 yr) from a captive red panda ( Ailurus fulgens styani) population at the Chengdu Research Base for Giant Panda Breeding in Sichuan Province, People's Republic of China. Individuals were anesthetized using combinations of ketamine, dexmedetomidine, diazepam, isoflurane, and tiletamine/zolazepam. Whereas physical exams revealed no abnormalities for 40% of red pandas, 24% had dental abnormalities and 18% had orthopedic abnormalities. As the red panda is the only member of the family Ailuridae, complete blood count and serum biochemistry samples were collected and used to develop reference intervals for this species. When hematologic and serum chemistry values of male and female red pandas were compared within this A. f. styani population, males had higher mean cell hemoglobin, mean cell hemoglobin concentration, and blood urea nitrogen concentrations, whereas females had higher alkaline phosphatase, cholesterol, and iron. Adult red pandas (≥2 yr) had higher lymphocyte percentage, total protein, globulin, and chloride levels, whereas juveniles (<2 yr) had higher white blood cell concentrations, neutrophil percentage and absolute neutrophil values, alkaline phosphatase, creatine kinase, cholesterol, potassium, total and ionized calcium, and phosphorus levels. Reference values and expected age and sex differences will assist with health management of the captive A. f. styani population.
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Choudhary JS, Naaz N, Lemtur M, Das B, Singh AK, Bhatt BP, Prabhakar CS. Genetic analysis of Bactrocera zonata (Diptera: Tephritidae) populations from India based on cox1 and nad1 gene sequences. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:727-736. [PMID: 28712341 DOI: 10.1080/24701394.2017.1350952] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The peach fruit fly, Bactrocera zonata, is among the most serious and polyphagous insect pest of fruit crops in many parts of the world under genus Bactrocera. In the present study, the genetic structure, diversity and demographic history of B. zonata in India were inferred from mitochondrial cytochrome oxidase 1 (cox1) and NADH dehydrogenase 1 (nad1) sequences. The efficiency of DNA barcodes for identification of B. zonata was also tested. Genetic diversity indices [number of haplotypes (H), haplotype diversity (Hd), nucleotide diversity (π) and average number of nucleotide differences (k)] of B. zonata populations across India maintain high level of genetic diversity without isolation by distance among the geographic regions. Non-significant negative correlation between pairwise Fst and geographic distance suggests a high level of gene flow among studied populations of B. zonata. The possibility of sudden expansion of B. zonata revealed through mismatch distribution analysis as well as negative Tajima's D and Fu's Fs values further supported by star-like network of haplotypes. DNA barcoding analysis suggests that B. zonata specimens can be clearly differentiated from other species with 100% accuracy of identification. Therefore, cytochrome oxidase 1 (cox1) barcode sequences generated in the present study could be a valuable source for the rapid identification and global population genetic study of B. zonata.
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Affiliation(s)
- Jaipal S Choudhary
- a ICAR Research Complex for Eastern Region , Research Centre , Ranchi , India
| | - Naiyar Naaz
- a ICAR Research Complex for Eastern Region , Research Centre , Ranchi , India
| | - Moanaro Lemtur
- a ICAR Research Complex for Eastern Region , Research Centre , Ranchi , India
| | - Bikash Das
- a ICAR Research Complex for Eastern Region , Research Centre , Ranchi , India
| | - Arun Kumar Singh
- a ICAR Research Complex for Eastern Region , Research Centre , Ranchi , India
| | - Bhagwati P Bhatt
- b ICAR Research Complex for Eastern Region , ICAR Parisar, P. O. Bihar Veterinary College , Patna , India
| | - Chandra S Prabhakar
- a ICAR Research Complex for Eastern Region , Research Centre , Ranchi , India.,c Department of Entomology, Veer Kunwar Singh College of Agriculture ( Bihar Agricultural University, Sabour) , Dumraon , India
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15
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Fei Y, Hou R, Spotila JR, Paladino FV, Qi D, Zhang Z. Metabolic rate of the red panda, Ailurus fulgens, a dietary bamboo specialist. PLoS One 2017; 12:e0173274. [PMID: 28306740 PMCID: PMC5356995 DOI: 10.1371/journal.pone.0173274] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 02/17/2017] [Indexed: 11/22/2022] Open
Abstract
The red panda (Ailurus fulgens) has a similar diet, primarily bamboo, and shares the same habitat as the giant panda, Ailuropoda melanoleuca. There are considerable efforts underway to understand the ecology of the red panda and to increase its populations in natural reserves. Yet it is difficult to design an effective strategy for red panda reintroduction if we do not understand its basic biology. Here we report the resting metabolic rate of the red panda and find that it is higher than previously measured on animals from a zoo. The resting metabolic rate was 0.290 ml/g/h (range 0.204–0.342) in summer and 0.361 ml/g/h in winter (range 0.331–0.406), with a statistically significant difference due to season and test temperature. Temperatures in summer were probably within the thermal neutral zone for metabolism but winter temperatures were below the thermal neutral zone. There was no difference in metabolic rate between male and female red pandas and no difference due to mass. Our values for metabolic rate were much higher than those measured by McNab for 2 red pandas from a zoo. The larger sample size (17), more natural conditions at the Panda Base and improved accuracy of the metabolic instruments provided more accurate metabolism measurements. Contrary to our expectations based on their low quality bamboo diet, the metabolic rates of red pandas were similar to mammals of the same size. Based on their metabolic rates red pandas would not be limited by their food supply in natural reserves.
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Affiliation(s)
- Yuxiang Fei
- Department of Biodiversity, Earth and Environmental Science, Drexel University, Philadelphia, PA United States of America
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Northern Suburb, FuTou Shan, Chengdu, Sichuan Province, People’s Republic of China
| | - Rong Hou
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Northern Suburb, FuTou Shan, Chengdu, Sichuan Province, People’s Republic of China
| | - James R. Spotila
- Department of Biodiversity, Earth and Environmental Science, Drexel University, Philadelphia, PA United States of America
- * E-mail: (JRS); (ZZ)
| | - Frank V. Paladino
- Department of Biology, Indiana Purdue University at Fort Wayne, 2101 E. Coliseum Blvd, Fort Wayne, IN United States of America
| | - Dunwu Qi
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Northern Suburb, FuTou Shan, Chengdu, Sichuan Province, People’s Republic of China
| | - Zhihe Zhang
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Northern Suburb, FuTou Shan, Chengdu, Sichuan Province, People’s Republic of China
- * E-mail: (JRS); (ZZ)
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16
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Kumar A, Rai U, Roka B, Jha AK, Reddy PA. Genetic assessment of captive red panda ( Ailurus fulgens) population. SPRINGERPLUS 2016; 5:1750. [PMID: 27795893 PMCID: PMC5055525 DOI: 10.1186/s40064-016-3437-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 09/29/2016] [Indexed: 11/21/2022]
Abstract
Red panda (Ailurus fulgens) is threatened across its range by detrimental human activities and rapid habitat changes necessitating captive breeding programs in various zoos globally to save this flagship species from extinction. One of the ultimate aims of ex situ conservation is reintroduction of endangered animals into their natural habitats while maintaining 90 % of the founder genetic diversity. Advances in molecular genetics and microsatellite genotyping techniques make it possible to accurately estimate genetic diversity of captive animals of unknown ancestry. Here we assess genetic diversity of the red panda population in Padmaja Naidu Himalayan Zoological Park, Darjeeling, which plays a pivotal role in ex situ conservation of red panda in India. We generated microsatellite genotypes of fifteen red pandas with a set of fourteen loci. This population is genetically diverse with 68 % observed heterozygosity (HO) and mean inbreeding (FIS) coefficient of 0.05. However population viability analysis reveals that this population has a very low survival probability (<2 %) and will rapidly loose its genetic diversity to 37 % mainly due to small population size and skewed male-biased sex ratio. Regular supplementation with a pair of adult individuals every five years will increase survival probability and genetic diversity to 99 and 61 % respectively and will also support future harvesting of individuals for reintroduction into the wild and exchange with other zoos.
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Affiliation(s)
- Arun Kumar
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500 007 India
| | - Upashna Rai
- Padmaja Naidu Himalayan Zoological Park, Darjeeling, 734101 India
| | - Bhupen Roka
- Padmaja Naidu Himalayan Zoological Park, Darjeeling, 734101 India
| | - Alankar K Jha
- Padmaja Naidu Himalayan Zoological Park, Darjeeling, 734101 India
| | - P Anuradha Reddy
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500 007 India
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17
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Jing M, Yu HT, Bi X, Lai YC, Jiang W, Huang L. Phylogeography of Chinese house mice (Mus musculus musculus/castaneus): distribution, routes of colonization and geographic regions of hybridization. Mol Ecol 2014; 23:4387-405. [PMID: 25065953 DOI: 10.1111/mec.12873] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2013] [Revised: 07/22/2014] [Accepted: 07/23/2014] [Indexed: 11/27/2022]
Abstract
House mice (Mus musculus) are human commensals and have served as a primary model in biomedical, ecological and evolutionary research. Although there is detailed knowledge of the biogeography of house mice in Europe, little is known of the history of house mice in China, despite the fact that China encompasses an enormous portion of their range. In the present study, 535 house mice caught from 29 localities in China were studied by sequencing the mitochondrial D-loop and genotyping 10 nuclear microsatellite markers distributed on 10 chromosomes. Phylogenetic analyses revealed two evolutionary lineages corresponding to Mus musculus castaneus and Mus musculus musculus in the south and north, respectively, with the Yangtze River approximately representing the boundary. More detailed analyses combining published sequence data from mice sampled in neighbouring countries revealed the migration routes of the two subspecies into China: M. m. castaneus appeared to have migrated through a southern route (Yunnan and Guangxi), whereas M. m. musculus entered China from Kazakhstan through the north-west border (Xinjiang). Bayesian analysis of mitochondrial sequences indicated rapid population expansions in both subspecies, approximately 4650-9300 and 7150-14 300 years ago for M. m. castaneus and M. m. musculus, respectively. Interestingly, the migration routes of Chinese house mice coincide with the colonization routes of modern humans into China, and the expansion times of house mice are consistent with the development of agriculture in southern and northern China, respectively. Finally, our study confirmed the existence of a hybrid zone between M. m. castaneus and M. m. musculus in China. Further study of this hybrid zone will provide a useful counterpart to the well-studied hybrid zone between M. m. musculus and Mus musculus domesticus in central Europe.
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Affiliation(s)
- Meidong Jing
- College of Life Sciences, Ludong University, Yantai, Shandong, 264025, China
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18
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Joshi J, Salar RK, Banerjee P, S U, Tantia MS, Vijh RK. Genetic variation and phylogenetic relationships of Indian buffaloes of uttar pradesh. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2014; 26:1229-36. [PMID: 25049904 PMCID: PMC4093408 DOI: 10.5713/ajas.2012.12669] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 03/05/2013] [Accepted: 02/17/2013] [Indexed: 11/27/2022]
Abstract
India possesses a total buffalo population of 105 million out of which 26.1% inhabit Uttar Pradesh. The buffalo of Uttar Pradesh are described as nondescript or local buffaloes. Currently, there is no report about the genetic diversity, phylogenetic relationship and matrilineal genetic structure of these buffaloes. To determine the origin and genetic diversity of UP buffaloes, we sequenced and analysed the mitochondrial DNA D-loop sequences in 259 samples from entire Uttar Pradesh. One hundred nine haplotypes were identified in UP buffaloes that were defined by 96 polymorphic sites. We implemented neutrality tests to assess signatures of recent historical demographic events like Tajima’s D test and Fu’s Fs test. The phylogenetic studies revealed that there was no geographic differentiation and UP buffaloes had a single maternal lineage while buffaloes of Eastern UP were distinctive from rest of the UP buffaloes.
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Affiliation(s)
- Jyoti Joshi
- Department of Animal Genetics, National Bureau of Animal Genetic Resources, POBox 129, GTBypass Road Karnal - 132001, Haryana, India
| | - R K Salar
- Department of Animal Genetics, National Bureau of Animal Genetic Resources, POBox 129, GTBypass Road Karnal - 132001, Haryana, India
| | - Priyanka Banerjee
- Department of Animal Genetics, National Bureau of Animal Genetic Resources, POBox 129, GTBypass Road Karnal - 132001, Haryana, India
| | - Upasna S
- Department of Animal Genetics, National Bureau of Animal Genetic Resources, POBox 129, GTBypass Road Karnal - 132001, Haryana, India
| | - M S Tantia
- Department of Animal Genetics, National Bureau of Animal Genetic Resources, POBox 129, GTBypass Road Karnal - 132001, Haryana, India
| | - R K Vijh
- Department of Animal Genetics, National Bureau of Animal Genetic Resources, POBox 129, GTBypass Road Karnal - 132001, Haryana, India
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Singh NS, Behera BK, Kunal SP, Das P, Paria P, Sharma AP. Genetic stock structure ofOsteobrama belangeri(Valenciennes, 1844) in Indian region. ACTA ACUST UNITED AC 2014; 27:232-7. [DOI: 10.3109/19401736.2014.883602] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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20
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Genetic diversity of Echinococcus granulosus in southwest China determined by the mitochondrial NADH dehydrogenase subunit 2 gene. ScientificWorldJournal 2014; 2014:867839. [PMID: 24592194 PMCID: PMC3925532 DOI: 10.1155/2014/867839] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 11/24/2013] [Indexed: 12/21/2022] Open
Abstract
We evaluated genetic diversity and structure of Echinococcus granulosus by analyzing the complete mitochondrial NADH dehydrogenase subunit 2 (ND2) gene in 51 isolates of E. granulosus sensu stricto metacestodes collected at three locations in this region. We detected 19 haplotypes, which formed a distinct clade with the standard sheep strain (G1). Hence, all 51 isolates were identified as E. granulosus sensu stricto (G1–G3). Genetic relationships among haplotypes were not associated with geographical divisions, and fixation indices (Fst) among sampling localities were low. Hence, regional populations of E. granulosus in the southwest China are not differentiated, as gene flow among them remains high. This information is important for formulating unified region-wide prevention and control measures. We found large negative Fu's Fs and Tajima's D values and a unimodal mismatch distribution, indicating that the population has undergone a demographic expansion. We observed high genetic diversity among the E. granulosus s. s. isolates, indicating that the parasite population in this important bioregion is genetically robust and likely to survive and spread. The data from this study will prove valuable for future studies focusing on improving diagnosis and prevention methods and developing robust control strategies.
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21
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Fasanella M, Bruno C, Cardoso Y, Lizarralde M. Historical demography and spatial genetic structure of the subterranean rodentCtenomys magellanicusin Tierra del Fuego (Argentina). Zool J Linn Soc 2013. [DOI: 10.1111/zoj.12067] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mariana Fasanella
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Centro Regional de Estudios Genómicos; Fac. Cs. Exactas; Universidad Nacional de La Plata; Fcio. Varela Buenos Aires Argentina
| | - Cecilia Bruno
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Centro Regional de Estudios Genómicos; Fac. Cs. Exactas; Universidad Nacional de La Plata; Fcio. Varela Buenos Aires Argentina
| | - Yamila Cardoso
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Centro Regional de Estudios Genómicos; Fac. Cs. Exactas; Universidad Nacional de La Plata; Fcio. Varela Buenos Aires Argentina
| | - Marta Lizarralde
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Centro Regional de Estudios Genómicos; Fac. Cs. Exactas; Universidad Nacional de La Plata; Fcio. Varela Buenos Aires Argentina
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22
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Devi KM, Ghosh SK. Molecular phylogeny of Indian horse breeds with special reference to Manipuri pony based on mitochondrial D-loop. Mol Biol Rep 2013; 40:5861-7. [DOI: 10.1007/s11033-013-2692-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 09/14/2013] [Indexed: 12/01/2022]
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23
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Hou X, Zhu F, Yin S, Zhang L, Hu Y, Wang Y, Jia Y, Zhang G, Li L. Genetic diversity of Odontobutis potamophila from different geographic populations inferred from mtDNA control region. ACTA ACUST UNITED AC 2013; 25:400-6. [PMID: 23841610 DOI: 10.3109/19401736.2013.803084] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Odontobutis potamophila is a Chinese endemic species and an economically important fishery resource in the Yangtze River. The genetic variability of O. potamophila was studied based on the sequence analysis of mitochondrial DNA control region from 150 individuals of five geographical populations including from Dangtu (n=30), Sheyang (n=30), Yuyao (n=30), Tai Lake nearby Dongxishan (n=30) and Minjiang (n=30). Among five populations, the genetic distance between Minjiang population and other populations (0.1186-0.1223) was larger than that among four populations except for Minjiang (0.0015-0.0198). In addition, 23 haplotypes were obtained and each population had special haplotypes. The samples from five sites had high haplotype diversity (0.80510) and low nucleotide diversity (0.04028). Through Tajima's D and Fu's F neutral testing and mismatch distribution test among all geographical populations, O. potamophila did not undergo recent population expansion. During the population evolution, O. potamophila experienced a balanced selection function and maintained a stable state and population size. Moreover, the haplotype Neighbor-Joining (NJ) tree was separated two haplotype groups. The NJ tree, TCS network and median-joining network could clearly separate the haplotypes of the specimens from different areas. Analysis of molecular variance and pairwise FST revealed an obvious genetic differentiation among different geographical populations, suggesting that O. potamophila in different geographical populations should be managed and conserved separately.
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Affiliation(s)
- Xinyuan Hou
- College of Life Sciences, Key Laboratory of Biodiversity and Biotechnology of Jiangsu Province, Nanjing Normal University , Nanjing 210023 , China
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24
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Mitochondrial DNA analysis reveals three stocks of yellowfin tuna Thunnus albacares (Bonnaterre, 1788) in Indian waters. CONSERV GENET 2013. [DOI: 10.1007/s10592-013-0445-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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25
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Kumar G, Kunal SP, Menezes MR, Meena RM. Single genetic stock of kawakawa Euthynnus affinis (Cantor, 1849) along the Indian coast inferred from sequence analyses of mitochondrial DNA D-loop region. CONSERV GENET 2012. [DOI: 10.1007/s10592-012-0359-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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26
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Population genetic structure and geographic differentiation in the hot spring snake Thermophis baileyi (Serpentes, Colubridae): indications for glacial refuges in southern-central Tibet. Mol Phylogenet Evol 2012; 63:396-406. [PMID: 22306823 DOI: 10.1016/j.ympev.2012.01.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Revised: 01/10/2012] [Accepted: 01/17/2012] [Indexed: 11/21/2022]
Abstract
The endangered hot spring snake (Thermophis baileyi) is endemic to the Tibetan Plateau and restricted to a few sites at high altitudes (>3500 m a.s.l.). Its strong preference for habitats with hot springs might be an early adaptation to the cooling climate during the plateau uplift. Some of these thermal sites may have been free of ice during the last glacial maximum (LGM) serving as refuges for the snake. To test this and to examine the population genetic structure data of 12 microsatellites and mitochondrial DNA were obtained from 153 individuals from 12 sites across the plateau. Four of the microsatellite loci were newly developed for this study. The results suggest that T. baileyi has at least two genetically diverse clades in Tibet, which developed during the Pleistocene and expanded after the LGM. Accordingly, the existence of separate glacial refuges on the central plateau can be assumed. Analyses of the genetic variation indicated a high level of geographic differentiation and population structure on a regional as well as on a range-wide scale. The study shows that, apart from the phylogeographic signatures, the diversification of current Thermophis populations is caused by (a) a limited dispersal due to mountain ranges, (b) a strong preference for hot springs and (c) the insular distribution of suitable habitats on the plateau. The present data should be taken into account in necessary monitoring and management plans for T. baileyi.
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27
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Mapelli FJ, Mora MS, Mirol PM, Kittlein MJ. Population structure and landscape genetics in the endangered subterranean rodent Ctenomys porteousi. CONSERV GENET 2011. [DOI: 10.1007/s10592-011-0273-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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28
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Genetic variation at mtDNA and microsatellite loci in Chinese longsnout catfish (Leiocassis longirostris). Mol Biol Rep 2011; 39:4605-17. [PMID: 21947845 DOI: 10.1007/s11033-011-1252-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Accepted: 09/14/2011] [Indexed: 10/17/2022]
Abstract
Genetic variability and population structure of the Chinese longsnout catfish Leiocassis longirostris Günther in the Yangtze River was examined with mitochondrial control region sequences and nuclear microsatellite markers. A 705-bp segment of the mitochondrial DNA control region was sequenced from 132 samples, which identified a total of 61 haplotypes. The Chinese longsnout catfish in the Yangtze River was characterized with high haplotype diversity (h = 0.9770 ± 0.0041) but low nucleotide diversity (π = 0.0081 ± 0.0043). Median-joining network analysis revealed a star-shaped pattern and mismatch distribution analysis found a smooth unimodal distribution, which suggested that this species in the Yangtze River underwent a population expansion following bottlenecks and/or they originated from a small size of founding population. It was estimated that the possible time of population expansion was 139,000-435,000 years before present, a time period in the middle Pleistocene. The analysis of molecular variance and phylogenetic reconstructions did not detect significant geographic structure between different river sections. This pattern of genetic variation was further evidenced with nuclear microsatellite markers. The genetic differentiation between above and below the Gezhouba Dam and Three Gorges Dam is very small at mitochondrial and nuclear levels, which suggested that these recently developed dams might have not significantly resulted in population genetic fragmentation in the Chinese longsnout catfish. However, the potential exacerbation of genetic structuring by the dams should not be overlooked in the future.
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29
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Genotyping faeces of red pandas (Ailurus fulgens): implications for population estimation. EUR J WILDLIFE RES 2011. [DOI: 10.1007/s10344-011-0556-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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30
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HU YIBO, GUO YU, QI DUNWU, ZHAN XIANGJIANG, WU HUA, BRUFORD MICHAELW, WEI FUWEN. Genetic structuring and recent demographic history of red pandas (Ailurus fulgens) inferred from microsatellite and mitochondrial DNA. Mol Ecol 2011; 20:2662-75. [DOI: 10.1111/j.1365-294x.2011.05126.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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31
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DING LI, GAN XIAONI, HE SHUNPING, ZHAO ERMI. A phylogeographic, demographic and historical analysis of the short-tailed pit viper (Gloydius brevicaudus): evidence for early divergence and late expansion during the Pleistocene. Mol Ecol 2011; 20:1905-22. [DOI: 10.1111/j.1365-294x.2011.05060.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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32
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Fan Z, Liu S, Liu Y, Zhang X, Yue B. How Quaternary geologic and climatic events in the southeastern margin of the Tibetan Plateau influence the genetic structure of small mammals: inferences from phylogeography of two rodents, Neodon irene and Apodemus latronum. Genetica 2011; 139:339-51. [DOI: 10.1007/s10709-011-9553-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Accepted: 01/19/2011] [Indexed: 10/18/2022]
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33
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LI YUZHI, XU XIAO, ZHANG LIANG, ZHANG ZHIHE, SHEN FUJUN, ZHANG WENPING, YUE BISONG. An ARMS-based technique for sex determination of red panda (Ailurus fulgens). Mol Ecol Resour 2010; 11:400-3. [DOI: 10.1111/j.1755-0998.2010.02934.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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34
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Chen W, Hao H, Liu Y, Chen S, Zhang X, Liu S, Yue B. Mitochondrial DNA genetic variation and phylogeography of the recently described vole speciesProedromys liangshanensisLiu, Sun, Zeng and Zhao, 2007 (Rodentia: Arvicolinae). J NAT HIST 2010. [DOI: 10.1080/00222933.2010.501911] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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35
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Chen W, Liu S, Liu Y, Hao H, Zeng B, Chen S, Peng H, Yue B, Zhang X. Phylogeography of the Large White-Bellied RatNiviventer excelsiorSuggests the Influence of Pleistocene Glaciations in the Hengduan Mountains. Zoolog Sci 2010; 27:487-93. [DOI: 10.2108/zsj.27.487] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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36
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Ci HX, Lin GH, Cai ZY, Tang LZ, Su JP, Liu JQ. Population history of the plateau pika endemic to the Qinghai-Tibetan Plateau based on mtDNA sequence data. J Zool (1987) 2009. [DOI: 10.1111/j.1469-7998.2009.00635.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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37
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WANG LP, DU YZ, HE YT, ZHENG FS, LU ZQ. Genetic Variation of Host Populations of Liriomyza sativae Blanchard. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/s1671-2927(08)60056-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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38
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Isolation and characterization of 12 novel microsatellite loci for the red panda (Ailurus fulgens). CONSERV GENET 2008. [DOI: 10.1007/s10592-008-9556-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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39
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Mora MS, Lessa EP, Kittlein MJ, Vassallo AI. PHYLOGEOGRAPHY OF THE SUBTERRANEAN RODENT CTENOMYS AUSTRALIS IN SAND-DUNE HABITATS: EVIDENCE OF POPULATION EXPANSION. J Mammal 2006. [DOI: 10.1644/05-mamm-a-399r1.1] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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40
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Okello JBA, Nyakaana S, Masembe C, Siegismund HR, Arctander P. Mitochondrial DNA variation of the common hippopotamus: evidence for a recent population expansion. Heredity (Edinb) 2006; 95:206-15. [PMID: 16030528 DOI: 10.1038/sj.hdy.6800711] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Mitochondrial DNA control region sequence variation was obtained and the population history of the common hippopotamus was inferred from 109 individuals from 13 localities covering six populations in sub-Saharan Africa. In all, 100 haplotypes were defined, of which 98 were locality specific. A relatively low overall nucleotide diversity was observed (pi = 1.9%), as compared to other large mammals so far studied from the same region. Within populations, nucleotide diversity varied from 1.52% in Zambia to 1.92% in Queen Elizabeth and Masai Mara. Overall, low but significant genetic differentiation was observed in the total data set (F(ST) = 0.138; P = 0.001), and at the population level, patterns of differentiation support previously suggested hippopotamus subspecies designations (F(CT) = 0.103; P = 0.015). Evidence that the common hippopotamus recently expanded were revealed by: (i) lack of clear geographical structure among haplotypes, (ii) mismatch distributions of pairwise differences (r = 0.0053; P = 0.012) and site-frequency spectra, (iii) Fu's neutrality statistics (F(S) = -155.409; P < 0.00001) and (iv) Fu and Li's statistical tests (D* = -3.191; P < 0.01, F* = -2.668; P = 0.01). Mismatch distributions, site-frequency spectra and neutrality statistics performed at subspecies level also supported expansion of Hippopotamus amphibius across Africa. We interpret observed common hippopotamus population history in terms of Pleistocene drainage overflow and suggest recognising the three subspecies that were sampled in this study as separate management units in future conservation planning.
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Affiliation(s)
- J B A Okello
- Molecular Biology Laboratory, Makerere University Institute of Environment & Natural Resources, PO Box 7298, Kampala, Uganda.
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41
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The molecular systematics and conservation of an endangered carnivore, the Owston's palm civet Chrotogale owstoni (Thomas, 1912) (Carnivora, Viverridae, Hemigalinae). Anim Conserv 2004. [DOI: 10.1017/s1367943003001136] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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42
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Nishibori M, Hayashi T, Tsudzuki M, Yamamoto Y, Yasue H. Complete sequence of the Japanese quail (Coturnix japonica) mitochondrial genome and its genetic relationship with related species. Anim Genet 2001; 32:380-5. [PMID: 11736810 DOI: 10.1046/j.1365-2052.2001.00795.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The Japanese quail (Coturnix japonica; JQ) is one of the domesticated fowl species of Japan. To provide DNA sequence information for examination of its phylogenetic position in the order Galliformes, the complete sequence of the JQ mitochondria was determined. Sequence analysis revealed that the JQ mitochondrial genome is a circular DNA of 16 697 basepairs (bp), which is smaller than the chicken mitochondrial DNA of 16 775 bp, but the genomic structure of JQ mitochondria was the same as that of the chicken. The sequence homologies of all mitochondrial genes including those for 12S and 16S ribosomal RNA (rRNA), between Japanese quail and chicken ranged from 78.0 to 89.9%. Because the sequences of NADH dehydrogenase subunit 2 and cytochrome b genes had been reported in five species [Phasianus colchicus (ring-neck pheasant: RP), Gallus gallus domesticus (chicken: CH), Perdix perdix (grey partridge: GP), Bambusicola thoracia (Chinese bamboo partridge: CP), and Aythya americana (redhead: RH)], the concatenated nucleotide sequences (2184 bp) and amino acid sequences of these two genes were used in a phylogenetic analysis of JQ against these five species using a maximum likelihood (ML) method. Using the first and second bases of the codons, and the third base of the codons indicated a phylogenic tree of [RH, (RP, GP), (JQ, (CH, CP))]. A phylogenic tree of [RH, JQ, (RP, GP), (CH, CP)] was determined using amino acid sequences. Because the local bootstrap values for the JQ branch in these trees are not high, additional sequence is necessary for construction of a reliable tree.
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Affiliation(s)
- M Nishibori
- Genome Research Department, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
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Strimmer K, Pybus OG. Exploring the demographic history of DNA sequences using the generalized skyline plot. Mol Biol Evol 2001; 18:2298-305. [PMID: 11719579 DOI: 10.1093/oxfordjournals.molbev.a003776] [Citation(s) in RCA: 161] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We present an intuitive visual framework, the generalized skyline plot, to explore the demographic history of sampled DNA sequences. This approach is based on a genealogy inferred from the sequences and provides a nonparametric estimate of effective population size through time. In contrast to previous related procedures, the generalized skyline plot is more applicable to cases where the underlying tree is not fully resolved and the data is not highly variable. This is achieved by the grouping of adjacent coalescent intervals. We employ a small-sample Akaike information criterion to objectively choose the optimal grouping strategy. We investigate the performance of our approach using simulation and subsequently apply it to HIV-1 sequences from central Africa and mtDNA sequences from red pandas.
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Affiliation(s)
- K Strimmer
- Department of Zoology, University of Oxford
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