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Salleh MHM, Esa Y, Pau SSN. Conservation Genetics of the Critically Endangered Southern River Terrapin ( Batagur affinis) in Malaysia: Genetic Diversity and Novel Subspecies Distribution Ranges. BIOLOGY 2023; 12:520. [PMID: 37106721 PMCID: PMC10136168 DOI: 10.3390/biology12040520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 03/05/2023] [Accepted: 03/09/2023] [Indexed: 03/31/2023]
Abstract
A population genetics study was carried out on the Southern River terrapin (Batagur affinis) from four places in Peninsular Malaysia: Pasir Gajah, Kemaman (KE), Terengganu; Bukit Pinang (BP), Kedah; Bota Kanan (BK), Perak; and Bukit Paloh, Kuala Berang (KB), Terengganu. The goal of this study is to identify genetic differences in two subspecies of B. affinis in Malaysia. No previous reports were available on the genetic diversity, phylogenetic relationships and matrilineal hereditary structure of these terrapin populations in Malaysia. The sequencing identified 46 single nucleotide polymorphisms that defined six mitochondrial haplotypes in the Southern River terrapins. Tajima's D test and Fu's Fs neutrality tests were performed to evaluate the signatures of recent historical demographic events. Based on the tests, the B. affinis edwardmolli was newly subspecies identified in the west coast-northern region of Kedah state. In addition, the B. affinis edwardmolli in Bukit Paloh, Kuala Berang (KB), Terengganu (Population 4), was shown to have a single maternal lineage compared to other populations. Low genetic diversity, but significant genetic differences, were detected among the studied Southern River terrapin populations.
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Affiliation(s)
- Mohd Hairul Mohd Salleh
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
- Royal Malaysian Customs Department, Persiaran Perdana, Presint 2, Putrajaya 62596, Putrajaya, Malaysia
| | - Yuzine Esa
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
- International Institute of Aquaculture and Aquatic Sciences, Universiti Putra Malaysia, Port Dickson 70150, Negeri Sembilan, Malaysia
| | - Suriyanti-Su Nyun Pau
- Department of Earth Sciences and Environment, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia
- Marine Ecosystem Research Centre (EKOMAR), Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia
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Zhang T, Du W, Lu H, Wang L. Genetic Diversity of Mitochondrial DNA of Chinese Black-bone Chicken. BRAZILIAN JOURNAL OF POULTRY SCIENCE 2018. [DOI: 10.1590/1806-9061-2018-0739] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- T Zhang
- Shaanxi University of technology, China
| | - W Du
- Shaanxi University of technology, China
| | - H Lu
- Shaanxi University of technology, China
| | - L Wang
- Shaanxi University of technology, China
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Abdoli R, Zamani P, Ghasemi M. Genetic similarities and phylogenetic analysis of human and farm animal species based on mitogenomic nucleotide sequences. Meta Gene 2018. [DOI: 10.1016/j.mgene.2017.10.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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Herrera MB, Thomson VA, Wadley JJ, Piper PJ, Sulandari S, Dharmayanthi AB, Kraitsek S, Gongora J, Austin JJ. East African origins for Madagascan chickens as indicated by mitochondrial DNA. ROYAL SOCIETY OPEN SCIENCE 2017; 4:160787. [PMID: 28405364 PMCID: PMC5383821 DOI: 10.1098/rsos.160787] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 02/20/2017] [Indexed: 06/07/2023]
Abstract
The colonization of Madagascar by Austronesian-speaking people during AD 50-500 represents the most westerly point of the greatest diaspora in prehistory. A range of economically important plants and animals may have accompanied the Austronesians. Domestic chickens (Gallus gallus) are found in Madagascar, but it is unclear how they arrived there. Did they accompany the initial Austronesian-speaking populations that reached Madagascar via the Indian Ocean or were they late arrivals with Arabian and African sea-farers? To address this question, we investigated the mitochondrial DNA control region diversity of modern chickens sampled from around the Indian Ocean rim (Southeast Asia, South Asia, the Arabian Peninsula, East Africa and Madagascar). In contrast to the linguistic and human genetic evidence indicating dual African and Southeast Asian ancestry of the Malagasy people, we find that chickens in Madagascar only share a common ancestor with East Africa, which together are genetically closer to South Asian chickens than to those in Southeast Asia. This suggests that the earliest expansion of Austronesian-speaking people across the Indian Ocean did not successfully introduce chickens to Madagascar. Our results further demonstrate the complexity of the translocation history of introduced domesticates in Madagascar.
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Affiliation(s)
- Michael B. Herrera
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, South Australia, Australia
| | - Vicki A. Thomson
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, South Australia, Australia
| | - Jessica J. Wadley
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, South Australia, Australia
| | - Philip J. Piper
- School of Archaeology and Anthropology, Faculty of Arts, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Sri Sulandari
- Genetic Laboratory, Division of Zoology, Research Center for Biology, The Indonesian Institute of Sciences (LIPI), Jl Raya Jakarta-Bogor Km.46, Cibinong 16911, Indonesia
| | - Anik Budhi Dharmayanthi
- Genetic Laboratory, Division of Zoology, Research Center for Biology, The Indonesian Institute of Sciences (LIPI), Jl Raya Jakarta-Bogor Km.46, Cibinong 16911, Indonesia
| | - Spiridoula Kraitsek
- Centre for Advanced Technologies in Animal Genetics and Reproduction, Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia
| | - Jaime Gongora
- Centre for Advanced Technologies in Animal Genetics and Reproduction, Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia
| | - Jeremy J. Austin
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, South Australia, Australia
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Langford S SM, Kraitsek S, Baskerville B, Ho SYW, Gongora J. Australian and Pacific contributions to the genetic diversity of Norfolk Island feral chickens. BMC Genet 2013; 14:91. [PMID: 24063717 PMCID: PMC3850513 DOI: 10.1186/1471-2156-14-91] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 09/12/2013] [Indexed: 11/10/2022] Open
Abstract
Background Norfolk Island has a population of feral chickens which could be the result of domestic stock introduced onto the island by British settlers in 1788. However, there is ongoing debate about their origins because multiple human arrivals to the island may have brought chickens with them. Here we investigate the genetic origins of these feral chickens by sequencing their mitochondrial control region. We infer their phylogenetic relationships using a large dataset of novel sequences from Australian mainland domestic chickens and published sequences from around the world. Results Eleven control region haplotypes were found among the Norfolk Island feral and Australian mainland domestic chickens. Six of the Norfolk Island haplotypes fall within haplogroup E, but given the worldwide distribution of this haplogroup, the putative European origin of these chickens requires further investigation. One haplotype common among Norfolk Island and Australian samples belonged to a subgroup of haplogroup D, which appears to be restricted to chickens from Indonesia, Vanuatu and Guam. Conclusions Our data show that at least two mitochondrial DNA haplogroups (D and E) have contributed to the genetic make-up of Norfolk Island feral chickens. In addition, we have provided insights into the discrete geographical distribution and diversity of the chicken haplogroup D. In view of the worldwide interest in the characterisation of poultry resources, further assessment of chicken populations of Island Southeast Asia and the Pacific region is warranted.
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Storey AA, Athens JS, Bryant D, Carson M, Emery K, deFrance S, Higham C, Huynen L, Intoh M, Jones S, Kirch PV, Ladefoged T, McCoy P, Morales-Muñiz A, Quiroz D, Reitz E, Robins J, Walter R, Matisoo-Smith E. Investigating the global dispersal of chickens in prehistory using ancient mitochondrial DNA signatures. PLoS One 2012; 7:e39171. [PMID: 22848352 PMCID: PMC3405094 DOI: 10.1371/journal.pone.0039171] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2012] [Accepted: 05/16/2012] [Indexed: 11/19/2022] Open
Abstract
Data from morphology, linguistics, history, and archaeology have all been used to trace the dispersal of chickens from Asian domestication centers to their current global distribution. Each provides a unique perspective which can aid in the reconstruction of prehistory. This study expands on previous investigations by adding a temporal component from ancient DNA and, in some cases, direct dating of bones of individual chickens from a variety of sites in Europe, the Pacific, and the Americas. The results from the ancient DNA analyses of forty-eight archaeologically derived chicken bones provide support for archaeological hypotheses about the prehistoric human transport of chickens. Haplogroup E mtDNA signatures have been amplified from directly dated samples originating in Europe at 1000 B.P. and in the Pacific at 3000 B.P. indicating multiple prehistoric dispersals from a single Asian centre. These two dispersal pathways converged in the Americas where chickens were introduced both by Polynesians and later by Europeans. The results of this study also highlight the inappropriate application of the small stretch of D-loop, traditionally amplified for use in phylogenetic studies, to understanding discrete episodes of chicken translocation in the past. The results of this study lead to the proposal of four hypotheses which will require further scrutiny and rigorous future testing.
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Affiliation(s)
- Alice A Storey
- Department of Archaeology and Palaeoanthropology, University of New England, Armidale, Australia.
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