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Garcia-Erill G, Hanghøj K, Heller R, Wiuf C, Albrechtsen A. Estimating admixture pedigrees of recent hybrids without a contiguous reference genome. Mol Ecol Resour 2023; 23:1604-1619. [PMID: 37400991 DOI: 10.1111/1755-0998.13830] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 05/30/2023] [Accepted: 06/15/2023] [Indexed: 07/05/2023]
Abstract
The genome of recently admixed individuals or hybrids has characteristic genetic patterns that can be used to learn about their recent admixture history. One of these are patterns of interancestry heterozygosity, which can be inferred from SNP data from either called genotypes or genotype likelihoods, without the need for information on genomic location. This makes them applicable to a wide range of data that are often used in evolutionary and conservation genomic studies, such as low-depth sequencing mapped to scaffolds and reduced representation sequencing. Here we implement maximum likelihood estimation of interancestry heterozygosity patterns using two complementary models. We furthermore develop apoh (Admixture Pedigrees of Hybrids), a software that uses estimates of paired ancestry proportions to detect recently admixed individuals or hybrids, and to suggest possible admixture pedigrees. It furthermore calculates several hybrid indices that make it easier to identify and rank possible admixture pedigrees that could give rise to the estimated patterns. We implemented apoh both as a command line tool and as a Graphical User Interface that allows the user to automatically and interactively explore, rank and visualize compatible recent admixture pedigrees, and calculate the different summary indices. We validate the performance of the method using admixed family trios from the 1000 Genomes Project. In addition, we show its applicability on identifying recent hybrids from RAD-seq data of Grant's gazelle (Nanger granti and Nanger petersii) and whole genome low-depth data of waterbuck (Kobus ellipsiprymnus) which shows complex admixture of up to four populations.
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Affiliation(s)
| | - Kristian Hanghøj
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Rasmus Heller
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Carsten Wiuf
- Department of Mathematical Sciences, University of Copenhagen, Copenhagen, Denmark
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2
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Koehler G, Hobson KA. Delineating origins of cheetah cubs in the illegal wildlife trade: Improvements based on the use of hair δ18O measurements. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1058985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Abstract
All African felids are listed as vulnerable or endangered according to the IUCN (International Union for Conservation of Nature) Red List of Threatened Species. Cheetahs (Acinonyx jubatus) in particular have declined rapidly as a result of human impacts so that development of effective strategies and tools for conservation of this highly vulnerable species, as well as African felids in general, are essential for their survival in the wild. Here we use the oxygen stable isotopic compositions of cheetah hair to determine origins of cheetah cubs destined for the illegal exotic pet trade by associating individual cubs with predicted δ18O isoscape locations. We found that cheetah cubs most likely originated in East Africa, close to the corridors responsible for this aspect of the illegal wildlife trade to the Middle East. Further refinement of these assignments using a two isotope analysis (δ18O and δ13C values) indicate that these cubs were likely sourced in Southern Ethiopia or possibly as far as Tanzania. We also demonstrate that δ18O values in tissues can provide provenance information in cases where results of δ2H analyses may be obscured by the effects of metabolic routing of nutrients during nursing, starvation, or dehydration. This study demonstrates the utility of stable isotopic tools for conservation and forensic uses for endangered mammalian species.
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Garcia-Erill G, Kjaer MM, Albrechtsen A, Siegismund HR, Heller R. Vicariance followed by secondary gene flow in a young gazelle species complex. Mol Ecol 2020; 30:528-544. [PMID: 33226701 PMCID: PMC7898927 DOI: 10.1111/mec.15738] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 11/03/2020] [Accepted: 11/11/2020] [Indexed: 01/03/2023]
Abstract
Grant's gazelles have recently been proposed to be a species complex comprising three highly divergent mtDNA lineages (Nanger granti, N. notata and N. petersii). The three lineages have nonoverlapping distributions in East Africa, but without any obvious geographical divisions, making them an interesting model for studying the early‐stage evolutionary dynamics of allopatric speciation in detail. Here, we use genomic data obtained by restriction site‐associated (RAD) sequencing of 106 gazelle individuals to shed light on the evolutionary processes underlying Grant's gazelle divergence, to characterize their genetic structure and to assess the presence of gene flow between the main lineages in the species complex. We date the species divergence to 134,000 years ago, which is recent in evolutionary terms. We find population subdivision within N. granti, which coincides with the previously suggested two subspecies, N. g. granti and N. g. robertsii. Moreover, these two lineages seem to have hybridized in Masai Mara. Perhaps more surprisingly given their extreme genetic differentiation, N. granti and N. petersii also show signs of prolonged admixture in Mkomazi, which we identified as a hybrid population most likely founded by allopatric lineages coming into secondary contact. Despite the admixed composition of this population, elevated X chromosomal differentiation suggests that selection may be shaping the outcome of hybridization in this population. Our results therefore provide detailed insights into the processes of allopatric speciation and secondary contact in a recently radiated species complex.
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Affiliation(s)
- Genís Garcia-Erill
- Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Michael Munkholm Kjaer
- Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Copenhagen N, Denmark.,Norwegian College of Fishery Science, UiT The Arctic University of Norway, Tromsø, Norway
| | - Anders Albrechtsen
- Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Hans Redlef Siegismund
- Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Rasmus Heller
- Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Copenhagen N, Denmark
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Ibrahim KM, Williams PC, Olson A, Torounsky R, Naser E, Ghebremariam FH, Masri MA. Genetic variation in morphologically divergent mainland and island populations of Soemmerring’s gazelles (Nanger soemmerringii). MAMMAL RES 2020. [DOI: 10.1007/s13364-020-00480-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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5
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Rakotoarivelo AR, O’Donoghue P, Bruford MW, Moodley Y. An ancient hybridization event reconciles mito-nuclear discordance among spiral-horned antelopes. J Mammal 2019. [DOI: 10.1093/jmammal/gyz089] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Abstract
The spiral-horned antelopes (genus Tragelaphus) are among the most phenotypically diverse of all large mammals, and evolved in Africa during an adaptive radiation that began in the late Miocene, around 6 million years ago. Tragelaphus was able to exploit the habitat heterogeneity created by Plio-Pleistocene paleoclimatic fluctuations and tectonic processes to eventually occupy almost every habitat type in present day sub-Saharan Africa. The smallest of the spiral-horned antelopes, the bushbuck (T. scriptus), is also widely distributed across Africa, but is genetically divided into polyphyletic Scriptus and Sylvaticus mitochondrial (mt)DNA superlineages that inhabit opposite halves of the continent, suggesting the convergent evolution of independent bushbuck species. In this study, we provide a species tree reconstruction for the genus Tragelaphus and show that Scriptus and Sylvaticus are reciprocally monophyletic at nuclear DNA loci, comprising a single species across its African range. Given that mtDNA will sort into species-specific lineages more quickly than nuclear DNA, only an ancient interspecific hybridization event between a female from a now-extinct Tragelaphus species and a proto-Scriptus bushbuck male can reconcile the mito-nuclear incongruence. This extinct species diverged from the nyala (T. angasii) in the Pliocene about 4.1 million years ago. This study adds to an increasing body of evidence that suggests interspecific hybridization may be more common than previously thought.
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Affiliation(s)
- Andrinajoro R Rakotoarivelo
- Department of Zoology, University of Venda, Thohoyandou, Republic of South Africa
- Natiora Ahy, Lot Bis, Ampahibe, Antananarivo, Madagascar
| | | | - Michael W Bruford
- Cardiff School of Biosciences, Sir Martin Evans Building, Cardiff University, Museum Avenue, Cardiff, United Kingdom
| | - Yoshan Moodley
- Department of Zoology, University of Venda, Thohoyandou, Republic of South Africa
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Farré M, Li Q, Zhou Y, Damas J, Chemnick LG, Kim J, Ryder OA, Ma J, Zhang G, Larkin DM, Lewin HA. A near-chromosome-scale genome assembly of the gemsbok (Oryx gazella): an iconic antelope of the Kalahari desert. Gigascience 2019; 8:5289690. [PMID: 30649288 PMCID: PMC6351727 DOI: 10.1093/gigascience/giy162] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 12/12/2018] [Indexed: 12/22/2022] Open
Abstract
Background The gemsbok (Oryx gazella) is one of the largest antelopes in Africa. Gemsbok are heterothermic and thus highly adapted to live in the desert, changing their feeding behavior when faced with extreme drought and heat. A high-quality genome sequence of this species will assist efforts to elucidate these and other important traits of gemsbok and facilitate research on conservation efforts. Findings Using 180 Gbp of Illumina paired-end and mate-pair reads, a 2.9 Gbp assembly with scaffold N50 of 1.48 Mbp was generated using SOAPdenovo. Scaffolds were extended using Chicago library sequencing, which yielded an additional 114.7 Gbp of DNA sequence. The HiRise assembly using SOAPdenovo + Chicago library sequencing produced a scaffold N50 of 47 Mbp and a final genome size of 2.9 Gbp, representing 90.6% of the estimated genome size and including 93.2% of expected genes according to Benchmarking Universal Single-Copy Orthologs analysis. The Reference-Assisted Chromosome Assembly tool was used to generate a final set of 47 predicted chromosome fragments with N50 of 86.25 Mbp and containing 93.8% of expected genes. A total of 23,125 protein-coding genes and 1.14 Gbp of repetitive sequences were annotated using de novo and homology-based predictions. Conclusions Our results provide the first high-quality, chromosome-scale genome sequence assembly for gemsbok, which will be a valuable resource for studying adaptive evolution of this species and other ruminants.
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Affiliation(s)
- Marta Farré
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, UK
| | - Qiye Li
- State Key Laboratory of Genetic Resources and Department of Comparative Biomedical Sciences Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,China National Genebank, BGI-Shenzhen, Dapeng New District, Shenzhen 518120, China
| | - Yang Zhou
- China National Genebank, BGI-Shenzhen, Dapeng New District, Shenzhen 518120, China.,Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Joana Damas
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, UK
| | - Leona G Chemnick
- Institute for Conservation Research, San Diego Zoo, Escondido, California, USA
| | - Jaebum Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, South Korea
| | - Oliver A Ryder
- Institute for Conservation Research, San Diego Zoo, Escondido, California, USA
| | - Jian Ma
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, USA
| | - Guojie Zhang
- State Key Laboratory of Genetic Resources and Department of Comparative Biomedical Sciences Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,China National Genebank, BGI-Shenzhen, Dapeng New District, Shenzhen 518120, China.,Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Denis M Larkin
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, UK
| | - Harris A Lewin
- The UC Davis Genome Center, Department of Evolution and Ecology, College of Biological Sciences, and the Department of Reproduction and Population Health, School of Veterinary Medicine, University of California, Davis, USA
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7
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Effect of landscape features on genetic structure of the goitered gazelle (Gazella subgutturosa) in Central Iran. CONSERV GENET 2017. [DOI: 10.1007/s10592-017-1002-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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8
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Pan-African genetic structure in the African buffalo (Syncerus caffer): investigating intraspecific divergence. PLoS One 2013; 8:e56235. [PMID: 23437100 PMCID: PMC3578844 DOI: 10.1371/journal.pone.0056235] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 01/11/2013] [Indexed: 11/19/2022] Open
Abstract
The African buffalo (Syncerus caffer) exhibits extreme morphological variability, which has led to controversies about the validity and taxonomic status of the various recognized subspecies. The present study aims to clarify these by inferring the pan-African spatial distribution of genetic diversity, using a comprehensive set of mitochondrial D-loop sequences from across the entire range of the species. All analyses converged on the existence of two distinct lineages, corresponding to a group encompassing West and Central African populations and a group encompassing East and Southern African populations. The former is currently assigned to two to three subspecies (S. c. nanus, S. c. brachyceros, S. c. aequinoctialis) and the latter to a separate subspecies (S. c. caffer). Forty-two per cent of the total amount of genetic diversity is explained by the between-lineage component, with one to seventeen female migrants per generation inferred as consistent with the isolation-with-migration model. The two lineages diverged between 145 000 to 449 000 years ago, with strong indications for a population expansion in both lineages, as revealed by coalescent-based analyses, summary statistics and a star-like topology of the haplotype network for the S. c. caffer lineage. A Bayesian analysis identified the most probable historical migration routes, with the Cape buffalo undertaking successive colonization events from Eastern toward Southern Africa. Furthermore, our analyses indicate that, in the West-Central African lineage, the forest ecophenotype may be a derived form of the savanna ecophenotype and not vice versa, as has previously been proposed. The African buffalo most likely expanded and diverged in the late to middle Pleistocene from an ancestral population located around the current-day Central African Republic, adapting morphologically to colonize new habitats, hence developing the variety of ecophenotypes observed today.
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9
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Chen B, Harbach RE, Walton C, He Z, Zhong D, Yan G, Butlin RK. Population genetics of the malaria vector Anopheles aconitus in China and Southeast Asia. INFECTION GENETICS AND EVOLUTION 2012; 12:1958-67. [PMID: 22982161 DOI: 10.1016/j.meegid.2012.08.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Revised: 08/07/2012] [Accepted: 08/08/2012] [Indexed: 11/20/2022]
Abstract
Anopheles aconitus is a well-known vector of malaria and is broadly distributed in the Oriental Region, yet there is no information on its population genetic characteristics. In this study, the genetic differentiation among populations was examined using 140 mtDNA COII sequences from 21 sites throughout Southern China, Myanmar, Vietnam, Thailand, Laos and Sri Lanka. The population in Sri Lanka has characteristic rDNA D3 and ITS2, mtDNA COII and ND5 haplotypes, and may be considered a distinct subspecies. Clear genetic structure was observed with highly significant genetic variation present among population groups in Southeast Asia. The greatest genetic diversity exists in Yunnan and Myanmar population groups. All population groups are significantly different from one another in pairwise Fst values, except Northern Thailand with Central Thailand. Mismatch distributions and extremely significant F(s) values suggest that the populations passed through a recent demographic expansion. These patterns are discussed in relation to the likely biogeographic history of the region and compared to other Anopheles species.
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Affiliation(s)
- Bin Chen
- Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Chongqing 401331, China.
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10
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Osmers B, Petersen BS, Hartl GB, Grobler JP, Kotze A, Van Aswegen E, Zachos FE. Genetic analysis of southern African gemsbok (Oryx gazella) reveals high variability, distinct lineages and strong divergence from the East African Oryx beisa. Mamm Biol 2012. [DOI: 10.1016/j.mambio.2011.08.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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11
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Schwab P, Debes PV, Witt T, Hartl GB, Hmwe SS, Zachos FE, Grobler JP. Genetic structure of the common impala (Aepyceros melampus melampus) in South Africa: phylogeography and implications for conservation. J ZOOL SYST EVOL RES 2011. [DOI: 10.1111/j.1439-0469.2011.00638.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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12
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Lerp H, Wronski T, Pfenninger M, Plath M. A phylogeographic framework for the conservation of Saharan and Arabian Dorcas gazelles (Artiodactyla: Bovidae). ORG DIVERS EVOL 2011. [DOI: 10.1007/s13127-011-0057-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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13
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Genetic diversity, population genetic structure and demographic history of Przewalski’s gazelle (Procapra przewalskii): implications for conservation. CONSERV GENET 2011. [DOI: 10.1007/s10592-011-0244-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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14
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Bitanyi S, Bjørnstad G, Ernest EM, Nesje M, Kusiluka LJ, Keyyu JD, Mdegela RH, Røed KH. Species identification of Tanzanian antelopes using DNA barcoding. Mol Ecol Resour 2011; 11:442-9. [PMID: 21481202 DOI: 10.1111/j.1755-0998.2011.02980.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Efficient tools for consistent species identification are important in wildlife conservation as it can provide information on the levels of species exploitation and assist in solving forensic-related problems. In this study, we evaluated the effectiveness of the mitochondrial cytochrome c oxidase subunit I (COI) barcode in species identification of Tanzanian antelope species. A 470 base-pair region of the COI gene was examined in 95 specimens representing 20 species of antelopes, buffalo and domestic Bovidae. All the Tanzanian species showed unique clades, and sequence divergence within species was <1%, whereas divergence between species ranged from 6.3% to 22%. Lowest interspecific divergence was noted within the Tragelaphus genus. Neighbour-joining phylogenetic analyses demonstrated that the examined COI region provided correct and highly supported species clustering using short fragments down to 100 base-pair lengths. This study demonstrates that even short COI fragments can efficiently identify antelope species, thus demonstrating its high potential for use in wildlife conservation activities.
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Affiliation(s)
- Stella Bitanyi
- Ministry of Livestock Development and Fisheries, Veterinary Investigation Centre, Temeke, Dar es Salaam, Tanzania
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15
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Kholodova MV, Kolpashchikov LA, Kuznetsova MV, Baranova AI. Genetic diversity of wild reindeer (Rangifer tarandus) of Taimyr: Analysis of polymorphism of the control region of mitochondrial DNA. BIOL BULL+ 2011. [DOI: 10.1134/s1062359011010067] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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16
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Zachos FE, Karami M, Ibenouazi Z, Hartl GB, Eckert I, Kirschning J. First genetic analysis of a free-living population of the threatened goitered gazelle (Gazella subgutturosa). Mamm Biol 2010. [DOI: 10.1016/j.mambio.2009.01.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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17
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Wronski T, Wacher T, Hammond RL, Winney B, Hundertmark KJ, Blacket MJ, Mohammed OB, Flores B, Omer SA, Macasero W, Plath M, Tiedemann R, Bleidorn C. Two reciprocally monophyletic mtDNA lineages elucidate the taxonomic status of Mountain gazelles (Gazella gazella). SYST BIODIVERS 2010. [DOI: 10.1080/14772001003613192] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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AVTZIS DIMITRIOSN, ARTHOFER WOLFGANG, STAUFFER CHRISTIAN. Sympatric occurrence of diverged mtDNA lineages of Pityogenes chalcographus (Coleoptera, Scolytinae) in Europe. Biol J Linn Soc Lond 2008. [DOI: 10.1111/j.1095-8312.2008.01004.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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20
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Wu HL, Wan QH, Fang SG. Microsatellite analysis of genetic variation and population subdivision for the black muntjac, Muntiacus crinifrons. Biochem Genet 2007; 45:775-88. [PMID: 17939033 DOI: 10.1007/s10528-007-9117-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2006] [Accepted: 07/31/2007] [Indexed: 11/29/2022]
Abstract
The black muntjac (Muntiacus crinifrons) is a rare deer found only in a restricted region in east China. Recent studies of mitochondrial DNA diversity have shown a markedly low level of nucleotide diversity for the species, and the Suichang population was genetically differentiated from the two other populations, in Huangshan and Tianmushan mountains. In this study, we extended the analysis of genetic diversity and population subdivision for the black muntjac using data from 11 highly polymorphic nuclear DNA microsatellite loci. Contrary to the results based on mtDNA data, the microsatellite loci revealed that the black muntjac retained a rather high nuclear genetic diversity (overall average H (E) = 0.78). Nevertheless, both types of markers supported the idea that the extant black muntjac population is genetically disrupted (overall phi (ST) = 0.16 for mtDNA and overall F (ST) = 0.053 for microsatellite, both P < 0.001). The correlation between genetic differentiation and geographic distance was not significant (Mantel test; P > 0.05), implying that the patterns of genetic differentiation observed in this study might result from recent habitat fragmentation or loss. Based on the results from the mtDNA and nuclear DNA data sets, two management units were defined for the species, Huangshan/Tianmushan and Suichang. We also recommend that a new captive population be established with individuals from the Suichang region as a founder source.
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Affiliation(s)
- Hai-Long Wu
- College of Life Sciences, State Conservation Center for Gene Resources of Endangered Wildlife, and Key Lab. of Conservation Genetics and Reproductive Biology for Endangered Wild Animals, Ministry of Education, Zhejiang University, Hangzhou, P.R. China
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21
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Lorenzen ED, Arctander P, Siegismund HR. Three reciprocally monophyletic mtDNA lineages elucidate the taxonomic status of Grant’s gazelles. CONSERV GENET 2007. [DOI: 10.1007/s10592-007-9375-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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22
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Patenaude NJ, Portway VA, Schaeff CM, Bannister JL, Best PB, Payne RS, Rowntree VJ, Rivarola M, Baker CS. Mitochondrial DNA diversity and population structure among southern right whales (Eubalaena australis). ACTA ACUST UNITED AC 2007; 98:147-57. [PMID: 17416933 DOI: 10.1093/jhered/esm005] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The population structure and mitochondrial (mt) DNA diversity of southern right whales (Eubalaena australis) are described from 146 individuals sampled on 4 winter calving grounds (Argentina, South Africa, Western Australia, and the New Zealand sub-Antarctic) and 2 summer feeding grounds (South Georgia and south of Western Australia). Based on a consensus region of 275 base pairs of the mtDNA control region, 37 variable sites defined 37 unique haplotypes, of which only one was shared between regional samples of the Indo-Pacific and South Atlantic Oceans. Phylogenetic reconstruction of the southern right whale haplotypes revealed 2 distinct clades that differed significantly in frequencies between oceans. An analysis of molecular variance confirmed significant overall differentiation among the 4 calving grounds at both the haplotype and the nucleotype levels (F(ST) = 0.159; Phi(ST) = 0.238; P < 0.001). Haplotype diversity was significantly lower in the Indo-Pacific (h = 0.701 +/- 0.037) compared with the South Atlantic (h = 0.948 +/- 0.013), despite a longer history of exploitation and larger catches in the South Atlantic. In fact, the haplotype diversity in the Indo-Pacific basin was similar to that of the North Atlantic right whale that currently numbers about 300 animals. Multidimensional scaling of genetic differentiation suggests that gene flow occurred primarily between adjacent calving grounds within an ocean basin, with mixing of lineages from different calving grounds occurring on feeding grounds.
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Iyengar A, Diniz FM, Gilbert T, Woodfine T, Knowles J, Maclean N. Structure and evolution of the mitochondrial control region in oryx. Mol Phylogenet Evol 2006; 40:305-14. [PMID: 16616521 DOI: 10.1016/j.ympev.2006.02.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2005] [Revised: 02/06/2006] [Accepted: 02/16/2006] [Indexed: 11/22/2022]
Affiliation(s)
- Arati Iyengar
- School of Biological Sciences, University of Southampton, Southampton SO16 7PX, UK.
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24
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Kholodova MV, Prikhodko VI. Molecular genetic diversity of musk deer Moschus moschiferus L., 1758 (Ruminantia, Artiodactyla) from the northern subspecies group. RUSS J GENET+ 2006. [DOI: 10.1134/s1022795406070131] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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25
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Zhang F, Jiang Z. Mitochondrial phylogeography and genetic diversity of Tibetan gazelle (Procapra picticaudata): implications for conservation. Mol Phylogenet Evol 2006; 41:313-21. [PMID: 16837214 DOI: 10.1016/j.ympev.2006.05.024] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2005] [Revised: 03/21/2006] [Accepted: 05/21/2006] [Indexed: 11/24/2022]
Abstract
The Tibetan gazelle (Procapra picticaudata) is a threatened species and distributed on the Qinghai-Tibet Plateau of China (Qinghai Province, Tibet Autonomous Region and the adjacent Gansu Province, Sichuan Province, and Xinjiang Uigur Autonomous Region). Small peripheral populations of Tibetan gazelle were once found in northern Sikkim and Ladakh, but now these are close to extinction. To describe the evolutionary history and to assess the genetic diversity within this monotypic species and population structure among different geographic locations in China, we sequenced mitochondrial DNA from the control region (CR) and cytochrome (cyt) b gene for 46 individuals from 12 geographic localities in Qinghai, Tibet, Xinjiang, Gansu, and Sichuan. A total of 25 CR haplotypes and 16 cyt b haplotypes were identified from these gazelle samples. CR haplotype diversity (0.98+/-0.01) and nucleotide diversity (0.08+/-0.009) were both high. Phylogenetic trees indicate that the Tibetan gazelle in China can be divided into three main clades: Tibet, Sichuan (SCH) and Qinghai-Arjin Shan-Kekexili (QH-ARJ-KKXL). Analysis of molecular variance (AMOVA) and network analysis consistently support this geographic structure in both datasets. Significant differentiation between populations argues for the presence of management units (MUs). Such differentiation may reflect a geographic separation resulting from the uplift of the Qinghai-Tibet Plateau during the Late Pliocene and Pleistocene. Mismatch distribution analysis implies that Tibetan gazelle has undergone complex population changes. We suggest that the present population structure has resulted from habitat fragmentation during the recent glacial period on the Qinghai-Tibet Plateau and population expansion from glacial refugia after the glacial period. It is likely that the present populations of Tibetan gazelle exhibit a pattern reminiscent of several bottlenecks and expansions in the recent past.
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Affiliation(s)
- Fangfang Zhang
- Institute of Zoology, Chinese Academy of Sciences, No. 25 Beisihuanxilu, Beijing 100080, China
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Sorokin PA, Kiriliuk VE, Lushchekina AA, Kholodova MV. Genetic Diversity of the Mongolian Gazelle Procapra guttorosa Pallas, 1777. RUSS J GENET+ 2005. [DOI: 10.1007/s11177-005-0206-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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27
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Kholodova MV, Sorokin PA, Lushchekina AA. Changes in the genetic diversity of European Saiga tatarica during a drastic population depression. DOKLADY BIOLOGICAL SCIENCES : PROCEEDINGS OF THE ACADEMY OF SCIENCES OF THE USSR, BIOLOGICAL SCIENCES SECTIONS 2005; 404:358-9. [PMID: 16405115 DOI: 10.1007/s10630-005-0135-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Affiliation(s)
- M V Kholodova
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
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Stephen CL, Devos JC, Lee TE, Bickham JW, Heffelfinger JR, Rhodes OE. POPULATION GENETIC ANALYSIS OF SONORAN PRONGHORN(ANTILOCAPRA AMERICANA SONORIENSIS). J Mammal 2005. [DOI: 10.1644/1545-1542(2005)086[0782:pgaosp]2.0.co;2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Lorenzen ED, Siegismund HR. No suggestion of hybridization between the vulnerable black-faced impala (Aepyceros melampus petersi) and the common impala (A. m. melampus) in Etosha National Park, Namibia. Mol Ecol 2004; 13:3007-19. [PMID: 15367116 DOI: 10.1111/j.1365-294x.2004.02308.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
There are two recognized subspecies of impala in sub-Saharan Africa: the common impala (Aepyceros melampus melampus) -- widespread in southern and east Africa -- and the vulnerable black-faced impala (A. m. petersi) -- found naturally in only a small enclave in southwest Africa. The Etosha National Park (NP) in Namibia harbours the largest and only protected-area population of black-faced impala, numbering some 1500 individuals. Due to translocations of the exotic common impala to commercial farms in Namibia during the past decades, the black-faced impala in Etosha is faced with the potentially serious threat of hybridization posed by secondary contact with the common impala inhabiting bordering farms. Using eight microsatellite DNA markers, we analysed 127 black-faced impala individuals from the five subpopulations in Etosha NP, to determine the degree, if any, of hybridization within the park. We found that (a) the black-faced impala were highly genetically differentiated from the common impala (pairwise theta-values ranged from 0.18 to 0.39 between subspecies; overall value = 0.27) and (b) black-faced samples showed high levels of genetic variability [average expected heterozygosity (H(E)) = 0.61 +/- 0.01 SE], although not as high as that observed in the common impala (average H(E) = 0.69 +/- 0.02 SE). (c) No hybridization between the subspecies in Etosha was suggested. A Bayesian Markov Chain Monte Carlo approach revealed clear distinction of individuals into groups according to their subspecies of origin, with a zero level of 'genetic admixture' among subspecies.
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Affiliation(s)
- Eline D Lorenzen
- Institute of Biology, Department of Evolutionary Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark.
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Hulva P, Horácek I, Strelkov PP, Benda P. Molecular architecture of Pipistrellus pipistrellus/Pipistrellus pygmaeus complex (Chiroptera: Vespertilionidae): further cryptic species and Mediterranean origin of the divergence. Mol Phylogenet Evol 2004; 32:1023-35. [PMID: 15288073 DOI: 10.1016/j.ympev.2004.04.007] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2003] [Revised: 04/06/2004] [Indexed: 11/26/2022]
Abstract
Previous genetic analyses have demonstrated that two phonic types of one of the most common European bats, the Common pipistrelle, belong to distinct species, although they are almost identical morphologically (45 kHz Pipistrellus pipistrellus and 55 kHz Pipistrellus pygmaeus). To reconstruct the history of the species complex and explain the codistribution of both forms in Europe and the Mediterranean, we performed phylogenetic analysis based on a 402-bp portion of the cytochrome b gene. Particular attention was paid to the eastern and southern parts of the range where no data were available. We found further distinctive allopatric haplotypes from Libya and Morocco. The difference of about 6-7% described in the Libyan population suggests the occurrence of a new species in the southern Mediterranean. The species status of Moroccan population is also discussed. The phylogeographic patterns obtained and analysis of fossil records support the hypothesis of expansion of both species into Europe from the Mediterranean region during the Holocene. The allopatric speciation model fits our data best. The paleobiographic scenario envisaged is corroborated also by molecular clock estimations and correlations with Late Neogene environmental changes in the Mediterranean region which ended with the Messinian salinity crisis.
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Affiliation(s)
- Pavel Hulva
- Department of Zoology, Charles University, Vinicná 7, 128 44 Prague 2, Czech Republic.
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Muwanika VB, Nyakaana S, Siegismund HR, Arctander P. Phylogeography and population structure of the common warthog (Phacochoerus africanus) inferred from variation in mitochondrial DNA sequences and microsatellite loci. Heredity (Edinb) 2004; 91:361-72. [PMID: 14512951 DOI: 10.1038/sj.hdy.6800341] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Global climate fluctuated considerably throughout the Pliocene and Pleistocene, influencing the evolutionary history of a wide range of species. Using both mitochondrial sequences and microsatellites, we have investigated the evolutionary consequences of such environmental fluctuation for the patterns of genetic variation in the common warthog, sampled from 24 localities in Africa. In the sample of 181 individuals, 70 mitochondrial DNA haplotypes were identified and an overall nucleotide diversity of 4.0% was observed. The haplotypes cluster in three well-differentiated clades (estimated net sequence divergence of 3.1-6.6%) corresponding to the geographical origins of individuals (i.e. eastern, western and southern African clades). At the microsatellite loci, high polymorphism was observed both in the number of alleles per locus (6-21), and in the gene diversity (in each population 0.59-0.80). Analysis of population differentiation indicates greater subdivision at the mitochondrial loci (FST=0.85) than at nuclear loci (FST=0.20), but both mitochondrial and nuclear loci support the existence of the three warthog lineages. We interpret our results in terms of the large-scale climatic fluctuations of the Pleistocene.
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Affiliation(s)
- V B Muwanika
- Institute of Environment and Natural Resources, Makerere University, PO Box 7298, Kampala, Uganda.
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32
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Okumura H. Complete sequence of mitochondrial DNA control region of the Japanese serow Capricornis crispus (Bovidae: Caprinae). MAMMAL STUDY 2004. [DOI: 10.3106/mammalstudy.29.137] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Abstract
Mitochondrial DNA (mtDNA) is a widely employed molecular tool in phylogeography, in the inference of human evolutionary history, in dating the domestication of livestock and in forensic science. In humans and other vertebrates the popularity of mtDNA can be partially attributed to an assumption of strict maternal inheritance, such that there is no recombination between mitochondrial lineages. The recent demonstration that linkage disequilibrium (LD) declines as a function of distance between polymorphic sites in hominid mitochondrial genomes has been interpreted as evidence of recombination between mtDNA haplotypes, and hence nonclonal inheritance. However, critics of mtDNA recombination have suggested that this association is an artefact of an inappropriate measure of LD or of sequencing error, and subsequent studies of other populations have failed to replicate the initial finding. Here we report the analysis of 16 ruminant populations and present evidence that LD significantly declines with distance in five of them. A meta-analysis of the data indicates a nonsignificant trend of LD declining with distance. Most of the earlier criticisms of patterns between LD and distance in hominid mtDNA are not applicable to this data set. Our results suggest that either ruminant mtDNA is not strictly clonal or that compensatory selection has influenced patterns of variation at closely linked sites within the mitochondrial control region. The potential impact of these processes should be considered when using mtDNA as a tool in vertebrate population genetic, phylogenetic and forensic studies.
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Affiliation(s)
- J Slate
- AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand.
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Vernesi C, Crestanello B, Pecchioli E, Tartari D, Caramelli D, Hauffe H, Bertorelle G. The genetic impact of demographic decline and reintroduction in the wild boar (Sus scrofa): a microsatellite analysis. Mol Ecol 2003; 12:585-95. [PMID: 12675815 DOI: 10.1046/j.1365-294x.2003.01763.x] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The reintroduction of wild boar from central Europe after World War II has contributed substantially to the range expansion of this species in Italy, where indiscriminate hunting in earlier times resulted in extreme demographic reduction. However, the genetic impact of such processes is not well-understood. In this study, 105 individuals from Italian and Hungarian wild boar populations were characterized for nine autosomal microsatellite loci. The Hungarian samples, and two central Italian samples from protected areas (parks) where reintroduction is not documented, were assumed to be representative of the genetic composition of the source and the target populations in the reintroduction process, respectively. Animals hunted in the wild in the Florence area of Tuscany (Italy) were then studied to identify the effects of reintroduction. The results we obtained can be summarized as follows: (i) none of the populations analysed shows genetic evidence of demographic decline; (ii) the three parental populations from Italy and Hungary are genetically distinct; however, the low level of divergence appears in conflict with the naming of the Italian and the European subspecies (Sus scrofa majori and Sus scrofa scrofa, respectively); in addition, the Italian groups appear to be as divergent from each other as they are from the Hungarian population; (iii) most of the individuals hunted near Florence are genetically intermediate between the parental groups, suggesting that hybridization has occurred in this area, the average introgression of Hungarian genotypes is 13%, but approximately 45% of the genetic pool of these individuals can not be directly attributed to any of the parental populations we analysed; (iv) analysis of microsatellite loci, though in a limited number, is an important tool for estimating the genetic effect of reintroduction in the wild boar, and therefore for the development of conservation and management strategies for this species.
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Affiliation(s)
- C Vernesi
- Department of Biology, Università di Ferrara, Italy
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36
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Li M, Wei F, Groves P, Feng Z, Hu J. Genetic structure and phylogeography of the takin (Budorcas taxicolor) as inferred from mitochondrial DNA sequences. CAN J ZOOL 2003. [DOI: 10.1139/z03-029] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
To investigate the genetic structure within the takin (Budorcas taxicolor), a little-studied and threatened species, portions of the mitochondrial DNA control region and cytochrome b gene were sequenced from 40 takins from three subspecies and 10 separate geographical locations in China. Overall variation among individuals was low. Both neighbor-joining and parsimony analyses did separate animals into three distinct clades reflecting the subspecific definitions, with only one locality grouping with a clade distinct from its purported subspecies. Animals within each clade were genetically similar to each other, which we hypothesize is due to the mobility of the animals leading to significant gene flow within each region until recent habitat alteration limited movements. We also suggest that genetic bottlenecks survived by the species since the end of the Pleistocene may have contributed to overall low levels of variability within the species.
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RYDER OA. Genetic studies in zoological parks and their application to conservation: past, present and future. ACTA ACUST UNITED AC 2003. [DOI: 10.1111/j.1748-1090.2003.tb02069.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Fok KW, Wade CM, Parkin DT. Inferring the phylogeny of disjunct populations of the azure-winged magpie Cyanopica cyanus from mitochondrial control region sequences. Proc Biol Sci 2002; 269:1671-9. [PMID: 12204127 PMCID: PMC1691084 DOI: 10.1098/rspb.2002.2057] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The azure-winged magpie (AWM), Cyanopica cyanus, is found in Asia and Iberia. This remarkable disjunct distribution has been variously explained by either the sixteenth-century introduction of birds into Iberia from the Far East, or by the loss of individuals from the central part of their range as a result of Pleistocene glaciations. We have used the mitochondrial control region to undertake a molecular phylogenetic analysis of the AWM, with sequences examined from individuals collected from across the current distribution range and incorporating representatives of all currently defined subspecies. The Western birds are genetically distinct from their Asian congeners and their divergence is basal in the phylogenetic tree. This indicates that the AWM is native to Iberia and not the result of a recent introduction from Asia. In Asia, two major mitochondrial DNA lineages were identified. These correspond to an Inland Asia group and a Pacific Seaboard group, and are separated topographically by the Da Hingan Ling mountains and the Yellow Sea. Molecular clock estimates suggest that these divergences are associated with Pleistocene glaciations. Furthermore, our data do not support the current classification of the AWM into 10 subspecies, as defined based on morphology and geographical distribution.
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Affiliation(s)
- Koon Wah Fok
- Institute of Genetics, Queen's Medical Centre, University of Nottingham, UK.
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39
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Nyakaana S, Arctander P, Siegismund HR. Population structure of the African savannah elephant inferred from mitochondrial control region sequences and nuclear microsatellite loci. Heredity (Edinb) 2002; 89:90-8. [PMID: 12136410 DOI: 10.1038/sj.hdy.6800110] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2001] [Accepted: 04/22/2002] [Indexed: 11/08/2022] Open
Abstract
Two hundred and thirty-six mitochondrial DNA nucleotide sequences were used in combination with polymorphism at four nuclear microsatellite loci to assess the amount and distribution of genetic variation within and between African savannah elephants. They were sampled from 11 localities in eastern, western and southern Africa. In the total sample, 43 haplotypes were identified and an overall nucleotide diversity of 2.0% was observed. High levels of polymorphism were also observed at the microsatellite loci both at the level of number of alleles and gene diversity. Nine to 14 alleles per locus across populations and 44 alleles in the total sample were found. The gene diversity ranged from 0.51 to 0.72 in the localities studied. An analysis of molecular variance showed significant genetic differentiation between populations within regions and also between regions. The extent of subdivision between populations at the mtDNA control region was approximately twice as high as shown by the microsatellite loci (mtDNA F(ST) = 0.59; microsatellite R(ST) = 0.31). We discuss our results in the light of Pleistocene refugia and attribute the observed pattern to population divergence in allopatry accompanied by a recent population admixture following a recent population expansion.
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Affiliation(s)
- S Nyakaana
- Institute of Environment and Natural Resources, Makerere University, P.O. Box 7298, Kampala, Uganda.
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40
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Pitra C, Hansen AJ, Lieckfeldt D, Arctander P. An exceptional case of historical outbreeding in African sable antelope populations. Mol Ecol 2002; 11:1197-208. [PMID: 12074727 DOI: 10.1046/j.1365-294x.2002.01516.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Empirical investigations of intraspecific outbreeding and subsequent introgressive hybridization in natural populations are rare, particularly among conspecific populations of large mammals. Using mitochondrial DNA data [partial control region (496 basepairs - bp) and cytochrome b gene (343 bp) sequences analysed from 95 individuals representing 17 sampling locations scattered through the African miombo (Brachystegia) woodland ecosystem] and phylogeographical statistical procedures (gene genealogy, nested cladistic and admixture proportion analyses), we (i) give a detailed dissection of the geographical genetic structure of Hippotragus niger; (ii) infer the processes and events potentially involved in the population history; and (iii) trace extensive introgressive hybridization in the species. The present-day sable antelope population shows a tripartite pattern of genetic subdivision representing West Tanzanian, Kenya/East Tanzanian and Southern Africa locations. Nested clade analysis revealed that past allopatric fragmentation, caused probably by habitat discontinuities associated with the East African Rift Valley system, together with intermediary episodic long-distance colonization and restricted, recurrent gene flow have played an predominant role in shaping the extent of maternal genetic diversity (10.4%) and population structure. An extensive (average rate of admixture = 20.0%), but geographically circumscribed and unidirectional hybridization event in the past was inferred, resulting in an extreme (the highest discovered so far in mammals) intraspecific difference of 18.2% among morphologically monotypic sable antelopes from West Tanzania. The results are used to provide an evolutionary framework within which taxonomic implications and conservation decisions can be evaluated.
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Affiliation(s)
- Christian Pitra
- Institute for Zoo- and Wildlife Research, PF 601103, D-10252 Berlin, Germany.
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41
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Romualdi C, Balding D, Nasidze IS, Risch G, Robichaux M, Sherry ST, Stoneking M, Batzer MA, Barbujani G. Patterns of human diversity, within and among continents, inferred from biallelic DNA polymorphisms. Genome Res 2002; 12:602-12. [PMID: 11932244 PMCID: PMC187513 DOI: 10.1101/gr.214902] [Citation(s) in RCA: 164] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Previous studies have reported that about 85% of human diversity at Short Tandem Repeat (STR) and Restriction Fragment Length Polymorphism (RFLP) autosomal loci is due to differences between individuals of the same population, whereas differences among continental groups account for only 10% of the overall genetic variance. These findings conflict with popular notions of distinct and relatively homogeneous human races, and may also call into question the apparent usefulness of ethnic classification in, for example, medical diagnostics. Here, we present new data on 21 Alu insertions in 32 populations. We analyze these data along with three other large, globally dispersed data sets consisting of apparently neutral biallelic nuclear markers, as well as with a beta-globin data set possibly subject to selection. We confirm the previous results for the autosomal data, and find a higher diversity among continents for Y-chromosome loci. We also extend the analyses to address two questions: (1) whether differences between continental groups, although small, are nevertheless large enough to confidently assign individuals to their continent on the basis of their genotypes; (2) whether the observed genotypes naturally cluster into continental or population groups when the sample source location is ignored. Using a range of statistical methods, we show that classification errors are at best around 30% for autosomal biallelic polymorphisms and 27% for the Y chromosome. Two data sets suggest the existence of three and four major groups of genotypes worldwide, respectively, and the two groupings are inconsistent. These results suggest that, at random biallelic loci, there is little evidence, if any, of a clear subdivision of humans into biologically defined groups.
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Affiliation(s)
- Chiara Romualdi
- Department of Biology, University of Ferrara, via L. Borsari 46, I-44100 Ferrara, Italy
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Liautard C, Keller L. Restricted effective queen dispersal at a microgeographic scale in polygynous populations of the ant Formica exsecta. Evolution 2001; 55:2484-92. [PMID: 11831664 DOI: 10.1111/j.0014-3820.2001.tb00763.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Ecological constraints on effective dispersal have been suggested to be a key factor influencing social evolution in animal societies as well as the shift from single queen colonies (monogyny) to multiple queen colonies (polygyny) in ants. However, little is known about the effective dispersal patterns of ant queens. Here we investigate the microgeographic genetic structure of mitochondrial haplotypes in polygynous populations of the ant Formica exsecta, both between pastures and among nests within pastures. An analysis of molecular variance revealed a very high genetic differentiation (phiST = 0.72) between pastures, indicating that queens rarely disperse successfully between pastures, despite the fact that pastures were sometimes as close as 1 km. Most of the pastures contained only a single haplotype, and haplotypes were frequently distinct between nearby pastures and even between groups of nests within the same pasture. In the three pastures that contained several haplotypes, haplotypes were not randomly distributed, the genetic differentiation between nests being phiST = 0.17, 0.52, and 0.69. This indicates that most queens are recruited within their parental colonies. However, a large proportion of nests contained more than one haplotype, demonstrating that colonies will sometimes accept foreign queens. The relatedness of mitochondrial genes among nestmates varied between 0.62 and 0.75 when relatedness was measured within each pasture and ranged between 0.72 and 1.0 when relatedness was assessed with all pastures as a reference population. Neighboring nests were more genetically similar than distant ones, and there was significant isolation by distance. This pattern may be due to new nests being formed by budding or by limited effective queen dispersal, probably on foot between neighboring nests. These results show that effective queen dispersal is extremely restricted even at a small geographical scale, a pattern consistent with the idea that ecological constraints are an important selective force leading to the evolution and maintenance of polygyny.
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Affiliation(s)
- C Liautard
- Institute of Ecology, Bâtiment de Biologie, University of Lausanne, Switzerland.
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43
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Fleischer RC, Perry EA, Muralidharan K, Stevens EE, Wemmer CM. Phylogeography of the asian elephant (Elephas maximus) based on mitochondrial DNA. Evolution 2001; 55:1882-92. [PMID: 11681743 DOI: 10.1111/j.0014-3820.2001.tb00837.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Populations of the Asian elephant (Elephas maximus) have been reduced in size and become highly fragmented during the past 3,000 to 4,000 years. Historical records reveal elephant dispersal by humans via trade and war. How have these anthropogenic impacts affected genetic variation and structure of Asian elephant populations? We sequenced mitochondrial DNA (mtDNA) to assay genetic variation and phylogeography across much of the Asian elephant's range. Initially we compare cytochrome b sequences (cyt b) between nine Asian and five African elephants and use the fossil-based age of their separation (approximately 5 million years ago) to obtain a rate of about 0.013 (95% CI = 0.011-0.018) corrected sequence divergence per million years. We also assess variation in part of the mtDNA control region (CR) and adjacent tRNA genes in 57 Asian elephants from seven countries (Sri Lanka, India, Nepal, Myanmar, Thailand, Malaysia, and Indonesia). Asian elephants have typical levels of mtDNA variation, and coalescence analyses suggest their populations were growing in the late Pleistocene. Reconstructed phylogenies reveal two major clades (A and B) differing on average by HKY85/gamma-corrected distances of 0.020 for cyt b and 0.050 for the CR segment (corresponding to a coalescence time based on our cyt b rate of approximately 1.2 million years). Individuals of both major clades exist in all locations but Indonesia and Malaysia. Most elephants from Malaysia and all from Indonesia are in well-supported, basal clades within clade A. thus supporting their status as evolutionarily significant units (ESUs). The proportion of clade A individuals decreases to the north, which could result from retention and subsequent loss of ancient lineages in long-term stable populations or, perhaps more likely, via recent mixing of two expanding populations that were isolated in the mid-Pleistocene. The distribution of clade A individuals appears to have been impacted by human trade in elephants among Myanmar, Sri Lanka, and India, and the subspecies and ESU statuses of Sri Lankan elephants are not supported by molecular data.
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Affiliation(s)
- R C Fleischer
- Molecular Genetics Laboratory, Conservation and Research Center, Smithsonian Institution, Washington, DC 20008, USA.
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Abstract
The phylogeography of the bush habituated African bovid species impala (Aepyceros melampus) and greater kudu (Tragelaphus strepsiceros) is investigated using mitochondrial DNA (mtDNA) markers. Combined analysis of individual lineages, relationships and population genetics suggest a colonization process from Southern Africa toward Eastern regions in the greater kudu. Results are less clear for the impala, although remaining consistent with a similar pattern of historical dispersion. The study reveals a similar pattern, that is a marked divergence of lineages from South-western Africa relative to other regions. This pattern is opposed to previously published findings in other African bovid species. In the impala, the genetically isolated region is consistent with morphology because it is recognized as the subspecies A. m. petersi, the black-faced impala. In contrast, the similar split of South-western mitochondrial lineages was not expected in the greater kudu on the basis of morphology. Both species show a significant population genetic differentiation. Beyond their phylogeographical value, our results should raise conservation concerns about South-western populations of both species. The black-faced impala is categorized as vulnerable and our data show indications of hybridization with common impala A. m. melampus. The previously unrecognized genetic status of the South-western kudus could also imply conservation regulations.
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Affiliation(s)
- L G Nersting
- Institute of Zoology, Department of Evolutionary Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
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45
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Liautard C, Keller L. RESTRICTED EFFECTIVE QUEEN DISPERSAL AT A MICROGEOGRAPHIC SCALE IN POLYGYNOUS POPULATIONS OF THE ANT FORMICA EXSECTA. Evolution 2001. [DOI: 10.1554/0014-3820(2001)055[2484:reqdaa]2.0.co;2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Fleischer RC, Perry EA, Muralidharan K, Stevens EE, Wemmer CM. PHYLOGEOGRAPHY OF THE ASIAN ELEPHANT (ELEPHAS MAXIMUS) BASED ON MITOCHONDRIAL DNA. Evolution 2001. [DOI: 10.1554/0014-3820(2001)055[1882:potaee]2.0.co;2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Birungi J, Arctander P. Large sequence divergence of mitochondrial DNA genotypes of the control region within populations of the african antelope, kob (Kobus kob). Mol Ecol 2000; 9:1997-2008. [PMID: 11123612 DOI: 10.1046/j.1365-294x.2000.01107.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The genetic differentiation among kob populations (Kobus kob) representing two recognized subspecies was examined using mitochondrial control region sequences. Two distinct lineages (estimated sequence divergence of 9.8%) exhibited different geographical distributions and do not coincide with previously recognized ranges of subspecies. The presence of the two lineages was further supported with sequences of mitochondrial cytochrome b gene. One lineage was predominant in the west and southern ranges of the populations studied and the other was commonly found in a more northern distribution (Murchison populations) in Uganda. Murchison and the geographically intermediate Toro populations (Uganda) represented the area of overlap. The existence of the two lineages in the area of overlap is hypothesized to have resulted from a range expansion and secondary contact of the two lineages of kob that evolved in allopatry. The existence of the kob during the Pleistocene offers a plausible explanation for the observed biogeographic pattern. Our mitochondrial data reveal two examples of discordance between a gene tree and presumed species tree as: (i) the two lineages co-occur in the kob subspecies, Kobus kob thomasi (Uganda kob); and (ii) the puku, which was included in the analysis because of its controversial taxonomic status (currently recognized as a distinct species from the kob), is paraphyletic with respect to the kob. Significant degrees of heterogeneity were detected between populations. Relatively high genetic variation was observed in the populations, however, the inclusion of distinct lineages influences the population structure and nucleotide diversity of the kob populations.
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Affiliation(s)
- J Birungi
- Zoological Institute, Department of Population Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen O, Denmark.
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Van Hooft WF, Groen AF, Prins HH. Microsatellite analysis of genetic diversity in African buffalo (Syncerus caffer) populations throughout Africa. Mol Ecol 2000; 9:2017-25. [PMID: 11123614 DOI: 10.1046/j.1365-294x.2000.01101.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Genetic diversity in nine African buffalo (Syncerus caffer) populations throughout Africa was analysed with 14 microsatellites to study the effects of rinderpest epidemics and habitat fragmentation during the 20th century. A gradient of declining expected heterozygosity was observed among populations in Save Valley Conservancy (Zimbabwe), and northern and southern Kruger National Park (South Africa). This was explained by a high mortality in northern Kruger National Park during the rinderpest pandemic at the end of the 19th century followed by recolonization from neighbouring populations, resulting in intermediate heterozygosity levels in northern Kruger National Park. In other populations expected heterozygosity was very high, indicating that rinderpest and recent habitat fragmentation had a limited effect on genetic diversity. From expected heterozygosity, estimates of long-term effective population size were derived. Migration rates among populations in eastern and southern Africa were very high, as shown by a weak isolation by distance and significant correlation in allele frequencies between populations. However, there were indications that dry habitats could limit migration. Genetic distances within buffalo in central Africa were relatively large, supporting their status as distinct subspecies. Finally, it was observed that the higher polymorphic microsatellites were less sensitive at detecting isolation by distance and differences in Ne, which may be a result of the high mutation pressure at these loci.
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Affiliation(s)
- W F Van Hooft
- Wageningen University, Department of Environmental Sciences, Tropical Nature Conservation and Vertebrate Ecology Group, Bornsesteeg 69, 6708 PD Wageningen, The Netherlands.
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Abstract
We investigate the shape of a phylogenetic tree reconstructed from sequences evolving under the coalescent with recombination. The motivation is that evolutionary inferences are often made from phylogenetic trees reconstructed from population data even though recombination may well occur (mtDNA or viral sequences) or does occur (nuclear sequences). We investigate the size and direction of biases when a single tree is reconstructed ignoring recombination. Standard software (PHYLIP) was used to construct the best phylogenetic tree from sequences simulated under the coalescent with recombination. With recombination present, the length of terminal branches and the total branch length are larger, and the time to the most recent common ancestor smaller, than for a tree reconstructed from sequences evolving with no recombination. The effects are pronounced even for small levels of recombination that may not be immediately detectable in a data set. The phylogenies when recombination is present superficially resemble phylogenies for sequences from an exponentially growing population. However, exponential growth has a different effect on statistics such as Tajima's D. Furthermore, ignoring recombination leads to a large overestimation of the substitution rate heterogeneity and the loss of the molecular clock. These results are discussed in relation to viral and mtDNA data sets.
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Affiliation(s)
- M H Schierup
- Department of Ecology and Genetics, University of Aarhus, DK-8000 Aarhus C., Denmark.
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50
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Nagata J, Masuda R, Tamate HB, Hamasaki SI, Ochiai K, Asada M, Tatsuzawa S, Suda K, Tado H, Yoshida MC. Two genetically distinct lineages of the sika deer, Cervus nippon, in Japanese islands: comparison of mitochondrial D-loop region sequences. Mol Phylogenet Evol 1999; 13:511-9. [PMID: 10620409 DOI: 10.1006/mpev.1999.0668] [Citation(s) in RCA: 113] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
To investigate genetic diversity among populations of the sika deer, Cervus nippon, nucleotide sequences (705-824 bases) of the mitochondrial D-loop regions were determined in animals from 13 localities in the Japanese islands. Phylogenetic trees constructed by the sequences indicated that the Japanese sika deer is separated into two distinct lineages: the northern Japan group (the Hokkaido island and most of the Honshu mainland) and the southern Japan group (a part of the southern Honshu mainland, the Kyushu island, and small islands around the Kyushu island). All sika deer examined in this study shared four to seven units of repetitive sequences (37 to 40 bases each) within the D-loop sequences. The number of tandem repeats was different among the populations, and it was specific to each population. Six or seven repeats occurred in populations of the northern Japan group, while four or five repeats occurred in populations of the southern Japan group. Each repeat unit included several nucleotide substitutions, compared with others, and 26 types were identified from 31 animals. Sequences of the first, second, and third units in arrays were clearly different between the northern and the southern groups. Based on these D-loop data, colonization and separation of the sika deer populations in the Japanese islands were estimated to have occurred less than 0.5 million years before present. Our results provide an invaluable insight into better understanding the evolutionary history, phylogeny, taxonomy, and population genetics of the sika deer.
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Affiliation(s)
- J Nagata
- Wildlife Management Laboratory, Forestry and Forest Products Research Institute, Ibaraki, 305-8687, Japan
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