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Escobedo-Morales LA, Castañeda-Rico S, Mandujano S, León-Paniagua L, Maldonado JE. First description of the mitochondrial genomes of the Central American brocket deer Mazama temama (Kerr, 1792) and the Yucatán Peninsula brocket deer Odocoileus pandora Merriam, 1901. Mol Biol Rep 2023; 50:4851-4863. [PMID: 37039999 DOI: 10.1007/s11033-023-08407-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 03/24/2023] [Indexed: 04/12/2023]
Abstract
BACKGROUND The Central American (Mazama temama) and the Yucatán Peninsula brocket deer (Odocoileus pandora) are deer species with cryptic habits, and little is known about their biology. Odocoileus pandora is listed as Vulnerable on the 2015 IUCN Red List of Threatened Species, while M. temama is considered Data Deficient; however, it currently faces a decreasing population trend. METHODS AND RESULTS We assembled the complete mitochondrial genome for two M. temama specimens and one complete and one partial for O. pandora from Illumina 150 bp paired-end reads. The mitogenomes of M. temama and O. pandora have a length of 16,479-16,480 and 16,419 bp, respectively, AT-biased; they consist of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and one non-coding control region, most of them follow a transcription direction in the heavy strand of the molecule. The mitochondrial genome of O. pandora shows some particularities compared to other deer species, like a shorter control region of 987-990 bp and a cytochrome b gene with a length of 1,143 bp. Our phylogenetic analyses confirm the close affinity of M. temama to South American M. americana and the nested position of the genus Odocoileus, including O. pandora, into the genus Mazama. CONCLUSIONS Here, we described for the first time the complete mitochondrial genome for these two species. While our study provides additional information about the taxonomic status of the northern neotropical brocket deer, further research is needed to solve the complicated taxonomy of neotropical deer.
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Affiliation(s)
- Luis A Escobedo-Morales
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Edificio D, Primer piso, Circuito de Posgrados, AP 70-153, Ciudad Universitaria, Mexico City, 04510, Mexico.
- Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, 3001 Connecticut Ave., NW, Washington, DC, 20008, USA.
| | - Susette Castañeda-Rico
- Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, 3001 Connecticut Ave., NW, Washington, DC, 20008, USA
- Smithsonian-Mason School of Conservation, 1500 Remount Road, Front Royal, VA, 22630, USA
- Department of Biology, George Mason University, 4400 University Drive, Fairfax, VA, 22030, USA
| | - Salvador Mandujano
- Red de Biología y Conservación de Vertebrados, Instituto de Ecología, A.C., Carretera antigua a Coatepec 351, Xalapa, Veracruz, 91070, Mexico
| | - Livia León-Paniagua
- Museo de Zoología Alfonso L. Herrera, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Mexico City, 04510, Mexico
| | - Jesús E Maldonado
- Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, 3001 Connecticut Ave., NW, Washington, DC, 20008, USA
- Smithsonian-Mason School of Conservation, 1500 Remount Road, Front Royal, VA, 22630, USA
- Department of Biology, George Mason University, 4400 University Drive, Fairfax, VA, 22030, USA
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Molecular Evidence Reveals the Sympatric Distribution of Cervus nippon yakushimae and Cervus nippon taiouanus on Jeju Island, South Korea. Animals (Basel) 2022; 12:ani12080998. [PMID: 35454244 PMCID: PMC9029077 DOI: 10.3390/ani12080998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/09/2022] [Accepted: 04/10/2022] [Indexed: 11/17/2022] Open
Abstract
Non-native species threaten native ecosystems and species, particularly on islands where rates of endemism and vulnerability to threats are high. Understanding species invasion will aid in providing insights into ecological and evolutionary processes. To identify the non-native sika deer (Cervus nippon) population in Jeju, South Korea, and their phylogenetic affinities, we collected tissue samples from roadkill and the World Natural Heritage Headquarters in Jeju. Mitochondrial DNA cytochrome B (CytB) gene sequences were analyzed to determine two distinct CytB haplotypes. Phylogenetic analysis using maximum likelihood tree revealed two haplotypes of CytB clustered into two different groups representing two subspecies: C. n. yakushimae, native to Japan, and C. n. taiouanus, native to Taiwan. The tentative divergence time between the two subspecies was estimated at 1.81 million years. Our study confirmed that the two subspecies of sika deer are sympatric in the natural ecosystem of Jeju Island. This study provides valuable information to help government and conservation agencies understand alien species and determine control policies for conserving native biodiversity in South Korea.
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Zhao W, Liu D, Jia Q, Wu X, Zhang H. Characterization of the complete mitochondrial genome of Myrmuslateralis (Heteroptera, Rhopalidae) and its implication for phylogenetic analyses. Zookeys 2021; 1070:13-30. [PMID: 34819768 PMCID: PMC8599289 DOI: 10.3897/zookeys.1070.72742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/25/2021] [Indexed: 11/23/2022] Open
Abstract
Mitochondrial genomes (mitogenomes) are widely used in research studies on phylogenetic relationships and evolutionary history. Here, we sequenced and analyzed the mitogenome of the scentless plant bug Myrmuslateralis Hsiao, 1964 (Heteroptera, Rhopalidae). The complete 17,309 bp genome encoded 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a control region. The mitogenome revealed a high A+T content (75.8%), a positive AT-skew (0.092), and a negative GC-skew (-0.165). All 13 PCGs were found to start with ATN codons, except for cox1, in which TTG was the start codon. The Ka/Ks ratios of 13 PCGs were all lower than 1, indicating that purifying selection evolved in these genes. All tRNAs could be folded into the typical cloverleaf secondary structure, except for trnS1 and trnV, which lack dihydrouridine arms. Phylogenetic trees were constructed and analyzed based on the PCG+rRNA from 38 mitogenomes, using maximum likelihood and Bayesian inference methods, showed that M.lateralis and Chorosomamacilentum Stål, 1858 grouped together in the tribe Chorosomatini. In addition, Coreoidea and Pyrrhocoroidea were sister groups among the superfamilies of Trichophora, and Rhopalidae was a sister group to Alydidae + Coreidae.
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Affiliation(s)
- Wanqing Zhao
- Department of Biology, Xinzhou Teachers University, Xinzhou 034000, Shanxi, ChinaXinzhou Teachers UniversityXinzhouChina
| | - Dajun Liu
- Department of Biology, Xinzhou Teachers University, Xinzhou 034000, Shanxi, ChinaXinzhou Teachers UniversityXinzhouChina
| | - Qian Jia
- Department of Biology, Xinzhou Teachers University, Xinzhou 034000, Shanxi, ChinaXinzhou Teachers UniversityXinzhouChina
| | - Xin Wu
- Department of Biology, Xinzhou Teachers University, Xinzhou 034000, Shanxi, ChinaXinzhou Teachers UniversityXinzhouChina
| | - Hufang Zhang
- Department of Biology, Xinzhou Teachers University, Xinzhou 034000, Shanxi, ChinaXinzhou Teachers UniversityXinzhouChina
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Fan H, Wang T, Li Y, Liu H, Dong Y, Zhang R, Wang H, Shang L, Xing X. Development and validation of a 1 K sika deer (Cervus nippon) SNP Chip. BMC Genom Data 2021; 22:35. [PMID: 34535071 PMCID: PMC8447661 DOI: 10.1186/s12863-021-00994-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 09/09/2021] [Indexed: 11/10/2022] Open
Abstract
Background China is the birthplace of the deer family and the country with the most abundant deer resources. However, at present, China’s deer industry faces the problem that pure sika deer and hybrid deer cannot be easily distinguished. Therefore, the development of a SNP identification chip is urgently required. Results In this study, 250 sika deer, 206 red deer, 23 first-generation hybrid deer (F1), 20 s-generation hybrid deer (F2), and 20 third-generation hybrid deer (F3) were resequenced. Using the chromosome-level sika deer genome as the reference sequence, mutation detection was performed on all individuals, and a total of 130,306,923 SNP loci were generated. After quality control filtering was performed, the remaining 31,140,900 loci were confirmed. From molecular-level and morphological analyses, the sika deer reference population and the red deer reference population were established. The Fst values of all SNPs in the two reference populations were calculated. According to customized algorithms and strict screening principles, 1000 red deer-specific SNP sites were finally selected for chip design, and 63 hybrid individuals were determined to contain red deer-specific SNP loci. The results showed that the gene content of red deer gradually decreased in subsequent hybrid generations, and this decrease roughly conformed to the law of statistical genetics. Reaction probes were designed according to the screening sites. All candidate sites met the requirements of the Illumina chip scoring system. The average score was 0.99, and the MAF was in the range of 0.3277 to 0.3621. Furthermore, 266 deer (125 sika deer, 39 red deer, 56 F1, 29 F2,17 F3) were randomly selected for 1 K SNP chip verification. The results showed that among the 1000 SNP sites, 995 probes were synthesized, 4 of which could not be typed, while 973 loci were polymorphic. PCA, random forest and ADMIXTURE results showed that the 1 K sika deer SNP chip was able to clearly distinguish sika deer, red deer, and hybrid deer and that this 1 K SNP chip technology may provide technical support for the protection and utilization of pure sika deer species resources. Conclusion We successfully developed a low-density identification chip that can quickly and accurately distinguish sika deer from their hybrid offspring, thereby providing technical support for the protection and utilization of pure sika deer germplasm resources. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-021-00994-z.
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Affiliation(s)
- Huanhuan Fan
- Key Laboratory of Molecular Biology of Special Economic Animals, Institute of Special Products, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Tianjiao Wang
- Key Laboratory of Molecular Biology of Special Economic Animals, Institute of Special Products, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Yang Li
- Key Laboratory of Molecular Biology of Special Economic Animals, Institute of Special Products, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Huitao Liu
- Key Laboratory of Molecular Biology of Special Economic Animals, Institute of Special Products, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Yimeng Dong
- Key Laboratory of Molecular Biology of Special Economic Animals, Institute of Special Products, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Ranran Zhang
- Key Laboratory of Molecular Biology of Special Economic Animals, Institute of Special Products, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Hongliang Wang
- Key Laboratory of Molecular Biology of Special Economic Animals, Institute of Special Products, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Liyuan Shang
- Jilin Animal Husbandry and Veterinary Research Institute Changchun, Changchun, 130112, China
| | - Xiumei Xing
- Key Laboratory of Molecular Biology of Special Economic Animals, Institute of Special Products, Chinese Academy of Agricultural Sciences, Changchun, 130112, China.
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Variation of craniometrical characters in an artificial population of Cervus nippon from Askania-Nova, Ukraine. THERIOLOGIA UKRAINICA 2020. [DOI: 10.15407/tu1906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Craniometrical characters of adult sika deer from an artificial population, which was created by import of animals from a natural population from the Primorsky Krai of Russia, are analysed. It was revealed that the mean value of variation (by 11 characters) of skulls of sika deer is 3.56 ± 0.35 in males and 3.89 ± 0.33 in females. Males are significantly larger than females (p < 0.001) by all characters. The study of craniometrical characters of the sika deer using principal component analysis showed that 93.3 % of total variance is described by the first principal component (PC1). The highest, though quite equal, factor loadings on PC1 have characters of length (full length, condylobasal length, basic length). Study results suggest that sex-related differences in C. nippon by craniometrical characters are expressed by general linear dimensions and by proportions of the skull. The correlation matrix of craniometrical characters of adult sika deer from the Askanian subpopulation shows a relatively weak dependence between different parameters. It was established that the coefficient of correlation in most pairs of characters varies from 0.02 to 0.96 in males and from 0.01 to 0.97 in females. The highest coefficients of correlation in both males and females (r = 0.96 and r = 0.97, respectively) are revealed between the condylobasal and basal lengths of the skull. Correlations between cranial indices are significantly lower compared to craniometrical characters. The highest coefficient of correlation in both males and females has the variation of the index of mastoid width in relation to the relative largest skull width (r = 0.72). Skulls of sika deer from the Askanian subpopulation (of both males and females) have significantly larger dimensions compared to those in animals from the natural population from the Primorsky Krai.
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McFarlane SE, Hunter DC, Senn HV, Smith SL, Holland R, Huisman J, Pemberton JM. Increased genetic marker density reveals high levels of admixture between red deer and introduced Japanese sika in Kintyre, Scotland. Evol Appl 2020; 13:432-441. [PMID: 31993087 PMCID: PMC6976951 DOI: 10.1111/eva.12880] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 09/01/2019] [Accepted: 10/10/2019] [Indexed: 12/14/2022] Open
Abstract
Hybridization is a natural process at species range boundaries, but increasing numbers of species are hybridizing due to direct or indirect human activities. In such cases of anthropogenic hybridization, subsequent introgression can threaten the survival of native species. To date, many such systems have been studied with too few genetic markers to assess the level of threat resulting from advanced backcrossing. Here, we use 44,999 single nucleotide polymorphisms (SNPs) and the ADMIXTURE program to study two areas of Scotland where a panel of 22 diagnostic microsatellites previously identified introgression between native red deer (Cervus elaphus) and introduced Japanese sika (Cervus nippon). In Kintyre, we reclassify 26% of deer from the pure species categories to the hybrid category whereas in the NW Highlands we only reclassify 2%. As expected, the reclassified individuals are mostly advanced backcrosses. We also investigate the ability of marker panels selected on different posterior allele frequency criteria to find hybrids assigned by the full marker set and show that in our data, ancestry informative markers (i.e. those that are highly differentiated between the species, but not fixed) are better than diagnostic markers (those markers that are fixed between the species) because they are more evenly distributed in the genome. Diagnostic loci are concentrated on the X chromosome to the detriment of autosomal coverage.
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Affiliation(s)
- S. Eryn McFarlane
- Institute of Evolutionary BiologySchool of Biological ScienceUniversity of EdinburghEdinburghUK
- Department of BiologyLund UniversityLundSweden
| | - Darren C. Hunter
- Institute of Evolutionary BiologySchool of Biological ScienceUniversity of EdinburghEdinburghUK
- Department of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
| | - Helen V. Senn
- Institute of Evolutionary BiologySchool of Biological ScienceUniversity of EdinburghEdinburghUK
- WildGenes LaboratoryRoyal Zoological Society of ScotlandEdinburghUK
| | - Stephanie L. Smith
- Institute of Evolutionary BiologySchool of Biological ScienceUniversity of EdinburghEdinburghUK
- The Royal (Dick) School of Veterinary StudiesUniversity of EdinburghEaster Bush CampusMidlothian, EdinburghUK
| | - Rebecca Holland
- Institute of Evolutionary BiologySchool of Biological ScienceUniversity of EdinburghEdinburghUK
| | - Jisca Huisman
- Institute of Evolutionary BiologySchool of Biological ScienceUniversity of EdinburghEdinburghUK
| | - Josephine M. Pemberton
- Institute of Evolutionary BiologySchool of Biological ScienceUniversity of EdinburghEdinburghUK
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7
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Jebb D, Foley NM, Whelan CV, Touzalin F, Puechmaille SJ, Teeling EC. Population level mitogenomics of long-lived bats reveals dynamic heteroplasmy and challenges the Free Radical Theory of Ageing. Sci Rep 2018; 8:13634. [PMID: 30206380 PMCID: PMC6134106 DOI: 10.1038/s41598-018-31093-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 07/26/2018] [Indexed: 12/30/2022] Open
Abstract
Bats are the only mammals capable of true, powered flight, which drives an extremely high metabolic rate. The "Free Radical Theory of Ageing" (FTRA) posits that a high metabolic rate causes mitochondrial heteroplasmy and the progressive ageing phenotype. Contrary to this, bats are the longest-lived order of mammals given their small size and high metabolic rate. To investigate if bats exhibit increased mitochondrial heteroplasmy with age, we performed targeted, deep sequencing of mitogenomes and measured point heteroplasmy in wild, long lived Myotis myotis. Blood was sampled from 195 individuals, aged between <1 and at 6+ years old, and whole mitochondria deep-sequenced, with a subset sampled over multiple years. The majority of heteroplasmies were at a low frequency and were transitions. Oxidative mutations were present in only a small number of individuals, suggesting local oxidative stress events. Cohort data showed no significant increase in heteroplasmy with age, while longitudinal data from recaptured individuals showed heteroplasmy is dynamic, and does not increase uniformly over time. We show that bats do not suffer from the predicted, inevitable increase in heteroplasmy as posited by the FRTA, instead heteroplasmy was found to be dynamic, questioning its presumed role as a primary driver of ageing.
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Affiliation(s)
- David Jebb
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Nicole M Foley
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Conor V Whelan
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Frédéric Touzalin
- Laboratoire Evolution et Diversité Biologique, Université Toulouse 3, Paul Sabatier, 31062, Toulouse Cedex 09, France
| | - Sebastien J Puechmaille
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
- Applied Zoology and Conservation, Zoological Institute, Greifswald University, Greifswald, Germany
| | - Emma C Teeling
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland.
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Smith SL, Senn HV, Pérez‐Espona S, Wyman MT, Heap E, Pemberton JM. Introgression of exotic Cervus ( nippon and canadensis) into red deer ( Cervus elaphus) populations in Scotland and the English Lake District. Ecol Evol 2018; 8:2122-2134. [PMID: 29468030 PMCID: PMC5817139 DOI: 10.1002/ece3.3767] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 11/04/2017] [Accepted: 11/14/2017] [Indexed: 11/10/2022] Open
Abstract
Since the mid-19th century, multiple introductions of Japanese sika deer (Cervus nippon nippon) and North American wapiti (C. canadensis) have taken place in the British Isles. While wapiti have generally been unsuccessful, sika have been very successful, especially in Scotland where they now overlap at least 40% of the range of native red deer (C. elaphus). Hybridization between these two species and red deer has been demonstrated in captivity and in the wild. Using a panel of 22 microsatellite loci that are highly diagnostic between red deer and sika, and moderately diagnostic between red deer and wapiti, we investigated the extent of introgression between these species in 2,943 deer sampled from around Scotland and from the English Lake District using the Bayesian clustering software STRUCTURE. We also used a diagnostic mitochondrial marker for red deer and sika. Our survey extends previous studies indicating little introgression of wapiti nuclear alleles into red deer, in particular in Northern Scotland, Kintyre, and the Lake District. We found a new area of extensive sika introgression in South Kintyre. In the North Highlands, we show for the first time geographically scattered evidence of past hybridization followed by extensive backcrossing, including one red-like individual with sika introgression, two sika-like individuals with red deer introgression, and six individuals that were apparently pure sika at the nuclear markers assessed but which carried red deer mitochondria. However, there has not been a collapse of assortative mating in this region. Similarly, in the English Lake District red deer, we found only traces of past sika introgression. No sika alleles were detected in the Central Highlands or the Hebridean red deer refugia. We make suggestions for management to prevent further spread of sika alleles into red deer and vice versa.
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Affiliation(s)
- Stephanie L. Smith
- Institute of Evolutionary BiologySchool of Biological SciencesUniversity of EdinburghEdinburghUK
| | - Helen V. Senn
- WildGenes LaboratoryRoyal Zoological Society of ScotlandEdinburghUK
| | | | - Megan T. Wyman
- Mammal Vocal Communication and Cognition ResearchSchool of PsychologyUniversity of SussexFalmerUK
| | - Elizabeth Heap
- Institute of Evolutionary BiologySchool of Biological SciencesUniversity of EdinburghEdinburghUK
| | - Josephine M. Pemberton
- Institute of Evolutionary BiologySchool of Biological SciencesUniversity of EdinburghEdinburghUK
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Hayashi K, Tang W, Ohari Y, Ohtori M, Mohanta UK, Matsuo K, Sato H, Itagaki T. Phylogenetic relationships between Dicrocoelium chinensis populations in Japan and China based on mitochondrial nad1 gene sequences. Parasitol Res 2017; 116:2605-2609. [PMID: 28735469 DOI: 10.1007/s00436-017-5557-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 07/07/2017] [Indexed: 11/25/2022]
Abstract
We carried out phylogenetic analyses of the relationships between Dicrocoelium chinensis populations in Japan and China using molecular markers. One hundred nine lancet flukes collected from Japan and China were identified as D. chinensis based on their testis orientation and the nucleotide sequences of their ribosomal ITS2. These flukes were analyzed phylogenetically using mitochondrial nad1 gene sequences. An analysis of molecular variance found that the percentage of variation between the countries was extremely high, indicating that the D. chinensis populations in Japan and China are differentiated genetically. D. chinensis mainly parasitizes wild sika deer, which is thought to originate in northeast Asia and to have colonized into Japan from the Eurasia continent in the Pleistocene glaciations. In addition, phylogenic analyses indicated that Japanese sika deer is genetically differentiated from Chinese population; therefore, we hypothesize that D. chinensis might have been introduced into Japan along with the migration of infected wild ruminants in the Pleistocene, and then the population became differentiated from the Chinese population. This study provides the nucleotide sequences of the nad1 gene of D. chinensis in Japan for the first time and shows that these sequences are useful for elucidating the phylogenetic relationships of the Dicrocoelium species prevalent in Asia.
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Affiliation(s)
- Kei Hayashi
- Laboratory of Veterinary Parasitology, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, 020-8550, Japan
- Department of Pathogenic Veterinary Science, United Graduate School of Veterinary Science, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
| | - WenQiang Tang
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, 56 Duodi Road, Lhasa, Tibet, 850009, China
| | - Yuma Ohari
- Laboratory of Veterinary Parasitology, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, 020-8550, Japan
- Department of Pathogenic Veterinary Science, United Graduate School of Veterinary Science, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
| | - Maiko Ohtori
- Laboratory of Veterinary Parasitology, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, 020-8550, Japan
| | - Uday Kumar Mohanta
- Laboratory of Veterinary Parasitology, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, 020-8550, Japan
- Department of Pathogenic Veterinary Science, United Graduate School of Veterinary Science, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
| | - Kayoko Matsuo
- Hida Region Livestock Hygiene Service Center, 7-468 Kamiokamotomachi, Takayama, 506-8688, Japan
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
| | - Hiroshi Sato
- Laboratory of Parasitology, United Graduated School of Veterinary Science, Yamaguchi University, 1677-1 Yoshida, Yamaguchi, 753-8515, Japan
| | - Tadashi Itagaki
- Laboratory of Veterinary Parasitology, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, 020-8550, Japan.
- Department of Pathogenic Veterinary Science, United Graduate School of Veterinary Science, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan.
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Krojerová-Prokešová J, Barančeková M, Kawata Y, Oshida T, Igota H, Koubek P. Genetic differentiation between introduced Central European sika and source populations in Japan: effects of isolation and demographic events. Biol Invasions 2017. [DOI: 10.1007/s10530-017-1424-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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11
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A complete history of the establishment of Japanese sika deer on the Delmarva Peninsula: 100 years post-introduction. Biol Invasions 2017. [DOI: 10.1007/s10530-017-1387-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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12
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Mitochondrial and Nuclear DNA Based Genetic Assessment Indicated Distinct Variation and Low Genetic Exchange Among the Three Subspecies of Swamp Deer (Rucervus duvaucelii). Evol Biol 2016. [DOI: 10.1007/s11692-016-9387-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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13
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Ai J, Wang X, Gao L, Xia W, Li M, Yuan G, Niu J, Zhang L. PCR-fingerprint profiles of mitochondrial and genomic DNA extracted from Fetus cervi using different extraction methods. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:781-786. [PMID: 27247076 DOI: 10.1080/24701394.2016.1186666] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The use of Fetus cervi, which is derived from the embryo and placenta of Cervus Nippon Temminck or Cervs elaphus Linnaeus, has been documented for a long time in China. There are abundant species of deer worldwide. Those recorded by China Pharmacopeia (2010 edition) from all the species were either authentic or adulterants/counterfeits. Identification of their origins or authenticity became a key in the preparation of the authentic products. The traditional SDS alkaline lysis and salt-outing methods were modified to extract mt DNA and genomic DNA from fresh and dry Fetus cervi in addition to Fetus from false animals, respectively. A set of primers were designed by bioinformatics to target the intra-and inter-variation. The mt DNA and genomic DNA extracted from Fetus cervi using the two methods meet the requirement for authenticity. Extraction of mt DNA by SDS alkaline lysis is more practical and accurate than extraction of genomic DNA by salt-outing method. There were differences in length and number of segments amplified by PCR between mt DNA from authentic Fetus cervi and false animals Fetus. The distinctive PCR-fingerprint patterns can distinguish the Fetus cervi from adulterants and counterfeit animal Fetus.
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Affiliation(s)
- Jinxia Ai
- a School of Laboratory Medicine , Beihua University , Jilin , China
| | - Xuesong Wang
- a School of Laboratory Medicine , Beihua University , Jilin , China
| | - Lijun Gao
- a School of Laboratory Medicine , Beihua University , Jilin , China
| | - Wei Xia
- a School of Laboratory Medicine , Beihua University , Jilin , China
| | - Mingcheng Li
- a School of Laboratory Medicine , Beihua University , Jilin , China
| | - Guangxin Yuan
- b School of Pharmacy , Beihua University , Jilin , China
| | - Jiamu Niu
- a School of Laboratory Medicine , Beihua University , Jilin , China
| | - Lihua Zhang
- c Jilin Leibo Scientific Co. Ltd , Jilin , China
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Amaral DT, Mitani Y, Oliveira G, Ohmiya Y, Viviani VR. Revisiting Coleoptera a + T-rich region: structural conservation, phylogenetic and phylogeographic approaches in mitochondrial control region of bioluminescent Elateridae species (Coleoptera). Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:671-680. [PMID: 27159725 DOI: 10.3109/24701394.2016.1174220] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The control region (CR) or A + T-rich region in Coleoptera mt genome is poorly characterized, including the Elateroidea bioluminescent species. Here, we provided the first attempt to characterize and compare the structure and organization of the CR of different species within Elateridae. We also revisited some sequenced Coleoptera CR and observed consensus T-stretches, non-conserved sequences near the stem-loop and unusual inner tRNAs-like sequences. All these features are probably involved in the replication start of the mt genome. The phylogenetic relationships in Elateridae bioluminescent groups using partial sequence of CR showed the monophyly of Pyrearinus pumilus group and Pyrearinus as a polyphyletic genus, corroborating our previous results. The wider genetic variation obtained by CR analysis could separate two different lineages that occur within P. termitilluminans populations. In Elateridae, the CR exhibited high polymorphism within and between populations, which was also observed in other Coleoptera species, suggesting that the CR could be described as a suitable molecular marker to be applied in phylogenetic and phylogeographic studies.
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Affiliation(s)
- Danilo T Amaral
- a Graduate School of Biotechnology and Environmental Monitoring (UFSCar) , Sorocaba , SP , Brazil.,b Graduate School of Evolutive Genetics and Molecular Biology , Federal University of São Carlos (UFSCar) , São Carlos , SP , Brazil
| | - Yasuo Mitani
- c Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) , Tsukuba , Japan
| | - Gabriela Oliveira
- a Graduate School of Biotechnology and Environmental Monitoring (UFSCar) , Sorocaba , SP , Brazil.,b Graduate School of Evolutive Genetics and Molecular Biology , Federal University of São Carlos (UFSCar) , São Carlos , SP , Brazil
| | - Yoshihiro Ohmiya
- d Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) , Tsukuba , Japan
| | - Vadim R Viviani
- a Graduate School of Biotechnology and Environmental Monitoring (UFSCar) , Sorocaba , SP , Brazil.,b Graduate School of Evolutive Genetics and Molecular Biology , Federal University of São Carlos (UFSCar) , São Carlos , SP , Brazil
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Patra AK, Kwon YM, Kang SG, Fujiwara Y, Kim SJ. The complete mitochondrial genome sequence of the tubeworm Lamellibrachia satsuma and structural conservation in the mitochondrial genome control regions of Order Sabellida. Mar Genomics 2016; 26:63-71. [PMID: 26776396 DOI: 10.1016/j.margen.2015.12.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 12/30/2015] [Accepted: 12/30/2015] [Indexed: 11/18/2022]
Abstract
The control region of the mitochondrial genomes shows high variation in conserved sequence organizations, which follow distinct evolutionary patterns in different species or taxa. In this study, we sequenced the complete mitochondrial genome of Lamellibrachia satsuma from the cold-seep region of Kagoshima Bay, as a part of whole genome study and extensively studied the structural features and patterns of the control region sequences. We obtained 15,037 bp of mitochondrial genome using Illumina sequencing and identified the non-coding AT-rich region or control region (354 bp, AT=83.9%) located between trnH and trnR. We found 7 conserved sequence blocks (CSB), scattered throughout the control region of L. satsuma and other taxa of Annelida. The poly-TA stretches, which commonly form the stem of multiple stem-loop structures, are most conserved in the CSB-I and CSB-II regions. The mitochondrial genome of L. satsuma encodes a unique repetitive sequence in the control region, which forms a unique secondary structure in comparison to Lamellibrachia luymesi. Phylogenetic analyses of all protein-coding genes indicate that L. satsuma forms a monophyletic clade with L. luymesi along with other tubeworms found in cold-seep regions (genera: Lamellibrachia, Escarpia, and Seepiophila). In general, the control region sequences of Annelida could be aligned with certainty within each genus, and to some extent within the family, but with a higher rate of variation in conserved regions.
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Affiliation(s)
- Ajit Kumar Patra
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Ansan 426-744, Republic of Korea; Department of Marine Biotechnology, Korea University of Science and Technology, Daejeon 305-333, Republic of Korea.
| | - Yong Min Kwon
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Ansan 426-744, Republic of Korea.
| | - Sung Gyun Kang
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Ansan 426-744, Republic of Korea; Department of Marine Biotechnology, Korea University of Science and Technology, Daejeon 305-333, Republic of Korea.
| | - Yoshihiro Fujiwara
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka 237-0061, Japan.
| | - Sang-Jin Kim
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Ansan 426-744, Republic of Korea; Department of Marine Biotechnology, Korea University of Science and Technology, Daejeon 305-333, Republic of Korea; National Marine Biodiversity Institute of Korea, Seocheon 325-902, Republic of Korea.
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Quinto CA, Tinoco R, Hellberg RS. DNA barcoding reveals mislabeling of game meat species on the U.S. commercial market. Food Control 2016. [DOI: 10.1016/j.foodcont.2015.05.043] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Gupta SK, Kumar A, Gaur A, Hussain SA. Detection of 40 bp insertion-deletion (INDEL) in mitochondrial control region among sambar (Rusa unicolor) populations in India. BMC Res Notes 2015; 8:581. [PMID: 26483190 PMCID: PMC4617744 DOI: 10.1186/s13104-015-1573-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 10/12/2015] [Indexed: 11/22/2022] Open
Abstract
Background The mitochondrial DNA (mtDNA) control region is extensively used in the phylogeography of species. We examined sequence variations in the mtDNA control region of sambar (Rusa unicolor) populations from the South, Central and North India. Results Most of the samples collected from the south India exhibited a 40 bp insertion in the mtDNA control region. This insertion was not observed in the North and Central Indian populations. Conclusion This study provided a potential marker for molecular screening and identification of sambar populations in the form of a distinct 40 bp insertion. Some populations in South India did not exhibit this insertion. It indicates that there could be an ecological barrier that might be preventing the expansion of insertion-positive sambar population.
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Affiliation(s)
| | - Ajit Kumar
- Wildlife Institute of India, Chandrabani, Dehra Dun, 248 001, India.
| | - Ajay Gaur
- Laboratory for the Conservation of Endangered Species (LaCONES), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.
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Gao L, Xia W, Ai J, Li M, Yuan G, Niu J, Fu G, Zhang L. Development of multiplex PCR assay for authentication of Cornu Cervi Pantotrichum in traditional Chinese medicine based on cytochrome b and C oxidase subunit 1 genes. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2989-92. [PMID: 26287950 DOI: 10.3109/19401736.2015.1060475] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
This study describes a method for discriminating the true Cervus antlers from its counterfeits using multiplex PCR. Bioinformatics were carried out to design the specific alleles primers for mitochondrial (mt) cytochrome b (Cyt b) and cytochrome C oxidase subunit 1 (Cox 1) genes. The mt DNA and genomic DNA were extracted from Cervi Cornu Pantotrichum through the modified alkaline and the salt-extracting method in addition to its counterfeits, respectively. Sufficient DNA templates were extracted from all samples used in two methods, and joint fragments of 354 bp and 543 bp that were specifically amplified from both of true Cervus antlers served as a standard control. The data revealed that the multiplex PCR-based assays using two primer sets can be used for forensic and quantitative identification of original Cervus deer products from counterfeit antlers in a single step.
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Affiliation(s)
- Lijun Gao
- a School of Laboratory Medicine, Beihua University , Jilin , People's Republic of China
| | - Wei Xia
- a School of Laboratory Medicine, Beihua University , Jilin , People's Republic of China
| | - Jinxia Ai
- a School of Laboratory Medicine, Beihua University , Jilin , People's Republic of China
| | - Mingcheng Li
- a School of Laboratory Medicine, Beihua University , Jilin , People's Republic of China
| | - Guanxin Yuan
- b School of Pharmacy, Beihua University , Jilin , People's Republic of China , and
| | - Jiamu Niu
- a School of Laboratory Medicine, Beihua University , Jilin , People's Republic of China
| | - Guilian Fu
- c Jilin Leibo Scientific Co. Ltd , Jilin , People's Republic of China
| | - Lihua Zhang
- c Jilin Leibo Scientific Co. Ltd , Jilin , People's Republic of China
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Ba H, Wu L, Liu Z, Li C. An examination of the origin and evolution of additional tandem repeats in the mitochondrial DNA control region of Japanese sika deer (Cervus Nippon). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:276-81. [PMID: 24621225 DOI: 10.3109/19401736.2014.892077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Tandem repeat units are only detected in the left domain of the mitochondrial DNA control region in sika deer. Previous studies showed that Japanese sika deer have more tandem repeat units than its cousins from the Asian continent and Taiwan, which often have only three repeat units. To determine the origin and evolution of these additional repeat units in Japanese sika deer, we obtained the sequence of repeat units from an expanded dataset of the control region from all sika deer lineages. The functional constraint is inferred to act on the first repeat unit because this repeat has the least sequence divergence in comparison to the other units. Based on slipped-strand mispairing mechanisms, the illegitimate elongation model could account for the addition or deletion of these additional repeat units in the Japanese sika deer population. We also report that these additional repeat units could be occurring in the internal positions of tandem repeat regions, possibly via coupling with a homogenization mechanism within and among these lineages. Moreover, the increased number of repeat units in the Japanese sika deer population could reflect a balance between mutation and selection, as well as genetic drift.
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Affiliation(s)
- Hengxing Ba
- a Institute of Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences , Jilin , People's Republic of China .,b State Key Laboratory for Molecular Biology of Special Economical Animals , Chinese Academy of Agricultural Sciences , Jilin , People's Republic of China , and
| | - Lang Wu
- c Center for Clinical and Translational Science, Mayo Clinic , Rochester , MN , USA
| | - Zongyue Liu
- a Institute of Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences , Jilin , People's Republic of China .,b State Key Laboratory for Molecular Biology of Special Economical Animals , Chinese Academy of Agricultural Sciences , Jilin , People's Republic of China , and
| | - Chunyi Li
- a Institute of Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences , Jilin , People's Republic of China .,b State Key Laboratory for Molecular Biology of Special Economical Animals , Chinese Academy of Agricultural Sciences , Jilin , People's Republic of China , and
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Smith SL, Carden RF, Coad B, Birkitt T, Pemberton JM. A survey of the hybridisation status of Cervus deer species on the island of Ireland. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0582-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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21
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Meiri M, Lister AM, Collins MJ, Tuross N, Goebel T, Blockley S, Zazula GD, van Doorn N, Dale Guthrie R, Boeskorov GG, Baryshnikov GF, Sher A, Barnes I. Faunal record identifies Bering isthmus conditions as constraint to end-Pleistocene migration to the New World. Proc Biol Sci 2014; 281:20132167. [PMID: 24335981 PMCID: PMC3871309 DOI: 10.1098/rspb.2013.2167] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 11/21/2013] [Indexed: 11/12/2022] Open
Abstract
Human colonization of the New World is generally believed to have entailed migrations from Siberia across the Bering isthmus. However, the limited archaeological record of these migrations means that details of the timing, cause and rate remain cryptic. Here, we have used a combination of ancient DNA, 14C dating, hydrogen and oxygen isotopes, and collagen sequencing to explore the colonization history of one of the few other large mammals to have successfully migrated into the Americas at this time: the North American elk (Cervus elaphus canadensis), also known as wapiti. We identify a long-term occupation of northeast Siberia, far beyond the species's current Old World distribution. Migration into North America occurred at the end of the last glaciation, while the northeast Siberian source population became extinct only within the last 500 years. This finding is congruent with a similar proposed delay in human colonization, inferred from modern human mitochondrial DNA, and suggestions that the Bering isthmus was not traversable during parts of the Late Pleistocene. Our data imply a fundamental constraint in crossing Beringia, placing limits on the age and mode of human settlement in the Americas, and further establish the utility of ancient DNA in palaeontological investigations of species histories.
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Affiliation(s)
- Meirav Meiri
- Zoological Museum and Department of Zoology, Institute of Archaeology, The Steinhardt National Collection of Natural History, Tel Aviv University, Tel Aviv 69978, Israel
| | - Adrian M. Lister
- Earth Sciences Department, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Matthew J. Collins
- Department of Archaeology, University of York, Heslington, York YO10 5YW, UK
| | - Noreen Tuross
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Ted Goebel
- Center for the Study of the First Americans, Department of Anthropology, Texas A&M University, College Station, TX 77843, USA
| | - Simon Blockley
- Department of Geography, University of London, Egham, Surrey TW20 0EX, UK
| | - Grant D. Zazula
- Department of Tourism and Culture, Government of Yukon, PO Box 2703, Whitehorse, Yukon, CanadaY1A 2C6
| | - Nienke van Doorn
- Department of Archaeology, University of York, Heslington, York YO10 5YW, UK
| | - R. Dale Guthrie
- Institute of Arctic Biology, University of Alaska, Fairbanks, AK 99709, USA
| | - Gennady G. Boeskorov
- Siberian Branch of Russian Academy of Sciences (SB RAS), Diamond and Precious Metals Geology Institute, 39 Prospect Lenina, Yakutsk 677980, Russia
- M. K. Ammosov's North-Eastern Federal University, 48 Kulakovsky street, Yakutsk 677013, Russia
| | - Gennady F. Baryshnikov
- Zoological Institute, Russian Academy of Sciences, Universitetskaya nab. 1, St Petersburg 199034, Russia
| | | | - Ian Barnes
- Earth Sciences Department, Natural History Museum, Cromwell Road, London SW7 5BD, UK
- School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK
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Dalmasso A, Chiesa F, Civera T, Bottero MT. A novel minisequencing test for species identification of salted and dried products derived from species belonging to Gadiformes. Food Control 2013. [DOI: 10.1016/j.foodcont.2013.04.031] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Ba H, Yang F, Xing X, Li C. Classification and phylogeny of sika deer (Cervus nippon) subspecies based on the mitochondrial control region DNA sequence using an extended sample set. ACTA ACUST UNITED AC 2013; 26:373-9. [DOI: 10.3109/19401736.2013.836509] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Meiri M, Lister AM, Higham TFG, Stewart JR, Straus LG, Obermaier H, González Morales MR, Marín-Arroyo AB, Barnes I. Late-glacial recolonization and phylogeography of European red deer (Cervus elaphusL.). Mol Ecol 2013; 22:4711-22. [DOI: 10.1111/mec.12420] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 06/09/2013] [Accepted: 06/11/2013] [Indexed: 11/27/2022]
Affiliation(s)
- Meirav Meiri
- Department of Zoology; Institute of Archaeology; Tel Aviv University; Tel Aviv 69978 Israel
| | - Adrian M. Lister
- Department of Earth Sciences; Natural History Museum; Cromwell Road London SW7 5BD UK
| | - Thomas F. G. Higham
- Research Lab for Archaeology and the History of Art; University of Oxford; Oxford OX1 3QY UK
| | - John R. Stewart
- School of Applied Sciences; Bournemouth University; Poole Dorset BH12 5BB UK
| | - Lawrence G. Straus
- Department of Anthropology; University of New Mexico; Albuquerque NM 87131-0001 USA
- Instituto Internacional de Investigaciones Prehistóricas de Cantabria; Universidad de Cantabria; Santander 39005 Spain
| | - Henriette Obermaier
- Bavarian State Collection for Anthropology and Palaeoanatomy Munich; Munich 80539 Germany
| | - Manuel R. González Morales
- Instituto Internacional de Investigaciones Prehistóricas de Cantabria; Universidad de Cantabria; Santander 39005 Spain
| | - Ana B. Marín-Arroyo
- Instituto Internacional de Investigaciones Prehistóricas de Cantabria; Universidad de Cantabria; Santander 39005 Spain
| | - Ian Barnes
- School of Biological Sciences; Royal Holloway; University of London; Egham Surrey TW20 0EX UK
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Li B, Xu Y, Ma J. Allelic characterization of the second DRB locus of major histocompatibility complex class II in Ussuri sika deer (Cervus nippon hortulorum): highlighting the trans-species evolution of DRB alleles within Cervidae. Anim Cells Syst (Seoul) 2013. [DOI: 10.1080/19768354.2013.826280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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Krojerová-Prokesová J, Baranceková M, Voloshina I, Myslenkov A, Lamka J, Koubek P. Dybowski's sika deer (Cervus nippon hortulorum): genetic divergence between natural primorian and introduced Czech populations. ACTA ACUST UNITED AC 2013; 104:312-26. [PMID: 23454911 DOI: 10.1093/jhered/est006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Dybowski's sika deer (Cervus nippon hortulorum) originally inhabited the majority of the Primorsky Krai in Far Eastern Russia, north-eastern China, and Korean Peninsula. At present, only the Russian population seems to be stable, even though this taxon is still classified as endangered by the Russian Federation. Almost 100 years ago, this subspecies, among others, was imported to several European countries including the Czech Republic. We used both mitochondrial (mtDNA; the cytochrome b gene and the control region) and nuclear DNA markers to examine the actual taxonomic status of modern Czech Dybowski's sika population and to compare the genetic diversity between the introduced and the native populations. Altogether, 124 Czech samples and 109 Primorian samples were used in the analyses. Within the samples obtained from individuals that were all morphologically classified as Dybowski's sika, we detected mtDNA haplotypes of Dybowski's sika (84 samples), as well as those belonging to other sika subspecies: northern Japanese sika (25 samples), southern Japanese sika (6 samples), and south-eastern Chinese sika (8 samples). Microsatellite analysis revealed a certain level of heterozygote deficiency and a high level of inbreeding in both populations. The high number of private alleles, factorial correspondence analysis, and Bayesian clustering analysis indicate a high level of divergence between both populations. The large degree of differentiation and the high number of population-specific alleles could be a result of a founder effect, could be a result of a previously suggested bottleneck within the Primorian population, and could also be affected by the crossbreeding of captive individuals with other sika subspecies.
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Affiliation(s)
- Jarmila Krojerová-Prokesová
- Institute of Vertebrate Biology Academy of Sciences of the Czech Republic, v.v.i., Květná 8, Brno, Czech Republic
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Barančeková M, Krojerová-Prokešová J, Voloshina IV, Myslenkov AI, Kawata Y, Oshida T, Lamka J, Koubek P. The origin and genetic variability of the Czech sika deer population. Ecol Res 2012. [DOI: 10.1007/s11284-012-0992-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Yang C, Li P, Zhang X, Guo Y, Gao Y, Xiong Y, Wang L, Qi W, Yue B. The complete mitochondrial genome of the Chinese Sika deer (Cervus nipponTemminck, 1838), and phylogenetic analysis among Cervidae, Moschidae and Bovidae. J NAT HIST 2012. [DOI: 10.1080/00222933.2012.693959] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Wada K, Okumura K, Nishibori M, Kikkawa Y, Yokohama M. The complete mitochondrial genome of the domestic red deer (Cervus elaphus) of New Zealand and its phylogenic position within the family Cervidae. Anim Sci J 2010; 81:551-7. [PMID: 20887306 DOI: 10.1111/j.1740-0929.2010.00799.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We determined the complete nucleotide sequence of the mitochondrial genome of the semidomestic red deer (Cervus elaphus) of New Zealand. The genome was 16,357 bp long and contained 13 protein-coding genes, 12SrRNA, 16SrRNA, 22 tRNAs and a D-loop as found in other mammals. Database homology searches showed that the mitochondrial DNA (mtDNA) sequence from the New Zealand semidomestic deer was similar to partial mtDNA sequences from the European, Norwegian (C. e. atlanticus) and Spanish red deer (C. e. hispanicus). Phylogenetic analysis of the mitochondrial protein-coding regions revealed two well-defined monophyletic clades in subfamilies Cervinae and Muntiacinae. However, red deer and Sika deer were not found to be close relatives. The analysis did identify the red deer as a sister taxon of a Samber/Sika deer clade, although it was more closely related to the Samber than the Sika group.
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Affiliation(s)
- Kenta Wada
- Faculty of Bioindustry, Department of Bioproduction Graduate School of Bioindustry, Tokyo University of Agriculture, Abashiri, Japan
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Organization and variation of the mitochondrial DNA control region in five Caprinae species. Genes Genomics 2010. [DOI: 10.1007/s13258-010-0023-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Authentication of meat from game and domestic species by SNaPshot minisequencing analysis. Meat Sci 2008; 80:216-24. [DOI: 10.1016/j.meatsci.2007.11.027] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2007] [Revised: 10/25/2007] [Accepted: 11/26/2007] [Indexed: 11/19/2022]
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Ozaki M, Suwa G, Kaji K, Ohba T, Hosoi E, Koizumi T, Takatsuki S. Correlations between feeding type and mandibular morphology in the sika deer. J Zool (1987) 2007. [DOI: 10.1111/j.1469-7998.2006.00264.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Wada K, Nishibori M, Yokohama M. The complete nucleotide sequence of mitochondrial genome in the Japanese Sika deer (Cervus nippon), and a phylogenetic analysis between Cervidae and Bovidae. Small Rumin Res 2007. [DOI: 10.1016/j.smallrumres.2005.12.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Qi D, Li T, Zhao X, Guo S, Li J. Mitochondrial cytochrome b sequence variation and phylogenetics of the highly specialized Schizothoracine fishes (Teleostei: Cyprinidae) in the Qinghai-Tibet plateau. Biochem Genet 2006; 44:270-85. [PMID: 16941235 DOI: 10.1007/s10528-006-9022-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2005] [Accepted: 09/24/2005] [Indexed: 10/24/2022]
Abstract
The complete 1140 bp mitochondrial cytochrome b sequences were obtained from 39 individuals representing five species of all four genera of highly specialized schizothoracine fishes distributed in the Qinghai-Tibet plateau. Sequence variation of the cytochrome b gene was surveyed among the 39 individuals as well as three primitive schizothoracines and one outgroup. Phylogenetic analysis suggested that the group assignment based on 1140 bp of the cytochrome b sequence is obviously different from previous assignments, and the highly specialized schizothoracine fishes (Schizopygopsis pylzovi, Gymnocypris przewalskii, G. eckloni, Chuanchia labiosa, and Platypharodon extremus) form a monophyletic group that is sister to the clade formed by the primitive schizothoracine fishes (Schizothorax prenanti, S. pseudaksaiensis, and S. argentatus). The haplotypes of Schizopygopsis pylzovi and G. przewalskii were paraphyletic based on cytochrome b data, which most likely reflected incomplete sorting of mitochondrial DNA lineages. The diploid chromosome numbers of Schizothoracinae were considered in phylogenetic analysis and provided a clear pattern of relationships. Molecular dating estimated for highly specialized schizothoracine fishes suggested that the highly specialized schizothoracine fishes diverged in the late Miocene Pliocene to Pleistocene (4.5 x 10(4)-4.05 x 10(6 ) years BP). The relationship between the cladogenesis of highly specialized schizothoracine fishes and geographical events of the Qinghai-Tibet plateau is discussed.
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Affiliation(s)
- Delin Qi
- Northwest Plateau Institute of Biology, Chinese Academy of Science, Xining, 810001, PR China
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Genetic diversity among Chinese sika deer (Cervus nippon) populations and relationships between Chinese and Japanese sika deer. ACTA ACUST UNITED AC 2006. [DOI: 10.1007/s11434-006-0433-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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38
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39
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Pitra C, Lutz W. Population genetic structure and the effect of founder events on the genetic variability of introduced sika deer, Cervus nippon, in Germany and Austria. EUR J WILDLIFE RES 2005. [DOI: 10.1007/s10344-005-0087-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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40
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Pitra C, Fickel J, Meijaard E, Groves PC. Evolution and phylogeny of old world deer. Mol Phylogenet Evol 2004; 33:880-95. [PMID: 15522810 DOI: 10.1016/j.ympev.2004.07.013] [Citation(s) in RCA: 146] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2004] [Revised: 07/14/2004] [Indexed: 10/26/2022]
Abstract
The phylogenetic pattern and timing of the radiation of Old World deer was determined based on the complete mitochondrial cytochrome b gene from 33 Cervinae taxa. Using rooted and unrooted phylogenies derived from distinct theoretical approaches, strong support was achieved for monophyly of the Old World deer with muntjacs as sister group as well as for the divergence of at least three distinct genera: Rucervus, Dama, and Cervus. The latter clade comprises what have previously been regarded as the genera or subgenera Panolia, Rusa, Cervus, Sika, and probably Przewalskium. Our data also consistently confirmed paraphyly of nominate C. elaphus and did not support the monophyly of Axis. We used these molecular phylogenies to assess the homoplastic evolution of morphological, geographical, ecological, and selected behavioural character state differences within the Cervinae. Reliable fossil calibrations, large molecular data sets, and improved dating methods are shaping a molecular time scale for the evolutionary radiation of Old World deer that occurred at the Miocene/Pliocene transition and is largely compatible with existing palaeontological evidence. Using node ages estimated from sequence data, we estimated an average per-lineage diversification rate of 0.51+/-0.1 species per million years (my) over roughly the last 6 mya.
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Affiliation(s)
- Christian Pitra
- Department of Evolutionary Genetics, Institute for Zoo and Wildlife Research, PF 60113, D-10252 Berlin, Germany.
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41
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WADA K, YOKOHAMA M. Analysis of mitochondrial DNA protein-coding region in the Yeso Sika deer (Cervus nippon yesoensis). Anim Sci J 2004. [DOI: 10.1111/j.1740-0929.2004.00189.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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42
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Ludt CJ, Schroeder W, Rottmann O, Kuehn R. Mitochondrial DNA phylogeography of red deer (Cervus elaphus). Mol Phylogenet Evol 2004; 31:1064-83. [PMID: 15120401 DOI: 10.1016/j.ympev.2003.10.003] [Citation(s) in RCA: 143] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2003] [Revised: 09/12/2003] [Indexed: 10/26/2022]
Abstract
In order to understand the origin, phylogeny, and phylogeography of the species Cervus elaphus, we examined the DNA sequence variation of the mitochondrial cytochrome b gene of 51 populations of deer from the entire distribution area of Cervinae with an emphasis on Europe and Asia. Several methods, including maximum parsimony, maximum likelihood, and nested clade analysis, revealed that red deer originated from the area between Kyrgyzstan and Northern India. We found two distinct groups of red deer: a western group consisting of four subgroups and an eastern group consisting of three subgroups. Our mtDNA data do not support the traditional classification of red deer as only one species nor its division into numerous subspecies. The discrepancies between the geographical pattern of differentiation based on mtDNA cytochrome b and the existing specific and subspecific taxonomy based on morphology are discussed.
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Affiliation(s)
- Christian J Ludt
- Department for Ecosystem and Landscape Management, Wildlife Biology and Wildlife Management Unit, Technical University Munich-Weihenstephan, Am Hochanger 13, Freising 85354, Germany
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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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44
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Phylogenetic relationships among deer in China derived from mitochondrial DNA cytochromeb sequences. ACTA ACUST UNITED AC 2003. [DOI: 10.1007/bf03194160] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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46
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Rajapaksha WRAKJS, Thilakaratne IDSIP, Chandrasiri ADN, Niroshan TD. Development of PCR assay for differentiation of some important wild animal meat of Sri Lanka. JOURNAL OF VETERINARY MEDICINE. B, INFECTIOUS DISEASES AND VETERINARY PUBLIC HEALTH 2002; 49:322-4. [PMID: 12420866 DOI: 10.1046/j.1439-0450.2002.00580.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A polymerase chain reaction (PCR) assay was developed to differentiate meat of Ceylon spotted deer (Axis axis ceylonensis), Ceylon hog deer (A. porcius oryzus), Ceylon sambhur (Cervus unicolor unicolor) and barking deer (Muntiacus muntijak malabaricus) from meat of cattle, goat, buffalo, pig, dog and sheep. A set of primers was designed according to the sequence of the mitochondrial cytochrome b gene of C. elaphus canadensis and by PCR amplification about 450 bp band was observed for all four animal species and these primers were not cross reacted with DNA of other animal species tested in the study under the tested reaction conditions. A band of 649 bp size was observed for all animal species when DNA was amplified with the universal primers and that indicated the presence of mitochondrial DNA in the samples. Further, the results indicated that this technique was sensitive enough to differentiate rotten meat, at least 5 days after the killing of an animal. Under these PCR conditions, the DNA of bacteria, which is involved in decomposition of meat, was not amplified with both universal and specific primers. However, the method was not sensitive enough in differentiating cooked meat of these species. Slaughtering of these four wild animal species is banned, but the animals are being killed illegally. Lack of meat identification methods has been identified as one of the major constraints to implement legal procedures and conserve biodiversity in the country.
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Affiliation(s)
- W R A K J S Rajapaksha
- Animal Breeding Division, Veterinary Research Institute, Gannoruwa, Peradeniya, Sri Lanka.
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47
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Polziehn RO, Strobeck C. A phylogenetic comparison of red deer and wapiti using mitochondrial DNA. Mol Phylogenet Evol 2002; 22:342-56. [PMID: 11884159 DOI: 10.1006/mpev.2001.1065] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A phylogeny was constructed for red deer/wapiti (Cervus elaphus) subspecies using sequence data from the control region of mitochondrial DNA (mtDNA). The tree was rooted using Cervus nippon (sika deer), Cervus albirostris (Thorold's white-lipped deer), and several Odocoileinae species. A division between the mtDNA haplotypes of red deer (European) and wapiti (Asian/North American) corresponds to subspecies found on opposite sides of the Himalayan Mountains and Gobi, which suggests wapiti should be reconsidered for the status of C. canadensis. Using parsimony and distance analysis, red deer and wapiti are derived from a single recent common ancestor, which is consistent with current taxonomy that recognizes the subspecies of Cervus elaphus as monophyletic group. However, maximum-likelihood analysis using weighted transitional substitutions caused red deer to form a sister group to sika deer (Cervus nippon) and wapiti. A phenetic comparison revealed wapiti also share more nucleotide similarities with sika deer, although approximately 5% sequence divergence separates wapiti, sika, and red deer. Phylogenetic evidence from the cytochrome b sequences corroborated observations from the control region. Observations from this study suggest that the species status of wapiti should be reinstated.
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Affiliation(s)
- Renee O Polziehn
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2V9, Canada.
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Hsieh HM, Chiang HL, Tsai LC, Lai SY, Huang NE, Linacre A, Lee JC. Cytochrome b gene for species identification of the conservation animals. Forensic Sci Int 2001; 122:7-18. [PMID: 11587860 DOI: 10.1016/s0379-0738(01)00403-0] [Citation(s) in RCA: 128] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
A partial DNA sequence of cytochrome b gene was used to identify the remains of endangered animals and species endemic to Taiwan. The conservation of animals species included in this study were: the formosan gem-faced civets, leopard cats, tigers, clouded leopards, lion, formosan muntjacs, formosan sika deers, formosan sambars, formosan serows, water buffalo, formosan pangolins and formosan macaques. The control species used included domestic cats, domestic dogs, domestic sheeps, domestic cattles, domestic pigs and humans. Heteroplasmy was detected in the formosan macaque, domestic pig and domestic cats. The frequencies of heteroplasmy in these animals were about 0.25% (1 in 402bp). Sequences were aligned by Pileup program of GCG computer package, and the phylogenetic tree was constructed by the neighbor-joining method. The results of sequence comparison showed that the percentage range of sequence diversity in the same species was from 0.25 to 2.74%, and that between the different species was from 5.97 to 34.83%. The results of phylogenetic analysis showed that the genetic distance between the different species was from 6.33 to 40.59. Animals of the same species, both the endangered animal species and domestic animals, were clustered together in the neighbor-joining tree. Three unknown samples of animal remains were identified by this system. The partial sequence of cytochrome b gene adopted in this study proved to be usable for animal identification.
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Affiliation(s)
- H M Hsieh
- Department of Forensic Science, Central Police University, 56 Shu-Jen Road, Kwei-San, 33334, ROC, Taoyuan, Taiwan
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Goodman SJ, Tamate HB, Wilson R, Nagata J, Tatsuzawa S, Swanson GM, Pemberton JM, McCullough DR. Bottlenecks, drift and differentiation: the population structure and demographic history of sika deer (Cervus nippon) in the Japanese archipelago. Mol Ecol 2001; 10:1357-70. [PMID: 11412360 DOI: 10.1046/j.1365-294x.2001.01277.x] [Citation(s) in RCA: 109] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We assessed genetic differentiation and diversity in 14 populations of sika deer (Cervus nippon) from Japan and four populations of sika deer introduced to the UK, using nine microsatellite loci. We observed extreme levels of differentiation and significant differences in diversity between populations. Our results do not support morphological subspecies designations, but are consistent with previous mitochondrial DNA analyses which suggest the existence of two genetically distinct lineages of sika deer in Japan. The source of sika introduced to the UK was identified as Kyushu. The underlying structure of Japanese populations probably derives from drift in separate glacial refugia and male dispersal limited by distance. This structure has been perturbed by bottlenecks and habitat fragmentation, resulting from human activity from the mid-nineteenth century. Most current genetic differentiation and differences in diversity among populations probably result from recent drift. Coalescent model analysis suggests sika on each of the main Japanese islands have experienced different recent population histories. Hokkaido, which has large areas of continuous habitat, has maintained high levels of gene flow. In Honshu the population is highly fragmented and is likely to have been evolving by drift alone. In Kyushu there has been a balance between gene flow and drift but all the populations have experienced high levels of drift. Habitat fragment size was not significantly associated with genetic diversity in populations but there was a significant correlation between habitat fragment size and effective population size.
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Affiliation(s)
- S J Goodman
- Institute of Cell, Animal and Population Biology, University of Edinburgh, West Mains Road, Edinburgh, EH9 3JT, UK.
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50
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A mitochondrial DNA control region phylogeny of the Cervinae: speciation in Cervus and implications for conservation. Anim Conserv 2001. [DOI: 10.1017/s1367943001001019] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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