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Werhahn G, Senn H, Macdonald DW, Sillero-Zubiri C. The Diversity in the Genus Canis Challenges Conservation Biology: A Review of Available Data on Asian Wolves. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.782528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Taxa belonging to the Genus Canis can challenge taxonomists because species boundaries and distribution ranges are often gradual. Species delineation within Canis is currently not based on consistent criteria, and is hampered by geographical bias and lack of taxonomic research. But a consistent taxonomy is critical, given its importance for assigning legal protection, conservation priorities, and financial resources. We carried out a qualitative review of the major wolf lineages so far identified from Asia from historical to contemporary time and considered relevant morphological, ecological, and genetic evidence. We present full mitochondrial phylogenies and genetic distances between these lineages. This review aims to summarize the available data on contemporary Asian wolf lineages within the context of the larger phylogenetic Canis group and to work toward a taxonomy that is consistent within the Canidae. We found support for the presence and taxon eligibility of Holarctic gray, Himalayan/Tibetan, Indian, and Arabian wolves in Asia and recommend their recognition at the taxonomic levels consistent within the group.
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Li YX, Gao YL, He XL, Cao SX. Exploration of mtDNA control region sequences in Chinese Tibetan Mastiffs. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:800-804. [PMID: 28756720 DOI: 10.1080/24701394.2017.1357714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The control region of mitochondrial DNA (mtDNA) was obtained from 40 purebred Chinese Tibetan Mastiffs (TMs). Sequence structure and genetic diversity were analyzed, and a phylogenetic tree was constructed. The TM mtDNA control region was composed of ETAS (extended termination associated sequences), CD (a central domain) and CSBs (conserved sequenced blocks) and sequence length showed some diversity, which was mainly caused by the number of 10 nucleotide repeat units [5'-GTA CAC GT (G/A) C-3'] between CSB I and CSB II, which ranged from 27 to 35 among individuals. Seventy-five polymorphic sites were identified, which defined 37 haplotypes; the haplotype diversity was 0.990, and the nucleotide diversity was 1.201. Based on the control region sequences, Chinese TMs were divided into three categories, which were consistent with the origin and geographical classification of TMs. Phylogenetic analysis of 538-bp HVR-I sequences revealed that TMs were most closely related to Labrador Retrievers.
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Affiliation(s)
- Yin-Xia Li
- a Institute of Animal Science , Jiangsu Academy of Agricultural Sciences , Nanjing , Jiangsu , China.,b Key Laboratory of Animal Breeding and Reproduction , Jiangsu Academy of Agricultural Sciences , Nanjing , Jiangsu , China
| | - Yi-Long Gao
- c Policedog Technology Key Laboratory of the Ministry of Public Security , Nanjing Policedog Research Institute of the Ministry of Public Security , Nanjing , Jiangsu , China
| | - Xing-Liang He
- c Policedog Technology Key Laboratory of the Ministry of Public Security , Nanjing Policedog Research Institute of the Ministry of Public Security , Nanjing , Jiangsu , China
| | - Shao-Xian Cao
- a Institute of Animal Science , Jiangsu Academy of Agricultural Sciences , Nanjing , Jiangsu , China.,b Key Laboratory of Animal Breeding and Reproduction , Jiangsu Academy of Agricultural Sciences , Nanjing , Jiangsu , China
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Ren Z, Chen H, Yang X, Zhang C. Phylogenetic analysis of Tibetan mastiffs based on mitochondrial hypervariable region I. J Genet 2017; 96:119-125. [PMID: 28360396 DOI: 10.1007/s12041-017-0753-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Recently, the number of Tibetan mastiffs, which is a precious germplasm resource and cultural heritage, is decreasing sharply. Therefore, the genetic diversity of Tibetan mastiffs needs to be studied to clarify its phylogenetics relationships and lay the foundation for resource protection, rational development and utilization of Tibetan mastiffs. We sequenced hypervariable region I of mitochondrial DNA (mtDNA) of 110 individuals from Tibet region and Gansu province. A total of 12 polymorphic sites were identified which defined eight haplotypes of which H4 and H8 were unique to Tibetan population with H8 being identified first. The haplotype diversity (Hd: 0.808), nucleotide diversity (Pi: 0.603%), the average number of nucleotide difference (K: 3.917) of Tibetan mastiffs from Gansu were higher than those from Tibet region (Hd: 0.794; Pi: 0.589%; K: 3.831), which revealed higher genetic diversity in Gansu. In terms of total population, the genetic variation was low. The median-joining network and phylogenetic tree based on the mtDNA hypervariable region I showed that Tibetan mastiffs originated from grey wolves, as the other domestic dogs and had different history of maternal origin. The mismatch distribution analysis and neutrality tests indicated that Tibetan mastiffs were in genetic equilibrium or in a population decline.
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Affiliation(s)
- Zhanjun Ren
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China.
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Fregel R, Suárez NM, Betancor E, González AM, Cabrera VM, Pestano J. Mitochondrial DNA haplogroup phylogeny of the dog: Proposal for a cladistic nomenclature. Mitochondrion 2015; 22:75-84. [PMID: 25869968 DOI: 10.1016/j.mito.2015.04.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 09/27/2014] [Accepted: 04/02/2015] [Indexed: 10/23/2022]
Abstract
Canis lupus familiaris mitochondrial DNA analysis has increased in recent years, not only for the purpose of deciphering dog domestication but also for forensic genetic studies or breed characterization. The resultant accumulation of data has increased the need for a normalized and phylogenetic-based nomenclature like those provided for human maternal lineages. Although a standardized classification has been proposed, haplotype names within clades have been assigned gradually without considering the evolutionary history of dog mtDNA. Moreover, this classification is based only on the D-loop region, proven to be insufficient for phylogenetic purposes due to its high number of recurrent mutations and the lack of relevant information present in the coding region. In this study, we design 1) a refined mtDNA cladistic nomenclature from a phylogenetic tree based on complete sequences, classifying dog maternal lineages into haplogroups defined by specific diagnostic mutations, and 2) a coding region SNP analysis that allows a more accurate classification into haplogroups when combined with D-loop sequencing, thus improving the phylogenetic information obtained in dog mitochondrial DNA studies.
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Affiliation(s)
- Rosa Fregel
- Department of Genetics, Faculty of Medicine, University of Las Palmas de Gran Canaria, Las Palmas, Spain; Department of Genetics, Faculty of Biology, University of La Laguna, La Laguna, Spain.
| | - Nicolás M Suárez
- Department of Genetics, Faculty of Medicine, University of Las Palmas de Gran Canaria, Las Palmas, Spain
| | - Eva Betancor
- Forensic Genetics Laboratory, Institute of Legal Medicine of Las Palmas, Las Palmas, Spain
| | - Ana M González
- Department of Genetics, Faculty of Biology, University of La Laguna, La Laguna, Spain
| | - Vicente M Cabrera
- Department of Genetics, Faculty of Biology, University of La Laguna, La Laguna, Spain
| | - José Pestano
- Department of Genetics, Faculty of Medicine, University of Las Palmas de Gran Canaria, Las Palmas, Spain; Forensic Genetics Laboratory, Institute of Legal Medicine of Las Palmas, Las Palmas, Spain
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Tu F, Fan Z, Murphy RW, Chen S, Zhang X, Yan C, Liu Y, Sun Z, Fu J, Liu S, Yue B. Molecular phylogenetic relationships among Asiatic shrewlike moles inferred from the complete mitogenomes. J ZOOL SYST EVOL RES 2014. [DOI: 10.1111/jzs.12081] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Feiyun Tu
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife; College of Life Sciences; Sichuan University; Chengdu China
- Jiangxi Academy of Forestry; Nanchang China
| | - Zhenxin Fan
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife; College of Life Sciences; Sichuan University; Chengdu China
| | - Robert W. Murphy
- Centre for Biodiversity and Conservation Biology; Royal Ontario Museum; Toronto M5S, 2C6 Canada
| | - Shunde Chen
- College of Life Sciences; Sichuan Normal University; Chengdu China
| | - Xiuyue Zhang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife; College of Life Sciences; Sichuan University; Chengdu China
| | - Chaochao Yan
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife; College of Life Sciences; Sichuan University; Chengdu China
| | - Yang Liu
- Sichuan Academy of Forestry; Chengdu China
| | - Zhiyu Sun
- Sichuan Academy of Forestry; Chengdu China
| | | | | | - Bisong Yue
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife; College of Life Sciences; Sichuan University; Chengdu China
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Verscheure S, Backeljau T, Desmyter S. Dog mitochondrial genome sequencing to enhance dog mtDNA discrimination power in forensic casework. Forensic Sci Int Genet 2014; 12:60-8. [PMID: 24905334 DOI: 10.1016/j.fsigen.2014.05.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 05/02/2014] [Indexed: 11/26/2022]
Abstract
A Belgian dog population sample and several population studies worldwide have confirmed that only a limited number of mtDNA control region haplotypes is observed in the majority of dogs. The high population frequency of these haplotypes negatively impacts both the exclusion probability of dog mtDNA analysis and the evidential value of a match with one of these haplotypes in casework. Variation within the mtDNA coding region was explored to improve the discrimination power of dog mtDNA analysis. In the current study, the entire mitochondrial genome of 161 dogs was sequenced applying a quality assured strategy and resulted in a total of 119 different mitochondrial genome sequences. Our research was focused on those dogs with the six most common control region haplotypes from a previous Belgian population study. We identified 33 informative SNPs that successfully divide the six most common control region haplotypes into 32 clusters of mitochondrial genome sequences. Determining the identity of these 33 polymorphic sites in addition to control region sequencing in case of a match with one of these 6 control region haplotypes could augment the exclusion probability of forensic dog mtDNA analysis from 92.5% to 97.5%.
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Affiliation(s)
- Sophie Verscheure
- National Institute of Criminalistics and Criminology, Vilvoordsesteenweg 100, B-1120 Brussels, Belgium; University of Antwerp (Evolutionary Ecology Group), Groenenborgerlaan 171, B-2020 Antwerp, Belgium.
| | - Thierry Backeljau
- University of Antwerp (Evolutionary Ecology Group), Groenenborgerlaan 171, B-2020 Antwerp, Belgium; Royal Belgian Institute of Natural Sciences (OD "Taxonomy and Phylogeny" and JEMU), Vautierstraat 29, B-1000 Brussels, Belgium
| | - Stijn Desmyter
- National Institute of Criminalistics and Criminology, Vilvoordsesteenweg 100, B-1120 Brussels, Belgium
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Verscheure S, Backeljau T, Desmyter S. Reviewing population studies for forensic purposes: Dog mitochondrial DNA. Zookeys 2013:381-411. [PMID: 24453568 PMCID: PMC3890688 DOI: 10.3897/zookeys.365.5859] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 12/14/2013] [Indexed: 02/02/2023] Open
Abstract
The identification of dog hair through mtDNA analysis has become increasingly important in the last 15 years, as it can provide associative evidence connecting victims and suspects. The evidential value of an mtDNA match between dog hair and its potential donor is determined by the random match probability of the haplotype. This probability is based on the haplotype’s population frequency estimate. Consequently, implementing a population study representative of the population relevant to the forensic case is vital to the correct evaluation of the evidence. This paper reviews numerous published dog mtDNA studies and shows that many of these studies vary widely in sampling strategies and data quality. Therefore, several features influencing the representativeness of a population sample are discussed. Moreover, recommendations are provided on how to set up a dog mtDNA population study and how to decide whether or not to include published data. This review emphasizes the need for improved dog mtDNA population data for forensic purposes, including targeting the entire mitochondrial genome. In particular, the creation of a publicly available database of qualitative dog mtDNA population studies would improve the genetic analysis of dog traces in forensic casework.
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Affiliation(s)
- Sophie Verscheure
- National Institute of Criminalistics and Criminology, Vilvoordsesteenweg 100, B-1120, Brussels, Belgium ; University of Antwerp (Evolutionary Ecology Group), Groenenborgerlaan 171, B-2020, Antwerp, Belgium
| | - Thierry Backeljau
- University of Antwerp (Evolutionary Ecology Group), Groenenborgerlaan 171, B-2020, Antwerp, Belgium ; Royal Belgian Institute of Natural Sciences (OD "Taxonomy and Phylogeny" and JEMU), Vautierstraat 29, B-1000, Brussels, Belgium
| | - Stijn Desmyter
- National Institute of Criminalistics and Criminology, Vilvoordsesteenweg 100, B-1120, Brussels, Belgium
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Lu L, Tu F, Yan C, Zhang X, Yue B, Zeng T. The complete mitochondrial genome sequence of Shrew Gymnure,Neotetracus sinensis. ACTA ACUST UNITED AC 2012. [DOI: 10.3109/19401736.2012.744976] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Yue H, Fan Z, Liu S, Liu Y, Song Z, Zhang X. A mitogenome of the Chevrier's field mouse (Apodemus chevrieri) and genetic variations inferred from the cytochrome b gene. DNA Cell Biol 2011; 31:460-9. [PMID: 21870961 DOI: 10.1089/dna.2011.1301] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Chevrier's field mouse (Apodemus chevrieri) is an endemic species to China and is an important pest in agriculture and human diseases. In this study, the complete mitochondrial genome of this species was sequenced and its size was 16,298 bases (accession no.: HQ896683). The mitogenome structure was similar compared with other reported rodent mitochondrial genomes and includes 13 protein-coding genes, 2 rRNA genes (12S rRNA and 16S rRNA), 22 tRNA genes, and 1 control region. This was the first complete mitogenome sequenced in genus Apodemus. The phylogenetic analyses based on the sequences of 12 heavy-strand protein-coding genes demonstrated that A. chevrieri clustered together with genus Mus. Additionally, extremely high haplotype and nucleotide diversities (h=0.978, π=2.6%) were observed based on 44 mitochondrial cytochrome b (cyt b) gene sequences. This suggests adaptive divergence of this species to a variety of living habitats and potential refuges in the eastern margin of the Hengduan Mountains during the Quaternary ice ages. No population expansions or genetic bottlenecks were observed in demographic analyses. The phylogenetic analysis of cyt b sequences and haplotypes revealed a genetic differentiation between north and south populations. The divergence between north clade and south clade occurred probably in the middle Pleistocene 1.1815 million years ago (Mya) (95% highest posterior density 2.3189-0.2737 Mya), which was congruent with the periods of the most tense uplift events in the Tibetan Plateau.
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Affiliation(s)
- Hao Yue
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, People's Republic of China
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The origin of the Tibetan Mastiff and species identification of Canis based on mitochondrial cytochrome c oxidase subunit I (COI) gene and COI barcoding. Animal 2011; 5:1868-73. [DOI: 10.1017/s1751731111001042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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