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Thai QK, Nguyen TC, Le CT, Chung AD, Nguyen TML, Tran QD, Savolainen P, Quan QD, Tran DL, Tran HD. HV1 mtDNA Reveals the High Genetic Diversity and the Ancient Origin of Vietnamese Dogs. Animals (Basel) 2023; 13:ani13061036. [PMID: 36978577 PMCID: PMC10044065 DOI: 10.3390/ani13061036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/27/2023] [Accepted: 03/01/2023] [Indexed: 03/14/2023] Open
Abstract
In this study, samples from 429 dog individuals across three main regions of Vietnam (Southern Vietnam (SVN), Central Vietnam (CVN), and Northern Vietnam (NVN)) were collected to analyze the 582 bp region mtDNA HVI, so as to study the genetic diversity and to screen the rare haplotype E in the Vietnamese village dog population. Nine new haplotypes A, two new haplotypes B, and three haplotypes C were unique to Vietnam dogs, in which the new haplotypes An3, An7, Cn1, and Cn3 concerned mutations at new polymorphism sites (15,517, 15,505, 15,479, and 15,933, respectively) which have not been previously reported. The detection of haplotypes A9 and A29, and the appearance of haplotype A200 in the two individual dogs sampled support that the Southeast Asian dog is the ancestor of today’s Australian dingo and Polynesian dog. The two rare haplotypes E (E1 and E4) were reconfirmed in Vietnamese dogs and discussed. This study also contributes to strengthening the theory of domestication of dogs to the south of the Yangtze River and the Southeast Asian origin of the dingo.
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Affiliation(s)
- Quan Ke Thai
- Faculty of Natural science Education, Saigon University, 273 An Duong Vuong, Ward 3, District 5, Ho Chi Minh City 72710, Vietnam
- Correspondence: (Q.K.T.); (H.-D.T.); Tel.: +84-918-297-640 (Q.K.T.); +84-772-999-537 (H-D.T.)
| | - Thanh-Cong Nguyen
- Faculty of Biotechnology, Nguyen-Tat-Thanh University, 298A-300A Nguyen-Tat-Thanh Street, District 04, Ho Chi Minh City 72820, Vietnam
| | - Cong-Trieu Le
- Soc Trang Vocational College, 176 Nam Ky Khoi Nghia Street, Ward 7, Soc Trang City 96114, Vietnam
| | - Anh-Dung Chung
- Biotechnology Division, Institute of Agricultural Sciences for Southern Viet Nam, 121 Nguyen Binh Khiem Street, Da Kao Ward, 1st District, Ho Chi Minh City 710302, Vietnam
| | - Tran Minh-Ly Nguyen
- Faculty of Business Administration, TU Bergakademie Freiberg, Akademiestraße 6, 09599 Freiberg, Germany
| | - Quoc-Dung Tran
- Faculty of Biology, University of Education, Hue University, 34 Le 5Loi Street, Hue City 49118, Vietnam
| | - Peter Savolainen
- Science for Life Laboratory, School of Biotechnology, Royal Institute of Technology (KTH), 171 65 Solna, Sweden
| | - Quoc-Dang Quan
- Agency for Southern Affairs of Ministry of Science and Technology, 31 Han Thuyen Street, Ben Nghe Ward, District 1, Ho Chi Minh City 70055, Vietnam
| | - Dai-Long Tran
- Department of Supervisor Inspector, Van Lang University, Nguyen Khac Nhu Street, Co Giang Ward, Distric 1, Ho Chi Minh City 700000, Vietnam
| | - Hoang-Dung Tran
- Faculty of Biology and Environment, Ho Chi Minh City University of Food Industry, 140 Le Trong Tan Street, Tay Thanh Ward, Tan Phu District, Ho Chi Minh City 72009, Vietnam
- Institute of Applied Research and Technology Transfer HUFI, Ho Chi Minh City University of Food Industry, 140 Le Trong Tan Street, Tay Thanh Ward, Tan Phu District, Ho Chi Minh City 72009, Vietnam
- Correspondence: (Q.K.T.); (H.-D.T.); Tel.: +84-918-297-640 (Q.K.T.); +84-772-999-537 (H-D.T.)
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2
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Serres-Armero A, Davis BW, Povolotskaya IS, Morcillo-Suarez C, Plassais J, Juan D, Ostrander EA, Marques-Bonet T. Copy number variation underlies complex phenotypes in domestic dog breeds and other canids. Genome Res 2021; 31:762-774. [PMID: 33863806 PMCID: PMC8092016 DOI: 10.1101/gr.266049.120] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 02/26/2021] [Indexed: 01/02/2023]
Abstract
Extreme phenotypic diversity, a history of artificial selection, and socioeconomic value make domestic dog breeds a compelling subject for genomic research. Copy number variation (CNV) is known to account for a significant part of inter-individual genomic diversity in other systems. However, a comprehensive genome-wide study of structural variation as it relates to breed-specific phenotypes is lacking. We have generated whole genome CNV maps for more than 300 canids. Our data set extends the canine structural variation landscape to more than 100 dog breeds, including novel variants that cannot be assessed using microarray technologies. We have taken advantage of this data set to perform the first CNV-based genome-wide association study (GWAS) in canids. We identify 96 loci that display copy number differences across breeds, which are statistically associated with a previously compiled set of breed-specific morphometrics and disease susceptibilities. Among these, we highlight the discovery of a long-range interaction involving a CNV near MED13L and TBX3, which could influence breed standard height. Integration of the CNVs with chromatin interactions, long noncoding RNA expression, and single nucleotide variation highlights a subset of specific loci and genes with potential functional relevance and the prospect to explain trait variation between dog breeds.
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Affiliation(s)
- Aitor Serres-Armero
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, Barcelona 08003, Spain
| | - Brian W Davis
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.,Department of Veterinary Integrative Biosciences, College of Veterinary Medicine, Texas A&M University, College Station, Texas 77843, USA
| | - Inna S Povolotskaya
- Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Carlos Morcillo-Suarez
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, Barcelona 08003, Spain
| | - Jocelyn Plassais
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - David Juan
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, Barcelona 08003, Spain
| | - Elaine A Ostrander
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Tomas Marques-Bonet
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, Barcelona 08003, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona 08028, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia 08010, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Catalonia 08201, Spain
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3
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Roccaro M, Bini C, Fais P, Merialdi G, Pelotti S, Peli A. Who killed my dog? Use of forensic genetics to investigate an enigmatic case. Int J Legal Med 2020; 135:387-392. [PMID: 32783156 PMCID: PMC7870635 DOI: 10.1007/s00414-020-02388-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 08/03/2020] [Indexed: 11/09/2022]
Abstract
Genetic testing of animal biological material has become a valuable tool in forensic investigations, and it is successfully used to identify unknown crime perpetrators, to unmask food frauds, or to clarify cases of animal attacks on humans or other animals. When DNA profiling is not possible due to inadequate amounts of nuclear DNA, mitochondrial DNA (mtDNA) testing is the only viable alternative, as in the case of shed hair samples. In this case, a dog was allegedly killed by wild animals while being hosted in a boarding house. Extraneous hair fragments recovered from the dog’s mouth and paws were subjected to genetic analysis: the cytochrome b gene located on mtDNA was amplified and sequenced in order to determine the species responsible for the killing. The mtDNA analysis provided evidence that the dog was killed by other dogs, thus unmasking a false wild animal attack and putting the case in an entirely different perspective.
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Affiliation(s)
- Mariana Roccaro
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano dell'Emilia, Italy.
| | - Carla Bini
- Department of Medical and Surgical Sciences, Unit of Legal Medicine, University of Bologna, Bologna, Italy
| | - Paolo Fais
- Department of Medical and Surgical Sciences, Unit of Legal Medicine, University of Bologna, Bologna, Italy
| | - Giuseppe Merialdi
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna "Bruno Ubertini", Bologna Unit, Bologna, Italy
| | - Susi Pelotti
- Department of Medical and Surgical Sciences, Unit of Legal Medicine, University of Bologna, Bologna, Italy
| | - Angelo Peli
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano dell'Emilia, Italy
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4
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Interval of detectability of predator DNA after livestock (and wild animal) predation. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.09.128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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5
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Serres-Armero A, Povolotskaya IS, Quilez J, Ramirez O, Santpere G, Kuderna LFK, Hernandez-Rodriguez J, Fernandez-Callejo M, Gomez-Sanchez D, Freedman AH, Fan Z, Novembre J, Navarro A, Boyko A, Wayne R, Vilà C, Lorente-Galdos B, Marques-Bonet T. Similar genomic proportions of copy number variation within gray wolves and modern dog breeds inferred from whole genome sequencing. BMC Genomics 2017; 18:977. [PMID: 29258433 PMCID: PMC5735816 DOI: 10.1186/s12864-017-4318-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 11/17/2017] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Whole genome re-sequencing data from dogs and wolves are now commonly used to study how natural and artificial selection have shaped the patterns of genetic diversity. Single nucleotide polymorphisms, microsatellites and variants in mitochondrial DNA have been interrogated for links to specific phenotypes or signals of domestication. However, copy number variation (CNV), despite its increasingly recognized importance as a contributor to phenotypic diversity, has not been extensively explored in canids. RESULTS Here, we develop a new accurate probabilistic framework to create fine-scale genomic maps of segmental duplications (SDs), compare patterns of CNV across groups and investigate their role in the evolution of the domestic dog by using information from 34 canine genomes. Our analyses show that duplicated regions are enriched in genes and hence likely possess functional importance. We identify 86 loci with large CNV differences between dogs and wolves, enriched in genes responsible for sensory perception, immune response, metabolic processes, etc. In striking contrast to the observed loss of nucleotide diversity in domestic dogs following the population bottlenecks that occurred during domestication and breed creation, we find a similar proportion of CNV loci in dogs and wolves, suggesting that other dynamics are acting to particularly select for CNVs with potentially functional impacts. CONCLUSIONS This work is the first comparison of genome wide CNV patterns in domestic and wild canids using whole-genome sequencing data and our findings contribute to study the impact of novel kinds of genetic changes on the evolution of the domestic dog.
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Affiliation(s)
- Aitor Serres-Armero
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain
| | - Inna S Povolotskaya
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain
| | - Javier Quilez
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Oscar Ramirez
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain.,Vetgenomics, 08193, Barcelona, Spain
| | - Gabriel Santpere
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain.,Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Lukas F K Kuderna
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain
| | - Jessica Hernandez-Rodriguez
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain
| | - Marcos Fernandez-Callejo
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Daniel Gomez-Sanchez
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain
| | - Adam H Freedman
- UCLA, Department of Ecology and Evolutionary Biology, Los Angeles, CA, 90095, USA
| | - Zhenxin Fan
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - John Novembre
- UCLA, Department of Ecology and Evolutionary Biology, Los Angeles, CA, 90095, USA
| | - Arcadi Navarro
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010, Barcelona, Catalonia, Spain
| | - Adam Boyko
- Cornell University, Department of Biological Statistics and Computational Biology, New York, NY, 14853, USA
| | - Robert Wayne
- UCLA, Department of Ecology and Evolutionary Biology, Los Angeles, CA, 90095, USA
| | - Carles Vilà
- Estación Biológica de Doñana EBD-CSIC, Department of Integrative Ecology, 41092, Sevilla, Spain
| | - Belen Lorente-Galdos
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain. .,Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA.
| | - Tomas Marques-Bonet
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain. .,CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. .,Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010, Barcelona, Catalonia, Spain.
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6
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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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7
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Thai QK, Chung DA, Tran HD. Canis mtDNA HV1 database: a web-based tool for collecting and surveying Canis mtDNA HV1 haplotype in public database. BMC Genet 2017; 18:60. [PMID: 28651548 PMCID: PMC5485557 DOI: 10.1186/s12863-017-0528-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 06/21/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Canine and wolf mitochondrial DNA haplotypes, which can be used for forensic or phylogenetic analyses, have been defined in various schemes depending on the region analyzed. In recent studies, the 582 bp fragment of the HV1 region is most commonly used. 317 different canine HV1 haplotypes have been reported in the rapidly growing public database GenBank. These reported haplotypes contain several inconsistencies in their haplotype information. To overcome this issue, we have developed a Canis mtDNA HV1 database. This database collects data on the HV1 582 bp region in dog mitochondrial DNA from the GenBank to screen and correct the inconsistencies. It also supports users in detection of new novel mutation profiles and assignment of new haplotypes. DESCRIPTION The Canis mtDNA HV1 database (CHD) contains 5567 nucleotide entries originating from 15 subspecies in the species Canis lupus. Of these entries, 3646 were haplotypes and grouped into 804 distinct sequences. 319 sequences were recognized as previously assigned haplotypes, while the remaining 485 sequences had new mutation profiles and were marked as new haplotype candidates awaiting further analysis for haplotype assignment. Of the 3646 nucleotide entries, only 414 were annotated with correct haplotype information, while 3232 had insufficient or lacked haplotype information and were corrected or modified before storing in the CHD. The CHD can be accessed at http://chd.vnbiology.com . It provides sequences, haplotype information, and a web-based tool for mtDNA HV1 haplotyping. The CHD is updated monthly and supplies all data for download. CONCLUSIONS The Canis mtDNA HV1 database contains information about canine mitochondrial DNA HV1 sequences with reconciled annotation. It serves as a tool for detection of inconsistencies in GenBank and helps identifying new HV1 haplotypes. Thus, it supports the scientific community in naming new HV1 haplotypes and to reconcile existing annotation of HV1 582 bp sequences.
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Affiliation(s)
- Quan Ke Thai
- Saigon University, 273 An Duong Vuong street, District 5, Ho Chi Minh city, Vietnam
| | - Dung Anh Chung
- Institute of Agricultural science for Southern Vietnam, 121 Nguyen Binh Khiem street, District 1, Ho Chi Minh city, Vietnam
| | - Hoang-Dung Tran
- Nguyen Tat Thanh University, 300A Nguyen Tat Thanh street, District 4, Ho Chi Minh city, Vietnam
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8
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Montana L, Caniglia R, Galaverni M, Fabbri E, Randi E. A new mitochondrial haplotype confirms the distinctiveness of the Italian wolf (Canis lupus) population. Mamm Biol 2017. [DOI: 10.1016/j.mambio.2017.01.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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9
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Janssens L, Miller R, Van Dongen S. The morphology of the mandibular coronoid process does not indicate that Canis lupus chanco is the progenitor to dogs. ZOOMORPHOLOGY 2016; 135:269-277. [PMID: 27340333 PMCID: PMC4871911 DOI: 10.1007/s00435-015-0298-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 12/12/2015] [Accepted: 12/30/2015] [Indexed: 12/18/2022]
Abstract
The domestication of wolves is currently under debate. Where, when and from which wolf sub-species dogs originated are being investigated both by osteoarchaeologists and geneticists. While DNA research is rapidly becoming more active and popular, morphological methods have been the gold standard in the past. But even today morphological details are routinely employed to discern archaeological wolves from dogs. One such morphological similarity between Canis lupus chanco and dogs was published in 1977 by Olsen and Olsen. This concerns the “turned back” anatomy of the dorsal part of the vertical ramus of the mandible that was claimed to be specific to domestic dogs and Chinese wolves C. lupus chanco, and “absent from other canids”. Based on this characteristic, C. lupus chanco was said to be the progenitor of Asian and American dogs, and this specific morphology has been continuously used as an argument to assign archaeological specimens, including non-Asian and non-American, to the dog clade. We challenged this statement by examining 384 dog skulls of 72 breeds and 60 skulls of four wolf sub-species. Only 20 % of dog mandibles and 80 % of C. lupus chanco showed the specific anatomy. In addition, 12 % of Canis lupus pallipes mandibles showed the “turned back” morphology. It can be concluded that the shape of the coronoid process of the mandible cannot be used as a morphological trait to determine whether a specimen belongs to a dog or as an argument in favour of chanco as the progenitor to dogs.
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Affiliation(s)
- Luc Janssens
- Department of Archaeology, Leiden University, Einsteinweg 2, 2333 CC Leiden, The Netherlands
| | - Rebecca Miller
- Service of Prehistory, University of Liège, quai Roosevelt, 1, 4000 Liège, Belgium
| | - Stefan Van Dongen
- Department of Evolutionary Ecology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
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10
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Janssens L, Spanoghe I, Miller R, Van Dongen S. Can orbital angle morphology distinguish dogs from wolves? ZOOMORPHOLOGY 2015; 135:149-158. [PMID: 26893534 PMCID: PMC4742516 DOI: 10.1007/s00435-015-0294-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Revised: 12/06/2015] [Accepted: 12/08/2015] [Indexed: 02/03/2023]
Abstract
For more than a century, the orbital angle has been studied by many authors to distinguish dog skulls from their progenitor, the wolf. In early studies, the angle was reported to be different between dogs (49°-55°) and wolves (39°-46°). This clear difference was, however, questioned in a more recent Scandinavian study that shows some overlap. It is clear that in all studies several methodological issues were unexplored or unclear and that group sizes and the variety of breeds and wolf subspecies were small. Archaeological dog skulls had also not been studied. Our goal was to test larger and more varied groups and add archaeological samples as they are an evolutionary stage between wolves and modern dogs. We also tested the influence of measuring methods, intra- and inter-reliability, angle symmetry, the influence of variations in skull position and the possibility of measuring and comparing this angle on 3D CT scan images. Our results indicate that there is about 50 % overlap between the angle range in wolves and modern dogs. However, skulls with a very narrow orbital angle were only found in wolves and those with a very wide angle only in dogs. Archaeological dogs have a mean angle very close to the one of the wolves. Symmetry is highest in wolves and lowest in archaeological dogs. The measuring method is very reliable, for both inter- and intra-reliability (0.99-0.97), and most skull position changes have no statistical influence on the angle measured. Three-dimensional CT scan images can be used to measure OA, but the angles differ from direct measuring and cannot be used for comparison. Evolutionary changes in dog skulls responsible for the wider OA compared to wolf skulls are mainly the lateralisation of the zygomatic process of the frontal bone. Our conclusion is that the orbital angle can be used as an additional morphological measuring method to discern wolves from recent and archaeological dogs. Angles above 60° are certainly from recent dogs. Angles under 35° are certainly of wolves.
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Affiliation(s)
- Luc Janssens
- Department of Archaeology, Leiden University, Einsteinweg 2, 2333 CC Leiden, The Netherlands
| | | | - Rebecca Miller
- Service of Prehistory, University of Liège, Quai Roosevelt, 1, 4000 Liège, Belgium
| | - Stefan Van Dongen
- Department of Evolutionary Ecology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
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11
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Kanthaswamy S. Review: domestic animal forensic genetics - biological evidence, genetic markers, analytical approaches and challenges. Anim Genet 2015; 46:473-84. [DOI: 10.1111/age.12335] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2015] [Indexed: 01/09/2023]
Affiliation(s)
- S. Kanthaswamy
- School of Mathematical and Natural Sciences; Arizona State University (ASU) at the West Campus; 4701 W Thunderbird Road Glendale AZ 85306-4908 USA
- California National Primate Research Center; University of California; Davis CA 95616 USA
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12
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Spadaro A, Ream K, Braham C, Webb KM. Local mitochondrial DNA haplotype databases needed for domestic dog populations that have experienced founder effect. Forensic Sci Int 2015; 248:113-8. [PMID: 25612881 DOI: 10.1016/j.forsciint.2014.12.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 11/19/2014] [Accepted: 12/27/2014] [Indexed: 10/24/2022]
Abstract
Biological material from pets is often collected as evidence from crime scenes. Due to sample type and quality, mitochondrial DNA (mtDNA) is frequently evaluated to identify the potential contributor. MtDNA has a lower discriminatory power than nuclear DNA with multiple individuals in a population potentially carrying the same mtDNA sequence, or haplotype. The frequency distribution of mtDNA haplotypes in a population must be known in order to determine the evidentiary value of a match between crime scene evidence and the potential contributor of the biological material. This is especially important in geographic areas that include remote and/or isolated populations where founder effect may have lead to a decrease in genetic diversity and a non-random distribution of haplotypes relative to the population at large. Here we compared the haplotype diversity in dogs from the noncontiguous states of Alaska and Hawaii relative to the contiguous United States (US). We report a greater proportion of dogs carrying an A haplotype in Alaska relative to any other US population. Significant variation in the distribution of haplotype frequencies was discovered when comparing the haplotype diversity of dogs in Hawaii to that of the continental US. Each of these regions exhibits reduced genetic diversity relative to the contiguous US, likely due to founder effect. We recommend that specific databases be created to accurately represent the mitochondrial haplotype diversity in these remote areas. Furthermore, our work demonstrates the importance of local surveys for populations that may have experienced found effect.
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Affiliation(s)
- Amanda Spadaro
- Department of Biology, Allegheny College, Meadville, PA, United States
| | - Kelsey Ream
- Department of Natural Resources and Environmental Science, University of Illinois, Urbana, IL, United States
| | - Caitlyn Braham
- Department of Graduate Studies, John Carroll University, University Heights, OH, United States
| | - Kristen M Webb
- Department of Biology, Allegheny College, Meadville, PA, United States.
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Verscheure S, Backeljau T, Desmyter S. Length heteroplasmy of the polyC-polyT-polyC stretch in the dog mtDNA control region. Int J Legal Med 2014; 129:927-35. [PMID: 25394743 DOI: 10.1007/s00414-014-1106-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 10/30/2014] [Indexed: 10/24/2022]
Abstract
Previously, the mitochondrial control region of 214 Belgian dogs was sequenced. Analysis of this data indicated length heteroplasmy of the polyT stretch in the polyC-polyT-polyC stretch from positions 16661 to 16674. Nine polyC-polyT-polyC haplotype combinations were observed, consisting of seven major haplotypes (highest signal intensity) combined with minor haplotypes (lower signal intensity) one T shorter than the major haplotype in all but three dogs. The longer the polyT stretch, the smaller was the difference in signal intensity between the major and minor haplotype peaks. Additional sequencing, cloning, and PCR trap experiments were performed to further study the intra-individual variation of this mitochondrial DNA (mtDNA) region. Cloning experiments demonstrated that the proportion of clones displaying the minor haplotypes also increased with the length of the polyT stretch. Clone amplification showed that in vitro polymerase errors might contribute to the length heteroplasmy of polyT stretches with at least 10 Ts. Although major and minor polyC-polyT-polyC haplotypes did not differ intra-individually within and between tissues in this study, interpretation of polyT stretch variation should be handled with care in forensic casework.
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Affiliation(s)
- Sophie Verscheure
- National Institute of Criminalistics and Criminology, Vilvoordsesteenweg 100, 1120, Brussels, Belgium,
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Lyons LA, Grahn RA, Kun TJ, Netzel LR, Wictum EE, Halverson JL. Acceptance of domestic cat mitochondrial DNA in a criminal proceeding. Forensic Sci Int Genet 2014; 13:61-7. [PMID: 25086413 DOI: 10.1016/j.fsigen.2014.07.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 06/20/2014] [Accepted: 07/07/2014] [Indexed: 02/06/2023]
Abstract
Shed hair from domestic animals readily adheres to clothing and other contact items, providing a source of transfer evidence for criminal investigations. Mitochondrial DNA is often the only option for DNA analysis of shed hair. Human mitochondrial DNA analysis has been accepted in the US court system since 1996. The murder trial of the State of Missouri versus Henry L. Polk, Jr. represents the first legal proceeding where cat mitochondrial DNA analysis was introduced into evidence. The mitochondrial DNA evidence was initially considered inadmissible due to concerns about the cat dataset and the scientific acceptance of the marker. Those concerns were subsequently addressed, and the evidence was deemed admissible. This report reviews the case in regards to the cat biological evidence and its ultimate admission as generally accepted and reliable. Expansion and saturation analysis of the cat mitochondrial DNA control region dataset supported the initial interpretation of the evidence.
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Affiliation(s)
- Leslie A Lyons
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, One Shields Avenue, Davis, CA 95616, United States.
| | - Robert A Grahn
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, One Shields Avenue, Davis, CA 95616, United States; Forensics Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California - Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Teri J Kun
- Forensics Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California - Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Linda R Netzel
- Kansas City Police Crime Laboratory, 6633 Troost Avenue, Kansas City, MO 64131, United States
| | - Elizabeth E Wictum
- Forensics Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California - Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Joy L Halverson
- Zoogen Services, 1046 Olive Drive Suite 1, Davis, CA 95616, United States
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15
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Pilli E, Casamassima R, Vai S, Virgili A, Barni F, D’Errico G, Berti A, Lago G, Caramelli D. Pet fur or fake fur? A forensic approach. INVESTIGATIVE GENETICS 2014; 5:7. [PMID: 24991403 PMCID: PMC4079164 DOI: 10.1186/2041-2223-5-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 04/29/2014] [Indexed: 11/10/2022]
Abstract
BACKGROUND In forensic science there are many types of crime that involve animals. Therefore, the identification of the species has become an essential investigative tool. The exhibits obtained from such offences are very often a challenge for forensic experts. Indeed, most biological materials are traces, hair or tanned fur. With hair samples, a common forensic approach should proceed from morphological and structural microscopic examination to DNA analysis. However, the microscopy of hair requires a lot of experience and a suitable comparative database to be able to recognize with a high degree of accuracy that a sample comes from a particular species and then to determine whether it is a protected one. DNA analysis offers the best opportunity to answer the question, 'What species is this?' In our work, we analyzed different samples of fur coming from China used to make hats and collars. Initially, the samples were examined under a microscope, then the mitochondrial DNA was tested for species identification. For this purpose, the genetic markers used were the 12S and 16S ribosomal RNA, while the hypervariable segment I of the control region was analyzed afterwards, to determine whether samples belonged to the same individual. RESULTS Microscopic examination showed that the fibres were of animal origin, although it was difficult to determine with a high degree of confidence which species they belonged to and if they came from a protected species. Therefore, DNA analysis was essential to try to clarify the species of these fur samples. CONCLUSIONS Macroscopic and microscopic analysis confirmed the hypothesis regarding the analyzed hair belonging to real animals, although it failed to prove with any kind of certainty which actual family it came from, therefore, the species remains unknown. Sequence data analysis and comparisons with the samples available in GenBank showed that the hair, in most cases, belonged to the Canidae family, and in one case only to Felidae.
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Affiliation(s)
- Elena Pilli
- Dipartimento di Biologia, Università di Firenze, via del Proconsolo 12, 50122 Florence, Italy
| | - Rosario Casamassima
- Reparto Carabinieri Investigazioni Scientifiche di Roma, Sezione di Chimica, viale Tor di Quinto 119, Rome, Italy
| | - Stefania Vai
- Dipartimento di Biologia, Università di Firenze, via del Proconsolo 12, 50122 Florence, Italy
| | - Antonino Virgili
- Istituto Superiore di Tecniche Investigative dei Carabinieri, viale Salvo D’Acquisto 2, 00049 Velletri (Roma), Italy
| | - Filippo Barni
- Reparto Carabinieri Investigazioni Scientifiche di Roma, Sezione di Biologia, viale Tor di Quinto 119, Rome, Italy
| | - Giancarlo D’Errico
- Reparto Carabinieri Investigazioni Scientifiche di Roma, Sezione di Biologia, viale Tor di Quinto 119, Rome, Italy
| | - Andrea Berti
- Reparto Carabinieri Investigazioni Scientifiche di Roma, Sezione di Biologia, viale Tor di Quinto 119, Rome, Italy
| | - Giampietro Lago
- Reparto Carabinieri Investigazioni Scientifiche di Parma, Parco Ducale 3, Parma, Italy
| | - David Caramelli
- Dipartimento di Biologia, Università di Firenze, via del Proconsolo 12, 50122 Florence, Italy
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16
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Aghbolaghi MA, Rezaei HR, Scandura M, Kaboli M. Low gene flow between Iranian Grey Wolves(Canis lupus)and dogs documented using uniparental genetic markers. ZOOLOGY IN THE MIDDLE EAST 2014. [DOI: 10.1080/09397140.2014.914708] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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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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18
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Spicer AM, Kun TJ, Sacks BN, Wictum EJ. Mitochondrial DNA sequence heteroplasmy levels in domestic dog hair. Forensic Sci Int Genet 2014; 11:7-12. [PMID: 24631692 DOI: 10.1016/j.fsigen.2014.02.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 02/01/2014] [Accepted: 02/13/2014] [Indexed: 11/25/2022]
Abstract
To assess the level of mtDNA sequence heteroplasmy in dog hair, we sequenced a 612 base pair fragment of the hypervariable region 1 (HVI) in 576 hairs from six dogs representing a range of age, sex, breed, and hair color. Blood and buccal samples were collected from each dog for reference. Three instances of sequence heteroplasmy were observed at nucleotide positions 15627 (G/A), 15628 (T/C) and 15639 (G/A) in two hairs from different dogs. An HVI sequence heteroplasmy frequency of 0.0034 was obtained. The Probability of Identity (PI) value, or probability that two random, unrelated dog hairs share an HVI sequence, and the Power of Discrimination (PD), or probability that two random unrelated dog hairs have different HVI sequences, were determined from the 88 HVI haplotypes represented in the Veterinary Genetics Laboratory database (n=1006) and found to be 0.086 and 0.914, respectively.
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Affiliation(s)
- Ashley M Spicer
- Forensic Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA, USA.
| | - Teri J Kun
- Forensic Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA, USA.
| | - Benjamin N Sacks
- Canid Diversity and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA, USA; Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, USA.
| | - Elizabeth J Wictum
- Forensic Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA, USA.
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19
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Iyengar A, Hadi S. Use of non-human DNA analysis in forensic science: a mini review. MEDICINE, SCIENCE, AND THE LAW 2014; 54:41-50. [PMID: 23929675 DOI: 10.1177/0025802413487522] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Analysis of non-human DNA in forensic science, first reported about two decades ago, is now commonplace. Results have been used as evidence in court in a variety of cases ranging from abduction and murder to patent infringement and dog attack. DNA from diverse species, including commonly encountered pets such as dogs and cats, to plants, viruses and bacteria has been used and the sheer potential offered by such analyses has been proven. In this review, using case examples throughout, we detail the considerable literature in this field.
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Affiliation(s)
- Arati Iyengar
- School of Forensic & Investigative Sciences, University of Central Lancashire, Preston, UK
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20
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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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21
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Analysis of mitochondrial DNA HVR1 haplotype of pure-bred domestic dogs in Japan. Leg Med (Tokyo) 2013; 15:303-9. [PMID: 24120304 DOI: 10.1016/j.legalmed.2013.08.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 08/29/2013] [Accepted: 08/30/2013] [Indexed: 11/20/2022]
Abstract
To develop DNA markers for forensic analysis, we examined the hypervariable region 1 (HVR1) sequences of 447 pure-bred domestic dogs (Canis lupus familiaris) that had been bred and raised in Japan. HVR1 is a 660-bp stretch of mitochondrial (mt) DNA. Among the 447 HVR1 sequences examined, we identified 58 haplotypes from 47 single nucleotide polymorphisms (SNPs) and two insertion-deletion (InDel) polymorphisms. The haplotype diversity inferred from inter-breed analysis (N=154, 88 breeds) was 0.929±0.011. Intra-breed analysis showed that the haplotype diversity of Golden Retrievers (N=53), Labrador Retrievers (N=67), Miniature Dachshunds (N=61), Toy Poodles (N=62), and Welsh Corgis (N=50) was 0.624±0.052, 0.722±0.029, 0.922±0.010, 0.877±0.020, and 0.443±0.084, respectively. The results of this genotype analysis were used to construct a dataset consisting of dog mtDNA HVR1 sequences for use in forensic applications in Japan.
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22
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McCallum J, Hall S, Lissone I, Anderson J, Huynen L, Lambert DM. Highly informative ancient DNA 'snippets' for New Zealand moa. PLoS One 2013; 8:e50732. [PMID: 23341875 PMCID: PMC3547012 DOI: 10.1371/journal.pone.0050732] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 10/24/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Analysis of ancient DNA has provided invaluable information on past ecologies, ancient populations, and extinct species. We used a short snippet of highly variable mitochondrial control region sequence from New Zealand's moa to characterise a large number of bones previously intractable to DNA analysis as well as bone fragments from swamps to gain information about the haplotype diversity and phylogeography that existed in five moa species. METHODOLOGY/PRINCIPAL FINDINGS By targeting such 'snippets', we show that moa populations differed substantially in geographic structure that is likely to be related to population mobility and history. We show that populations of Pachyornis geranoides, Dinornis novaezealandiae, and Dinornis robustus were highly structured and some appear to have occupied the same geographic location for hundreds of thousands of years. In contrast, populations of the moa Anomalopteryx didiformis and Euryapteryx curtus were widespread, with specific populations of the latter occupying both the North and South Islands of New Zealand. We further show that for a specific area, in this case a North Island swamp, complete haplotype diversity and even sex can be recovered from collections of small, often discarded, bone fragments. CONCLUSIONS/SIGNIFICANCE Short highly variable mitochondrial 'snippets' allow successful typing of environmentally damaged and fragmented skeletal material, and can provide useful information about ancient population diversity and structure without the need to sample valuable, whole bones often held by museums.
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Affiliation(s)
- Jonathan McCallum
- Griffith School of Environment and School of Biomolecular and Physical Sciences, Griffith University, Nathan, Queensland, Australia
| | - Samantha Hall
- Griffith School of Environment and School of Biomolecular and Physical Sciences, Griffith University, Nathan, Queensland, Australia
| | - Iman Lissone
- Institute of Natural Resources, Massey University, North Shore City, New Zealand
| | - Jennifer Anderson
- Institute of Natural Resources, Massey University, North Shore City, New Zealand
| | - Leon Huynen
- Griffith School of Environment and School of Biomolecular and Physical Sciences, Griffith University, Nathan, Queensland, Australia
| | - David M. Lambert
- Griffith School of Environment and School of Biomolecular and Physical Sciences, Griffith University, Nathan, Queensland, Australia
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23
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Frynta D, Baudyšová J, Hradcová P, Faltusová K, Kratochvíl L. Allometry of sexual size dimorphism in domestic dog. PLoS One 2012; 7:e46125. [PMID: 23049956 PMCID: PMC3458007 DOI: 10.1371/journal.pone.0046125] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Accepted: 08/28/2012] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND The tendency for male-larger sexual size dimorphism (SSD) to scale with body size - a pattern termed Rensch's rule - has been empirically supported in many animal lineages. Nevertheless, its theoretical elucidation is a subject of debate. Here, we exploited the extreme morphological variability of domestic dog (Canis familiaris) to gain insights into evolutionary causes of this rule. METHODOLOGY/PRINCIPAL FINDINGS We studied SSD and its allometry among 74 breeds ranging in height from less than 19 cm in Chihuahua to about 84 cm in Irish wolfhound. In total, the dataset included 6,221 individuals. We demonstrate that most dog breeds are male-larger, and SSD in large breeds is comparable to SSD of their wolf ancestor. Among breeds, SSD becomes smaller with decreasing body size. The smallest breeds are nearly monomorphic. CONCLUSIONS/SIGNIFICANCE SSD among dog breeds follows the pattern consistent with Rensch's rule. The variability of body size and corresponding changes in SSD among breeds of a domestic animal shaped by artificial selection can help to better understand processes leading to emergence of Rensch's rule.
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Affiliation(s)
- Daniel Frynta
- Department of Zoology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Jana Baudyšová
- Department of Zoology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Petra Hradcová
- Department of Zoology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Kateřina Faltusová
- Department of Zoology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Lukáš Kratochvíl
- Department of Ecology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
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24
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Kim RN, Kim DS, Choi SH, Yoon BH, Kang A, Nam SH, Kim DW, Kim JJ, Ha JH, Toyoda A, Fujiyama A, Kim A, Kim MY, Park KH, Lee KS, Park HS. Genome analysis of the domestic dog (Korean Jindo) by massively parallel sequencing. DNA Res 2012; 19:275-87. [PMID: 22474061 PMCID: PMC3372376 DOI: 10.1093/dnares/dss011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Although pioneering sequencing projects have shed light on the boxer and poodle genomes, a number of challenges need to be met before the sequencing and annotation of the dog genome can be considered complete. Here, we present the DNA sequence of the Jindo dog genome, sequenced to 45-fold average coverage using Illumina massively parallel sequencing technology. A comparison of the sequence to the reference boxer genome led to the identification of 4 675 437 single nucleotide polymorphisms (SNPs, including 3 346 058 novel SNPs), 71 642 indels and 8131 structural variations. Of these, 339 non-synonymous SNPs and 3 indels are located within coding sequences (CDS). In particular, 3 non-synonymous SNPs and a 26-bp deletion occur in the TCOF1 locus, implying that the difference observed in cranial facial morphology between Jindo and boxer dogs might be influenced by those variations. Through the annotation of the Jindo olfactory receptor gene family, we found 2 unique olfactory receptor genes and 236 olfactory receptor genes harbouring non-synonymous homozygous SNPs that are likely to affect smelling capability. In addition, we determined the DNA sequence of the Jindo dog mitochondrial genome and identified Jindo dog-specific mtDNA genotypes. This Jindo genome data upgrade our understanding of dog genomic architecture and will be a very valuable resource for investigating not only dog genetics and genomics but also human and dog disease genetics and comparative genomics.
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Affiliation(s)
- Ryong Nam Kim
- Genome Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea
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25
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Imes DL, Wictum EJ, Allard MW, Sacks BN. Identification of single nucleotide polymorphisms within the mtDNA genome of the domestic dog to discriminate individuals with common HVI haplotypes. Forensic Sci Int Genet 2012; 6:630-9. [PMID: 22436122 DOI: 10.1016/j.fsigen.2012.02.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Revised: 02/08/2012] [Accepted: 02/09/2012] [Indexed: 11/26/2022]
Abstract
We sequenced the entire ∼16 kb canine mitochondrial genome (mtGenome) of 100 unrelated domestic dogs (Canis lupus familiaris) and compared these to 246 published sequences to assess hypervariable region I (HVI) haplotype frequencies. We then used all available sequences to identify informative single nucleotide polymorphisms (SNPs) outside of the control region for use in further resolving mtDNA haplotypes corresponding to common HVI haplotypes. Haplotype frequencies in our data set were highly correlated with previous ones (e.g., F(ST)=0.02, r=0.90), suggesting the total data set reasonably reflected the broader dog population. A total of 128 HVI haplotypes was represented. The 10 most common HVI haplotypes (n=184 dogs) represented 53.3% of the sample. We identified a total 71 SNPs in the mtGenomes (external to the control region) that resolved the 10 most common HVI haplotypes into 63 mtGenome subhaplotypes. The random match probability of the dataset based solely on the HVI sequence was 4%, whereas the random match probability of the mtGenome subhaplotypes was <1%. Thus, the panel of 71 SNPs identified in this study represents a useful forensic tool to further resolve the identity of individual dogs from mitochondrial DNA (mtDNA).
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Affiliation(s)
- Donna L Imes
- Canid Diversity and Conservation Laboratory, Center for Veterinary Genetics, University of California at Davis, Davis, CA 95616, USA.
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26
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Berger C, Berger B, Parson W. Sequence analysis of the canine mitochondrial DNA control region from shed hair samples in criminal investigations. Methods Mol Biol 2012; 830:331-348. [PMID: 22139671 DOI: 10.1007/978-1-61779-461-2_23] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
In recent years, evidence from domestic dogs has increasingly been analyzed by forensic DNA testing. Especially, canine hairs have proved most suitable and practical due to the high rate of hair transfer occurring between dogs and humans. Starting with the description of a contamination-free sample handling procedure, we give a detailed workflow for sequencing hypervariable segments (HVS) of the mtDNA control region from canine evidence. After the hair material is lysed and the DNA extracted by Phenol/Chloroform, the amplification and sequencing strategy comprises the HVS I and II of the canine control region and is optimized for DNA of medium-to-low quality and quantity. The sequencing procedure is based on the Sanger Big-dye deoxy-terminator method and the separation of the sequencing reaction products is performed on a conventional multicolor fluorescence detection capillary electrophoresis platform. Finally, software-aided base calling and sequence interpretation are addressed exemplarily.
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Affiliation(s)
- C Berger
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
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27
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Bekaert B, Larmuseau MHD, Vanhove MPM, Opdekamp A, Decorte R. Automated DNA extraction of single dog hairs without roots for mitochondrial DNA analysis. Forensic Sci Int Genet 2011; 6:277-81. [PMID: 21531187 DOI: 10.1016/j.fsigen.2011.04.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Revised: 04/04/2011] [Accepted: 04/05/2011] [Indexed: 11/29/2022]
Abstract
Dogs are intensely integrated in human social life and their shed hairs can play a major role in forensic investigations. The overall aim of this study was to validate a semi-automated extraction method for mitochondrial DNA analysis of telogenic dog hairs. Extracted DNA was amplified with a 95% success rate from 43 samples using two new experimental designs in which the mitochondrial control region was amplified as a single large (± 1260 bp) amplicon or as two individual amplicons (HV1 and HV2; ± 650 and 350 bp) with tailed-primers. The results prove that the extraction of dog hair mitochondrial DNA can easily be automated to provide sufficient DNA yield for the amplification of a forensically useful long mitochondrial DNA fragment or alternatively two short fragments with minimal loss of sequence in case of degraded samples.
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Affiliation(s)
- Bram Bekaert
- Laboratory of Forensic Genetics and Molecular Archaeology, UZ Leuven, Kapucijnenvoer 33, B-3000 Leuven, Belgium.
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28
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Desmyter S, Gijsbers L. Belgian canine population and purebred study for forensics by improved mitochondrial DNA sequencing. Forensic Sci Int Genet 2011; 6:113-20. [PMID: 21489897 DOI: 10.1016/j.fsigen.2011.03.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Revised: 03/02/2011] [Accepted: 03/09/2011] [Indexed: 11/19/2022]
Abstract
In canine population studies for forensics, the mitochondrial DNA is profiled by sequencing the two hyper variable regions, HV1 and HV2 of the control region. In a first effort to create a Belgian population database some samples showed partially poor sequence quality. We demonstrated that a nuclear pseudogene was co-amplified with the mtDNA control region. Using a new combination of primers this adverse result was no longer observed and sequencing quality was improved. All former samples with poor sequence data were reanalyzed. Furthermore, the forensic canine population study was extended to 208 breed and mixed dogs. In total, 58 haplotypes were identified, resulting in an exclusion capacity of 0.92. The profile distribution of the Belgian population sample was not significantly different from those observed in population studies of three other countries. In addition to the total population study 107 Belgian registered pedigree dogs of six breeds were profiled. Per breed, the obtained haplotypes were supplemented with those from population and purebred studies. The combined data revealed that some haplotypes were more or less prominent present in particular dog breeds. The statistically significant differences in haplotype distribution between breeds and population sample can have consequences on mtDNA databasing and matching probabilities in forensics.
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Affiliation(s)
- Stijn Desmyter
- National Institute of Criminalistics and Criminology, Vilvoordsesteenweg 100, B-1120 Brussels, Belgium.
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Complete sequence of the Tibetan Mastiff mitochondrial genome and its phylogenetic relationship with other Canids (Canis, Canidae). Animal 2011; 5:18-25. [DOI: 10.1017/s1751731110001370] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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30
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Klütsch CFC, Seppälä EH, Uhlén M, Lohi H, Savolainen P. Segregation of point mutation heteroplasmy in the control region of dog mtDNA studied systematically in deep generation pedigrees. Int J Legal Med 2010; 125:527-35. [PMID: 21049272 PMCID: PMC3115052 DOI: 10.1007/s00414-010-0524-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Accepted: 10/18/2010] [Indexed: 12/04/2022]
Abstract
Heteroplasmy, the presence of two or more variants in an organism, may render mitochondrial DNA (mtDNA)-based individual identification challenging in forensic analysis. However, the variation of heteroplasmic proportions and the segregation of heteroplasmic variants through generations and within families have not been systematically described at a large scale in animals such as the domestic dog. Therefore, we performed the largest study to date in domestic dogs and screened a 582-bp-long fragment of the mtDNA control region in 180 individuals in 58 pedigrees for signs of heteroplasmy. We identified three pedigrees (5.17%) with heteroplasmic point mutations. To follow the segregation of the point mutations, we then analyzed 131 samples from these three independent pedigrees and found significant differences in heteroplasmy between generations and among siblings. Frequently (10% of cases), the proportion of one base changed from 0–10% to 80–90% (as judged from Sanger electropherograms) between generations and varied to a similar extent among siblings. We included also a literature review of heteroplasmic and potential mutational hot spot positions in the studied region which showed that all heteroplasmic positions appear to be mutational hot spots. Thus, although heteroplasmy may be used to increase the significance of a match in forensic case work, it may also cause erroneous exclusion of related individuals because of sharp switches from one state to the other within a single generation or among siblings especially in the presented mutational hot spots.
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Affiliation(s)
- Cornelya F C Klütsch
- KTH-Royal Institute of Technology, Gene Technology, Roslagstullsbacken 21, 10691 Stockholm, Sweden
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31
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Grahn RA, Kurushima JD, Billings NC, Grahn JC, Halverson JL, Hammer E, Ho CK, Kun TJ, Levy JK, Lipinski MJ, Mwenda JM, Ozpinar H, Schuster RK, Shoorijeh SJ, Tarditi CR, Waly NE, Wictum EJ, Lyons LA. Feline non-repetitive mitochondrial DNA control region database for forensic evidence. Forensic Sci Int Genet 2010; 5:33-42. [PMID: 20457082 DOI: 10.1016/j.fsigen.2010.01.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2009] [Revised: 01/08/2010] [Accepted: 01/20/2010] [Indexed: 01/26/2023]
Abstract
The domestic cat is the one of the most popular pets throughout the world. A by-product of owning, interacting with, or being in a household with a cat is the transfer of shed fur to clothing or personal objects. As trace evidence, transferred cat fur is a relatively untapped resource for forensic scientists. Both phenotypic and genotypic characteristics can be obtained from cat fur, but databases for neither aspect exist. Because cats incessantly groom, cat fur may have nucleated cells, not only in the hair bulb, but also as epithelial cells on the hair shaft deposited during the grooming process, thereby generally providing material for DNA profiling. To effectively exploit cat hair as a resource, representative databases must be established. The current study evaluates 402 bp of the mtDNA control region (CR) from 1394 cats, including cats from 25 distinct worldwide populations and 26 breeds. Eighty-three percent of the cats are represented by 12 major mitotypes. An additional 8.0% are clearly derived from the major mitotypes. Unique sequences are found in 7.5% of the cats. The overall genetic diversity for this data set is 0.8813±0.0046 with a random match probability of 11.8%. This region of the cat mtDNA has discriminatory power suitable for forensic application worldwide.
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Affiliation(s)
- R A Grahn
- Department of Population Health & Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA
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Webb K, Allard M. Assessment of minimum sample sizes required to adequately represent diversity reveals inadequacies in datasets of domestic dog mitochondrial DNA. ACTA ACUST UNITED AC 2010; 21:19-31. [DOI: 10.3109/19401730903532044] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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33
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Belgian dog mitochondrial DNA database for forensics. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2009. [DOI: 10.1016/j.fsigss.2009.08.110] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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34
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Complex population structure in African village dogs and its implications for inferring dog domestication history. Proc Natl Acad Sci U S A 2009; 106:13903-8. [PMID: 19666600 DOI: 10.1073/pnas.0902129106] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
High genetic diversity of East Asian village dogs has recently been used to argue for an East Asian origin of the domestic dog. However, global village dog genetic diversity and the extent to which semiferal village dogs represent distinct, indigenous populations instead of admixtures of various dog breeds has not been quantified. Understanding these issues is critical to properly reconstructing the timing, number, and locations of dog domestication. To address these questions, we sampled 318 village dogs from 7 regions in Egypt, Uganda, and Namibia, measuring genetic diversity >680 bp of the mitochondrial D-loop, 300 SNPs, and 89 microsatellite markers. We also analyzed breed dogs, including putatively African breeds (Afghan hounds, Basenjis, Pharaoh hounds, Rhodesian ridgebacks, and Salukis), Puerto Rican street dogs, and mixed breed dogs from the United States. Village dogs from most African regions appear genetically distinct from non-native breed and mixed-breed dogs, although some individuals cluster genetically with Puerto Rican dogs or United States breed mixes instead of with neighboring village dogs. Thus, African village dogs are a mosaic of indigenous dogs descended from early migrants to Africa, and non-native, breed-admixed individuals. Among putatively African breeds, Pharaoh hounds, and Rhodesian ridgebacks clustered with non-native rather than indigenous African dogs, suggesting they have predominantly non-African origins. Surprisingly, we find similar mtDNA haplotype diversity in African and East Asian village dogs, potentially calling into question the hypothesis of an East Asian origin for dog domestication.
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Webb KM, Allard MW. Identification of forensically informative SNPs in the domestic dog mitochondrial control region. J Forensic Sci 2009; 54:289-304. [PMID: 19261051 DOI: 10.1111/j.1556-4029.2008.00953.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dog hair is often found at crime scenes either due to the dog's involvement in the crime or secondary transfer. As little nuclear DNA is present in shed hair, a 1000 base pair fragment of the mitochondrial control region (mtCR) from 552 dogs was assessed for forensically useful sequence variation. Through pairwise alignment to a standard reference sequence, existing haplotypes were further described and 36 new haplotypes and 24 new single nucleotide polymorphisms were identified. The probability of exclusion was found to be 0.957. Breeds were found to have similar sequences, although not identical. No genetic basis was found for grouping dogs by either purebred or mixed or geographic location within the continental United States. Our research demonstrates that the domestic dog mtCR has not been thoroughly surveyed for sequence variation and that a single database comprised of purebred and mixed breed dogs is sufficient for the continental United States.
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Affiliation(s)
- Kristen M Webb
- Animal Parasitic Diseases Laboratory, Agricultural Research Service, United States Department of Agriculture, Building 1180, Beltsville, MD 20705, USA
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Webb KM, Allard MW. Mitochondrial genome DNA analysis of the domestic dog: identifying informative SNPs outside of the control region. J Forensic Sci 2009; 54:275-88. [PMID: 19261050 DOI: 10.1111/j.1556-4029.2008.00952.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
While the mitochondrial control region has proven successful for human forensic evaluations by indicating ethnic origin, domestic dogs (Canis lupus familiaris) of seemingly unrelated breeds often form large groups based on identical control region sequences. In an attempt to break up these large haplotype groups, we have analyzed the remaining c. 15,484 base pairs of the canine mitochondrial genome for 79 dogs and used phylogenetic and population genetic methods to search for additional variability in the form of single nucleotide polymorphisms (SNPs). We have identified 356 SNPs and 65 haplotypes in the remainder of the mitochondrial genome excluding the control region. The exclusion capacity was found to be 0.018. The mitochondrial control region was also evaluated for the same 79 dogs. The signals from the different fragments do not conflict, but instead support one another and provide a larger fragment of DNA that can be analyzed as forensic evidence.
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Affiliation(s)
- Kristen M Webb
- Animal Parasitic Diseases Laboratory, Agricultural Research Service, United States Department of Agriculture Building 1180, Beltsville, MD 20705, USA
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van Asch B, Albarran C, Alonso A, Angulo R, Alves C, Betancor E, Catanesi CI, Corach D, Crespillo M, Doutremepuich C, Estonba A, Fernandes AT, Fernandez E, Garcia AM, Garcia MA, Gilardi P, Gonçalves R, Hernández A, Lima G, Nascimento E, de Pancorbo MM, Parra D, Pinheiro MDF, Prat E, Puente J, Ramírez JL, Rendo F, Rey I, Di Rocco F, Rodríguez A, Sala A, Salla J, Sanchez JJ, Solá D, Silva S, Pestano Brito JJ, Amorim A. Forensic analysis of dog (Canis lupus familiaris) mitochondrial DNA sequences: an inter-laboratory study of the GEP-ISFG working group. Forensic Sci Int Genet 2009; 4:49-54. [PMID: 19948334 DOI: 10.1016/j.fsigen.2009.04.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2009] [Revised: 04/20/2009] [Accepted: 04/20/2009] [Indexed: 11/25/2022]
Abstract
A voluntary collaborative exercise aiming at the mitochondrial analysis of canine biological samples was carried out in 2006-2008 by the Non-Human Forensic Genetics Commission of the Spanish and Portuguese Working Group (GEP) of the International Society for Forensic Genetics (ISFG). The participating laboratories were asked to sequence two dog samples (one bloodstain and one hair sample) for the mitochondrial D-loop region comprised between positions 15,372 and 16,083 using suggested primers and PCR conditions, and to compare their results against a reference sequence. Twenty-one participating laboratories reported a total of 67.5% concordant results, 15% non-concordant results, and 17.5% no results. The hair sample analysis presented more difficulty to the participants than the bloodstain analysis, with a high percentage (29%) failing to obtain a result. The high level of participation showed the interest of the community in the analysis of dog forensic samples but the results reveal that crucial methodological issues need to be addressed and further training is required in order to respond proficiently to the demands of forensic casework.
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Affiliation(s)
- Barbara van Asch
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Rua Dr. Roberto Frias s/n, 4200-465 Porto, Portugal.
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Affiliation(s)
- T. A. Brettell
- Department of Chemical and Physical Sciences, Cedar Crest College, 100 College Drive, Allentown, Pennsylvania 18104-6196
| | - J. M. Butler
- Biochemical Science Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8312
| | - J. R. Almirall
- Department of Chemistry and Biochemistry and International Forensic Research Institute, Florida International University, University Park, Miami, Florida 33199
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Baute DT, Satkoski JA, Spear TF, Smith DG, Dayton MR, Malladi VS, Goyal V, Kou A, Kinaga JL, Kanthaswamy S. Analysis of forensic SNPs in the canine mtDNA HV1 mutational hotspot region. J Forensic Sci 2008; 53:1325-33. [PMID: 18808373 DOI: 10.1111/j.1556-4029.2008.00880.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A 60 bp sequence variation hotspot in the canine mitochondrial DNA hypervariable region 1 was evaluated for its use in forensic investigations. Nineteen haplotypes containing 18 single nucleotide polymorphisms were observed among laboratory-generated and GenBank-derived domestic dog sequences representing five regional localities in the U.S. Samples from the different localities were highly variable with the levels of intra-population variability being similar among the populations studied. AMOVA further confirmed that there was no significant genetic structuring of the populations. Assays using these haplotypes were robust, canid specific and portend a rapid method for correctly excluding individual dogs as noncontributors of forensic evidence. Species-specificity of the primers was confirmed by means of in-tube polymerase chain reaction of human and cat DNA and in-silico assessment of the genomes of several animal species. Breed-specific fragments were not detected among the common haplotypes but there is evidence that this assay may be capable of differentiating domestic dog, wolf, and coyote sequences.
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Affiliation(s)
- Danielle T Baute
- The Jan Bashinski DNA Laboratory, California Department of Justice, Richmond, CA 94804, USA
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Mitochondrial DNA analysis of domestic dogs in the UK. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2008. [DOI: 10.1016/j.fsigss.2007.10.187] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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41
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Himmelberger AL, Spear TF, Satkoski JA, George DA, Garnica WT, Malladi VS, Smith DG, Webb KM, Allard MW, Kanthaswamy S. Forensic Utility of the Mitochondrial Hypervariable Region 1 of Domestic Dogs, in Conjunction with Breed and Geographic Information. J Forensic Sci 2008; 53:81-9. [DOI: 10.1111/j.1556-4029.2007.00615.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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