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Brajkovic V, Pocrnic I, Kaps M, Špehar M, Cubric-Curik V, Ristov S, Novosel D, Gorjanc G, Curik I. Quantifying the effects of the mitochondrial genome on milk production traits in dairy cows: empirical results and modelling challenges. J Dairy Sci 2024:S0022-0302(24)01221-9. [PMID: 39414016 DOI: 10.3168/jds.2024-25203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 09/17/2024] [Indexed: 10/18/2024]
Abstract
Significant advances in livestock traits have been achieved primarily through selection strategies targeting variation in the nuclear genome, with little attention given to mitogenome variation. We analyzed the influence of the mitogenome on milk production traits of Holstein cattle in Croatia based on strategically generated next-generation sequencing data for 109 cows pedigree-linked to 7115 milk production records (milk, fat and protein yield) from 3006 cows (first 5 lactations). Since little is known about the biology of the relationship between mitogenome variation and production traits, our quantitative genetic modeling was complex. Thus, the proportion of total variance explained by mitogenome inheritance was estimated using 5 different models: (1) cytoplasmic model with maternal lineages (CYTO), (2) haplotypic model with mitogenome sequences (HAPLO), (3) amino acid model with unique amino acid sequences (AMINO), (4) evolutionary model based on a phylogenetic analysis using Bayesian Evolutionary Analysis Sampling Trees phylogenetic analysis (EVOL), and (5) mitogenome SNP model (SNPmt). The polygenic autosomal and X chromosome additive genetic effects based on pedigree were modeled, together with the effects of herd-year-season interaction, permanent environment, location, and age at first calving. The estimated proportions of phenotypic variance explained by mitogenome in 4 different models (CYTO, HAPLO, AMINO, and SNPmt) were found to be substantial given the size of mitogenome, ranging from 5% to 7% for all 3 milk traits. At the same time, a negligible proportion of the phenotypic variance was explained by mitogenome with the EVOL model. Similarly, in all models, no proportion of phenotypic variance was explained by the X chromosome. Although our results should be confirmed in other dairy cattle populations, including a large number of sequenced mitogenomes and nuclear genomes, the potential of utilizing mitogenome information in animal breeding is promising, especially as the acquisition of complete genome sequences becomes cost-effective.
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Affiliation(s)
- Vladimir Brajkovic
- Department of Animal Science, University of Zagreb, Faculty of Agriculture, Zagreb 10000, Croatia;.
| | - Ivan Pocrnic
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Midlothian EH25 9RG, UK
| | - Miroslav Kaps
- Department of Animal Science, University of Zagreb, Faculty of Agriculture, Zagreb 10000, Croatia
| | - Marija Špehar
- Croatian Agency for Agriculture and Food, Zagreb 10000
| | - Vlatka Cubric-Curik
- Department of Animal Science, University of Zagreb, Faculty of Agriculture, Zagreb 10000, Croatia
| | | | - Dinko Novosel
- Croatian Veterinary Institute, Zagreb 10000, Croatia; Department of Animal Science, University of Zagreb, Faculty of Agriculture, Zagreb 10000, Croatia
| | - Gregor Gorjanc
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Midlothian EH25 9RG, UK
| | - Ino Curik
- Department of Animal Science, University of Zagreb, Faculty of Agriculture, Zagreb 10000, Croatia;; Institute of Animal Sciences, Hungarian University of Agriculture and Life Sciences (MATE), Guba Sándor u. 40, 7400 Kaposvár, Hungary.
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2
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Gautier M, Micol T, Camus L, Moazami-Goudarzi K, Naves M, Guéret E, Engelen S, Lemainque A, Colas F, Flori L, Druet T. Genomic Reconstruction of the Successful Establishment of a Feralized Bovine Population on the Subantarctic Island of Amsterdam. Mol Biol Evol 2024; 41:msae121. [PMID: 38889245 PMCID: PMC11339654 DOI: 10.1093/molbev/msae121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 05/13/2024] [Accepted: 06/13/2024] [Indexed: 06/20/2024] Open
Abstract
The feral cattle of the subantarctic island of Amsterdam provide an outstanding case study of a large mammalian population that was established by a handful of founders and thrived within a few generations in a seemingly inhospitable environment. Here, we investigated the genetic history and composition of this population using genotyping and sequencing data. Our inference showed an intense but brief founding bottleneck around the late 19th century and revealed contributions from European taurine and Indian Ocean Zebu in the founder ancestry. Comparative analysis of whole-genome sequences further revealed a moderate reduction in genetic diversity despite high levels of inbreeding. The brief and intense bottleneck was associated with high levels of drift, a flattening of the site frequency spectrum and a slight relaxation of purifying selection on mildly deleterious variants. Unlike some populations that have experienced prolonged reductions in effective population size, we did not observe any significant purging of highly deleterious variants. Interestingly, the population's success in the harsh environment can be attributed to preadaptation from their European taurine ancestry, suggesting no strong bioclimatic challenge, and also contradicting evidence for insular dwarfism. Genome scan for footprints of selection uncovered a majority of candidate genes related to nervous system function, likely reflecting rapid feralization driven by behavioral changes and complex social restructuring. The Amsterdam Island cattle offers valuable insights into rapid population establishment, feralization, and genetic adaptation in challenging environments. It also sheds light on the unique genetic legacies of feral populations, raising ethical questions according to conservation efforts.
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Affiliation(s)
- Mathieu Gautier
- CBGP, INRAE, CIRAD, IRD, L’institut Agro, Université de Montpellier, Montpellier, France
| | | | - Louise Camus
- CBGP, INRAE, CIRAD, IRD, L’institut Agro, Université de Montpellier, Montpellier, France
| | | | | | - Elise Guéret
- MGX-Montpellier GenomiX, University of Montpellier, CNRS, INSERM, Montpellier, France
| | - Stefan Engelen
- Retired, CEA, Institut de biologie François-Jacob, Genoscope, Université Paris-Saclay, Evry, France
| | - Arnaud Lemainque
- Retired, CEA, Institut de biologie François-Jacob, Genoscope, Université Paris-Saclay, Evry, France
| | - François Colas
- Retired, Saint-Paul and Amsterdam District, Terres Australes et Antarctiques Françaises, France
| | - Laurence Flori
- SELMET, INRAE, CIRAD, L’institut Agro, Université de Montpellier, Montpellier, France
| | - Tom Druet
- Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
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3
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Larsson MNA, Morell Miranda P, Pan L, Başak Vural K, Kaptan D, Rodrigues Soares AE, Kivikero H, Kantanen J, Somel M, Özer F, Johansson AM, Storå J, Günther T. Ancient Sheep Genomes Reveal Four Millennia of North European Short-Tailed Sheep in the Baltic Sea Region. Genome Biol Evol 2024; 16:evae114. [PMID: 38795367 PMCID: PMC11162877 DOI: 10.1093/gbe/evae114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 04/24/2024] [Accepted: 05/21/2024] [Indexed: 05/27/2024] Open
Abstract
Sheep are among the earliest domesticated livestock species, with a wide variety of breeds present today. However, it remains unclear how far back this diversity goes, with formal documentation only dating back a few centuries. North European short-tailed (NEST) breeds are often assumed to be among the oldest domestic sheep populations, even thought to represent relicts of the earliest sheep expansions during the Neolithic period reaching Scandinavia <6,000 years ago. This study sequenced the genomes (up to 11.6X) of five sheep remains from the Baltic islands of Gotland and Åland, dating from the Late Neolithic (∼4,100 cal BP) to historical times (∼1,600 CE). Our findings indicate that these ancient sheep largely possessed the genetic characteristics of modern NEST breeds, suggesting a substantial degree of long-term continuity of this sheep type in the Baltic Sea region. Despite the wide temporal spread, population genetic analyses show high levels of affinity between the ancient genomes and they also exhibit relatively high genetic diversity when compared to modern NEST breeds, implying a loss of diversity in most breeds during the last centuries associated with breed formation and recent bottlenecks. Our results shed light on the development of breeds in Northern Europe specifically as well as the development of genetic diversity in sheep breeds, and their expansion from the domestication center in general.
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Affiliation(s)
- Martin N A Larsson
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Pedro Morell Miranda
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Li Pan
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Kıvılcım Başak Vural
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Damla Kaptan
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | | | - Hanna Kivikero
- Department of Culture, University of Helsinki, Helsinki, Finland
| | - Juha Kantanen
- Natural Resources Institute Finland, Jokioinen, Finland
| | - Mehmet Somel
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Füsun Özer
- Department of Anthropology, Hacettepe University, Ankara, Turkey
| | - Anna M Johansson
- Department of Animal Biosciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jan Storå
- Osteoarchaeological Research Laboratory, Stockholm University, Stockholm, Sweden
| | - Torsten Günther
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
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4
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Zhang M, Song Y, Wang C, Sun G, Zhuang L, Guo M, Ren L, Wangdue S, Dong G, Dai Q, Cao P, Yang R, Liu F, Feng X, Bennett EA, Zhang X, Chen X, Wang F, Luan F, Dong W, Lu G, Hao D, Hou H, Wang H, Qiao H, Wang Z, Hu X, He W, Xi L, Wang W, Shao J, Sun Z, Yue L, Ding Y, Tashi N, Tsho Y, Tong Y, Yang Y, Zhu S, Miao B, Wang W, Zhang L, Hu S, Ni X, Fu Q. Ancient Mitogenomes Reveal the Maternal Genetic History of East Asian Dogs. Mol Biol Evol 2024; 41:msae062. [PMID: 38507661 PMCID: PMC11003542 DOI: 10.1093/molbev/msae062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 02/27/2024] [Accepted: 03/11/2024] [Indexed: 03/22/2024] Open
Abstract
Recent studies have suggested that dogs were domesticated during the Last Glacial Maximum (LGM) in Siberia, which contrasts with previous proposed domestication centers (e.g. Europe, the Middle East, and East Asia). Ancient DNA provides a powerful resource for the study of mammalian evolution and has been widely used to understand the genetic history of domestic animals. To understand the maternal genetic history of East Asian dogs, we have made a complete mitogenome dataset of 120 East Asian canids from 38 archaeological sites, including 102 newly sequenced from 12.9 to 1 ka BP (1,000 years before present). The majority (112/119, 94.12%) belonged to haplogroup A, and half of these (55/112, 49.11%) belonged to sub-haplogroup A1b. Most existing mitochondrial haplogroups were present in ancient East Asian dogs. However, mitochondrial lineages in ancient northern dogs (northeastern Eurasia and northern East Asia) were deeper and older than those in southern East Asian dogs. Results suggests that East Asian dogs originated from northeastern Eurasian populations after the LGM, dispersing in two possible directions after domestication. Western Eurasian (Europe and the Middle East) dog maternal ancestries genetically influenced East Asian dogs from approximately 4 ka BP, dramatically increasing after 3 ka BP, and afterwards largely replaced most primary maternal lineages in northern East Asia. Additionally, at least three major mitogenome sub-haplogroups of haplogroup A (A1a, A1b, and A3) reveal at least two major dispersal waves onto the Qinghai-Tibet Plateau in ancient times, indicating eastern (A1b and A3) and western (A1a) Eurasian origins.
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Affiliation(s)
- Ming Zhang
- China-Central Asia “the Belt and Road” Joint Laboratory on Human and Environment Research, Key Laboratory of Cultural Heritage Research and Conservation, School of Culture Heritage, Northwest University, Xi’an, China
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
| | - Yanbo Song
- School of Archaeology, Shandong University, Jinan, China
| | - Caihui Wang
- China-Central Asia “the Belt and Road” Joint Laboratory on Human and Environment Research, Key Laboratory of Cultural Heritage Research and Conservation, School of Culture Heritage, Northwest University, Xi’an, China
| | - Guoping Sun
- Zhejiang Provincial Institute of Cultural Relics and Archaeology, Hangzhou, China
| | | | | | - Lele Ren
- School of History and Culture, Lanzhou University, Lanzhou, China
| | - Shargan Wangdue
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, China
| | - Guanghui Dong
- Key Laboratory of Western China's Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou, China
| | - Qingyan Dai
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
| | - Peng Cao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
| | - Ruowei Yang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
| | - Feng Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
| | - Xiaotian Feng
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
| | - E Andrew Bennett
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
| | - Xiaoling Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
| | - Xi Chen
- Department of Cultural Heritage and Museology, Nanjing Normal University, Nanjing, China
| | - Fen Wang
- School of Archaeology, Shandong University, Jinan, China
| | - Fengshi Luan
- School of Archaeology, Shandong University, Jinan, China
| | - Wenbin Dong
- Shandong Provincial Institute of Cultural Relics and Archaeology, Jinan, China
| | - Guoquan Lu
- School of Archaeology, Shandong University, Jinan, China
| | - Daohua Hao
- Shandong Provincial Institute of Cultural Relics and Archaeology, Jinan, China
| | - Hongwei Hou
- Gansu Provincial Institute of Cultural Relics and Archaeology, Lanzhou, China
| | - Hui Wang
- Gansu Provincial Institute of Cultural Relics and Archaeology, Lanzhou, China
- Fudan Archaeological Science Institute, Fudan University, Shanghai, China
| | - Hong Qiao
- Qinghai Provincial Cultural Relics and Archaeology Institute, Xining, China
| | - Zhongxin Wang
- Qinghai Provincial Cultural Relics and Archaeology Institute, Xining, China
| | - Xiaojun Hu
- Qinghai Provincial Cultural Relics and Archaeology Institute, Xining, China
| | - Wei He
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, China
| | - Lin Xi
- Shaanxi Academy of Archaeology, Xi’an, China
| | - Weilin Wang
- School of Archaeology and Museology, Shanxi University, Taiyuan, China
| | - Jing Shao
- Shaanxi Academy of Archaeology, Xi’an, China
| | | | | | - Yan Ding
- Shaanxi Academy of Archaeology, Xi’an, China
| | - Norbu Tashi
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, China
| | - Yang Tsho
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, China
| | - Yan Tong
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, China
| | - Yangheshan Yang
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Shilun Zhu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Bo Miao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
| | - Wenjun Wang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
- Science and Technology Archaeology, National Centre for Archaeology, Beijing, China
| | - Lizhao Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
| | - Songmei Hu
- Joint International Research Laboratory of Environmental and Social Archaeology, Shandong University, Qingdao, China
- Shaanxi Academy of Archaeology, Xi’an, China
| | - Xijun Ni
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
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Koshkina O, Deniskova T, Dotsev A, Kunz E, Selionova M, Medugorac I, Zinovieva N. Phylogenetic Analysis of Russian Native Sheep Breeds Based on mtDNA Sequences. Genes (Basel) 2023; 14:1701. [PMID: 37761841 PMCID: PMC10531259 DOI: 10.3390/genes14091701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 08/22/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
Eurasia is represented by all climatic zones and various environments. A unique breed variety of farm animals has been developed in Russia, whose territory covers a large area of the continent. A total of 69 local breeds and types of dairy, wool, and meat sheep (Ovis aries) are maintained here. However, the genetic diversity and maternal origin of these local breeds have not been comprehensively investigated. In this study, we describe the diversity and phylogeny of Russian sheep breeds inhabiting different geographical regions based on the analysis of complete sequences of mitochondrial genomes (mtDNA). Complete mtDNA sequences of the studied sheep were obtained using next-generation sequencing technology (NGS). All investigated geographical groups of sheep were characterized by high haplotype (Hd = 0.9992) and nucleotide diversity (π = 0.00378). Analysis of the AMOVA results showed that genetic diversity was majorly determined by within-population differences (77.87%). We identified 128 haplotypes in all studied sheep. Haplotypes belonged to the following haplogroups: B (64.8%), A (28.9%), C (5.5%), and D (0.8%). Haplogroup B was predominant in the western part of Russia. A high level of mtDNA polymorphism in the studied groups of local sheep indicates the presence of a significant reserve of unique genotypes in Russia, which is to be explored.
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Affiliation(s)
- Olga Koshkina
- L.K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy 60, Podolsk Municipal District, Moscow 142132, Russia; (O.K.); (A.D.); (N.Z.)
| | - Tatiana Deniskova
- L.K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy 60, Podolsk Municipal District, Moscow 142132, Russia; (O.K.); (A.D.); (N.Z.)
| | - Arsen Dotsev
- L.K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy 60, Podolsk Municipal District, Moscow 142132, Russia; (O.K.); (A.D.); (N.Z.)
| | - Elisabeth Kunz
- Population Genomics Group, Department of Veterinary Sciences, Ludwig-Maximilians-University Munich, 82152 Munich, Germany; (E.K.); (I.M.)
| | - Marina Selionova
- Timiryazev Agricultural Academy, Russian State Agrarian University-Moscow, Timiryazevskaya Street, 41, Moscow 127550, Russia;
| | - Ivica Medugorac
- Population Genomics Group, Department of Veterinary Sciences, Ludwig-Maximilians-University Munich, 82152 Munich, Germany; (E.K.); (I.M.)
| | - Natalia Zinovieva
- L.K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy 60, Podolsk Municipal District, Moscow 142132, Russia; (O.K.); (A.D.); (N.Z.)
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6
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Demir E, Moravčíková N, Argun Karsli B, Kasarda R, Aytekin I, Bilginer U, Karsli T. Mitochondrial DNA diversity of D-loop region in three native Turkish cattle breeds. Arch Anim Breed 2023; 66:31-40. [PMID: 36756623 PMCID: PMC9901521 DOI: 10.5194/aab-66-31-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 01/05/2023] [Indexed: 01/26/2023] Open
Abstract
This study aimed to reveal the genetic variability of mitochondrial DNA (mtDNA) displacement-loop (D-loop) region in 62 animals belonging to three native Turkish cattle breeds, namely Anatolian Black (AB), East Anatolian Red (EAR) and Zavot (ZAV), and to conduct phylogenetic relationship analyses to obtain deeper information on their genetic origin and breeding history by comparison of 6 taurine and 11 indicine breeds, together with 66 polymorphic sites, a total of 31 haplotypes, of which 15, 10 and 6 were detected in AB, EAR and ZAV, respectively. Mean nucleotide and haplotype diversity were 0.01 and 0.891, respectively, whereas the genetic differentiation derived from Wright's F ST index was 0.174 across the breeds. A significant level of total variation (17.42 %) was observed among breeds in molecular variance analysis. Six main haplogroups (T, T1, T2, T3, Q and I2) were detected in Anatolian cattle populations, where T3 was the most frequent among breeds (43.55 %), whereas I2, an indicine specific haplogroup, was observed only in ZAV. At the breed level, phylogenetic analyses supported by 198 sequences of 17 cattle breeds and 3 outgroup species retrieved from the GenBank clustered native Turkish cattle breeds with the taurine group rather than the indicine one, as expected. However, indicine admixture at low frequency (8.89 %) was detected in the ZAV breed for the first time due to more likely gene flow from indicine cattle breeds raised in neighbour countries, particularly Iran. This finding should be further investigated in all native Turkish and indicine cattle breeds from nearby countries to clarify gene flow and indicine admixture in Anatolian cattle.
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Affiliation(s)
- Eymen Demir
- Department of Animal Science, Faculty of Agriculture, Akdeniz
University, Antalya, 07058, Türkiye,Institute of Nutrition and Genomics, Faculty of Agrobiology and Food
Resources, Slovak University of Agriculture in Nitra 94976, Slovak Republic
| | - Nina Moravčíková
- Institute of Nutrition and Genomics, Faculty of Agrobiology and Food
Resources, Slovak University of Agriculture in Nitra 94976, Slovak Republic
| | - Bahar Argun Karsli
- Department of Agricultural Biotechnology, Faculty of Agriculture,
Eskisehir Osmangazi University, Eskisehir 26040, Türkiye
| | - Radovan Kasarda
- Institute of Nutrition and Genomics, Faculty of Agrobiology and Food
Resources, Slovak University of Agriculture in Nitra 94976, Slovak Republic
| | - Ibrahim Aytekin
- Department of Animal Science, Faculty of Agriculture, University of
Selçuk, Konya 42130, Türkiye
| | - Umit Bilginer
- Department of Animal Science, Faculty of Agriculture, Akdeniz
University, Antalya, 07058, Türkiye
| | - Taki Karsli
- Department of Animal Science, Faculty of Agriculture, Eskisehir
Osmangazi University, Eskisehir 26160, Türkiye
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7
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Godinez CJP, Layos JKN, Yamamoto Y, Kunieda T, Duangjinda M, Liao LM, Huang XH, Nishibori M. Unveiling new perspective of phylogeography, genetic diversity, and population dynamics of Southeast Asian and Pacific chickens. Sci Rep 2022; 12:14609. [PMID: 36028749 PMCID: PMC9418149 DOI: 10.1038/s41598-022-18904-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 08/22/2022] [Indexed: 11/10/2022] Open
Abstract
The complex geographic and temporal origins of chicken domestication have attracted wide interest in molecular phylogeny and phylogeographic studies as they continue to be debated up to this day. In particular, the population dynamics and lineage-specific divergence time estimates of chickens in Southeast Asia (SEA) and the Pacific region are not well studied. Here, we analyzed 519 complete mitochondrial DNA control region sequences and identified 133 haplotypes with 70 variable sites. We documented 82.7% geographically unique haplotypes distributed across major haplogroups except for haplogroup C, suggesting high polymorphism among studied individuals. Mainland SEA (MSEA) chickens have higher overall genetic diversity than island SEA (ISEA) chickens. Phylogenetic trees and median-joining network revealed evidence of a new divergent matrilineage (i.e., haplogroup V) as a sister-clade of haplogroup C. The maximum clade credibility tree estimated the earlier coalescence age of ancestral D-lineage (i.e., sub-haplogroup D2) of continental chickens (3.7 kya; 95% HPD 1985-4835 years) while island populations diverged later at 2.1 kya (95% HPD 1467-2815 years). This evidence of earlier coalescence age of haplogroup D ancestral matriline exemplified dispersal patterns to the ISEA, and thereafter the island clade diversified as a distinct group.
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Affiliation(s)
- Cyrill John P Godinez
- Laboratory of Animal Genetics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8528, Japan.
- Department of Animal Science, College of Agriculture and Food Science, Visayas State University, Visca, Baybay City, Leyte, 6521, Philippines.
| | - John King N Layos
- Laboratory of Animal Genetics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8528, Japan
- College of Agriculture and Forestry, Capiz State University, Burias, Mambusao, Capiz, 5807, Philippines
| | - Yoshio Yamamoto
- Laboratory of Animal Genetics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8528, Japan
| | - Tetsuo Kunieda
- Faculty of Veterinary Medicine, Okayama University of Science, Imabari, Ehime, 794-8555, Japan
| | - Monchai Duangjinda
- Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Lawrence M Liao
- Laboratory of Aquatic Botany, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8528, Japan
| | - Xun-He Huang
- School of Life Sciences, Jiaying University, Meizhou, 514015, China
| | - Masahide Nishibori
- Laboratory of Animal Genetics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8528, Japan.
- Department of Animal Science, College of Agriculture and Food Science, Visayas State University, Visca, Baybay City, Leyte, 6521, Philippines.
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8
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Kharzinova VR, Akopyan NA, Dotsev AV, Deniskova TE, Sermyagin AA, Karpushkina TV, Solovieva AD, Brem G, Zinovieva NA. Genetic Diversity and Phylogenetic Relationships of Russian Pig Breeds Based on the Analysis of mtDNA D-Loop Polymorphism. RUSS J GENET+ 2022. [DOI: 10.1134/s102279542208004x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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Dorji J, Vander Jagt CJ, Chamberlain AJ, Cocks BG, MacLeod IM, Daetwyler HD. Recovery of mitogenomes from whole genome sequences to infer maternal diversity in 1883 modern taurine and indicine cattle. Sci Rep 2022; 12:5582. [PMID: 35379858 PMCID: PMC8980051 DOI: 10.1038/s41598-022-09427-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 03/18/2022] [Indexed: 11/09/2022] Open
Abstract
Maternal diversity based on a sub-region of mitochondrial genome or variants were commonly used to understand past demographic events in livestock. Additionally, there is growing evidence of direct association of mitochondrial genetic variants with a range of phenotypes. Therefore, this study used complete bovine mitogenomes from a large sequence database to explore the full spectrum of maternal diversity. Mitogenome diversity was evaluated among 1883 animals representing 156 globally important cattle breeds. Overall, the mitogenomes were diverse: presenting 11 major haplogroups, expanding to 1309 unique haplotypes, with nucleotide diversity 0.011 and haplotype diversity 0.999. A small proportion of African taurine (3.5%) and indicine (1.3%) haplogroups were found among the European taurine breeds and composites. The haplogrouping was largely consistent with the population structure derived from alternate clustering methods (e.g. PCA and hierarchical clustering). Further, we present evidence confirming a new indicine subgroup (I1a, 64 animals) mainly consisting of breeds originating from China and characterised by two private mutations within the I1 haplogroup. The total genetic variation was attributed mainly to within-breed variance (96.9%). The accuracy of the imputation of missing genotypes was high (99.8%) except for the relatively rare heteroplasmic genotypes, suggesting the potential for trait association studies within a breed.
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Affiliation(s)
- Jigme Dorji
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia.
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia.
| | - Christy J Vander Jagt
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Amanda J Chamberlain
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Benjamin G Cocks
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Iona M MacLeod
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia.
| | - Hans D Daetwyler
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
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10
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Ren T, Nunome M, Suzuki T, Matsuda Y. Genetic diversity and population genetic structure of Cambodian indigenous chickens. Anim Biosci 2022; 35:826-837. [PMID: 34991210 PMCID: PMC9066038 DOI: 10.5713/ab.21.0351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 11/29/2021] [Indexed: 11/27/2022] Open
Abstract
Objective Cambodia is located within the distribution range of the red junglefowl, the common ancestor of domestic chickens. Although a variety of indigenous chickens have been reared in Cambodia since ancient times, their genetic characteristics have yet to be sufficiently defined. Here, we conducted a large-scale population genetic study to investigate the genetic diversity and population genetic structure of Cambodian indigenous chickens and their phylogenetic relationships with other chicken breeds and native chickens worldwide. Methods A Bayesian phylogenetic tree was constructed based on 625 mitochondrial DNA D-loop sequences, and Bayesian clustering analysis was performed for 666 individuals with 23 microsatellite markers, using samples collected from 28 indigenous chicken populations in 24 provinces and three commercial chicken breeds. Results A total of 92 haplotypes of mitochondrial D-loop sequences belonging to haplogroups A to F and J were detected in Cambodian chickens; in the indigenous chickens, haplogroup D (44.4%) was the most common, and haplogroups A (21.0%) and B (13.2%) were also dominant. However, haplogroup J, which is rare in domestic chickens but abundant in Thai red junglefowl, was found at a high frequency (14.5%), whereas the frequency of haplogroup E was considerably lower (4.6%). Population genetic structure analysis based on microsatellite markers revealed the presence of three major genetic clusters in Cambodian indigenous chickens. Their genetic diversity was relatively high, which was similar to findings reported for indigenous chickens from other Southeast Asian countries. Conclusion Cambodian indigenous chickens are characterized by mitochondrial D-loop haplotypes that are common to indigenous chickens throughout Southeast Asia, and may retain many of the haplotypes that originated from wild ancestral populations. These chickens exhibit high population genetic diversity, and the geographical distribution of three major clusters may be attributed to inter-regional trade and poultry transportation routes within Cambodia or international movement between Cambodia and other countries.
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Affiliation(s)
- Theary Ren
- General Directorate of Animal Health and Production, National Animal Health and Production Research Institute, Phnom Penh 12352, Cambodia.,Asian Satellite Campuses Institute, Nagoya University, Nagoya 464-8601, Japan
| | - Mitsuo Nunome
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Takayuki Suzuki
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan.,Laboratory of Avian Bioscience, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Yoichi Matsuda
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan.,Laboratory of Avian Bioscience, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
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11
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Cubric‐Curik V, Novosel D, Brajkovic V, Rota Stabelli O, Krebs S, Sölkner J, Šalamon D, Ristov S, Berger B, Trivizaki S, Bizelis I, Ferenčaković M, Rothammer S, Kunz E, Simčič M, Dovč P, Bunevski G, Bytyqi H, Marković B, Brka M, Kume K, Stojanović S, Nikolov V, Zinovieva N, Schönherz AA, Guldbrandtsen B, Čačić M, Radović S, Miracle P, Vernesi C, Curik I, Medugorac I. Large‐scale mitogenome sequencing reveals consecutive expansions of domestic taurine cattle and supports sporadic aurochs introgression. Evol Appl 2021; 15:663-678. [PMID: 35505892 PMCID: PMC9046920 DOI: 10.1111/eva.13315] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 10/01/2021] [Accepted: 10/11/2021] [Indexed: 11/29/2022] Open
Affiliation(s)
- Vlatka Cubric‐Curik
- Department of Animal Science University of Zagreb Faculty of Agriculture Zagreb Croatia
| | - Dinko Novosel
- Department of Animal Science University of Zagreb Faculty of Agriculture Zagreb Croatia
- Department of Pathology Croatian Veterinary Institute Zagreb Croatia
| | - Vladimir Brajkovic
- Department of Animal Science University of Zagreb Faculty of Agriculture Zagreb Croatia
| | - Omar Rota Stabelli
- Department of Sustainable Agro‐Ecosystems and Bioresources, Research and Innovation Centre Fondazione Edmund Mach S. Michele all' Adige Italy
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis Gene Center Ludwig Maximilians University Munich Munich Germany
| | - Johann Sölkner
- Division of Livestock Sciences Department of Sustainable Agricultural Systems BOKU‐University of Natural Resources and Life Sciences Vienna Vienna Austria
| | - Dragica Šalamon
- Department of Animal Science University of Zagreb Faculty of Agriculture Zagreb Croatia
| | | | - Beate Berger
- AREC Raumberg‐Gumpenstein Institute of Organic Farming and Biodiversity of Farm Animals Thalheim Austria
| | | | - Iosif Bizelis
- Faculty of Animal Science and Aquaculture Department of Animal Breeding & Husbandry Agricultural University of Athens Athens Greece
| | - Maja Ferenčaković
- Department of Animal Science University of Zagreb Faculty of Agriculture Zagreb Croatia
| | - Sophie Rothammer
- Population Genomics Group Faculty of Veterinary Medicine Department of Veterinary Sciences LMU Munich Munich Germany
| | - Elisabeth Kunz
- Population Genomics Group Faculty of Veterinary Medicine Department of Veterinary Sciences LMU Munich Munich Germany
| | - Mojca Simčič
- Biotechnical Faculty Department of Animal Science University of Ljubljana Ljubljana Slovenia
| | - Peter Dovč
- Biotechnical Faculty Department of Animal Science University of Ljubljana Ljubljana Slovenia
| | - Gojko Bunevski
- Faculty of Agricultural Sciences and Food University Ss. Cyril and Methodius Skopje Macedonia
| | - Hysen Bytyqi
- Faculty of Agriculture and Veterinary Department of Animal Science University of Prishtina Prishtina Kosovo
| | - Božidarka Marković
- Biotechnical Faculty Department of Livestock Science University of Montenegro Podgorica Montenegro
| | - Muhamed Brka
- Faculty of Agriculture and Food Science Institute of Animal Sciences University of Sarajevo Sarajevo Bosnia and Herzegovina
| | | | - Srđan Stojanović
- Ministry of Agriculture, Forestry and Water Management Beograd Serbia
| | - Vasil Nikolov
- Executive Agency for Selection and Reproduction in Animal Breeding Sofia Bulgaria
| | - Natalia Zinovieva
- Center of Biotechnology and Molecular Diagnostics of the L.K. Ernst Institute of Animal Husbandry Moscow Region Russia
| | | | - Bernt Guldbrandtsen
- Department of Animal Sciences Rheinische Friedrich‐Wilhelms‐Universität Bonn Bonn Germany
| | - Mato Čačić
- Croatian Agricultural Agency Zagreb Croatia
| | - Siniša Radović
- Institute for Quaternary Palaeontology and Geology Croatian Academy of Sciences and Arts Zagreb Croatia
| | - Preston Miracle
- Department of Archaeology University of Cambridge Cambridge UK
| | - Cristiano Vernesi
- Department of Sustainable Agro‐Ecosystems and Bioresources, Research and Innovation Centre Fondazione Edmund Mach S. Michele all' Adige Italy
| | - Ino Curik
- Department of Animal Science University of Zagreb Faculty of Agriculture Zagreb Croatia
| | - Ivica Medugorac
- Population Genomics Group Faculty of Veterinary Medicine Department of Veterinary Sciences LMU Munich Munich Germany
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12
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Huang X, Weng Z, He Y, Miao Y, Luo W, Zhang X, Zhong F, Du B. Mitochondrial DNA diversity and demographic history of Black-boned chickens in China. Mitochondrial DNA B Resour 2021; 6:1462-1467. [PMID: 33969196 PMCID: PMC8079009 DOI: 10.1080/23802359.2021.1912668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 03/29/2021] [Indexed: 11/30/2022] Open
Abstract
Black-boned chickens (Gallus domesticus, herein abbreviated BBCs) are well known for their unique appearance and medicinal properties and have a long breeding history in China. However, the genetic diversity and demographic history of BBCs remain unclear. In this study, we analyzed 844 mitochondrial DNA D-loop sequences, including 346 de novo sequences and 498 previously published sequences from 20 BBC breeds. We detected a generally high level of genetic diversity among the BBCs, with average haplotype and nucleotide diversities of 0.917 ± 0.0049 and 0.01422, respectively. Nucleotide diversity was highest in populations from Southwest China (0.01549 ± 0.00026), particularly in Yunnan Province (0.01624 ± 0.00025). Significant genetic divergence was detected between most breeds, particularly between Yunnan chickens and those from all other provinces. Haplogroups F and G had the highest levels of genetic diversity and were restricted to Southwest China, particularly Yunnan Province. Based on neutrality tests and mismatch distribution analyses, we did not obtain evidence for rapid population expansions and observed similar demographic histories in BBCs and local non-BBCs. Our results suggest that Chinese BBCs have complex breeding histories and may be selected in situ from local domestic chickens. These results improve our understanding of the genetic heritage and breeding histories of these desirable chickens.
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Affiliation(s)
- Xunhe Huang
- Guangdong Provincial Key Laboratory of Conservation and Precision Utilization of Characteristic Agricultural Resources in Mountainous Areas, Guangdong Innovation Centre for Science and Technology of Wuhua Yellow Chicken, School of Life Science, JiaYing University, Meizhou, China
| | - Zhuoxian Weng
- Guangdong Provincial Key Laboratory of Conservation and Precision Utilization of Characteristic Agricultural Resources in Mountainous Areas, Guangdong Innovation Centre for Science and Technology of Wuhua Yellow Chicken, School of Life Science, JiaYing University, Meizhou, China
- College of Animal Science and Technology, Hunan Agricultural University,Changsha, China
| | - Yujing He
- Guangdong Provincial Key Laboratory of Conservation and Precision Utilization of Characteristic Agricultural Resources in Mountainous Areas, Guangdong Innovation Centre for Science and Technology of Wuhua Yellow Chicken, School of Life Science, JiaYing University, Meizhou, China
| | - Yongwang Miao
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Wei Luo
- College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Xiquan Zhang
- College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Fusheng Zhong
- Guangdong Provincial Key Laboratory of Conservation and Precision Utilization of Characteristic Agricultural Resources in Mountainous Areas, Guangdong Innovation Centre for Science and Technology of Wuhua Yellow Chicken, School of Life Science, JiaYing University, Meizhou, China
- College of Animal Science and Technology, Hunan Agricultural University,Changsha, China
| | - Bingwang Du
- Guangdong Provincial Key Laboratory of Conservation and Precision Utilization of Characteristic Agricultural Resources in Mountainous Areas, Guangdong Innovation Centre for Science and Technology of Wuhua Yellow Chicken, School of Life Science, JiaYing University, Meizhou, China
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13
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Zhang M, Sun G, Ren L, Yuan H, Dong G, Zhang L, Liu F, Cao P, Ko AMS, Yang MA, Hu S, Wang GD, Fu Q. Ancient DNA Evidence from China Reveals the Expansion of Pacific Dogs. Mol Biol Evol 2021; 37:1462-1469. [PMID: 31913480 DOI: 10.1093/molbev/msz311] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The ancestral homeland of Australian dingoes and Pacific dogs is proposed to be in South China. However, the location and timing of their dispersal and relationship to dog domestication is unclear. Here, we sequenced 7,000- to 2,000-year-old complete mitochondrial DNA (mtDNA) genomes of 27 ancient canids (one gray wolf and 26 domestic dogs) from the Yellow River and Yangtze River basins (YYRB). These are the first complete ancient mtDNA of Chinese dogs from the cradle of early Chinese civilization. We found that most ancient dogs (18/26) belong to the haplogroup A1b lineage that is found in high frequency in present-day Australian dingoes and precolonial Pacific Island dogs but low frequency in present-day China. Particularly, a 7,000-year-old dog from the Tianluoshan site in Zhejiang province possesses a haplotype basal to the entire haplogroup A1b lineage. We propose that A1b lineage dogs were once widely distributed in the YYRB area. Following their dispersal to South China, and then into Southeast Asia, New Guinea and remote Oceania, they were largely replaced by dogs belonging to other lineages in the last 2,000 years in present-day China, especially North China.
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Affiliation(s)
- Ming Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Life and Paleoenvironment, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Guoping Sun
- Zhejiang Provincial Institute of Relics and Archaeology, Hangzhou, China
| | - Lele Ren
- School of History and Culture, Lanzhou University, Lanzhou, China
| | - Haibing Yuan
- National Demonstration Center for Experimental Archaeology Education, Department of Archaeology, Sichuan University, Chengdu, China
| | - Guanghui Dong
- Key Laboratory of Western China's Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou, China
| | - Lizhao Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | - Feng Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | - Peng Cao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | - Albert Min-Shan Ko
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | - Melinda A Yang
- Department of Biology, University of Richmond, Richmond, VA
| | - Songmei Hu
- Shaanxi Academy of Archaeology, Xi'an, China
| | - Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Life and Paleoenvironment, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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14
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Mauki DH, Adeola AC, Ng’ang’a SI, Tijjani A, Akanbi IM, Sanke OJ, Abdussamad AM, Olaogun SC, Ibrahim J, Dawuda PM, Mangbon GF, Gwakisa PS, Yin TT, Peng MS, Zhang YP. Genetic variation of Nigerian cattle inferred from maternal and paternal genetic markers. PeerJ 2021; 9:e10607. [PMID: 33717663 PMCID: PMC7938780 DOI: 10.7717/peerj.10607] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 11/29/2020] [Indexed: 01/29/2023] Open
Abstract
The African cattle provide unique genetic resources shaped up by both diverse tropical environmental conditions and human activities, the assessment of their genetic diversity will shade light on the mechanism of their remarkable adaptive capacities. We therefore analyzed the genetic diversity of cattle samples from Nigeria using both maternal and paternal DNA markers. Nigerian cattle can be assigned to 80 haplotypes based on the mitochondrial DNA (mtDNA) D-loop sequences and haplotype diversity was 0.985 + 0.005. The network showed two major matrilineal clustering: the dominant cluster constituting the Nigerian cattle together with other African cattle while the other clustered Eurasian cattle. Paternal analysis indicates only zebu haplogroup in Nigerian cattle with high genetic diversity 1.000 ± 0.016 compared to other cattle. There was no signal of maternal genetic structure in Nigerian cattle population, which may suggest an extensive genetic intermixing within the country. The absence of Bos indicus maternal signal in Nigerian cattle is attributable to vulnerability bottleneck of mtDNA lineages and concordance with the view of male zebu genetic introgression in African cattle. Our study shades light on the current genetic diversity in Nigerian cattle and population history in West Africa.
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Affiliation(s)
- David H. Mauki
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Chinese Academy of Sciences, Sino-Africa Joint Research Center, Kunming, Yunnan, China
- University of Academy of Sciences, Kunming College of Life Science, Kunming, Yunnan, China
| | - Adeniyi C. Adeola
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Chinese Academy of Sciences, Sino-Africa Joint Research Center, Kunming, Yunnan, China
| | - Said I. Ng’ang’a
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Chinese Academy of Sciences, Sino-Africa Joint Research Center, Kunming, Yunnan, China
- University of Academy of Sciences, Kunming College of Life Science, Kunming, Yunnan, China
| | | | - Ibikunle Mark Akanbi
- Ministry of Agriculture and Rural Development, Secretariat, Ibadan, Oyo, Nigeria
| | - Oscar J. Sanke
- Taraba State Ministry of Agriculture and Natural Resources, Jalingo, Taraba, Nigeria
| | | | - Sunday C. Olaogun
- Department of Veterinary Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Jebi Ibrahim
- College of veterinary medicine, department of theriogenology, University of agriculture, Makurdi, Makurdi, Benue, Nigeria
| | - Philip M. Dawuda
- Department of Veterinary Surgery and Theriogenology, College of Veterinary Medicine, University of Agriculture Makurdi, Makurdi, Benue, Nigeria
| | | | - Paul S. Gwakisa
- Department of Microbiology, Parasitology and Biotechnology/ Genome Science Center, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Ting-Ting Yin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Chinese Academy of Sciences, Sino-Africa Joint Research Center, Kunming, Yunnan, China
- University of Academy of Sciences, Kunming College of Life Science, Kunming, Yunnan, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Chinese Academy of Sciences, Sino-Africa Joint Research Center, Kunming, Yunnan, China
- University of Academy of Sciences, Kunming College of Life Science, Kunming, Yunnan, China
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan, China
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15
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Koupadi K, Fontani F, Ciucani MM, Maini E, De Fanti S, Cattani M, Curci A, Nenzioni G, Reggiani P, Andrews AJ, Sarno S, Bini C, Pelotti S, Caniglia R, Luiselli D, Cilli E. Population Dynamics in Italian Canids between the Late Pleistocene and Bronze Age. Genes (Basel) 2020; 11:genes11121409. [PMID: 33256122 PMCID: PMC7761486 DOI: 10.3390/genes11121409] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/21/2020] [Accepted: 11/23/2020] [Indexed: 12/20/2022] Open
Abstract
Dog domestication is still largely unresolved due to time-gaps in the sampling of regions. Ancient Italian canids are particularly understudied, currently represented by only a few specimens. In the present study, we sampled 27 canid remains from Northern Italy dated between the Late Pleistocene and Bronze Age to assess their genetic variability, and thus add context to dog domestication dynamics. They were targeted at four DNA fragments of the hypervariable region 1 of mitochondrial DNA. A total of 11 samples had good DNA preservation and were used for phylogenetic analyses. The dog samples were assigned to dog haplogroups A, C and D, and a Late Pleistocene wolf was set into wolf haplogroup 2. We present our data in the landscape of ancient and modern dog genetic variability, with a particular focus on the ancient Italian samples published thus far. Our results suggest there is high genetic variability within ancient Italian canids, where close relationships were evident between both a ~24,700 years old Italian canid, and Iberian and Bulgarian ancient dogs. These findings emphasize that disentangling dog domestication dynamics benefits from the analysis of specimens from Southern European regions.
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Affiliation(s)
- Kyriaki Koupadi
- Hellenic Ministry of Culture and Sports, Ephorate of Antiquities of the City of Athens, Makriyianni 2-4, 11742 Athens, Greece;
- Department of Cultural Heritage, University of Bologna, Via Degli Ariani 1, 48121 Ravenna, Italy; (F.F.); (A.J.A.); (D.L.)
| | - Francesco Fontani
- Department of Cultural Heritage, University of Bologna, Via Degli Ariani 1, 48121 Ravenna, Italy; (F.F.); (A.J.A.); (D.L.)
| | - Marta Maria Ciucani
- Section for Evolutionary Genomics, the GLOBE Institute, University of Copenhagen, Oester Voldgade 5-7, 1350 Copenhagen, Denmark;
| | - Elena Maini
- ArcheoLaBio—Research Centre for Bioarchaeology, Department of History and Cultures, University of Bologna, Via San Vitale 30, 48121 Ravenna, Italy; (E.M.); (A.C.)
| | - Sara De Fanti
- Department of Biological Geological and Environmental Sciences, University of Bologna, via Selmi 3, 40126 Bologna, Italy; (S.D.F.); (S.S.)
- Interdepartmental Centre “Alma Mater Research Institute on Global Challenges and Climate Change (Alma Climate)”, University of Bologna, Via Petroni 26, 40126 Bologna, Italy
| | - Maurizio Cattani
- Department of History and Cultures, University of Bologna, Via San Vitale 30, 48121 Ravenna, Italy;
| | - Antonio Curci
- ArcheoLaBio—Research Centre for Bioarchaeology, Department of History and Cultures, University of Bologna, Via San Vitale 30, 48121 Ravenna, Italy; (E.M.); (A.C.)
| | - Gabriele Nenzioni
- Museo della Preistoria “Luigi Donini”, Via Fratelli Canova 49, 40068 San Lazzaro di Savena, BO, Italy;
| | - Paolo Reggiani
- Paleostudy, Via Martiri delle Foibe 1, 35028 Piove di Sacco, PD, Italy;
| | - Adam J. Andrews
- Department of Cultural Heritage, University of Bologna, Via Degli Ariani 1, 48121 Ravenna, Italy; (F.F.); (A.J.A.); (D.L.)
- Department of Biological Geological and Environmental Sciences, University of Bologna, via Selmi 3, 40126 Bologna, Italy; (S.D.F.); (S.S.)
| | - Stefania Sarno
- Department of Biological Geological and Environmental Sciences, University of Bologna, via Selmi 3, 40126 Bologna, Italy; (S.D.F.); (S.S.)
| | - Carla Bini
- Department of Medical and Surgical Sciences, University of Bologna, Via Irnerio 49, 40126 Bologna, Italy; (C.B.); (S.P.)
| | - Susi Pelotti
- Department of Medical and Surgical Sciences, University of Bologna, Via Irnerio 49, 40126 Bologna, Italy; (C.B.); (S.P.)
| | - Romolo Caniglia
- Unit for Conservation Genetics (BIO-CGE), Italian Institute for Environmental Protection and Research (ISPRA), Via Ca’ Fornacetta 9, 40064 Ozzano dell’Emilia, BO, Italy;
| | - Donata Luiselli
- Department of Cultural Heritage, University of Bologna, Via Degli Ariani 1, 48121 Ravenna, Italy; (F.F.); (A.J.A.); (D.L.)
| | - Elisabetta Cilli
- Department of Cultural Heritage, University of Bologna, Via Degli Ariani 1, 48121 Ravenna, Italy; (F.F.); (A.J.A.); (D.L.)
- Correspondence:
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16
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Hata A, Takenouchi A, Kinoshita K, Hirokawa M, Igawa T, Nunome M, Suzuki T, Tsudzuki M. Geographic Origin and Genetic Characteristics of Japanese Indigenous Chickens Inferred from Mitochondrial D-Loop Region and Microsatellite DNA Markers. Animals (Basel) 2020; 10:E2074. [PMID: 33182330 PMCID: PMC7695345 DOI: 10.3390/ani10112074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 10/30/2020] [Accepted: 11/03/2020] [Indexed: 01/10/2023] Open
Abstract
Japanese indigenous chickens have a long breeding history, possibly beginning 2000 years ago. Genetic characterization of Japanese indigenous chickens has been performed using mitochondrial D-loop region and microsatellite DNA markers. Their phylogenetic relationships with chickens worldwide and genetic variation within breeds have not yet been examined. In this study, the genetic characteristics of 38 Japanese indigenous chicken breeds were assessed by phylogenetic analyses of mitochondrial D-loop sequences compared with those of indigenous chicken breeds overseas. To evaluate the genetic relationships among Japanese indigenous chicken breeds, a STRUCTURE analysis was conducted using 27 microsatellite DNA markers. D-loop sequences of Japanese indigenous chickens were classified into five major haplogroups, A-E, among 15 haplogroups found in chickens worldwide. The haplogroup composition suggested that Japanese indigenous chickens originated mainly from China, with some originating from Southeast Asia. The STRUCTURE analyses revealed that Japanese indigenous chickens are genetically differentiated from chickens overseas; Japanese indigenous chicken breeds possess distinctive genetic characteristics, and Jidori breeds, which have been reared in various regions of Japan for a long time, are genetically close to each other. These results provide new insights into the history of chickens around Asia in addition to novel genetic data for the conservation of Japanese indigenous chickens.
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Affiliation(s)
- Ayano Hata
- Laboratory of Avian Bioscience, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan;
| | - Atsushi Takenouchi
- Laboratory of Animal Breeding and Genetics, Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan;
- Japanese Avian Bioresource Project Research Center, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan;
| | - Keiji Kinoshita
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan;
| | - Momomi Hirokawa
- Laboratory of Animal Genetics, Department of Applied Molecular Biosciences, School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan;
| | - Takeshi Igawa
- Japanese Avian Bioresource Project Research Center, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan;
- Amphibian Research Center, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Mitsuo Nunome
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan;
| | - Takayuki Suzuki
- Laboratory of Avian Bioscience, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan;
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan;
| | - Masaoki Tsudzuki
- Laboratory of Animal Breeding and Genetics, Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan;
- Japanese Avian Bioresource Project Research Center, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan;
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17
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Weng Z, Huang X. Highlighting the classification of mitochondrial DNA haplogroups C and D in chickens. Mitochondrial DNA A DNA Mapp Seq Anal 2020; 31:218-219. [PMID: 32516055 DOI: 10.1080/24701394.2020.1773452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Zhuoxian Weng
- Guangdong Provincial Key Laboratory of Conservation and Precision Utilization of Characteristic Agricultural Resources in Mountainous Areas; Guangdong Innovation Centre for Science and Technology of Wuhua Yellow Chicken; School of Life Science of Jiaying University, Meizhou, China
| | - Xunhe Huang
- Guangdong Provincial Key Laboratory of Conservation and Precision Utilization of Characteristic Agricultural Resources in Mountainous Areas; Guangdong Innovation Centre for Science and Technology of Wuhua Yellow Chicken; School of Life Science of Jiaying University, Meizhou, China
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18
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Yankova I, Marinov M, Neov B, Petrova M, Spassov N, Hristov P, Radoslavov G. Evidence for Early European Neolithic Dog Dispersal: New Data on Southeastern European Subfossil Dogs from the Prehistoric and Antiquity Ages. Genes (Basel) 2019; 10:genes10100757. [PMID: 31561553 PMCID: PMC6826387 DOI: 10.3390/genes10100757] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/20/2019] [Accepted: 09/22/2019] [Indexed: 01/03/2023] Open
Abstract
The history of dog domestication is still under debate, but it is doubtless the process of an ancient partnership between dogs (Canis familiaris) and humans. Although data on ancient DNA for dog diversity are still incomplete, it is clear that several regional dog populations had formed in Eurasia up to the Holocene. During the Neolithic Revolution and the transition from hunter-gatherer to farmer societies, followed by civilization changes in the Antiquity period, the dog population structure also changed. This process was due to replacement with newly formed dog populations. In this study, we present for the first time mitochondrial data of ancient dog remains from the Early Neolithic (8000 years before present (BP)) to Late Antiquity (up to 3th century AD) from southeastern Europe (the Balkans). A total of 16 samples were analyzed, using the mitochondrial D-loop region (HVR1). The results show the presence of A (70%) and B (25%) clades throughout the Early and Late Neolithic Period. In order to clarify the position of our results within the ancient dog population in Eneolithic Eurasia, we performed phylogenetic analysis with the available genetic data sets. This data showed a similarity of the ancient Bulgarian dogs to Italian (A, B, and C clades) and Iberian (clades A and C) dogs’ populations. A clear border can be seen between southern European genetic dog structure, on the one hand, and on the other hand, central-western (clade C), eastern (clade D) and northern Europe (clades A and C). This corresponds to genetic data for European humans during the same period, without admixture between dog populations. Also, our data have shown the presence of clade B in ancient Eurasia. This is not unexpected, as the B haplogroup is widely distributed in extant Balkan dogs and wolves. The presence of this clade both in dogs and in wolves on the Balkans may be explained with hybridization events before the Neolithic period. The spreading of this clade across Europe, together with the A clade, is related to the possible dissemination of newly formed dog breeds from Ancient Greece, Thrace, and the Roman Empire.
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Affiliation(s)
- Iskra Yankova
- Department of Animal Diversity and Resources, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1040 Sofia, Bulgaria.
| | - Miroslav Marinov
- Department of Animal Diversity and Resources, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1040 Sofia, Bulgaria.
| | - Boyko Neov
- Department of Animal Diversity and Resources, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1040 Sofia, Bulgaria.
| | - Maria Petrova
- Department of Structure and Function of Chromatin, Institute of Molecular Biology, Bulgarian Academy of Sciences, 1040 Sofia, Bulgaria.
| | - Nikolai Spassov
- Palaeontology and Mineralogy Department, National Museum of Natural History, Bulgarian Academy of Sciences, 1040 Sofia, Bulgaria.
| | - Peter Hristov
- Department of Animal Diversity and Resources, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1040 Sofia, Bulgaria.
| | - Georgi Radoslavov
- Department of Animal Diversity and Resources, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1040 Sofia, Bulgaria.
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19
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Genetic analysis identifies the missing parchment of New Zealand's founding document, the Treaty of Waitangi. PLoS One 2019; 14:e0210528. [PMID: 30650155 PMCID: PMC6334937 DOI: 10.1371/journal.pone.0210528] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 12/26/2018] [Indexed: 11/19/2022] Open
Abstract
Genetic analyses provide a powerful tool with which to identify the biological components of historical objects. Te Tiriti o Waitangi | The Treaty of Waitangi is New Zealand’s founding document, intended to be a partnership between the indigenous Māori and the British Crown. Here we focus on an archived piece of blank parchment that has been proposed to be the missing portion of the lower parchment of the Waitangi Sheet of the Treaty. However, its physical dimensions and characteristics are not consistent with this hypothesis. We perform genetic analyses on the parchment membranes of the Treaty, plus the blank piece of parchment. We find that all three parchments were made from ewes and that the blank parchment is highly likely to be a portion cut from the lower membrane of the Waitangi Sheet because they share identical whole mitochondrial genomes, including an unusual heteroplasmic site. We suggest that the differences in size and characteristics between the two pieces of parchment may have resulted from the Treaty’s exposure to water in the early 20th century and the subsequent repair work, light exposure during exhibition or the later conservation treatments in the 1970s and 80s. The blank piece of parchment will be valuable for comparison tests to study the effects of earlier treatments and to monitor the effects of long-term display on the Treaty.
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20
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Phylogenetic Studies on Red Junglefowl ( Gallus gallus) and Native Chicken ( Gallus gallus domesticus) in Samar Island, Philippines using the Mitochondrial DNA D-Loop Region. J Poult Sci 2019; 56:237-244. [PMID: 32055220 PMCID: PMC7005397 DOI: 10.2141/jpsa.0180131] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
A study was conducted to provide genetic information on the matrilineal phylogeny and genetic diversity of Red junglefowl (RJF) and native chickens in Samar Island, Philippines and to identify the genetic distance between Philippine junglefowls and other RJF species in Southeast Asia using complete mitochondrial DNA D-loop sequences. A total of 5 RJFs and 43 native chickens from Samar Island were included in this study. The results showed that Samar RJFs had a nucleotide diversity of 0.0050±0.0016, which was lower than those of three subspecies of Gallus gallus: G. g. gallus, G. g. spadiceus, and G. g. jabouillei. Meanwhile, Samar native chickens showed lower nucleotide diversity (0.0056±0.0004) than domestic fowls in some neighboring Southeast Asian countries, but higher than those in African and European countries. Phylogenetic analysis showed that 3 haplotypes of Samar RJFs clustered to haplogroup D1, and that 2 haplotypes clustered to haplogroup D2. Chickens native to Samar Island showed 100% resemblance to those in the haplogroup shared by domestic chickens and RJFs. Haplogroups A and B and sub-haplogroups D1 and E1 were the more widely distributed matrilineal lineages in Samar Island. Phylogenetic analysis of Samar RJFs showed that they were closely related to Myanmar RJFs (99.6%), Indonesia RJFs (99.5%), and Thailand RJFs (99.1%). This study is an initial investigation estimating the matrilineal phylogeny and genetic diversity of chicken populations in Samar Island, Philippines for developing strategies aimed at the future conservation and improvement of valuable genetic resources.
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21
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Nunome M, Kinoshita K, Ishishita S, Ohmori Y, Murai A, Matsuda Y. Genetic diversity of 21 experimental chicken lines with diverse origins and genetic backgrounds. Exp Anim 2018; 68:177-193. [PMID: 30542001 PMCID: PMC6511517 DOI: 10.1538/expanim.18-0139] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The genetic characteristics and diversity of 21 experimental chicken lines registered with the National BioResource Project of Japan were examined using mitochondrial D-loop sequences and 54 microsatellite DNA markers. A total of 12 haplotypes were detected in the 500-bp mitochondrial DNA sequences of the hypervariable segment I for 349 individuals of 21 lines. The 12 haplotypes belonged to three (A, D, and E) haplogroups, out of the eight (A‒H) common haplogroups in domestic chickens and red junglefowls. The haplogroups A and D were widely represented in indigenous chickens in the Asian and Pacific regions, and the haplogroup E was the most prevalent in domestic chickens. Genetic clustering by discriminant analysis of principal components with microsatellite markers divided 681 individuals of 21 lines into three groups that consisted of Fayoumi-, European-, and Asian- derived lines. In each of the cladograms constructed with Nei's genetic distances based on allele frequencies and the membership coefficients provided by STRUCTURE and with the genetic distance based on the proportion of shared alleles, the genetic relationships coincided well with the breeding histories of the lines. Microsatellite markers showed remarkably lower genetic heterozygosities (less than 0.1 observed heterozygosity) for eight lines (GSP, GSN/1, YL, PNP, BM-C, WL-G, BL-E, and #413), which have been maintained as closed colonies for more than 40 years (except for #413), indicating their usefulness as experimental chicken lines in laboratory animal science research.
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Affiliation(s)
- Mitsuo Nunome
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Keiji Kinoshita
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Satoshi Ishishita
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Yasushige Ohmori
- Laboratory of Animal Morphology, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Atsushi Murai
- Laboratory of Nutrition Science, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Yoichi Matsuda
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan.,Laboratory of Avian Bioscience, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
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22
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St John JC, Tsai TS. The association of mitochondrial DNA haplotypes and phenotypic traits in pigs. BMC Genet 2018; 19:41. [PMID: 29980191 PMCID: PMC6035439 DOI: 10.1186/s12863-018-0629-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Accepted: 06/19/2018] [Indexed: 11/29/2022] Open
Abstract
Background The mitochondrial genome (mtDNA) is an emerging determiner of phenotypic traits and disease. mtDNA is inherited in a strict maternal fashion from the population of mitochondria present in the egg at fertilisation. Individuals are assigned to mtDNA haplotypes and those with sequences that cluster closely have common origins and their migration patterns can be mapped. Previously, we identified five mtDNA haplotypes in the commercial breeding lines of Australian pigs, which defined their common origins, and showed how these mtDNA haplotypes influenced litter size and reproductive function in terms of egg and embryo quality and fertilisation efficiency. Results We have determined whether mtDNA haplotypes influence other phenotypic traits. These include fat density; muscle depth; fat to leanness ratios; lifetime daily gain; teat quality; muscle score; front and rear leg assessments; percentage offspring weaned; weaning to oestrus intervals; gilt age at selection; and gestational length. In all, we assessed 5687 pigs of which 2762 were females and 2925 were males. We assessed all animals together and then by gender. We further assessed by gender based on whether a sire had joined with females from only one haplotype or from more than one haplotype. We determined that fat density, muscle depth, fat to leanness ratios, lifetime daily gain and teat quality were influenced by mtDNA haplotype and that there were gender specific effects on teat quality. Conclusions Our data illustrate that mtDNA haplotypes are associated with a number of important phenotypic traits indicative of economic breeding values in breeding pigs with gender-specific differences. Interestingly, there are ‘trade offs’ whereby some mtDNA haplotypes perform better for one selection criterion, such as muscle depth, but less so for another, for example teat quality, indicating that pig mtDNA haplotypes are afforded an advantage in one respect but a disadvantage in another. Electronic supplementary material The online version of this article (10.1186/s12863-018-0629-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Justin C St John
- Centre for Genetic Diseases, Hudson Institute of Medical Research and Department of Molecular and Translational Science, Monash University, 27-31 Wright Street, Clayton, Vic 3168, Australia.
| | - Te-Sha Tsai
- Centre for Genetic Diseases, Hudson Institute of Medical Research and Department of Molecular and Translational Science, Monash University, 27-31 Wright Street, Clayton, Vic 3168, Australia
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23
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Marinov M, Teofanova D, Gadjev D, Radoslavov G, Hristov P. Mitochondrial diversity of Bulgarian native dogs suggests dual phylogenetic origin. PeerJ 2018; 6:e5060. [PMID: 29967734 PMCID: PMC6026455 DOI: 10.7717/peerj.5060] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 06/04/2018] [Indexed: 11/20/2022] Open
Abstract
The dog has been the first domesticated animal to have a central role in human society from ancient times to present day. Although there have been numerous investigations of dog phylogeny and origin, genetic data of dogs in the region of the Balkan Peninsula (South-Eastern Europe) are still scarce. Therefore, the aim of the present study was to perform phylogenetic analysis of three native Bulgarian dog breeds. A total of 130 samples were analyzed at HVR1 (hypervariable region, D-loop region). The samples were taken from two hunting dog breeds (Bulgarian Hound Dog: Barak, n = 34; Bulgarian Scenthound Dog: Gonche, n = 45) as well as from a Bulgarian Shepherd Dog (n = 51). The first two breeds are reared in a flat region of the country (the Northern part of Bulgaria, the Danubian Plain), while the last breed is a typical representative of the mountainous part of the country. The results have shown the presence of almost all main clades—A, B, C and D—in the three dog breeds taken together, except clades E and F, as expected. With regard to haplogroups distribution, there are clear differences among investigated breeds. While hunting breeds exhibit a prevalence of clade C, the mountainous Shepherd dog shows presence of the D2 haplogroup but absence of the C clade. In conclusion, the present study has been the first to investigate the mitochondrial DNA diversity of native dog breeds in Bulgaria. The results have revealed a clear difference of haplogroups dissemination in native hunting and shepherd dogs, which suggests a dual independent phylogenetic origin, without hybridization events between these dogs.
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Affiliation(s)
- Miroslav Marinov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Denitsa Teofanova
- Department of Biochemistry, Faculty of Biology, Sofia University "St. Kliment Ohridski", Sofia, Bulgaria
| | - Dimitar Gadjev
- Agricultural and Stockbreeding Experimental Station, Agricultural Academy, Smolyan, Bulgaria
| | - Georgi Radoslavov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Peter Hristov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, Bulgaria
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24
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Huang XH, Wu YJ, Miao YW, Peng MS, Chen X, He DL, Suwannapoom C, Du BW, Li XY, Weng ZX, Jin SH, Song JJ, Wang MS, Chen JB, Li WN, Otecko NO, Geng ZY, Qu XY, Wu YP, Yang XR, Jin JQ, Han JL, Zhong FS, Zhang XQ, Zhang YP. Was chicken domesticated in northern China? New evidence from mitochondrial genomes. Sci Bull (Beijing) 2018; 63:743-746. [PMID: 36658946 DOI: 10.1016/j.scib.2017.12.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 11/14/2017] [Accepted: 11/16/2017] [Indexed: 01/21/2023]
Affiliation(s)
- Xun-He Huang
- School of Life Sciences, Jiaying University, Meizhou 514015, China
| | - Ya-Jiang Wu
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan University, Kunming 650091, China
| | - Yong-Wang Miao
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Xing Chen
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Dan-Lin He
- College of Animal Sciences, South China Agricultural University, Guangzhou 510642, China
| | | | - Bing-Wang Du
- College of Agriculture, Guangdong Ocean University, Zhanjiang 524088, China
| | - Xian-Yao Li
- College of Animal Science and Technology, Shandong Agricultural University, Taian 271018, China
| | - Zhuo-Xian Weng
- School of Life Sciences, Jiaying University, Meizhou 514015, China; College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Si-Hua Jin
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Jiao-Jiao Song
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Ming-Shan Wang
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Jie-Bo Chen
- School of Life Sciences, Jiaying University, Meizhou 514015, China
| | - Wei-Na Li
- School of Life Sciences, Jiaying University, Meizhou 514015, China
| | - Newton Otieno Otecko
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Zhao-Yu Geng
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Xiang-Yong Qu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Yan-Ping Wu
- Institute of Animal Science, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Xiu-Rong Yang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Jie-Qiong Jin
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences (CAS-SEABRI), Yezin 05282, Myanmar
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; International Livestock Research Institute (ILRI), Nairobi 00100, Kenya
| | - Fu-Sheng Zhong
- School of Life Sciences, Jiaying University, Meizhou 514015, China.
| | - Xi-Quan Zhang
- College of Animal Sciences, South China Agricultural University, Guangzhou 510642, China.
| | - Ya-Ping Zhang
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan University, Kunming 650091, China; State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China.
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25
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Ma H, Wu Y, Xiang H, Yang Y, Wang M, Zhao C, Wu C. Some maternal lineages of domestic horses may have origins in East Asia revealed with further evidence of mitochondrial genomes and HVR-1 sequences. PeerJ 2018; 6:e4896. [PMID: 29868288 PMCID: PMC5985762 DOI: 10.7717/peerj.4896] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 05/13/2018] [Indexed: 11/20/2022] Open
Abstract
Objectives There are large populations of indigenous horse (Equus caballus) in China and some other parts of East Asia. However, their matrilineal genetic diversity and origin remained poorly understood. Using a combination of mitochondrial DNA (mtDNA) and hypervariable region (HVR-1) sequences, we aim to investigate the origin of matrilineal inheritance in these domestic horses. Methods To investigate patterns of matrilineal inheritance in domestic horses, we conducted a phylogenetic study using 31 de novo mtDNA genomes together with 317 others from the GenBank. In terms of the updated phylogeny, a total of 5,180 horse mitochondrial HVR-1 sequences were analyzed. Results Eightteen haplogroups (Aw-Rw) were uncovered from the analysis of the whole mitochondrial genomes. Most of which have a divergence time before the earliest domestication of wild horses (about 5,800 years ago) and during the Upper Paleolithic (35-10 KYA). The distribution of some haplogroups shows geographic patterns. The Lw haplogroup contained a significantly higher proportion of European horses than the horses from other regions, while haplogroups Jw, Rw, and some maternal lineages of Cw, have a higher frequency in the horses from East Asia. The 5,180 sequences of horse mitochondrial HVR-1 form nine major haplogroups (A-I). We revealed a corresponding relationship between the haplotypes of HVR-1 and those of whole mitochondrial DNA sequences. The data of the HVR-1 sequences also suggests that Jw, Rw, and some haplotypes of Cw may have originated in East Asia while Lw probably formed in Europe. Conclusions Our study supports the hypothesis of the multiple origins of the maternal lineage of domestic horses and some maternal lineages of domestic horses may have originated from East Asia.
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Affiliation(s)
- Hongying Ma
- College of Animal Science and Technology, China Agricultural University, Beijing, China.,Equine Center, China Agricultural University, Beijing, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Beijing, China
| | - Yajiang Wu
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan University, Kunming, China
| | - Hai Xiang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yunzhou Yang
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Science, Shanghai, China
| | - Min Wang
- College of Animal Science and Technology, China Agricultural University, Beijing, China.,Equine Center, China Agricultural University, Beijing, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Beijing, China
| | - Chunjiang Zhao
- College of Animal Science and Technology, China Agricultural University, Beijing, China.,Equine Center, China Agricultural University, Beijing, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Beijing, China.,Beijing Key Laboratory for Genetic Improvement of Livestock and Poultry, Beijing, China
| | - Changxin Wu
- College of Animal Science and Technology, China Agricultural University, Beijing, China.,Equine Center, China Agricultural University, Beijing, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Beijing, China
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26
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Suwannapoom C, Wu YJ, Chen X, Adeola AC, Chen J, Wang WZ. Complete mitochondrial genome of the Thai Red Junglefowl (Gallus gallus) and phylogenetic analysis. Zool Res 2018. [PMID: 29515095 PMCID: PMC5885385 DOI: 10.24272/j.issn.2095-8137.2017.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Affiliation(s)
- Chatmongkon Suwannapoom
- School of Agriculture and Natural Resources, University of Phayao, Phayao 56000, Thailand.,Southeast Asia Biodiversity Research Institute (CAS-SEABRI), Chinese Academy of Sciences, Yezin Nay Pyi Taw 05282, Myanmar
| | - Ya-Jiang Wu
- State Key Laboratory for Conservation and Utilization of Bio-resource in Yunnan, Yunnan University, Kunming Yunnan 650091, China
| | - Xing Chen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China.
| | - Adeniyi C Adeola
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China.
| | - Jing Chen
- Wildlife Forensics Science Service Centre, Kunming Yunnan 650203, China
| | - Wen-Zhi Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China. .,Wildlife Forensics Science Service Centre, Kunming Yunnan 650203, China.,Guizhou Academy of Testing and Analysis, Guizhou Academy of Sciences, Guiyang Guizhou 550002, China
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27
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Hirimuthugoda NY, Adeola AC, Anthony Perera PW, Chen X, Dewar Asoka Gunawardena WW, Thilini Nisanka Gunawardana HG, Yin TT, Wang MS, Li GM, Ding ZL, Wang WZ, Xie HB, Peng MS, Zhang YP. Sri Lankan pig ancestry revealed by mitochondrial DNA, Y-chromosome, and MC1R. Anim Genet 2017; 48:622-623. [PMID: 28748531 DOI: 10.1111/age.12577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/17/2017] [Indexed: 12/01/2022]
Affiliation(s)
| | - Adeniyi C Adeola
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | | | - Xing Chen
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | | | | | - Ting-Ting Yin
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Ming-Shan Wang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Gui-Mei Li
- Kunming Biological Diversity Regional Center of Large Apparatus and Equipments, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Zhao-Li Ding
- Kunming Biological Diversity Regional Center of Large Apparatus and Equipments, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Wen-Zhi Wang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Hai-Bing Xie
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, 650091, China
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28
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Huang XH, Li GM, Chen X, Wu YJ, Li WN, Zhong FS, Wang WZ, Ding ZL. Identification of a novel mtDNA lineage B3 in chicken ( Gallus gallus domesticus). Zool Res 2017; 38:208-210. [PMID: 28825453 PMCID: PMC5571479 DOI: 10.24272/j.issn.2095-8137.2017.039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Xun-He Huang
- School of Life Sciences, Jiaying University, Meizhou Guangdong 514015, China
| | - Gui-Mei Li
- Kunming Biological Diversity Regional Center of Large Apparatus and Equipments, Chinese Academy of Sciences, Kunming Yunnan 650223, China; Public Technical Service Center, Kunming Institute of Zoology, Chinese Academy of Science, Kunming Yunnan 650223, China
| | - Xing Chen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
| | - Ya-Jiang Wu
- State Key Laboratory for Conservation and Utilization of Bioresource in Yunnan, Yunnan University, Kunming Yunnan 650091, China
| | - Wei-Na Li
- School of Life Sciences, Jiaying University, Meizhou Guangdong 514015, China
| | - Fu-Sheng Zhong
- School of Life Sciences, Jiaying University, Meizhou Guangdong 514015, China
| | - Wen-Zhi Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China; Forensic Science Service of Yunnan Endangered Species Scientific Commission, Kunming Yunnan 650223, China
| | - Zhao-Li Ding
- Kunming Biological Diversity Regional Center of Large Apparatus and Equipments, Chinese Academy of Sciences, Kunming Yunnan 650223, China; Public Technical Service Center, Kunming Institute of Zoology, Chinese Academy of Science, Kunming Yunnan 650223, China.
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29
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Adeola AC, Oluwole OO, Oladele BM, Olorungbounmi TO, Boladuro B, Olaogun SC, Nneji LM, Sanke OJ, Dawuda PM, Omitogun OG, Frantz L, Murphy RW, Xie HB, Peng MS, Zhang YP. Analysis of the genetic variation in mitochondrial DNA, Y-chromosome sequences, and MC1R sheds light on the ancestry of Nigerian indigenous pigs. Genet Sel Evol 2017. [PMID: 28651519 PMCID: PMC5485568 DOI: 10.1186/s12711-017-0326-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background The history of pig populations in Africa remains controversial due to insufficient evidence from archaeological and genetic data. Previously, a Western ancestry for West African pigs was reported based on loci that are involved in the determination of coat color. We investigated the genetic diversity of Nigerian indigenous pigs (NIP) by simultaneously analyzing variation in mitochondrial DNA (mtDNA), Y-chromosome sequence and the melanocortin receptor 1 (MC1R) gene. Results Median-joining network analysis of mtDNA D-loop sequences from 201 NIP and previously characterized loci clustered NIP with populations from the West (Europe/North Africa) and East/Southeast Asia. Analysis of partial sequences of the Y-chromosome in 57 Nigerian boars clustered NIP into lineage HY1. Finally, analysis of MC1R in 90 NIP resulted in seven haplotypes, among which the European wild boar haplotype was carried by one individual and the European dominant black by most of the other individuals (93%). The five remaining unique haplotypes differed by a single synonymous substitution from European wild type, European dominant black and Asian dominant black haplotypes. Conclusions Our results demonstrate a European and East/Southeast Asian ancestry for NIP. Analyses of MC1R provide further evidence. Additional genetic analyses and archaeological studies may provide further insights into the history of African pig breeds. Our findings provide a valuable resource for future studies on whole-genome analyses of African pigs. Electronic supplementary material The online version of this article (doi:10.1186/s12711-017-0326-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Adeniyi C Adeola
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China
| | - Olufunke O Oluwole
- Institute of Agricultural Research and Training, Obafemi Awolowo University, Ibadan, Nigeria
| | - Bukola M Oladele
- Institute of Agricultural Research and Training, Obafemi Awolowo University, Ibadan, Nigeria
| | | | - Bamidele Boladuro
- Institute of Agricultural Research and Training, Obafemi Awolowo University, Ibadan, Nigeria
| | - Sunday C Olaogun
- Department of Veterinary Medicine, University of Ibadan, Ibadan, Nigeria
| | - Lotanna M Nneji
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Oscar J Sanke
- Taraba State Ministry of Agriculture and Natural Resources, Jalingo, Nigeria
| | - Philip M Dawuda
- Department of Veterinary Surgery and Theriogenology, College of Veterinary Medicine, University of Agriculture Makurdi, Makurdi, Nigeria
| | - Ofelia G Omitogun
- Department of Animal Sciences, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Laurent Frantz
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology, University of Oxford, Oxford, UK.,School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, Canada
| | - Hai-Bing Xie
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China. .,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China. .,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China. .,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China. .,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China. .,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China.
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30
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Schroeder O, Benecke N, Frölich K, Peng Z, Kaniuth K, Sverchkov L, Reinhold S, Belinskiy A, Ludwig A. Endogenous Retroviral Insertions Indicate a Secondary Introduction of Domestic Sheep Lineages to the Caucasus and Central Asia between the Bronze and Iron Age. Genes (Basel) 2017. [PMID: 28632161 PMCID: PMC5485529 DOI: 10.3390/genes8060165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Sheep were one of the first livestock species domesticated by humans. After initial domestication in the Middle East they were spread across Eurasia. The modern distribution of endogenous Jaagsiekte sheep retrovirus insertions in domestic sheep breeds suggests that over the course of millennia, successive introductions of improved lineages and selection for wool quality occurred in the Mediterranean region and most of Asia. Here we present a novel ancient DNA approach using data of endogenous retroviral insertions in Bronze and Iron Age domestic sheep from the Caucasus and Pamir mountain areas. Our findings support a secondary introduction of wool sheep from the Middle East between the Late Bronze Age and Iron Age into most areas of Eurasia.
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Affiliation(s)
- Oskar Schroeder
- Leibniz-Institute for Zoo and Wildlife Research, Department of Evolutionary Genetics, Alfred-Kowalke-Straße 17, 10315 Berlin, Germany.
- German Archaeological Institute, Im Dol 2-6, 14195 Berlin, Germany.
| | - Norbert Benecke
- German Archaeological Institute, Im Dol 2-6, 14195 Berlin, Germany.
| | - Kai Frölich
- Tierpark Arche Warder e.V., Langwedeler Weg 11, 24646 Warder, Germany.
| | - Zuogang Peng
- Southwest University School of Life Sciences, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Chongqing 400715, China.
| | - Kai Kaniuth
- Institut für Vorderasiatische Archäologie, Ludwig-Maximilians-Universität München, Geschwister-Scholl-Platz 1, 80539 Munich, Germany.
| | - Leonid Sverchkov
- Institute of Fine Arts, Academy of Sciences of the Republic of Uzbekistan, Afrosiab Street 5/19, Tashkent 100029, Uzbekistan.
| | - Sabine Reinhold
- German Archaeological Institute, Im Dol 2-6, 14195 Berlin, Germany.
| | - Andrey Belinskiy
- Nasledie Ltd., Prospekt Karla Marksa 56, 355017 Stavropol, Russia.
| | - Arne Ludwig
- Leibniz-Institute for Zoo and Wildlife Research, Department of Evolutionary Genetics, Alfred-Kowalke-Straße 17, 10315 Berlin, Germany.
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31
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Amiri Ghanatsaman Z, Adeola AC, Asadi Fozi M, Ma YP, Peng MS, Wang GD, Esmailizadeh A, Zhang YP. Mitochondrial DNA sequence variation in Iranian native dogs. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:394-402. [PMID: 28303732 DOI: 10.1080/24701394.2017.1289375] [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 dog mtDNA diversity picture from wide geographical sampling but from a small number of individuals per region or breed, displayed little geographical correlation and high degree of haplotype sharing between very distant breeds. For a clear picture, we extensively surveyed Iranian native dogs (n = 305) in comparison with published European (n = 443) and Southwest Asian (n = 195) dogs. Twelve haplotypes related to haplogroups A, B and C were shared by Iranian, European, Southwest Asian and East Asian dogs. In Iran, haplotype and nucleotide diversities were highest in east, southeast and northwest populations while western population had the least. Sarabi and Saluki dog populations can be assigned into haplogroups A, B, C and D; Qahderijani and Kurdi to haplogroups A, B and C, Torkaman to haplogroups A, B and D while Sangsari and Fendo into haplogroups A and B, respectively. Evaluation of population differentiation using pairwise FST generally revealed no clear population structure in most Iranian dog populations. The genetic signal of a recent demographic expansion was detected in East and Southeast populations. Further, in accordance with previous studies on dog-wolf hybridization for haplogroup d2 origin, the highest number of d2 haplotypes in Iranian dog as compared to other areas of Mediterranean basin suggests Iran as the probable center of its origin. Historical evidence showed that Silk Road linked Iran to countries in South East Asia and other parts of the world, which might have probably influenced effective gene flow within Iran and these regions. The medium nucleotide diversity observed in Iranian dog calls for utilization of appropriate management techniques in increasing effective population size.
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Affiliation(s)
- Zeinab Amiri Ghanatsaman
- a Department of Animal Science, Faculty of Agriculture , Shahid Bahonar University of Kerman , Kerman , Iran.,b Yong Researchers Society , Shahid Bahonar University of Kerman , Kerman , Iran
| | - Adeniyi C Adeola
- c State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals , Kunming Institute of Zoology, Chinese Academy of Sciences No. 32 Jiaochang Donglu , Kunming , Yunnan , China
| | - Masood Asadi Fozi
- a Department of Animal Science, Faculty of Agriculture , Shahid Bahonar University of Kerman , Kerman , Iran
| | - Ya-Ping Ma
- d State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan , Yunnan University , Kunming , China
| | - Min-Sheng Peng
- c State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals , Kunming Institute of Zoology, Chinese Academy of Sciences No. 32 Jiaochang Donglu , Kunming , Yunnan , China
| | - Guo-Dong Wang
- c State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals , Kunming Institute of Zoology, Chinese Academy of Sciences No. 32 Jiaochang Donglu , Kunming , Yunnan , China
| | - Ali Esmailizadeh
- a Department of Animal Science, Faculty of Agriculture , Shahid Bahonar University of Kerman , Kerman , Iran.,c State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals , Kunming Institute of Zoology, Chinese Academy of Sciences No. 32 Jiaochang Donglu , Kunming , Yunnan , China
| | - Ya-Ping Zhang
- c State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic Animals , Kunming Institute of Zoology, Chinese Academy of Sciences No. 32 Jiaochang Donglu , Kunming , Yunnan , China.,d State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan , Yunnan University , Kunming , China
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32
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Zhang L, Zhang P, Li Q, Gaur U, Liu Y, Zhu Q, Zhao X, Wang Y, Yin H, Hu Y, Liu A, Li D. Genetic evidence from mitochondrial DNA corroborates the origin of Tibetan chickens. PLoS One 2017; 12:e0172945. [PMID: 28241078 PMCID: PMC5328412 DOI: 10.1371/journal.pone.0172945] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 12/27/2016] [Indexed: 01/23/2023] Open
Abstract
Chicken is the most common poultry species and is important to human societies. Tibetan chicken (Gallus gallus domesticus) is a breed endemic to China that is distributed mainly on the Qinghai-Tibet Plateau. However, its origin has not been well characterized. In the present study, we sequenced partial mitochondrial DNA (mtDNA) control region of 239 and 283 samples from Tibetan and Sichuan indigenous chickens, respectively. Incorporating 1091 published sequences, we constructed the matrilineal genealogy of Tibetan chickens to further document their domestication history. We found that the genetic structure of the mtDNA haplotypes of Tibetan chickens are dominated by seven major haplogroups (A-G). In addition, phylogenetic and network analyses showed that Tibetan chickens are not distinguishable from the indigenous chickens in surrounding areas. Furthermore, some clades of Tibetan chickens may have originated from game fowls. In summary, our results collectively indicated that Tibetan chickens may have diverged from indigenous chickens in the adjacent regions and hybridized with various chickens.
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Affiliation(s)
- Long Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Pu Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Qingqing Li
- Life Science College, Southwest Forestry University, Kunming, China
| | - Uma Gaur
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yiping Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Qing Zhu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Xiaoling Zhao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yan Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Huadong Yin
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yaodong Hu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Aiping Liu
- College of Food Science, Sichuan Agricultural University, Ya'an, China
| | - Diyan Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- * E-mail:
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33
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Luzuriaga-Neira A, Villacís-Rivas G, Cueva-Castillo F, Escudero-Sánchez G, Ulloa-Nuñez A, Rubilar-Quezada M, Monteiro R, Miller MR, Beja-Pereira A. On the origins and genetic diversity of South American chickens: one step closer. Anim Genet 2017; 48:353-357. [PMID: 28094447 DOI: 10.1111/age.12537] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/08/2016] [Indexed: 11/27/2022]
Abstract
Local chicken populations are a major source of food in the rural areas of South America. However, very little is known about their genetic composition and diversity. Here, we analyzed five populations from South America to investigate their maternal genetic origin and diversity, hoping to mitigate the lack of information on local chicken populations from this region. We also included three populations of chicken from the Iberian Peninsula and one from Easter Island, which are potential sources of the first chickens introduced in South America. The obtained sequencing data from South American chickens indicate the presence of four haplogroups (A, B, E and D) that can be further subdivided into nine sub-haplogroups. Of these, four (B1, D1a, E1a(b), E1b) were absent from local Iberian Peninsula chickens and one (D1a) was present only on Easter Island. The presence of the sub-haplogroups A1a(b) and E1a(b) in South America, previously only observed in Eastern Asia, and the significant population differentiation between Iberian Peninsula and South American populations, suggest a second maternal source of the extant genetic pool in South American chickens.
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Affiliation(s)
- A Luzuriaga-Neira
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO-InBIO), Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas 7, 4485-661, Vairão, Portugal
| | - G Villacís-Rivas
- Centro de Biotecnología, Universidad Nacional de Loja, Pio Jaramillo Alvarado s/n sector La Argelia, 1101, Loja, Ecuador
| | - F Cueva-Castillo
- Centro de Biotecnología, Universidad Nacional de Loja, Pio Jaramillo Alvarado s/n sector La Argelia, 1101, Loja, Ecuador
| | - G Escudero-Sánchez
- Universidad Nacional de Loja, Pio Jaramillo Alvarado s/n sector La Argelia, 1101, Loja, Ecuador
| | - A Ulloa-Nuñez
- Facultad de Ciencias Veterinarias, Universidad de Concepción, Av. Vicente Mendez 595, Chillán, Chile
| | - M Rubilar-Quezada
- Facultad de Ciencias Veterinarias, Universidad de Concepción, Av. Vicente Mendez 595, Chillán, Chile
| | - R Monteiro
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO-InBIO), Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas 7, 4485-661, Vairão, Portugal
| | - M R Miller
- Department of Animal Science, University of California, Davis, CA, 95616, USA
| | - A Beja-Pereira
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO-InBIO), Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas 7, 4485-661, Vairão, Portugal.,Department of Biology, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre S/N, Porto, Portugal
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34
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A cryptic mitochondrial DNA link between North European and West African dogs. J Genet Genomics 2016; 44:163-170. [PMID: 28302420 DOI: 10.1016/j.jgg.2016.10.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 08/17/2016] [Accepted: 10/21/2016] [Indexed: 01/25/2023]
Abstract
Domestic dogs have an ancient origin and a long history in Africa. Nevertheless, the timing and sources of their introduction into Africa remain enigmatic. Herein, we analyse variation in mitochondrial DNA (mtDNA) D-loop sequences from 345 Nigerian and 37 Kenyan village dogs plus 1530 published sequences of dogs from other parts of Africa, Europe and West Asia. All Kenyan dogs can be assigned to one of three haplogroups (matrilines; clades): A, B, and C, while Nigerian dogs can be assigned to one of four haplogroups A, B, C, and D. None of the African dogs exhibits a matrilineal contribution from the African wolf (Canis lupus lupaster). The genetic signal of a recent demographic expansion is detected in Nigerian dogs from West Africa. The analyses of mitochondrial genomes reveal a maternal genetic link between modern West African and North European dogs indicated by sub-haplogroup D1 (but not the entire haplogroup D) coalescing around 12,000 years ago. Incorporating molecular anthropological evidence, we propose that sub-haplogroup D1 in West African dogs could be traced back to the late-glacial dispersals, potentially associated with human hunter-gatherer migration from southwestern Europe.
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35
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O'Sullivan NJ, Teasdale MD, Mattiangeli V, Maixner F, Pinhasi R, Bradley DG, Zink A. A whole mitochondria analysis of the Tyrolean Iceman's leather provides insights into the animal sources of Copper Age clothing. Sci Rep 2016; 6:31279. [PMID: 27537861 PMCID: PMC4989873 DOI: 10.1038/srep31279] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 07/15/2016] [Indexed: 02/07/2023] Open
Abstract
The attire of the Tyrolean Iceman, a 5,300-year-old natural mummy from the Ötzal Italian Alps, provides a surviving example of ancient manufacturing technologies. Research into his garments has however, been limited by ambiguity surrounding their source species. Here we present a targeted enrichment and sequencing of full mitochondrial genomes sampled from his clothes and quiver, which elucidates the species of production for nine fragments. Results indicate that the majority of the samples originate from domestic ungulate species (cattle, sheep and goat), whose recovered haplogroups are now at high frequency in today’s domestic populations. Intriguingly, the hat and quiver samples were produced from wild species, brown bear and roe deer respectively. Combined, these results suggest that Copper Age populations made considered choices of clothing material from both the wild and domestic populations available to them. Moreover, these results show the potential for the recovery of complete mitochondrial genomes from degraded prehistoric artefacts.
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Affiliation(s)
- Niall J O'Sullivan
- Institute for Mummies and the Iceman, EURAC research, 39100 Bolzano, Italy.,School of Archaeology and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Matthew D Teasdale
- Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland
| | - Valeria Mattiangeli
- Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland
| | - Frank Maixner
- Institute for Mummies and the Iceman, EURAC research, 39100 Bolzano, Italy
| | - Ron Pinhasi
- School of Archaeology and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Daniel G Bradley
- Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland
| | - Albert Zink
- Institute for Mummies and the Iceman, EURAC research, 39100 Bolzano, Italy
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36
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Frantz LAF, Mullin VE, Pionnier-Capitan M, Lebrasseur O, Ollivier M, Perri A, Linderholm A, Mattiangeli V, Teasdale MD, Dimopoulos EA, Tresset A, Duffraisse M, McCormick F, Bartosiewicz L, Gál E, Nyerges ÉA, Sablin MV, Bréhard S, Mashkour M, Bălăşescu A, Gillet B, Hughes S, Chassaing O, Hitte C, Vigne JD, Dobney K, Hänni C, Bradley DG, Larson G. Genomic and archaeological evidence suggest a dual origin of domestic dogs. Science 2016; 352:1228-31. [PMID: 27257259 DOI: 10.1126/science.aaf3161] [Citation(s) in RCA: 222] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 04/25/2016] [Indexed: 01/19/2023]
Abstract
The geographic and temporal origins of dogs remain controversial. We generated genetic sequences from 59 ancient dogs and a complete (28x) genome of a late Neolithic dog (dated to ~4800 calendar years before the present) from Ireland. Our analyses revealed a deep split separating modern East Asian and Western Eurasian dogs. Surprisingly, the date of this divergence (~14,000 to 6400 years ago) occurs commensurate with, or several millennia after, the first appearance of dogs in Europe and East Asia. Additional analyses of ancient and modern mitochondrial DNA revealed a sharp discontinuity in haplotype frequencies in Europe. Combined, these results suggest that dogs may have been domesticated independently in Eastern and Western Eurasia from distinct wolf populations. East Eurasian dogs were then possibly transported to Europe with people, where they partially replaced European Paleolithic dogs.
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Affiliation(s)
- Laurent A F Frantz
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK.
| | - Victoria E Mullin
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Maud Pionnier-Capitan
- CNRS/ENS de Lyon, IGFL, UMR 5242 and French National Platform of Paleogenetics, PALGENE, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon Cedex 07, France/Université Grenoble Alpes, Laboratoire d'Ecologie Alpine (LECA), F-38000 Grenoble, France. CNRS/Muséum National d'Histoire Naturelle/Sorbonne Universités, Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnement (UMR 7209), CP56, 55 rue Buffon, F-75005 Paris, France
| | - Ophélie Lebrasseur
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Morgane Ollivier
- CNRS/ENS de Lyon, IGFL, UMR 5242 and French National Platform of Paleogenetics, PALGENE, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon Cedex 07, France/Université Grenoble Alpes, Laboratoire d'Ecologie Alpine (LECA), F-38000 Grenoble, France
| | - Angela Perri
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Anna Linderholm
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK. Department of Anthropology, Texas A&M University, College Station, TX 77843-4352, USA
| | | | - Matthew D Teasdale
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Evangelos A Dimopoulos
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK. School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Anne Tresset
- CNRS/Muséum National d'Histoire Naturelle/Sorbonne Universités, Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnement (UMR 7209), CP56, 55 rue Buffon, F-75005 Paris, France
| | - Marilyne Duffraisse
- CNRS/ENS de Lyon, IGFL, UMR 5242 and French National Platform of Paleogenetics, PALGENE, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon Cedex 07, France/Université Grenoble Alpes, Laboratoire d'Ecologie Alpine (LECA), F-38000 Grenoble, France
| | - Finbar McCormick
- School of Geography, Archaeology and Palaeoecology, Queen's University Belfast, University Road, Belfast, Northern Ireland, UK
| | - László Bartosiewicz
- Osteoarchaeological Research Laboratory, University of Stockholm, Stockholm, Sweden
| | - Erika Gál
- Archaeological Institute, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest, Hungary
| | - Éva A Nyerges
- Archaeological Institute, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest, Hungary
| | - Mikhail V Sablin
- Zoological Institute, Russian Academy of Sciences, Universitetskaya Nab. 1, 199034 Saint-Petersburg, Russia
| | - Stéphanie Bréhard
- CNRS/Muséum National d'Histoire Naturelle/Sorbonne Universités, Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnement (UMR 7209), CP56, 55 rue Buffon, F-75005 Paris, France
| | - Marjan Mashkour
- CNRS/Muséum National d'Histoire Naturelle/Sorbonne Universités, Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnement (UMR 7209), CP56, 55 rue Buffon, F-75005 Paris, France
| | - Adrian Bălăşescu
- The National Museum of Romanian History, 12 Calea Victoriei, 030026 Bucharest, Romania
| | - Benjamin Gillet
- CNRS/ENS de Lyon, IGFL, UMR 5242 and French National Platform of Paleogenetics, PALGENE, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon Cedex 07, France/Université Grenoble Alpes, Laboratoire d'Ecologie Alpine (LECA), F-38000 Grenoble, France
| | - Sandrine Hughes
- CNRS/ENS de Lyon, IGFL, UMR 5242 and French National Platform of Paleogenetics, PALGENE, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon Cedex 07, France/Université Grenoble Alpes, Laboratoire d'Ecologie Alpine (LECA), F-38000 Grenoble, France
| | - Olivier Chassaing
- CNRS/ENS de Lyon, IGFL, UMR 5242 and French National Platform of Paleogenetics, PALGENE, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon Cedex 07, France/Université Grenoble Alpes, Laboratoire d'Ecologie Alpine (LECA), F-38000 Grenoble, France
| | - Christophe Hitte
- Institut de Génétique et Développement de Rennes, CNRS-UMR6290, Université de Rennes 1, Rennes, France
| | - Jean-Denis Vigne
- CNRS/Muséum National d'Histoire Naturelle/Sorbonne Universités, Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnement (UMR 7209), CP56, 55 rue Buffon, F-75005 Paris, France
| | - Keith Dobney
- Department of Archaeology, School of Geosciences, University of Aberdeen, St. Mary's, Elphinstone Road, AB24 3UF, UK. Department of Archaeology, Classics and Egyptology, University of Liverpool, 12-14 Abercromby Square, Liverpool L69 7WZ, UK
| | - Catherine Hänni
- CNRS/ENS de Lyon, IGFL, UMR 5242 and French National Platform of Paleogenetics, PALGENE, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon Cedex 07, France/Université Grenoble Alpes, Laboratoire d'Ecologie Alpine (LECA), F-38000 Grenoble, France
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
| | - Greger Larson
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK.
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Sziszkosz N, Mihók S, Jávor A, Kusza S. Genetic diversity of the Hungarian Gidran horse in two mitochondrial DNA markers. PeerJ 2016; 4:e1894. [PMID: 27168959 PMCID: PMC4860319 DOI: 10.7717/peerj.1894] [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: 10/08/2015] [Accepted: 03/14/2016] [Indexed: 11/20/2022] Open
Abstract
The Gidran is a native Hungarian horse breed that has approached extinction several times. Phylogenetic analysis of two mitochondrial markers (D-loop and cytochrome-b) was performed to determine the genetic characterization of the Gidran for the first time as well as to detect errors in the management of the Gidran stud book. Sequencing of 686 bp of CYTB and 202 bp of the D-loop in 260 mares revealed 24 and 32 haplotypes, respectively, among 31 mare families. BLAST analysis revealed six novel CYTB and four D-loop haplotypes that have not been previously reported. The Gidran mares showed high haplotype (CYTB: 0.8735 ± 0.011; D-loop: 0.9136 ± 0.008) and moderate nucleotide (CYTB: 0.00472 ± 0.00017; D-loop: 0.02091 ± 0.00068) diversity. Of the 31 Gidran mare families, only 15 CYTB (48.4%) and 17 D-loop (54.8%) distinct haplotypes were formed using the two markers separately. Merged markers created 24 (77.4%) mare families, which were in agreement with the mare families in the stud book. Our key finding was that the Gidran breed still possesses high genetic diversity despite its history. The obtained haplotypes are mostly consistent with known mare families, particularly when the two mtDNA markers were merged. Our results could facilitate conservation efforts for preserving the genetic diversity of the Gidran.
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Affiliation(s)
- Nikolett Sziszkosz
- Institute of Animal Science, Biotechnology and Nature Conservation, University of Debrecen , Debrecen , Hungary
| | - Sándor Mihók
- Institute of Animal Science, Biotechnology and Nature Conservation, University of Debrecen , Debrecen , Hungary
| | - András Jávor
- Institute of Animal Science, Biotechnology and Nature Conservation, University of Debrecen , Debrecen , Hungary
| | - Szilvia Kusza
- Institute of Animal Science, Biotechnology and Nature Conservation, University of Debrecen , Debrecen , Hungary
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Song JJ, Wang WZ, Otecko NO, Peng MS, Zhang YP. Reconciling the conflicts between mitochondrial DNA haplogroup trees of Canis lupus. Forensic Sci Int Genet 2016; 23:83-85. [PMID: 27042801 DOI: 10.1016/j.fsigen.2016.03.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 03/25/2016] [Accepted: 03/25/2016] [Indexed: 11/18/2022]
Affiliation(s)
- Jiao-Jiao Song
- Institute of Health Sciences, Anhui University, 111 Jiulong Lu, 230601 Hefei, China; State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, and Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu, 650223 Kunming, China
| | - Wen-Zhi Wang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, and Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu, 650223 Kunming, China
| | - Newton O Otecko
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, and Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu, 650223 Kunming, China; Kunming College of Life Science, University of Chinese Academy of Sciences, 19 Qingsong Lu, 650204 Kunming, China
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, and Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu, 650223 Kunming, China; Kunming College of Life Science, University of Chinese Academy of Sciences, 19 Qingsong Lu, 650204 Kunming, China.
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, and Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu, 650223 Kunming, China; Kunming College of Life Science, University of Chinese Academy of Sciences, 19 Qingsong Lu, 650204 Kunming, China; State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, 2 Cuihu Beilu, 650091 Kunming, China.
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