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Articles

Maternal lineage of Nicobari pig (Sus scrofa nicobaricus) correlated with migration of Nicobarese, a native tribal population of Andaman and Nicobar Islands, India

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References

  • Larson G, Dobney K, Albarella U, et al. Worldwide phylogeography of wild boar reveals multiple centers of pig domestication. Science. 2005;307(5715):1618–1621.
  • Groenen MA. A decade of pig genome sequencing: a window on pig domestication and evolution. Genet Sel Evol. 2016;48:23.
  • Groenen MA, Archibald AL, Uenishi H, et al. Analyses of pig genomes provide insight into porcine demography and evolution. Nature. 2012;491(7424):393–398.
  • Li M, Tian S, Yeung CK, Meng X, et al. Whole-genome sequencing of Berkshire (European native pig) provides insights into its origin and domestication. Sci Rep. 2014;4:4678.
  • Darwin C. The Variation of Animals and Plants under Domestication. London: John Murray; 1868.
  • Giuffra E, Kijas JM, Amarger V, et al. The origin of the domestic pig: independent domestication and subsequent introgression. Genetics. 2000;154(4):1785–1791.
  • Okumura N, Kurosawa Y, Kobayashi E, et al. Genetic relationship amongst the major non-coding regions of mitochondrial DNAs in wild boars and several breeds of domesticated pigs. Anim Genet. 2001;32(3):139–147.
  • Watanobe T, Ishiguro N, Okumura N, et al. Ancient mitochondrial DNA reveals the origin of Sus scrofa from Rebun Island, Japan. J Mol Evol. 2001;52(3):281–289.
  • Kim TH, Kim KS, Choi BH, et al. Genetic structure of pig breeds from Korea and China using microsatellite loci analysis. J Anim Sci. 2005;83(10):2255–2263.
  • De AK, Ponraj P, Kundu MS, et al. Mitochondrial landscape of indigenous pig germplasm of Andaman and Nicobar Islands. Mitochondrial DNA B Resour. 2019; 4(2):2808–2810.
  • De AK, Jeyakumar S, Kundu MS, et al. Farming practices and genetic characterization of Nicobari pig, an indigenous pig germplasm of Nicobar group of islands, India. Trop Anim Health Prod. 2014;46(4):655–661.
  • Endicott P, Gilbert MTP, Stringer C, et al. The genetic origins of the Andaman Islanders. Am J Hum Genet. 2003;72(1):178–184.
  • Thangaraj K, Chaubey G, Kivisild T, et al. Reconstructing the origin of Andaman Islanders. Science. 2005;308(5724):996.
  • Ingman M, Kaessmann H, Paabo S, et al. Mitochondrial genome variation and the origin of modern humans. Nature. 2000;408(6813):708–713.
  • Chauhan N, Padalia H, Gupta S, et al. Nicobari tribe of the Car Nicobar Island: keeping in pace with time. J Hum Ecol. 2004;16(3):155–161.
  • Larson G, Liu R, Zhao X, et al. Patterns of East Asian pig domestication, migration, and turnover revealed by modern and ancient DNA. Proc Natl Acad Sci U S A. 2010;107(17):7686–7691.
  • Rosman A, Rubel PG. Stalking the wild pig: hunting and horticulture in Papua New Guinea. In: Kent S, ed. Farmers as Hunters: The Implications of Sedentism. Cambridge: Cambridge University Press, New Directions in Archaeology Series; 1989:27–36.
  • FAO. Molecular Genetic Characterization of Animal Genetic Resources. Rome: FAO Animal Production and Health Guidelines. No. 9; 2011.
  • Georgescu SE, Manea MA, Dudu A, et al. Phylogenetic relationships of the mangalitsa Swine breed inferred from mitochondrial DNA variation. Int J Mol Sci. 2012;13(7):8467–8481.
  • Okonechnikov K, Golosova O, Fursov M, Team U. Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics. 2012;28(8):1166–1167.
  • Bankevich A, Nurk S, Antipov D, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19(5):455–477.
  • Lowe TM, Chan PP. tRNAscan-SE on-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Res. 2016;44(W1):W54–W57.
  • Laslett D, Canbäck B. ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences. Bioinformatics. 2008;24(2):172–175.
  • Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994;22(22):4673–4680.
  • Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol. 2018;35(6):1547–1549.
  • Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987;4(4):406–425.
  • Bandelt HJ, Forster P, Röhl A. Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol. 1999;16(1):37–48.
  • Tamura K, Nei M, Kumar S. Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci U S A. 2004;101(30):11030–11035.
  • Rozas J, Ferrer-Mata A, Sánchez-DelBarrio JC, et al. DnaSP 6: DNA sequence polymorphism analysis of large data sets. Mol Biol Evol. 2017;34(12):3299–3302.
  • Quan J, Gao C, Cai Y, et al. Population genetics assessment model reveals priority protection of genetic resources in native pig breeds in China. Global Ecol Conserv. 2020;21:e00829.
  • Zhang J, Yang B, Wen X, et al. Genetic variation and relationships in the mitochondrial DNA D-loop region of Qinghai indigenous and commercial pig breeds. Cell Mol Biol Lett. 2018;23:31.
  • Zhang J, Jiao T, Zhao S. Genetic diversity in the mitochondrial DNA D-loop region of global swine (Sus scrofa) populations. Biochem Biophys Res Commun. 2016;473(4):814–820.
  • Charlesworth D. Effects of inbreeding on the genetic diversity of populations. Philos Trans R Soc Lond B Biol Sci. 2003;358(1434):1051–1070.
  • Zanella R, Peixoto JO, Cardoso FF, et al. Genetic diversity analysis of two commercial breeds of pigs using genomic and pedigree data. Genet Sel Evol. 2016;48:24.
  • Nidup K, Moran C. Genetic diversity of domestic pigs as revealed by microsatellites: a mini review. Genom Quant Genet. 2011;2:5–18.
  • Martinez AM, Delgado JV, Rodero A, et al. Genetic structure of the Iberian pig breed using microsatellites. Anim Genet. 2000;31(5):295–301.
  • Larson G, Piperno DR, Allaby RG, et al. Current perspectives and the future of domestication studies. Proc Natl Acad Sci U S A. 2014;111(17):6139–6146.
  • Larson G, Burger J. A population genetics view of animal domestication. Trends Genet. 2013;29(4):197–205.
  • Cai Y, Quan J, Gao C, et al. Multiple domestication centers revealed by the geographical distribution of Chinese native pigs. Animals. 2019;9(10):709.
  • Jinam TA, Hong LC, Phipps ME, et al. Evolutionary history of continental southeast Asians: “early train” hypothesis based on genetic analysis of mitochondrial and autosomal DNA data. Mol Biol Evol. 2012;29(11):3513–3527.
  • Bellwood P. The First Farmers: The Origins of Agricultural Societies. Victoria, Australia: Blackwell Publishing; 2005.
  • Anderson A. Crossing the Luzon Strait: archaeological chronology in the Batanes Islands, Philippines and the regional sequence of Neolithic dispersal. J Austronesian Stud. 2005;1:25–45.
  • Dobney K, Cucchi T, Larson G. The pigs of Island Southeast Asia and the Pacific: new evidence for taxonomic status and human-mediated dispersal. Asian Perspect. 2008;47(1):59–74.
  • Tumonggor MK, Karafet TM, Hallmark B, et al. The Indonesian archipelago: an ancient genetic highway linking Asia and the Pacific. J Hum Genet. 2013;58(3):165–173.
  • Bellwood P. Man's Conquest of the Pacific: The Prehistory of South-East Asia and Oceania. Auckland: William Collins; 1978:462.
  • Kutanan W, Kampuansai J, Brunelli A, et al. New insights from Thailand into the maternal genetic history of Mainland Southeast Asia. Eur J Hum Genet. 2018;26(6):898–911.
  • Underhill PA, Passarino G, Lin AA, et al. The phylogeography of Y chromosome binary haplotypes and the origins of modern human populations. Ann Hum Genet. 2001;65(Pt 1):43–62.
  • Trejaut JA, Kivisild T, Loo JH, et al. Traces of archaic mitochondrial lineages persist in Austronesian-speaking Formosan populations. PLoS Biol. 2005;3(8):e247.
  • Tabbada KA, Trejaut J, Loo JH, et al. Philippine mitochondrial DNA diversity: a populated viaduct between Taiwan and Indonesia? Mol Biol Evol. 2010;27(1):21–31.
  • Duong NT, Macholdt E, Ton ND, et al. Complete human mtDNA genome sequences from Vietnam and the phylogeography of Mainland Southeast Asia. Sci Rep. 2018;8(1):11651.
  • Reddy BM, Langstieh BT, Kumar V, et al. Austro-Asiatic tribes of Northeast India provide hitherto missing genetic link between South and Southeast Asia. PloS One. 2007;2(11):e1141.
  • Lipson M, Cheronet O, Mallick S, et al. Ancient genomes document multiple waves of migration in Southeast Asian prehistory. Science. 2018;361(6397):92–95.
  • Larson G, Cucchi T, Fujita M, et al. Phylogeny and ancient DNA of Sus provides insights into neolithic expansion in Island Southeast Asia and Oceania. Proc Natl Acad Sci U S A. 2007;104(12):4834–4839.
  • Leigh JW, Bryant D. Popart: full‐feature software for haplotype network construction. Methods Ecol Evol. 2015;6(9):1110–1116.
  • Fernández AI, Alves E, Óvilo C, et al. Divergence time estimates of East Asian and European pigs based on multiple near complete mitochondrial DNA sequences. Anim Genet. 2011;42(1):86–88.
  • Kijas JM, Andersson L. A phylogenetic study of the origin of the domestic pig estimated from the near-complete mtDNA genome. J Mol Evol. 2001;52(3):302–308.

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