Abstract
A short review of the current state in ethnogenomics was carried out. The main breakthroughs in the field are described, and small-scale historical overview is presented. The methods and approaches currently used in Y-chromosome, mitochondrial DNA and genome-wide studies are listed.
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Balanovskaia, E.V. and Rychkov, Iu.G., Ethnic genetics: ethnogeographic diversity of the gene pool of human populations around the world, Russ. J. Genet., 1990, vol. 26, no. 1, pp. 114–121.
Amorim, A., Archaeogenetics, J. Iberian Archaeol., 1999, no. 1, pp. 15–25.
Renfrew, C., Archaeogenetics: towards a population prehistory of Europe, in Archaeogenetics: DNA and the Population Prehistory of Europe, Cambridge: McDonald Institute for Archaeological Research, 2000, pp. 3–11.
Abecasis, G.R., Auton, A., Brooks, L.D., et al., An integrated map of genetic variation from 1092 human genomes, Nature, 2012, vol. 491, no. 7422, pp. 56–65.
Cavalli-Sforza, L.L., Piazza, A., Menozzi, P., and Mountain, J., Reconstruction of human evolution: bringing together genetic, archaeological, and linguistic data, Proc. Natl. Acad. Sci. U.S.A., 1988, vol. 85, no. 16, pp. 6002–6006.
Brown, W.M., Polymorphism in mitochondrial DNA of humans as revealed by restriction endonuclease analysis, Proc. Natl. Acad. Sci. U.S.A., 1980, vol. 77, no. 6, pp. 3605–3609.
Torroni, A., Schurr, T.G., Yang, C.C., et al., Native American mitochondrial DNA analysis indicates that the Amerind and the Nadene populations were founded by two independent migrations, Genetics, 1992, vol. 130, no. 1, pp. 153–162.
Torroni, A., Schurr, T.G., Cabell, M.F., et al., Asian affinities and continental radiation of the four founding native American mtDNAs, Am. J. Hum. Genet., 1993, vol. 53, no. 3, pp. 563–590.
Torroni, A., Achilli, A., Macaulay, V., et al., Harvesting the fruit of the human mtDNA tree, Trends Genet., 2006, vol. 22, no. 6, pp. 339–345.
Behar, D.M., Villems, R., Soodyall, H., et al., The dawn of human matrilineal diversity, Am. J. Hum. Genet., 2008, vol. 82, no. 5, pp. 1130–1140.
Renfrew, C., Archaeogenetics-towards a “new synthesis”?, Curr. Biol., 2010, vol. 20, no. 4, pp. R162–R165.
Kefi, R., Hsouna, S., Ben Halim, N., et al., Phylogeny and genetic structure of Tunisians and their position within Mediterranean populations, Mitochondrial DNA, 2014. doi 10.3109/194017.36.2013.879649
Limborskaya, S.A., Khusnutdinova, E.K., and Balanovskaya, E.V., Etnogenomika i genogeografiya narodov Votochnoi Evropy (Ethnogenomics and Gene Geography of Peoples in Eastern Europe), Moscow: Nauka, 2002.
Roostalu, U., Kutuev, I., Loogvali, E.L., et al., Origin and expansion of haplogroup H, the dominant human mitochondrial DNA lineage in West Eurasia: the Near Eastern and Caucasian perspective, Mol. Biol. Evol., 2007, vol. 24, no. 2, pp. 436–448.
Chaubey, G., Singh, M., Crivellaro, F., et al., Unravelling the distinct strains of Tharu ancestry, Eur. J. Hum. Genet., 2014. doi 10.1038/ejhg.2014.36
Bermisheva, M., Tambets, K., Villems, R., and Khusnutdinova, E., Diversity of mitochondrial DNA haplogroups in ethnic populations of the Volga-Ural region, Mol. Biol. (Moscow), 2002, vol. 36, no. 6, pp. 802–812.
Bermisheva, M.A., Kutuev, I.A., Korshunova, T.Yu., et al., Phylogeographic analysis of mitochondrial DNA in the Nogays: a strong mixture of maternal lineages from Eastern and Western Eurasia, Mol. Biol. (Moscow), 2004, vol. 38, no. 4, pp. 516–523.
Denisova, G.A., Malarchuk, B.A., Derenko, M.V., Population structure of Volga Tatars inferred from the mitochondrial DNA diversity data, Russ. J. Genet., 2011, vol. 47, no. 3, pp. 387–393.
Derenko, M., Malyarchuk, B., Grzybowski, T., et al., Origin and post-glacial dispersal of mitochondrial DNA haplogroups C and D in northern Asia, PLoS One, 2010, vol. 5, no. 12. e15214
Fedorova, S.A., Reidla, M., Metspalu, E., et al., Autosomal and uniparental portraits of the native populations of Sakha (Yakutia): implications for the peopling of Northeast Eurasia, BMC Evol. Biol., 2013, vol. 13, no. 1, p. 127.
Anderson, S., Bankier, A.T., Barrell, B.G., et al., Sequence and organization of the human mitochondrial genome, Nature, 1981, vol. 290, no. 5806, pp. 457–465.
Andrews, R.M., Kubacka, I., Chinnery, P.F., et al., Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA, Nat. Genet., 1999, vol. 23, no. 2, p. 147.
Behar, D.M., van Oven, M., Rosset, S., et al., A“Copernican” reassessment of the human mitochondrial DNA tree from its root, Am. J. Hum. Genet., 2012, vol. 90, no. 4, pp. 675–684.
van Oven, M. and Kayser, M., Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation, Hum. Mutat., 2009, vol. 30, no. 2, pp. E386–E394.
Loogvali, E.L., Roostalu, U., Malyarchuk, B.A., et al., Disuniting uniformity: a pied cladistic canvas of mtDNA haplogroup H in Eurasia, Mol. Biol. Evol., 2004, vol. 21, no. 11, pp. 2012–2021.
Brotherton, P., Haak, W., Templeton, J., et al., Neolithic mitochondrial haplogroup H genomes and the genetic origins of Europeans, Nat. Commun., 2013, vol. 4, p. 1764.
Olivieri, A., Pala, M., Gandini, F., et al., Mitogenomes from two uncommon haplogroups mark late glacial/postglacial expansions from the Near East and Neolithic dispersals within Europe, PLoS One, 2013, vol. 8, no. 7. e70492
Achilli, A., Iommarini, L., Olivieri, A., et al., Rare primary mitochondrial DNA mutations and probable synergistic variants in Leber’s hereditary optic neuropathy, PLoS One, 2012, vol. 7, no. 8. e42242
Khusnutdinova, E., Gilyazova, I., Ruiz-Pesini, E., et al., A mitochondrial etiology of neurodegenerative diseases: evidence from Parkinson’s disease, Ann. N.Y. Acad. Sci., 2008, vol. 1147, pp. 1–20.
Bourdon, V., Ng, C., Harris, J., et al., Optimization of human mtDNA control region sequencing for forensic applications, J. Forensic Sci., 2014, vol. 59, no. 4, pp. 1057–1063.
Underhill, P.A., Passarino, G., Lin, A.A., et al., The phylogeography of Y chromosome binary haplotypes and the origins of modern human populations, Ann. Hum. Genet., 2001, vol. 65, no. 1, pp. 43–62.
Jobling, M.A. and Tyler-Smith, C., The human Y chromosome: an evolutionary marker comes of age, Nat. Rev. Genet., 2003, vol. 4, no. 8, pp. 598–612.
Hammer, M.F., Karafet, T.M., Redd, A.J., et al., Hierarchical patterns of global human Y-chromosome diversity, Mol. Biol. Evol., 2001, vol. 18, no. 7, pp. 1189–1203.
Casanova, M., Leroy, P., Boucekkine, C., et al., A human Y-linked DNA polymorphism and its potential for estimating genetic and evolutionary distance, Science, 1985, vol. 230, no. 4732, pp. 1403–1406.
YCC, A nomenclature system for the tree of human Y-chromosomal binary haplogroups, Genome Res., 2002, vol. 12, no. 2, pp. 339–348.
Oefner, P.J. and Underhill, P.A., DNA mutation detection using denaturing high-performance liquid chromatography, in Current Protocols in Human Genetics, Dracopoli, N.C., Haines, J.L., Korff, B.R., et al., Eds., New York: Wiley, 1997, pp. 7.10.1–7.10.12.
Zhivotovskii, L.A., Microsatellite variation in human populations and the methods of their analysis, Vestn. VOGiS, 2006, vol. 10, no. 1, pp. 74–96.
Yunusbayev, B., Metspalu, M., Jarve, M., et al., The Caucasus as an asymmetric semipermeable barrier to ancient human migrations, Mol. Biol. Evol., 2012, vol. 29, no. 1, pp. 359–365.
Myres, N.M., Rootsi, S., Lin, A.A., et al., A major Y-chromosome haplogroup R1b Holocene era founder effect in central and Western Europe, Eur. J. Hum. Genet., 2011, vol. 19, no. 1, pp. 95–101.
Busby, G.B., Brisighelli, F., Sanchez-Diz, P., et al., The peopling of Europe and the cautionary tale of Y chromosome lineage R-M269, Proc. Biol. Sci., 2012, vol. 279, no. 1730, pp. 884–892.
Underhill, P.A., Poznik, G.D., Rootsi, S., et al., The phylogenetic and geographic structure of Y-chromosome haplogroup R1a, Eur. J. Hum. Genet., 2014.
Zhivotovsky, L.A., Akhmetova, V.L., Fedorova, S.A., et al., An STR database on the Volga-Ural population, Forensic Sci. Int. Genet., 2009, vol. 3, no. 4. e133–6
Kharkov, V.N., Khamina, K.V., Medvedeva, O.F., et al., Gene pool of Buryats: clinal variability and territorial subdivision based on data of Y-chromosome markers, Russ. J. Genet., 2014, vol. 50, no. 2, pp. 203–213.
Kharkov, V.N., Khamina, K.V., Medvedeva, O.F., et al., Gene-pool structure of Tuvinians inferred from Y-chromosome marker data, Russ. J. Genet., 2013, vol. 49, no. 12, pp. 1416–1425.
Calderon, S., Perez-Benedico, D., Mesa, L., et al., Phylogenetic and forensic studies of the Southeast Florida Hispanic population using the next-generation forensic PowerPlex(R) Y23 STR marker system, Leg. Med., (Tokyo), 2013, vol. 15, no. 6, pp. 289–292.
Karafet, T.M., Mendez, F.L., Meilerman, M.B., et al., New binary polymorphisms reshape and increase resolution of the human y chromosomal haplogroup tree, Genome Res., 2008, vol. 18, no. 5, pp. 830–838.
Mendez, F.L., Krahn, T., Schrack, B., et al., An African American paternal lineage adds an extremely ancient root to the human y chromosome phylogenetic tree, Am. J. Hum. Genet., 2013, vol. 92, no. 3, pp. 454–459.
Elhaik, E., Tatarinova, T.V., and Klyosov, A.A., The “extremely ancient” chromosome that isn’t: a forensic bioinformatic investigation of Albert Perry’s X-degenerate portion of the Y chromosome, Eur. J. Hum. Genet., 2014. doi 10.1038/ejhg.2013.303
International Society of Genetic Genealogy, 2014. http://www.isogg.org/tree/
Rootsi, S., Zhivotovsky, L.A., Baldovic, M., et al., A counter-clockwise northern route of the Y-chromosome haplogroup N from Southeast Asia towards Europe, Eur. J. Hum. Genet., 2007, vol. 15, no. 2, pp. 204–211.
Lobov, A.S., Gene pool structure of the Bashkir subpopulation, Extended Abstract of Cand. Sci. Dissertation, Inst. Biokhim. Genet., Ufa, 2009.
Kutuev, I.A., Litvinov, S.S., Yunusbaev, B.B., et al., Genetic structure of the Caucasus populations according to the Y-chromosome data, Med. Genet., 2010, vol. 9, no. 3, pp. 18–25.
Balanovsky, O., Dibirova, K., Dybo, A., et al., Parallel evolution of genes and languages in the Caucasus region, Mol. Biol. Evol., 2011, vol. 28, no. 10, pp. 2905–2920.
Underhill, P.A., Myres, N.M., Rootsi, S., et al., Separating the post-glacial coancestry of European and Asian Y chromosomes within haplogroup R1a, Eur. J. Hum. Genet., 2010, vol. 18, no. 4, pp. 479–484.
Balanovsky, O., Rootsi, S., Pshenichnov, A., et al., Two sources of the Russian patrilineal heritage in their Eurasian context, Am. J. Hum. Genet., 2008, vol. 82, no. 1, pp. 236–250.
Kasperaviciute, D., Kucinskas, V., and Stoneking, M., Y chromosome and mitochondrial DNA variation in Lithuanians, Ann. Hum. Genet., 2004, vol. 68, vol. 8, no. 5, pp. 438–452.
Alexander, D.H., Novembre, J., and Lange, K., Fast model-based estimation of ancestry in unrelated individuals, Genome Res., 2009, vol. 19, no. 9, pp. 1655–1664.
Patterson, N., Price, A.L., and Reich, D., Population structure and eigenanalysis, PLoS Genet., 2006, vol. 2, no. 12. e190
Li, J.Z., Absher, D.M., Tang, H., et al., Worldwide human relationships inferred from genome-wide patterns of variation, Science, 2008, vol. 319, no. 5866, pp. 1100–1104.
Novembre, J., Johnson, T., Bryc, K., et al., Genes mirror geography within Europe, Nature, 2008, vol. 456, no. 7218, pp. 98–101.
Tang, H., Peng, J., and Wang, P., Estimation of individual admixture: analytical and study design considerations, Genet. Epidemiol., 2005, vol. 28, no. 4, pp. 289–301.
Pritchard, J.K., Stephens, M., and Donnelly, P., Inference of population structure using multilocus genotype data, Genetics, 2000, vol. 155, no. 2, pp. 945–959.
Purcell, S., Neale, B., Todd-Brown, K., et al., PLINK: a tool set for whole-genome association and population-based linkage analyses, Am. J. Hum. Genet., 2007, vol. 81, no. 3, pp. 559–575.
Khusnutdinova, E.K., Litvinov, S.S., Kutuev, I.A., et al., Gene pool of ethnic groups of the Caucasus: results of integrated study of the Y chromosome and mitochondrial DNA and genome wide data, Russ. J. Genet., 2012, vol. 48, no. 6, pp. 640–650.
Tambets, K., Towards the Understanding of Post-Glacial Spread of Human Mitochondrial DNA Haplogroups in Europe and beyond: A Phylogenetic Approach, Tartu: University of Tartu, 2004.
Richards, M., Macaulay, V., Torroni, A., and Bandelt, H.J., In search of geographical patterns in European mitochondrial DNA, Am. J. Hum. Genet., 2002, vol. 71, no. 5, pp. 1168–1174.
Metspalu, M., Romero, I.G., Yunusbayev, B., et al., Shared and unique components of human population structure and genome-wide signals of positive selection in South Asia, Am. J. Hum. Genet., 2011, vol. 89, no. 6, pp. 731–744.
Pickrell, J.K. and Pritchard, J.K., Inference of population splits and mixtures from genome-wide allele frequency data, PLoS Genet., 2012, vol. 8, no. 11. e1002967
Browning, B.L. and Browning, S.R., A fast, powerful method for detecting identity by descent, Am. J. Hum. Genet., 2011, vol. 88, no. 2, pp. 173–182.
Howie, B.N., Donnelly, P., and Marchini, J., A flexible and accurate genotype imputation method for the next generation of genome-wide association studies, PLoS Genet., 2009, vol. 5, no. 6. e1000529
Delaneau, O., Marchini, J., and Zagury, J.F., A linear complexity phasing method for thousands of genomes, Nat. Methods, 2012, vol. 9, no. 2, pp. 179–181.
Hellenthal, G., Busby, G.B., Band, G., et al., A genetic atlas of human admixture history, Science, 2014, vol. 343, no. 6172, pp. 747–751.
Gusev, A., Lowe, J.K., Stoffel, M., et al., Whole population, genome-wide mapping of hidden relatedness, Genome Res., 2009, vol. 19, no. 2, pp. 318–326.
Lawson, D.J., Hellenthal, G., and Myers, S., Inference of population structure using dense haplotype data, PLoS Genet., 2012, vol. 8, no. 1. e1002453
Raghavan, M., Skoglund, P., Graf, K.E., et al., Upper Palaeolithic Siberian genome reveals dual ancestry of native Americans, Nature, 2014, vol. 505, no. 7481, pp. 87–91.
Lazaridis, I., Patterson, N., Mittnik, A., et al., Ancient human genomes suggest three ancestral populations for present-day Europeans, Nature, 2014. doi 10.1038/nature. 13673
Raghavan, M., DeGiorgio, M., Albrechtsen, A., et al., The genetic prehistory of the New World Arctic, Science, 2014, vol. 345, no. 6200. doi 10.1126/science. 1255832
Behar, D.M., Yunusbayev, B., Metspalu, M., et al., The genome-wide structure of the Jewish people, Nature, 2010, vol. 466, no. 7303, pp. 238–242.
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Original Russian Text © S.S. Litvinov, E.K. Khusnutdinova, 2015, published in Genetika, 2015, Vol. 51, No. 4, pp. 503–516.
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Litvinov, S.S., Khusnutdinova, E.K. Current state of research in ethnogenomics: Genome-wide analysis and uniparental markers. Russ J Genet 51, 418–429 (2015). https://doi.org/10.1134/S1022795415040080
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DOI: https://doi.org/10.1134/S1022795415040080