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The Genetic Legacy of the Expansion of Turkic-Speaking Nomads across Eurasia

Yunusbayev, Bayazit, Metspalu, Mait, Metspalu, Ene, Valeev, Albert, Litvinov, Sergei, Valiev, Ruslan, Akhmetova, Vita, Balanovska, Elena, Balanovsky, Oleg, Turdikulova, Shahlo, Dalimova, Dilbar, Nymadawa, Pagbajabyn, Bahmanimehr, Ardeshir, Sahakyan, Hovhannes, Tambets, Kristiina, Fedorova, Sardana, Barashkov, Nikolay, Khidiyatova, Irina, Mihailov, Evelin, Khusainova, Rita, Damba, Larisa, Derenko, Miroslava, Malyarchuk, Boris, Osipova, Ludmila, Voevoda, Mikhail, Yepiskoposyan, Levon, Kivisild, Toomas, Khusnutdinova, Elza, Villems, Richard·2015·PLOS Genetics
DOI 10.1371/journal.pgen.1005068PMC PMC4405460

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Fig 1 Geographic map of samples included in this study and linguistic tree of Turkic languages. Panel A) Non-Turkic-speaking populations are shown with light blue, light green, dark green, light brown, and yellow circles, depending on the region. Turkic-speaking populations are shown with red circles regardless of the region of sampling. Full population names are given in S1 Table Panel B) The linguistic tree of Turkic languages is adapted from Dybo 2004 and includes only those languages spoken by the Turkic peoples analyzed in this study. The x-axis shows the time scale in kilo-years (kya). Internal branches are shown with different colors.
Fig 1 Geographic map of samples included in this study and linguistic tree of Turkic languages. Panel A) Non-Turkic-speaking populations are shown with light blue, light green, dark green, light brown, and yellow circles, depending on the region. Turkic-speaking populations are shown with red circles regardless of the region of sampling. Full population names are given in S1 Table Panel B) The linguistic tree of Turkic languages is adapted from Dybo 2004 and includes only those languages spoken by the Turkic peoples analyzed in this study. The x-axis shows the time scale in kilo-years (kya). Internal branches are shown with different colors.CC BY · PubMed Central
Fig 2 Population structure inferred using ADMIXTURE analysis. ADMIXTURE results at K = 8 are shown. Each individual is represented by a vertical (100%) stacked column indicating the proportions of ancestry in K constructed ancestral populations. Turkic-speaking populations are shown in red. The upper barplot shows only Turkic-speaking populations.
Fig 2 Population structure inferred using ADMIXTURE analysis. ADMIXTURE results at K = 8 are shown. Each individual is represented by a vertical (100%) stacked column indicating the proportions of ancestry in K constructed ancestral populations. Turkic-speaking populations are shown in red. The upper barplot shows only Turkic-speaking populations.CC BY · PubMed Central
Fig 3 Populations with high and correlated signals of IBD sharing with western Turkic peoples. Circle positions correspond to population locations. Circle color indicates the amount of excess IBD sharing (shown in Legend) that a population shares with all 12 western Turkic populations. Populations with IBD sharing exceeding the 0.90 quantile are shown with a “plus symbol”. Panel A) IBD sharing signal based on IBD tracts of 1–2 cM. Panel B) IBD sharing signal based on IBD tracts of 2–3 cM. Panel C) IBD sharing signal based on IBD tracts of 3–4 cM
Fig 3 Populations with high and correlated signals of IBD sharing with western Turkic peoples. Circle positions correspond to population locations. Circle color indicates the amount of excess IBD sharing (shown in Legend) that a population shares with all 12 western Turkic populations. Populations with IBD sharing exceeding the 0.90 quantile are shown with a “plus symbol”. Panel A) IBD sharing signal based on IBD tracts of 1–2 cM. Panel B) IBD sharing signal based on IBD tracts of 2–3 cM. Panel C) IBD sharing signal based on IBD tracts of 3–4 cMCC BY · PubMed Central
Fig 4 Pairwise IBD sharing based on 1–2 cM long segments. For each population ordered along the x–axis, IBD sharing is computed with three SSM populations (Tuvans, Buryats, Mongols) and Evenkis. Each Turkic-speaking population (shown in red) is grouped with its respective geographic neighbors using parentheses. The grouped geographic neighbors were pooled and used to perform a permutation test as described in the M&M section. Red numbers under the Turkic population name indicate how many SSM populations demonstrate a statistically significant excess of IBD sharing with a given Turkic population. Note that, for example, Bashkirs, Tatars, and Chuvashes share their geographic neighbors.
Fig 4 Pairwise IBD sharing based on 1–2 cM long segments. For each population ordered along the x–axis, IBD sharing is computed with three SSM populations (Tuvans, Buryats, Mongols) and Evenkis. Each Turkic-speaking population (shown in red) is grouped with its respective geographic neighbors using parentheses. The grouped geographic neighbors were pooled and used to perform a permutation test as described in the M&M section. Red numbers under the Turkic population name indicate how many SSM populations demonstrate a statistically significant excess of IBD sharing with a given Turkic population. Note that, for example, Bashkirs, Tatars, and Chuvashes share their geographic neighbors.CC BY · PubMed Central
Fig 5 Admixture dates for Turkic-speaking populations on an absolute date scale. Blue circles show ALDER-inferred point estimates and error bars indicate 95% confidence intervals. Gray circles show SPCO-inferred point estimates and error bars in gray indicate 95% confidence intervals. The red bar shows the point estimate range (inferred using ALDER) across all the analyzed samples and the orange bar shows the same for SPCO-inferred dates. Admixture dates before Common Era (CE) are shown with a negative sign.
Fig 5 Admixture dates for Turkic-speaking populations on an absolute date scale. Blue circles show ALDER-inferred point estimates and error bars indicate 95% confidence intervals. Gray circles show SPCO-inferred point estimates and error bars in gray indicate 95% confidence intervals. The red bar shows the point estimate range (inferred using ALDER) across all the analyzed samples and the orange bar shows the same for SPCO-inferred dates. Admixture dates before Common Era (CE) are shown with a negative sign.CC BY · PubMed Central
Fig 6 Admixture dates for simulated populations. Simulated populations were generated by mixing two ancestral populations G generations ago as described in the M&M section. We repeated each admixture scenario 120 times and analyzed with two admixture dating methods: ALDER and SPCO. Circles represent admixture dates for one simulated population and circle color indicates the method of admixture inference as shown in the legend. Red “plus symbols” show the true admixture date.
Fig 6 Admixture dates for simulated populations. Simulated populations were generated by mixing two ancestral populations G generations ago as described in the M&M section. We repeated each admixture scenario 120 times and analyzed with two admixture dating methods: ALDER and SPCO. Circles represent admixture dates for one simulated population and circle color indicates the method of admixture inference as shown in the legend. Red “plus symbols” show the true admixture date.CC BY · PubMed Central

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Citations

Cites

Research works printed but not linked: 35

  1. C Renfrew, 2010, Archaeogenetics—towards a 'new synthesis'?, Curr Biol, 20, R162, 10.1016/j.cub.2009.11.056 · DOI
  2. D Sinor, 1990, The Cambridge History of Early Inner Asia, 285
  3. M Bermisheva, 2002, Diversity of mitochondrial DNA haplotypes in ethnic populations of the Volga-Ural region of Russia, Mol Biol (Mosk), 36, 990, 10.1023/A:1021677708482 · DOI
  4. I Nasidze, 2003, Testing hypotheses of language replacement in the Caucasus: evidence from the Y-chromosome, Hum Genet, 112, 255, 10.1007/s00439-002-0874-4 · DOI
  5. C Cinnioglu, 2004, Excavating Y-chromosome haplotype strata in Anatolia, Hum Genet, 114, 127, 10.1007/s00439-003-1031-4 · DOI · Paper page
  6. A Varzari, 2009, Searching for the origin of Gagauzes: inferences from Y-chromosome analysis, Am J Hum Biol, 21, 326, 10.1002/ajhb.20863 · DOI
  7. B Malyarchuk, 2010, Mitogenomic diversity in Tatars from the Volga-Ural region of Russia, Mol Biol Evol, 27, 2220, 10.1093/molbev/msq065 · DOI
  8. B Yunusbayev, 2012, The Caucasus as an Asymmetric Semipermeable Barrier to Ancient Human Migrations, Mol Biol Evol, 29, 359, 10.1093/molbev/msr221 · DOI
  9. D Comas, 2004, Admixture, migrations, and dispersals in Central Asia: evidence from maternal DNA lineages, Eur J Hum Genet, 12, 495, 10.1038/sj.ejhg.5201160 · DOI · Paper page
  10. L Quintana-Murci, 2004, Where West meets East: The complex mtDNA landscape of the Southwest and Central Asian corridor, Am J Hum Genet, 74, 827, 10.1086/383236 · DOI · Paper page
  11. M Derenko, 2006, Contrasting patterns of Y-chromosome variation in south Siberian populations from Baikal and Altai-Sayan regions, Hum Genet, 118, 591, 10.1007/s00439-005-0076-y · DOI
  12. M Derenko, 2007, Phylogeographic analysis of mitochondrial DNA in northern Asian Populations, Am J Hum Genet, 81, 1025, 10.1086/522933 · DOI
  13. JZ Li, 2008, Worldwide human relationships inferred from genome-wide patterns of variation, Science, 319, 1100, 10.1126/science.1153717 · DOI
  14. DM Behar, 2010, The genome-wide structure of the Jewish people, Nature, 466, 238, 10.1038/nature09103 · DOI
  15. SA Fedorova, 2013, Autosomal and uniparental portraits of the native populations of Sakha (Yakutia): implications for the peopling of Northeast Eurasia, BMC evolutionary biology, 13, 127, 10.1186/1471-2148-13-127 · DOI
  16. J Di Cristofaro, 2013, Afghan Hindu Kush: where Eurasian sub-continent gene flows converge, PLoS One, 8, e76748, 10.1371/journal.pone.0076748 · DOI · Paper page
  17. U Hodoglugil, 2012, Turkish population structure and genetic ancestry reveal relatedness among Eurasian populations, Ann Hum Genet, 76, 128, 10.1111/j.1469-1809.2011.00701.x · DOI
  18. G Hellenthal, 2014, A genetic atlas of human admixture history, Science, 343, 747, 10.1126/science.1243518 · DOI · Paper page
  19. JK Pritchard, 2000, Association mapping in structured populations, Am J Hum Genet, 67, 170, 10.1086/302959 · DOI
  20. DH Alexander, 2009, Fast model-based estimation of ancestry in unrelated individuals, Genome Research, 19, 1655, 10.1101/gr.094052.109 · DOI · Paper page
  21. M Metspalu, 2011, Shared and Unique Components of Human Population Structure and Genome-Wide Signals of Positive Selection in South Asia, Am J Hum Genet, 89, 731, 10.1016/j.ajhg.2011.11.010 · DOI
  22. P Ralph, 2013, The Geography of Recent Genetic Ancestry across Europe, PLoS Biol, 11, 10.1371/journal.pbio.1001555 · DOI
  23. SR Browning, 2008, Estimation of pairwise identity by descent from dense genetic marker data in a population sample of haplotypes, Genetics, 178, 2123, 10.1534/genetics.107.084624 · DOI
  24. PR Loh, 2013, Inferring admixture histories of human populations using linkage disequilibrium, Genetics, 193, 1233, 10.1534/genetics.112.147330 · DOI · Paper page
  25. I Pugach, 2011, Dating the age of admixture via wavelet transform analysis of genome-wide data, Genome Biology, 12, R19, 10.1186/gb-2011-12-2-r19 · DOI
  26. AL Williams, 2012, Phasing of many thousands of genotyped samples, Am J Hum Genet, 91, 238, 10.1016/j.ajhg.2012.06.013 · DOI
  27. JJ Saunders, 1971
  28. G Mako, 2011, The Islamization of the Volga Bulghars: A Question Reconsidered, Archivum Eurasiae Medii Aevi, 18, 199
  29. DM Behar, 2013, No Evidence from Genome-Wide Data of a Khazar Origin for the Ashkenazi Jews, Human Biology, 85, 859, 10.3378/027.085.0604 · DOI
  30. BL Browning, 2011, A fast, powerful method for detecting identity by descent, Am J Hum Genet, 88, 173, 10.1016/j.ajhg.2011.01.010 · DOI
  31. S Banerjee, 2005, On geodetic distance computations in spatial modelling, Biometrics, 61, 617, 10.1111/j.1541-0420.2005.00320.x · DOI
  32. HM Cann, 2002, A human genome diversity cell line panel, Science, 296, 261, 10.1126/science.296.5566.261b · DOI
  33. J Ma, 2012, Principal components analysis of population admixture, Plos One, 7, e40115, 10.1371/journal.pone.0040115 · DOI
  34. GK Chen, 2009, Fast and flexible simulation of DNA sequence data, Genome Research, 19, 136, 10.1101/gr.083634.108 · DOI
  35. SF Schaffner, 2005, Calibrating a coalescent simulation of human genome sequence variation, Genome Research, 15, 1576, 10.1101/gr.3709305 · DOI · Paper page

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Metadata

Authors
Yunusbayev, B., Metspalu, M., Metspalu, E., Valeev, A., Litvinov, S., Valiev, R., Akhmetova, V., Balanovska, E., Balanovsky, O., Turdikulova, S., Dalimova, D., Nymadawa, P., Bahmanimehr, A., Sahakyan, H., Tambets, K., Fedorova, S., Barashkov, N., Khidiyatova, I., Mihailov, E., Khusainova, R., Damba, L., Derenko, M., Malyarchuk, B., Osipova, L., Voevoda, M., Yepiskoposyan, L., Kivisild, T., Khusnutdinova, E., & Villems, R.
Venue
PLOS Genetics
Publisher
Public Library of Science (PLoS)
Published
2015-04-21
Volume
11
Issue
4
Pages
e1005068
ISSN
1553-7404
DOI
10.1371/journal.pgen.1005068
PMC
PMC4405460
Cited by
176
References
6
Language
en
Licence
creativecommons.org/licenses/by/4.0/ (vor)

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