Genetic landscape of populations along the Silk Road: admixture and migration patterns

BMC Genetics

Vincenza Colonna¹  Paolo Gasparini²  Pio d’Adamo²  Giorgia Girotto²  Nicola Pirastu²  Diego Vozzi³  Massimo Mezzavilla² 

[1] Institute of Genetics and Biophysics ‘A. Buzzati-Traverso’, National Research Council (CNR), via Pietro Castellino 111, Naples, 80131, Italy;Department of Medical Sciences, University of Trieste, Trieste, Italy;Institute for Maternal and Child Health - IRCCS “Burlo Garofolo”, Trieste, Italy

关键词: Tajikistan;    Kazakhstan;    Uzbekistan;    Azerbaijan;    Armenia;    Georgia;    Effective population size;    Central Asia;    Migration patterns;    Admixture;    Silk Road;   

Others  :  1085159
DOI  :  10.1186/s12863-014-0131-6

 received in 2014-06-17, accepted in 2014-11-19,  发布年份 2014

【 摘 要 】

Background

The ancient Silk Road has been a trading route between Europe and Central Asia from the 2^nd century BCE to the 15^th century CE. While most populations on this route have been characterized, the genetic background of others remains poorly understood, and little is known about past migration patterns. The scientific expedition “Marco Polo” has recently collected genetic and phenotypic data in six regions (Georgia, Armenia, Azerbaijan, Uzbekistan, Kazakhstan, Tajikistan) along the Silk Road to study the genetics of a number of phenotypes.

Results

We characterized the genetic structure of these populations within a worldwide context. We observed a West-East subdivision albeit the existence of a genetic component shared within Central Asia and nearby populations from Europe and Near East. We observed a contribution of up to 50% from Europe and Asia to most of the populations that have been analyzed. The contribution from Asia dates back to ~25 generations and is limited to the Eastern Silk Road. Time and direction of this contribution are consistent with the Mongolian expansion era.

Conclusions

We clarified the genetic structure of six populations from Central Asia and suggested a complex pattern of gene flow among them. We provided a map of migration events in time and space and we quantified exchanges among populations. Altogether these novel findings will support the future studies aimed at understanding the genetics of the phenotypes that have been collected during the Marco Polo campaign, they will provide insights into the history of these populations, and they will be useful to reconstruct the developments and events that have shaped modern Eurasians genomes.

【 授权许可】

   
2014 Mezzavilla et al.; licensee BioMed Central Ltd.

【 图 表 】

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【 参考文献 】

• [1]Cavalli-Sforza LL, Menozzi P, Piazza A: The History and Geography of Human Genes. Princeton University Press, Princetown, New Jersey; 1994.
• [2]Maca-Meyer N, González AM, Larruga JM, Flores C, Cabrera VM: Major genomic mitochondrial lineages delineate early human expansions. BMC Genet 2001, 2:13. BioMed Central Full Text
• [3]Comas D, Calafell F, Mateu E, Perez-Lezaun A, Bosch E, Martinez-Arias R, Clarimon J, Facchini F, Fiori G, Luiselli D: Trading genes along the silk road: mtDNA sequences and the origin of central Asian populations. Am J Hum Genet 1998, 63(6):1824-1838.
• [4]Wells RS, Yuldasheva N, Ruzibakiev R, Underhill PA, Evseeva I, Blue-Smith J, Jin L, Su B, Pitchappan R, Shanmugalakshmi S: The Eurasian heartland: a continental perspective on Y-chromosome diversity. Proc Natl Acad Sci U S A 2001, 98(18):10244-10249.
• [5]Karafet T, Xu L, Du R, Wang W, Feng S, Wells RS, Redd AJ, Zegura SL, Hammer MF: Paternal population history of East Asia: sources, patterns, and microevolutionary processes. Am J Hum Genet 2001, 69:615-628.
• [6]Martínez-Cruz B, Vitalis R, Ségurel L, Austerlitz F, Georges M, Théry S, Quintana-Murci L, Hegay T, Aldashev A, Nasyrova F: In the heartland of Eurasia: the multilocus genetic landscape of Central Asian populations. Eur J Hum Genet 2011, 19:216-223.
• [7]Colonna V, Boattini A, Guardiano C, Dall’Ara I, Pettener D, Longobardi G, Barbujani G: Long-range comparison between genes and languages based on syntactic distances. Hum Hered 2010, 70:245-254.
• [8]Hellenthal G, Busby GB, Band G, Wilson JF, Capelli C, Falush D, Myers S: A genetic atlas of human admixture history. Science 2014, 343:747-751.
• [9]Pirastu N, Robino A, Lanzara C, Athanasakis E, Esposito L, Tepper BJ, Gasparini P: Genetics of food preferences: a first view from silk road populations. J Food Sci 2012, 77:S413-S418.
• [10]Robino A, Mezzavilla M, Pirastu N, Dognini M, Tepper BJ, Gasparini P: A population-based approach to study the impact of PROP perception on food liking in populations along the Silk Road. PLoS One 2014, 9:e91716.
• [11]Ulivi S, Mezzavilla M, Gasparini P: Genetics of eye colours in different rural populations on the Silk Road. Eur J Hum Genet 2013, 21:1320-1323.
• [12]Girotto G, Pirastu N, Gasparini A, D'Adamo P, Gasparini P: Frequency of hearing loss in a series of rural communities of five developing countries located along the Silk Road. Audiol Med 2011, 9:135-140.
• [13]Li JZ, Absher DM, Tang H, Southwick AM, Casto AM, Ramachandran S, Cann HM, Barsh GS, Feldman M, Cavalli-Sforza LL: Worldwide human relationships inferred from genome-wide patterns of variation. Science 2008, 319:1100-1104.
• [14]Alexander DH, Novembre J, Lange K: Fast model-based estimation of ancestry in unrelated individuals. Genome Res 2009, 19:1655-1664.
• [15]Jakobsson M, Scholz SW, Scheet P, Gibbs JR, VanLiere JM, Fung H-C, Szpiech ZA, Degnan JH, Wang K, Guerreiro R: Genotype, haplotype and copy-number variation in worldwide human populations. Nature 2008, 451:998-1003.
• [16]McEvoy BP, Powell JE, Goddard ME, Visscher PM: Human population dispersal “Out of Africa” estimated from linkage disequilibrium and allele frequencies of SNPs. Genome Res 2011, 21:821-829.
• [17]Kirin M, McQuillan R, Franklin CS, Campbell H, McKeigue PM, Wilson JF: Genomic runs of homozygosity record population history and consanguinity. PLoS One 2010, 5:e13996.
• [18]Pemberton TJ, Absher D, Feldman MW, Myers RM, Rosenberg NA, Li JZ: Genomic patterns of homozygosity in worldwide human populations. Am J Hum Genet 2012, 91:275-292.
• [19]Weir BS, Hill WG: Effect of mating structure on variation in linkage disequilibrium. Genetics 1980, 95:477-488.
• [20]Tenesa A, Navarro P, Hayes BJ, Duffy DL, Clarke GM, Goddard ME, Visscher PM: Recent human effective population size estimated from linkage disequilibrium. Genome Res 2007, 17:520-526.
• [21]Hayes BJ, Visscher PM, McPartlan HC, Goddard ME: Novel multilocus measure of linkage disequilibrium to estimate past effective population size. Genome Res 2003, 13:635-643.
• [22]Reich D, Thangaraj K, Patterson N, Price AL, Singh L: Reconstructing Indian population history. Nature 2009, 461:489-494.
• [23]Pickrell JK, Pritchard JK: Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet 2012, 8:e1002967.
• [24]Loh P-R, Lipson M, Patterson N, Moorjani P, Pickrell JK, Reich D, Berger B: Inferring admixture histories of human populations using linkage disequilibrium. Genetics 2013, 193:1233-1254.
• [25]Dulik MC, Osipova LP, Schurr TG: Y-chromosome variation in Altaian Kazakhs reveals a common paternal gene pool for Kazakhs and the influence of Mongolian expansions. PLoS One 2011, 6:e17548.
• [26]Omberg L, Salit J, Hackett N, Fuller J, Matthew R, Chouchane L, Rodriguez-Flores JL, Bustamante C, Crystal RG, Mezey JG: Inferring genome-wide patterns of admixture in Qataris using fifty-five ancestral populations. BMC Genet 2012, 13:49. BioMed Central Full Text
• [27]Haber M, Platt DE, Bonab MA, Youhanna SC, Soria-Hernanz DF, Martínez-Cruz B, Douaihy B, Ghassibe-Sabbagh M, Rafatpanah H, Ghanbari M: Afghanistan’s ethnic groups share a Y-chromosomal heritage structured by historical events. PLoS One 2012, 7:e34288.
• [28]Ulivi S, Mezzavilla M, Gasparini P: Genetics of eye colours in different rural populations on the Silk Road. Eur J Hum Genet 2013, 21(11):1320-1323.
• [29]Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, De Bakker PI, Daly MJ: PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 2007, 81:559-575.
• [30]Rosenberg NA: Standardized subsets of the HGDP‐CEPH Human Genome Diversity Cell Line Panel, accounting for atypical and duplicated samples and pairs of close relatives. Ann Hum Genet 2006, 70:841-847.
• [31]Patterson N, Price AL, Reich D: Population structure and eigenanalysis. PLoS Genet 2006, 2:e190.
• [32][http:/ / www.unife.it/ dipartimento/ biologia-evoluzione/ ricerca/ evoluzione-e-genetica/ software] webcite NeON. []
• [33][http://cran.r-project.org/web/packages/ape/index.html] webcite ape. []
• [34]Browning SR, Browning BL: Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am J Hum Genet 2007, 81:1084-1097.