Genetic differentiation between upland and lowland populations shapes the Y-chromosomal landscape of West Asia

Abstract

Y-chromosomal variation in West Asian populations has so far been studied in less detail than in the neighboring Europe. Here, we analyzed 598 Y-chromosomes from two West Asian subregions—Transcaucasia and the Armenian plateau—using 40 Y-SNPs and 17 Y-STRs and combined them with previously published data from the region. The West Asian populations fell into two clusters: upland populations from the Anatolian, Armenian and Iranian plateaus, and lowland populations from the Levant, Mesopotamia and the Arabian Peninsula. This geographic subdivision corresponds with the linguistic difference between Indo-European and Turkic speakers, on the one hand, and Semitic speakers, on the other. This subdivision could be traced back to the Neolithic epoch, when upland populations from the Anatolian and Iranian plateaus carried similar haplogroup spectra but did not overlap with lowland populations from the Levant. We also found that the initial gene pool of the Armenian motherland population has been well preserved in most groups of the Armenian Diaspora. In view of the contribution of West Asians to the autosomal gene pool of the steppe Yamnaya archaeological culture, we sequenced a large portion of the Y-chromosome in haplogroup R1b samples from present-day East European steppe populations. The ancient Yamnaya samples are located on the “eastern” R-GG400 branch of haplogroup R1b-L23, showing that the paternal descendants of the Yamnaya still live in the Pontic steppe and that the ancient Yamnaya population was not an important source of paternal lineages in present-day West Europeans.

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Acknowledgements

We thank all sample donors whose participation made this study possible, and the Georgian church which approved and assisted in sampling in Georgia.

The Genographic Consortium includes: Li Jin, Hui Li, & Shilin Li (Fudan University, Shanghai, China); Pandikumar Swamikrishnan (IBM, Somers, New York, United States); Asif Javed, Laxmi Parida & Ajay K. Royyuru (IBM, Yorktown Heights, New York, United States); R. John Mitchell (La Trobe University, Melbourne, Victoria, Australia); Pierre A. Zalloua (Lebanese American University, Chouran, Beirut, Lebanon); Syama Adhikarla, ArunKumar, GaneshPrasad, Ramasamy Pitchappan, Arun Varatharajan Santhakumari, Kavitha Valampuri (Madurai Kamaraj University, Madurai, Tamil Nadu, India); R. Spencer Wells and Miguel G. Vilar (National Geographic Society, Washington, District of Columbia, United States); Himla Soodyall (National Health Laboratory Service, Johannesburg, South Africa); Elena Balanovska & Oleg Balanovsky (Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moscow, Russia); Chris Tyler-Smith (The Wellcome Trust Sanger Institute, Hinxton, United Kingdom); Fabrício R. Santos (Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil); Jaume Bertranpetit, Marc Haber, Marta Melé, & David Comas(Universitat Pompeu Fabra, Barcelona, Spain); Christina J. Adler, Alan Cooper, Clio S. I. Der Sarkissian & Wolfgang Haak (University of Adelaide, South Australia, Australia); Matthew E. Kaplan & Nirav C. Merchant (University of Arizona, Tucson, Arizona, United States); Colin Renfrew (University of Cambridge, Cambridge, United Kingdom); Andrew C. Clarke & Elizabeth A. Matisoo-Smith (University of Otago, Dunedin, New Zealand); Jill B. Gaieski & Theodore G. Schurr (University of Pennsylvania, Philadelphia, Pennsylvania, United States).

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Correspondence to O. Balanovsky.

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Ethical approval

All procedures performed in studies involving human participants were in accordance with the ethical standards of the Ethics Committee of the Research Centre for Medical Genetics, Moscow, Russia and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards.

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Informed consent was obtained from all individual participants included in the study.

Funding

This study received primary support from the Russian Science Foundation Grant 14-14-00827 (to OB, MC, AA, VZ), including data analysis and completing the paper. Y-chromosomal resequencing was done mainly using funding from the Historical Genetics lab in the Moscow Institute of Physics and Technology. Erzurum Armenian samples were genotyped with support from the Russian Foundation for Basic Research (Grant 16-36-00122 to MC), while the Hemsheni and Krasnodar Armenian samples were genotyped with support from the Russian Foundation for Basic Research (Grant 16-06-00364 to EP) and from the Genographic project. CTS was supported by The Wellcome Trust (098051).

Conflict of interest

On behalf of all authors, the corresponding author states that there is no conflict of interest.

Additional information

O. Balanovsky and M. Chukhryaeva have equally contributed to this article.

Affiliations for The Genographic Consortium are moved to Acknowledgements.

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Supplementary Figure 1. Map of the populations studied, and their documented migration routes during historical times. Armenian populations are designated as “A-”.The Hemsheni Armenian population was formed by migration of a small Armenian group into the coastal zone between Erzurum and Trabzon (modern Turkey). They were isolated from the rest of the Armenian people from the 7th to the 20th century, when due to the consequences of the World War I they migrated to the Russian Black Sea coast. Nowadays, about 300,000 Hemsheni live in the Krasnodar region of Russia (Simonian, 2007). Armenians of the Adygea and Krasnodar regions include not only immigrants into the province from the 10th to the 15th century from eastern Armenia, but also a later heterogeneous influx of immigrants. There are 250,000 non-Hemsheni Armenians in the Krasnodar region, and about 15,000 in Adygea. Armenians of Erzurum originated from the Taron area within historical Armenia. During the 19th century, they were moved into the growing area of the Russian empire. Nowadays, they live in the Shirac Province of Armenia and the south-western part of Georgia. Don Armenians have an even more complicated migration history. They claim to be descendants of residents of the medieval Armenian city Ani. The expansion of Seljuk Turks in the 13th century forced them to migrate to the North Caspian area. In the next century, they escaped from Nogais to Crimea, and in the 18th century they were relocated by the Russian government to the lower Don area. There are around 110,000 Don Armenians nowadays (Tololyan, 2001).Laz is a Georgian ethnic group inhabiting the historic region of Lazistan (modern Turkey). The Laz language belongs to the Kartvelian language family. There are about 20,000 Laz in Turkey. Imeretins are another ethnic group of Georgians inhabiting the Imereti province (western Georgia). Their language also belongs to the Kartvelian family. Eastern Georgians are a heterogenous group, including Pshavi, Tushi, Mtiul and Xevsur. All these groups live in mountainous eastern regions of Georgia, and speak different dialects of the Kartvelian family. Armenian Hemsheni and Erzurum samples were collected in Russia and Georgia, respectively, but in geographic-based analyses they were placed in their grandparent’s homeland: Trabzon and Erzurum. This reconstruction method was previously used (Herrera et al., 2012), and we also adopted this approach for relatively recent migrations. The Armenian populations from Iran were located in northwest Iran because the migration occurred a long time ago. Supplementary material 1 (TIF 2634kb)

Supplementary Figure 2. Phylogeographic summary of haplogroup R-L23 diversity in West Asia.Inset: R-L23 frequency distribution map. The map shows that within West Asia, haplogroup R-L23 reaches its highest frequencies among Armenians (around 20%) and the surrounding mountain populations of Turkey and Iran. Almost all Armenian and Georgian L23 samples fall into a newly-recognized “eastern” branch R-GG400. Populations in the Y-STR network are grouped by geography, as legend indicates: West Caucasus – Abkhazes, Cherkessians (Myres et al., 2010); Armenians - A-Krasnodar, A-Adygei, A-Don (this study); A-Ararat, A-Gardman, A-Van, A-Sasun (Herrera et al., 2012); Armenians (Myres et al., 2010); East Caucasus - Avars, Bagvalals, Balkars, Darginians, Lezgis, Tabasarans (Myres et al., 2010); Central Europe - Czech, Hungarians, Poles (Myres et al., 2010); West Europe - Danes, Germans, Swiss (Myres et al., 2010); North Europe - Estonians, Swades South (Malmo) (Myres et al., 2010); Transcaucasia - Georgians, Azeri (our unpublished data), Georgians Megrels (Myres et al., 2010); South Europe - Greeks, Italians, Romanians (Myres et al., 2010); South Asia - Jordanians, Pakistani, Palestinians (Myres et al., 2010); Central Caucasus - Ossets North (Myres et al., 2010); Anatolia - Turkey (Myres et al., 2010).The Y-STR network identifies some clusters of haplotypes, designated by Greek letters. Dotted lines indicate the boundaries of the clusters. Cluster β is specific to the Armenian populations. The cluster is 3000±1200 years old. Supplementary material 1 (TIF 482kb)

Supplementary Figure 3. Phylogeographic summary of haplogroup J-M67 diversity in West Asia.Inset: J-M67 frequency distribution map. Haplogroup J-M67 reaches its frequency peak among Nakh-speaking Chechens and Ingushes in East Caucasus, exhibits moderate frequencies among Armenians and is rare among other West Asians. The haplogroup J2a has been present in Transcaucasia since Upper Paleolithic times (Jones et al., 2015). Populations in the Y-STR network are grouped by geography, as the legend indicates: West Caucasus - Adyghes, Abkhazes (Balanovsky et al., 2011); Transcaucasia - Georgians, Azeri (our unpublished data); Armenians - A-Krasnodar, A-Adygei, A-Don, A-Hemsheni, A-Erzurum (this study); A-Ararat, A-Gardman, A-Van, A-Sasun (Lowery et al., 2013); East Caucasus - Ingush, Chechen (Balanovsky et al., 2011); Central Caucasus - Ossets (Balanovsky et al., 2011). The Y-STR network identifies some clusters of haplotypes, designated by Greek letters. Dotted lines indicate the boundaries of the clusters. There are some Nakh-specific haplotype clusters and an Armenian cluster (α), which originated 2000±500 years BP. As the Y-STR resolution is not enough to reveal the fine haplogroup substructure, further Y-chromosomal sequencing efforts are needed.Supplementary material 1 (TIF 510kb)

Supplementary Figure 4. Phylogeographic summary of haplogroup L-M317 diversity in West Asia.Inset: L-M317 frequency distribution map, which shows that haplogroup L-M317 is rare in most West Asian populations, except for the Laz. Populations in the Y-STR network are grouped by geography, as the legend indicates: West Caucasus – Abkhazes, Avars, (Balanovsky et al., 2011); Transcaucasia – Laz, Imeretins, Armenians Adygei, Armenians Krasnodar, Armenians Don (this study); A-Ararat, A-Gardman, A-Van, A-Sasun (Lowery et al., 2013); East Caucasus - Lezghins (Balanovsky et al., 2011); Central Caucasus - Ossets Iron (Balanovsky et al., 2011); West Asia – Iranians SE, Iranians NW, South Iran, Esfahan (Iran), Kordestan (Iran), Lebanese Maronite N, Lebanese Maronite (Mount), Lebanese Maronite S, Lebanese Shiite N, Pashtun-Kunduz (Haber et al., 2011; Cristofaro et al., 2013); Makrani (Cristofaro et al., 2013); Central Asia - Uzbek-Jawzjan (Cristofaro et al., 2013); Karakalpaks (our unpublished data); Siberia – Altai-Kizhi, Evenks (our unpublished data); Russians – Terek Cossacs, Russians Ryazan (our unpublished data).The Y-STR network did not identify a Laz-specific cluster and many Laz haplotypes were shared with other ethnic groups or are linked by one-step neighbors.Supplementary material 1 (TIF 326kb)

Supplementary Figure 5. Armenian and Georgian populations compared with other West Eurasians. This MDS plot is based on 21 haplogroups and only populations examined for all these haplogroups are shown. Population names follow Table 1.Supplementary material 1 (TIF 616kb)

Supplementary Figure 6. Genetic relationships between Armenian populations. A) Heatmap of the genetic distance matrix and corresponding dendrogram. B) MDS plot based on data from 21 haplogroups. Population names follow Table 1.Supplementary material 1 (TIF 391kb)

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Balanovsky, O., Chukhryaeva, M., Zaporozhchenko, V. et al. Genetic differentiation between upland and lowland populations shapes the Y-chromosomal landscape of West Asia. Hum Genet 136, 437–450 (2017). https://doi.org/10.1007/s00439-017-1770-2

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Keywords

  • Arabian Peninsula
  • Iranian Plateau
  • Eastern Branch
  • Haplogroup Frequency
  • Lowland Population