Pinpointing the Indian origin and revealing the Caucasus chapter in the genetic ancestry of the European Roma. M. Karmin1, M. Baldovič2, N. Jeran3, M. Reidla1, S. Cvjetan4, S. Rootsi1, T. Šaric3, J. Šarac3, M. Cenanovic5, T. Haller6, A. Raidvee7, R. Mägi6, A. Leskovac8, L. Kovacevic5, D. Marjanovic5, H. D. Auguštin3, N. Novokmet3, A. Ficek2, G. Chaubey1, P. Rudan3, V. Ferak2, E. Metspalu1, M. D. M. Behar1,9, M. Metspalu1, R. Villems1 1) Intitute of Molecular and Cellular Biology, University of Tartu and Estonian Biocenter, Tartu, Estonia; 2) Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia; 3) Institute for Anthropological Research, Zagreb, Croatia; 4) Mediterranean Institute for Life Sciences, Split, Croatia; 5) Institute for Genetic Engineering and Biotechnology, Sarajevo, Bosnia and Herzegovina; 6) Estonian Genome Center, University of Tartu, Tartu, Estonia; 7) University of Tartu, Faculty of Social Sciences and Education, Department of Psychology, Tartu, Estonia; 8) Vinca Institute of Nuclear Sciences , Belgrade, Serbia; 9) Molecular Medicine Laboratory, Rambam Health Care Campus, Haifa, Israel.

   According to linguistic evidence, the Indian exodus of the ancestors of the European Roma most probably took place around the end of the first millennium. By the 13th - 15th centuries, different groups of the Roma had spread throughout Europe. A virtual lack of written records prior to their arrival to Europe has left us with scarce knowledge about their historical migratory routes. Therefore, valuable insight comes from genetic studies. The origin of the maternal (mitochondrial DNA - mtDNA) and paternal lineages (Y chromosome - NRY) of the European Roma can be broadly classified as South Asian and West Eurasian. Out of the nearly 600 mtDNAs and 340 NRY lineages studied here, about 30% of the gene pool of both maternal and paternal lineages of the European Roma were classified as South Asian. To analyze the genetic ancestry of the Roma on the genome-wide level we genotyped ca 650 000 SNPs in 30 Roma individuals from six European countries with Illumina genotyping arrays. STRUCTURE-like analyses and principal component analyses (PCA) were performed in the context of Eurasian populations (N=1219). These analyses showed that in general the European Roma have a three-part genetic ancestry, with components from South Asia, the Caucasus area and Europe. Notably, on average, 38% of each Roma genome comprises the genetic component currently most abundant among populations in the Caucasus region, revealing a genetic legacy that has not received much attention until now. To further pinpoint the Indian origin of the Roma we used two methods based on haplotype data and a pre-defined reference population. 1) With the local ancestry deconvolution method we assigned the parts of genome with South Asian ancestry, and further used information only from those parts for PCA. 2) We used a novel in-house method assigning best-fit ancestry proportions for individuals as amalgamates of ancestral populations. The Roma formed a cluster bordering and overlapping with individuals from Uttar Pradesh and several South Indian states on PCA results, and the best-fit method revealed that the Indian ancestry of the Roma comes primarily from the Southern Indian populations. Thus, our results reveal a substantial amount of ancestry shared with populations from the Caucasus and several lines of evidence suggest a more southern origin of the Roma within India than previously thought.

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