Open Access Highly Accessed Research article

Most of the extant mtDNA boundaries in South and Southwest Asia were likely shaped during the initial settlement of Eurasia by anatomically modern humans

Mait Metspalu1*, Toomas Kivisild1, Ene Metspalu1, Jüri Parik1, Georgi Hudjashov1, Katrin Kaldma1, Piia Serk1, Monika Karmin1, Doron M Behar2, M Thomas P Gilbert6, Phillip Endicott7, Sarabjit Mastana4, Surinder S Papiha5, Karl Skorecki2, Antonio Torroni3 and Richard Villems1

Author Affiliations

1 Institute of Molecular and Cell Biology, Tartu University, Tartu, Estonia

2 Bruce Rappaport Faculty of Medicine and Research Institute, Technion and Rambam Medical Center, Haifa, Israel

3 Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy

4 Department of Human Sciences, Loughborough University, Loughborough, United Kingdom

5 Department of Human Genetics, University of Newcastle-upon-Tyne, United Kingdom

6 Ecology and Evolutionary Biology, The University of Arizona, Tucson, Arizona, USA

7 Henry Wellcome Ancient Biomolecules Centre, Department of Zoology, University of Oxford, Oxford OX1 3PS,United Kingdom

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BMC Genetics 2004, 5:26  doi:10.1186/1471-2156-5-26

Published: 31 August 2004



Recent advances in the understanding of the maternal and paternal heritage of south and southwest Asian populations have highlighted their role in the colonization of Eurasia by anatomically modern humans. Further understanding requires a deeper insight into the topology of the branches of the Indian mtDNA phylogenetic tree, which should be contextualized within the phylogeography of the neighboring regional mtDNA variation. Accordingly, we have analyzed mtDNA control and coding region variation in 796 Indian (including both tribal and caste populations from different parts of India) and 436 Iranian mtDNAs. The results were integrated and analyzed together with published data from South, Southeast Asia and West Eurasia.


Four new Indian-specific haplogroup M sub-clades were defined. These, in combination with two previously described haplogroups, encompass approximately one third of the haplogroup M mtDNAs in India. Their phylogeography and spread among different linguistic phyla and social strata was investigated in detail. Furthermore, the analysis of the Iranian mtDNA pool revealed patterns of limited reciprocal gene flow between Iran and the Indian sub-continent and allowed the identification of different assemblies of shared mtDNA sub-clades.


Since the initial peopling of South and West Asia by anatomically modern humans, when this region may well have provided the initial settlers who colonized much of the rest of Eurasia, the gene flow in and out of India of the maternally transmitted mtDNA has been surprisingly limited. Specifically, our analysis of the mtDNA haplogroups, which are shared between Indian and Iranian populations and exhibit coalescence ages corresponding to around the early Upper Paleolithic, indicates that they are present in India largely as Indian-specific sub-lineages. In contrast, other ancient Indian-specific variants of M and R are very rare outside the sub-continent.