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Phylogeography of mtDNA haplogroup R7 in the Indian peninsula

Gyaneshwer Chaubey12, Monika Karmin1, Ene Metspalu1, Mait Metspalu1, Deepa Selvi-Rani2, Vijay Kumar Singh2, Jüri Parik1, Anu Solnik1, B Prathap Naidu2, Ajay Kumar25, Niharika Adarsh25, Chandana Basu Mallick25, Bhargav Trivedi25, Swami Prakash25, Ramesh Reddy25, Parul Shukla25, Sanjana Bhagat25, Swati Verma25, Samiksha Vasnik25, Imran Khan25, Anshu Barwa25, Dipti Sahoo25, Archana Sharma25, Mamoon Rashid25, Vishal Chandra25, Alla G Reddy2, Antonio Torroni3, Robert A Foley4, Kumarasamy Thangaraj2, Lalji Singh2, Toomas Kivisild14* and Richard Villems1

Author Affiliations

1 Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu and Estonian Biocentre, Tartu, Estonia

2 Centre for Cellular and Molecular Biology, Hyderabad, India

3 Dipartimento di Genetica e Microbiologia, Università di Pavia, Via Ferrata 1, 27100 Pavia, Italy

4 Leverhulme Centre of Human Evolutionary Studies, The Henry Wellcome Building, University of Cambridge, Fitzwilliam Street, Cambridge, CB2 1QH, UK

5 Students of different Universities and Colleges of India studied (as a part of their curriculum) in CCMB Hyderabad, India

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BMC Evolutionary Biology 2008, 8:227  doi:10.1186/1471-2148-8-227

Published: 4 August 2008

Additional files

Additional file 1:

Phylogenetic tree of 22 Indian complete mtDNA sequences of superhaplogroup R. The tree includes data reported [[4] and references there in] Suffixes A, C, G, and T indicate transversions, "d" signifies a deletion; recurrent mutations are underlined. 16182C, 16183C and 16519 polymorphisms are omitted in phylogenetic reconstruction. The sample code, geographic and linguistic affiliations are described in Table 1. The sub-tree of haplogroup R7 sequences is displayed in Fig. 2.

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Additional file 2:

Haplogroup R5-8, R30 and R31 frequency plots with 95% credible regions. Data calculated from the posterior distribution of the proportion of a haplogroup/sub-haplogroup in the population. Linguistic affiliations of the populations are indicated by colors.

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Additional file 3:

Map of Indian subcontinent depicting the spatial frequency distribution of mtDNA haplogroup R7. Isofrequency maps were generated by using Surfer7 Golden software (Golden Software Inc., Golden, Colorado), following the Kriging procedure. The spread of R7 in India is centered around the AA "heartland" (Bihar, Jharkhand, and Chhattisgarh). Dots indicate the sampling locations.

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Additional file 4:

Spatial Autocorrelation Analyses Correlograms of haplogroup R7 in Indian subcontinent. The Moran's I coefficient was calculated with five distance classes in binary weight matrix. Significant values are shown as black (p < .05) whereas nonsignificant values as blank circles. Distances are given in Kilometers (KM's).

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Additional file 5:

Map of India showing the frequency distribution (%) of haplogroup R7 at the district level. Only 2,200 samples were available at this resolution. Nevertheless, it is still evident that the frequency peak of R7 is observed in Bihar, Jharkhand, Chhattisgarh, Madhya-Pradesh and the northern districts of Andhra-Pradesh (Adilabad, Warangal and Khammam).

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Additional file 6:

Details of the samples studied for hg R7 in the present study. Data shown are from the present work and from literature: [4,12,14,21,22,41-46].

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