Phylogeography of mtDNA haplogroup R7 in the Indian peninsula

Gyaneshwer Chaubey¹^,2 , Monika Karmin¹ , Ene Metspalu¹ , Mait Metspalu¹ , Deepa Selvi-Rani² , Vijay Kumar Singh² , Jüri Parik¹ , Anu Solnik¹ , B Prathap Naidu² , Ajay Kumar²^,5 , Niharika Adarsh²^,5 , Chandana Basu Mallick²^,5 , Bhargav Trivedi²^,5 , Swami Prakash²^,5 , Ramesh Reddy²^,5 , Parul Shukla²^,5 , Sanjana Bhagat²^,5 , Swati Verma²^,5 , Samiksha Vasnik²^,5 , Imran Khan²^,5 , Anshu Barwa²^,5 , Dipti Sahoo²^,5 , Archana Sharma²^,5 , Mamoon Rashid²^,5 , Vishal Chandra²^,5 , Alla G Reddy² , Antonio Torroni³ , Robert A Foley⁴ , Kumarasamy Thangaraj² , Lalji Singh² , Toomas Kivisild¹^,4 and Richard Villems¹

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

²Centre for Cellular and Molecular Biology, Hyderabad, India

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

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

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

author email corresponding author email

BMC Evolutionary Biology 2008, 8:227doi: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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