Background The phylogeny of the indigenous Indian-specific mitochondrial DNA (mtDNA) haplogroups have been determined and refined in previous reports. Similar to mtDNA superhaplogroups M and N, a profusion of reports are also available for superhaplogroup R. However, there is a dearth of information on South Asian subhaplogroups in particular, including R8. Therefore, we ought to access the genealogy and pre-historic expansion of haplogroup R8 which is considered one of the autochthonous lineages of South Asia. Methodology/Principal Findings Upon screening the mtDNA of 5,836 individuals belonging to 104 distinct ethnic populations of the Indian subcontinent, we found 54 individuals with the HVS-I motif that defines the R8 haplogroup. Complete mtDNA sequencing of these 54 individuals revealed two deep-rooted subclades: R8a and R8b. Furthermore, these subclades split into several fine subclades. An isofrequency contour map detected the highest frequency of R8 in the state of Orissa. Spearman's rank correlation analysis suggests significant correlation of R8 occurrence with geography. Conclusions/Significance The coalescent age of newly-characterized subclades of R8, R8a (15.4±7.2 Kya) and R8b (25.7±10.2 Kya) indicates that the initial maternal colonization of this haplogroup occurred during the middle and upper Paleolithic period, roughly around 40 to 45 Kya. These results signify that the southern part of Orissa currently inhabited by Munda speakers is likely the origin of these autochthonous maternal deep-rooted haplogroups. Our high-resolution study on the genesis of R8 haplogroup provides ample evidence of its deep-rooted ancestry among the Orissa (Austro-Asiatic) tribes.
References
[1]
Gadgil M, Joshi N, Manoharan S, Patil S, Prasad UVS (1998) Peopling of India. In: Balasubramanian D, Rao NA, editors. The Human Heritage. Hyderabad: Hyderabad University Press. pp. 100–129.
[2]
Kumar V, Reddy BM (2003) Status of Austro-Asiatic groups in the peopling of India: An exploratory study based on the available prehistoric, linguistic and biological evidences. J Biosci 28: 507–522.
[3]
Chaubey G, Karmin M, Metspalu E, Metspalu M, Selvi-Rani D, et al. (2008) Phylogeography of mtDNA haplogroup R7 in the Indian peninsula. BMC Evol Biol 8: 227.
[4]
Kumar V, Reddy ANS, Babu JP, Rao TN, Langstieh BT, et al. (2007) Y-chromosome evidence suggests a common paternal heritage of Austro-Asiatic populations. BMC Evol Biol 7: 47.
[5]
Thangaraj K, Sridhar V, Kivisild T, Reddy AG, Chaubey G, et al. (2005) Different population histories of the Mundari-and Mon-Khmer-speaking Austro-Asiatic tribes inferred from the mtDNA 9-bp deletion/insertion polymorphism in Indian populations. Hum Genet 116: 507–517.
[6]
Cordaux R, Saha N, Bentley GR, Aunger R, Sirajuddin SM, et al. (2003) Mitochondrial DNA analysis reveals diverse histories of tribal populations from India. Eur J Hum Genet 11: 253–264.
[7]
Kivisild T, Rootsi S, Metspalu M, Mastana S, Kaldma K, et al. (2003) The genetic heritage of the earliest settlers persists both in Indian tribal and caste populations. Am J Hum Genet 72: 313–332.
[8]
Metspalu M, Kivisild T, Metspalu E, Parik J, Hudjashov G, et al. (2004) Most of the extant mtDNA boundaries in south and southwest Asia were likely shaped during the initial settlement of Eurasia by anatomically modern humans. BMC Genet 5: 26.
[9]
Palanichamy MG, Sun C, Agrawal S, Bandelt HJ, Kong QP, et al. (2004) Phylogeny of mitochondrial DNA macrohaplogroup N in India, based on complete sequencing: implications for the peopling of Indian subcontinent. Am J Hum Genet 75: 966–978.
[10]
Reddy BM, Langstieh BT, Kumar V, Nagaraja T, Reddy ANS, et al. (2007) Austro-Asiatic tribes of Northeast India provide hitherto missing genetic link between South and Southeast Asia. PloS One 2: e1141.
[11]
Thangaraj K, Chaubey G, Singh VK, Vanniarajan A, Thanseem I, et al. (2006) In situ origin of deep rooting lineages of mitochondrial Macrohaplogroup ‘M’ in India. BMC Genomics 7: 151.
[12]
Rajkumar R, Banerjee J, Gunturi HB, Trivedi R, Kashyap VK (2005) Phylogeny and antiquity of M macrohaplogroup inferred from complete mtDNA sequence of Indian specific lineages. BMC Evol Biol 5: 26.
[13]
Kivisild T, Bamshad MJ, Kaldma K, Metspalu M, Metspalu E, et al. (1999) Deep common ancestry of Indian and western-Eurasian mitochondrial DNA lineages. Curr Biol 9: 1331–1334.
[14]
Thangaraj K, Chaubey G, Kivisild K, Reddy AG, Singh VK, et al. (2006) Response to Comment on “Reconstructing the Origin of Andaman Islanders”. Science 311: 470b.
[15]
Barik SS, Sahani R, Prasad BVR, Endicott P, Metspalu M, et al. (2008) Detailed mtDNA genotypes permit a reassessment of the settlement and population structure of the Andaman Islands. Am J Phys Anthropol 136: 19–27.
[16]
Andrews RM, Kubacka I, Chinnery PF, Lightowlers RN, Turnbull DM, et al. (1999) Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat genet 23: 147.
[17]
Bandelt H-J, Forster P, Rohl A (1999) Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16: 37–48.
[18]
Saitou N, Nei M (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406–425.
[19]
Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 24: 1596–1599.
[20]
Richards MB, Macaulay VA, Bandelt HJ, Sykes BC (1998) Phylogeography of mitochondrial DNA in western Europe. Ann Hum Genet 62: 241–260.
[21]
Delfiner P (1976) Linear estimation of non-stationary spatial phenomena. In: Guarasio M, David M, Haijbegts C, Dordrecht , Reidel , editors. Advanced geostatistics in the mining industry. Austria: pp. 49–68.
[22]
Mishmar D, Ruiz-Pesini E, Golik P, Macaulay V, Clark AG, et al. (2003) Natural selection shaped regional mtDNA variation in humans. Proc Natl Acad Sci USA 100: 171–176.
[23]
Saillard J, Forster P, Lynnerup N, Bandelt HJ, N？rby S (2000) mtDNA variation among Greenland Eskimos: The edge of the Beringian expansion. Am J Hum Genet 67: 718–726.
[24]
Schneider S, Roessli D, Excoffier L (2000) Arlequin ver. 2.000: Software for population genetics data analysis. Genetics and Biometry Laboratory, University of Geneva, Geneva, Switzerland.
