An Updated Phylogeny of mtDNA Haplogroup R8 Based on Complete Mitogenomes

Abstract

Mitochondrial DNA (mtDNA) sequences reveal maternal phylogeny to trace back the demographic histories to construct phylogeny of a population. In this study, we update the phylogeny of the autochthonous Indian-specific mtDNA haplogroup R8 to give regional relationships between the members of haplogroup R8 in India and neighbouring areas. A set of 31 complete mitogenomes sequences from a Melakudiya tribal population of Southern India revealed two subclades of R8-R8a and R8b clustered with other tribal and caste populations of India. The updated coalescence age of haplogroup R8 in South Asia is dated ~43.3 ± 8.1 Kya, subclades R8a and R8b are dated ~40.6 ± 8.8 Kya and 15.4 ± 4.3 Kya, respectively. This study updated the deep in situ distribution of Indian-specific R8 lineages and added new daughter branches to the previously described branches of the haplogroup R8 in India.

Keywords

mtDNA haplogroup R8 tribe Southern India

Get full access to this article

View all access options for this article.

References

Andrews

R. M.

Kubacka

Chinnery

P. F.

Lightowlers

R. N.

Turnbull

D. M.

Howell

(1999). Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nature Genetics , 23(2), 147.

Bandelt

H. J.

Forster

Röhl

(1999). Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution , 16(1), 37–48.

Behar

D. M.

Van Oven

Rosset

Metspalu

Loogväli

E. L.

Silva

N. M.

(2012). A “Copernican” reassessment of the human mitochondrial DNA tree from its root. The American Journal of Human Genetics , 90(4), 675–684.

Chaubey

Karmin

Metspalu

Selvi-Rani

Singh

V. K.

(2008). Phylogeography of mtDNA haplogroup R7 in the Indian peninsula. BMC Evolutionary Biology , 8(1), 227.

Derenko

Malyarchuk

Bahmanimehr

Denisova

Perkova

Farjadian

Yepiskoposyan

(2013). Complete mitochondrial DNA diversity in Iranians. PloS One , 8(11), e80673.

Excoffier

Lischer

H. E.

(2010). Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources , 10(3), 564–567.

Greenspan

(2010). GenBank accession number HM345949 . Unpublished. Houston, TX: Family Tree DNA/Genealogy by Genetics.

Hall

T. A.

(1999). BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series , 41(41), 95–98.

Khan

N. A.

Govindaraj

Jyothi

Meena

A. K.

Thangaraj

(2013). Co-occurrence of m. 1555A > G and m. 11778G > A mitochondrial DNA mutations in two Indian families with strikingly different clinical penetrance of Leber hereditary optic neuropathy. Molecular Vision , 19, 1282.

10.

Kivisild

Rootsi

Metspalu

Mastana

Kaldma

Parik

(2003). The genetic heritage of the earliest settlers persists both in Indian tribal and caste populations. American Journal of Human Genetics , 72, 313–332.

11.

Kumar

Stecher

Tamura

(2016). MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution , 33(7), 1870–1874.

12.

Larruga

J. M.

Marrero

Abu-Amero

K. K.

Golubenko

M. V.

Cabrera

V. M.

(2017). Carriers of mitochondrial DNA macrohaplogroup R colonized Eurasia and Australasia from a Southeast Asia core area. BMC Evolutionary Biology , 17(1), 115.

13.

Metspalu

Kivisild

Metspalu

Parik

Hudjashov

Kaldma

(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 Genetics , 5(1), 26.

14.

Mishmar

Ruiz-Pesini

Golik

Macaulay

Clark

A. G.

Hosseini

(2003). Natural selection shaped regional mtDNA variation in humans. Proceedings of the National Academy of Sciences , 100(1), 171–176.

15.

Palanichamy

M. G.

Sun

Agrawal

Bandelt

H. J.

Kong

Q. P.

Khan

(2004). Phylogeny of mitochondrial DNA macrohaplogroup N in India, based on complete sequencing: Implications for the peopling of South Asia. The American Journal of Human Genetics , 75(6), 966–978.

16.

Pradutkanchana

Ishida

Kimura

(2010). Mitochondrial diversity of the sea nomads of Thailand (Unpublished; GenBank accession number—GU810073). Songkhla: Pathology, Prince of Songkla University.

17.

Quintana-Murci

Chaix

Wells

R. S.

Behar

D. M.

Sayar

Scozzari

(2004). Where west meets east: The complex mtDNA landscape of the Southwest and Central Asian corridor. The American Journal of Human Genetics , 74(5), 827–845.

18.

Rieder

M. J.

Taylor

S. L.

Tobe

V. O.

Nickerson

D. A.

(1998). Automating the identification of DNA variations using quality-based fluorescence re-sequencing: Analysis of the human mitochondrial genome. Nucleic Acids Research , 26(4), 967–973.

19.

Saillard

Forster

Lynnerup

Bandelt

H. J.

Nørby

(2000). mtDNA variation among Greenland Eskimos: The edge of the Beringian expansion. The American Journal of Human Genetics , 67(3), 718–726.

20.

Sambrook

Fritsch

E. F.

Maniatis

(1989). Molecular cloning: A laboratory manual (2nd ed.). Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.

21.

Thangaraj

Nandan

Sharma

V. K.

Eaaswarkhanth

Patra

(2009). Deep rooting in-situ expansion of mtDNA Haplogroup R8 in South Asia. PloS One , 4(8), e6545.

22.

Wang

H. W.

Y. C.

Sun

Zhao

Mitra

Chaudhuri

T. K.

(2012). Revisiting the role of the Himalayas in peopling Nepal: Insights from mitochondrial genomes. Journal of Human Genetics , 57(4), 228.

Supplementary Material

Please find the following supplemental material available below.

For Open Access articles published under a Creative Commons License, all supplemental material carries the same license as the article it is associated with.

For non-Open Access articles published, all supplemental material carries a non-exclusive license, and permission requests for re-use of supplemental material or any part of supplemental material shall be sent directly to the copyright owner as specified in the copyright notice associated with the article.

0.00 MB

0.05 MB