Human mtDNA hypervariable regions, HVR I and II, hint at deep common maternal founder and subsequent maternal gene flow in Indian population groups

AbstractWe have analysed the hypervariable regions (HVR I and II) of human mitochondrial DNA (mtDNA) in individuals from Uttar Pradesh (UP), Bihar (BI) and Punjab (PUNJ), belonging to the Indo-European linguistic group, and from South India (SI), that have their linguistic roots in Dravidian language. Our analysis revealed the presence of known and novel mutations in both hypervariable regions in the studied population groups. Median joining network analyses based on mtDNA showed extensive overlap in mtDNA lineages despite the extensive cultural and linguistic diversity. MDS plot analysis based on Fst distances suggested increased maternal genetic proximity for the studied population groups compared with other world populations. Mismatch distribution curves, respective neighbour joining trees and other statistical analyses showed that there were significant expansions. The study revealed an ancient common ancestry for the studied population groups, most probably through common founder female lineage(s), and also indicated that human migrations occurred (maybe across and within the Indian subcontinent) even after the initial phase of female migration to India.

[1]  M. Stoneking,et al.  Extent of heterogeneity in mitochondrial DNA of European populations. , 1997, Journal of forensic sciences.

[2]  Y. Fu,et al.  Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. , 1997, Genetics.

[3]  Shamkant B. Navathe,et al.  MITOMAP: a human mitochondrial genome database--1998 update , 1998, Nucleic Acids Res..

[4]  L. Kunkel,et al.  Analysis of human Y-chromosome-specific reiterated DNA in chromosome variants. , 1977, Proceedings of the National Academy of Sciences of the United States of America.

[5]  R Trivedi,et al.  Phylogeny and antiquity of M macrohaplogroup inferred from complete mt DNA sequence of Indian specific lineages , 2005, BMC Evolutionary Biology.

[6]  Wen-Hsiung Li,et al.  Low nucleotide diversity in man. , 1991, Genetics.

[7]  B. Greenberg,et al.  Intraspecific nucleotide sequence variability surrounding the origin of replication in human mitochondrial DNA. , 1983, Gene.

[8]  M. Hammer,et al.  Y-chromosome lineages trace diffusion of people and languages in southwestern Asia. , 2001, American journal of human genetics.

[9]  Shamkant B. Navathe,et al.  MITOMAP: a human mitochondrial genome database—2004 update , 2004, Nucleic Acids Res..

[10]  Erratum to: Most of the extant mtDNA boundaries in South and Southwest Asia were likely shaped during the initial settlement of Eurasia by anatomically modern humans , 2004, BMC Genetics.

[11]  Personal Identification from Human Remains by Mitochondrial DNA Sequencing , 2002, The American journal of forensic medicine and pathology.

[12]  H. Bandelt,et al.  Single, Rapid Coastal Settlement of Asia Revealed by Analysis of Complete Mitochondrial Genomes , 2005, Science.

[13]  P. Majumder,et al.  Genomic Diversities and Affinities among Four Endogamous Groups of Punjab (India) Based on Autosomal and Mitochondrial DNA Polymorphisms , 2002, Human biology.

[14]  S T Sherry,et al.  Mismatch distributions of mtDNA reveal recent human population expansions. , 1994, Human biology.

[15]  O. Semino,et al.  Pre-Caucasoid and Caucasoid genetic features of the Indian population, revealed by mtDNA polymorphisms. , 1996, American journal of human genetics.

[16]  T. Nakayama,et al.  Mitochondrial DNA and STR typing of matter adhering to an earphone. , 2002, Journal of forensic sciences.

[17]  M. Hammer,et al.  Genetic Evidence on the Origins of Indian Caste Populations Material Supplemental , 2022 .

[18]  Bruce Budowle,et al.  Correlation of microscopic and mitochondrial DNA hair comparisons. , 2002, Journal of forensic sciences.

[19]  N. Freimer,et al.  A fine-scale comparison of the human and chimpanzee genomes: linkage, linkage disequilibrium and sequence analysis. , 1996, Human molecular genetics.

[20]  M. Stoneking.  Mitochondrial DNA and human evolution , 1994, Journal of bioenergetics and biomembranes.

[21]  P. Forster,et al.  Did Early Humans Go North or South? , 2005, Science.

[22]  Julio Rozas,et al.  DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis , 1999, Bioinform..

[23]  F. Sanger,et al.  Sequence and organization of the human mitochondrial genome , 1981, Nature.

[24]  M. Dixon,et al.  Deep common ancestry of Indian and western-Eurasian mitochondrial DNA lineages , 1999, Current Biology.

[25]  Sudhir Kumar,et al.  MEGA2: molecular evolutionary genetics analysis software , 2001, Bioinform..

[26]  H. Bandelt,et al.  Median-joining networks for inferring intraspecific phylogenies. , 1999, Molecular biology and evolution.

[27]  H. Bandelt,et al.  Genetic evidence of an early exit of Homo sapiens sapiens from Africa through eastern Africa , 1999, Nature Genetics.

[28]  H. Harpending,et al.  Population growth makes waves in the distribution of pairwise genetic differences. , 1992, Molecular biology and evolution.

[29]  P. Majumder,et al.  FUNDAMENTAL GENOMIC UNITY OF ETHNIC INDIA IS REVEALED BY ANALYSIS OF MITOCHONDRIAL DNA , 2000 .

[30]  G. Chaubey,et al.  Reconstructing the Origin of Andaman Islanders , 2005, Science.

[31]  P. Majumder,et al.  Genomic structures and population histories of linguistically distinct tribal groups of India , 2001, Human Genetics.

[32]  P. Underhill,et al.  The genetic heritage of the earliest settlers persists both in Indian tribal and caste populations. , 2003, American journal of human genetics.

[33]  Yun-Xin Fu,et al.  Genetic relationship of Chinese ethnic populations revealed by mtDNA sequence diversity. , 2002, American journal of physical anthropology.

[34]  R. Sukernik,et al.  Analysis of mitochondrial DNA diversity in the aleuts of the commander islands and its implications for the genetic history of beringia. , 2002, American journal of human genetics.

[35]  P. Underhill,et al.  Origins and divergence of the Roma (gypsies). , 2001, American journal of human genetics.

[36]  P. Majumder,et al.  Ethnic India: a genomic view, with special reference to peopling and structure. , 2003, Genome research.

[37]  S. Pääbo,et al.  Extensive nuclear DNA sequence diversity among chimpanzees. , 1999, Science.

[38]  F. Tajima.  Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. , 1989, Genetics.

[39]  Mark R. Wilson,et al.  Critique of interpretation of high levels of heteroplasmy in the human mitochondrial DNA hypervariable region I from hair. , 2002, Forensic science international.

[40]  H. Bandelt,et al.  Origin and evolution of Native American mtDNA variation: a reappraisal. , 1996, American journal of human genetics.

[41]  U. Gyllensten,et al.  Analysis of the complete human mtDNA genome: methodology and inferences for human evolution. , 2001, The Journal of heredity.

[42]  Hans-Jürgen Bandelt,et al.  Phylogeny of mitochondrial DNA macrohaplogroup N in India, based on complete sequencing: implications for the peopling of South Asia. , 2004, American journal of human genetics.

[43]  M Slatkin,et al.  A measure of population subdivision based on microsatellite allele frequencies. , 1995, Genetics.

[44]  A. Torroni,et al.  Extensive female-mediated gene flow from sub-Saharan Africa into near eastern Arab populations. , 2003, American journal of human genetics.

[45]  Ya-ping Zhang,et al.  Phylogeographic analysis of mtDNA variation in four ethnic populations from Yunnan Province: new data and a reappraisal , 2002, Journal of Human Genetics.

[46]  V. Kashyap,et al.  Haplotype diversity in mitochondrial DNA hypervariable regions I and II in three communities of Southern India. , 2003, Forensic science international.