The Q2 Mitochondrial Haplogroup in Oceania

Many details surrounding the origins of the peoples of Oceania remain to be resolved, and as a step towards this we report seven new complete mitochondrial genomes from the Q2a haplogroup, from Papua New Guinea, Fiji and Kiribati. This brings the total to eleven Q2 genomes now available. The Q haplogroup (that includes Q2) is an old and diverse lineage in Near Oceania, and is reasonably common; within our sample set of 430, 97 are of the Q haplogroup. However, only 8 are Q2, and we report 7 here. The tree with all complete Q genomes is proven to be minimal. The dating estimate for the origin of Q2 (around 35 Kya) reinforces the understanding that humans have been in Near Oceania for tens of thousands of years; nevertheless the Polynesian maternal haplogroups remain distinctive. A major focus now, with regard to Polynesian ancestry, is to address the differences and timing of the ‘Melanesian’ contribution to the maternal and paternal lineages as people moved further and further into Remote Oceania. Input from other fields such as anthropology, history and linguistics is required for a better understanding and interpretation of the genetic data.

[1]  Marcus W. Feldman,et al.  The great human expansion , 2012, Resonance.

[2]  D. Penny,et al.  Correcting the apparent mutation rate acceleration at shorter time scales under a Jukes-Cantor model. , 2011, Molecular biology and evolution.

[3]  Christopher R. Gignoux,et al.  Rapid, global demographic expansions after the origins of agriculture , 2011, Proceedings of the National Academy of Sciences.

[4]  M. Hurles,et al.  Genomic Analysis of Hepatitis B Virus Reveals Antigen State and Genotype as Sources of Evolutionary Rate Variation , 2011, Viruses.

[5]  M. Stoneking,et al.  Demographic History of Oceania Inferred from Genome-wide Data , 2010, Current Biology.

[6]  Simon J. Greenhill,et al.  Rise and fall of political complexity in island South-East Asia and the Pacific , 2010, Nature.

[7]  Richard Fullagar,et al.  Human Adaptation and Plant Use in Highland New Guinea 49,000 to 44,000 Years Ago , 2010, Science.

[8]  Patrick J. Biggs,et al.  Index-Free De Novo Assembly and Deconvolution of Mixed Mitochondrial Genomes , 2010, Genome biology and evolution.

[9]  Jin Ok Yang,et al.  Mapping Human Genetic Diversity in Asia , 2009, Science.

[10]  M. Stoneking,et al.  Genetic admixture history of Eastern Indonesia as revealed by Y-chromosome and mitochondrial DNA analysis. , 2009, Molecular biology and evolution.

[11]  Arne Röhl,et al.  Correcting for purifying selection: an improved human mitochondrial molecular clock. , 2009, American journal of human genetics.

[12]  R. Villems,et al.  Mitochondrial haplogroup U5b3: a distant echo of the epipaleolithic in Italy and the legacy of the early Sardinians. , 2009, American journal of human genetics.

[13]  Simon J. Greenhill,et al.  Matrilocal residence is ancestral in Austronesian societies , 2009, Proceedings of the Royal Society B: Biological Sciences.

[14]  Scott M. Williams,et al.  The Genetic Structure and History of Africans and African Americans , 2009, Science.

[15]  Manfred Kayser,et al.  Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation , 2009, Human mutation.

[16]  D. Graham,et al.  The Peopling of the Pacific from a Bacterial Perspective , 2009, Science.

[17]  Simon J. Greenhill,et al.  Language Phylogenies Reveal Expansion Pulses and Pauses in Pacific Settlement , 2009, Science.

[18]  M. Cox Accuracy of Molecular Dating with the Rho Statistic: Deviations from Coalescent Expectations Under a Range of Demographic Models , 2008, Human biology.

[19]  R. Gray,et al.  Bayesian coalescent inference of major human mitochondrial DNA haplogroup expansions in Africa , 2009, Proceedings of the Royal Society B: Biological Sciences.

[20]  Mark Stoneking,et al.  The impact of the Austronesian expansion: evidence from mtDNA and Y chromosome diversity in the Admiralty Islands of Melanesia. , 2008, Molecular biology and evolution.

[21]  Jaume Bertranpetit,et al.  The dawn of human matrilineal diversity. , 2008, American journal of human genetics.

[22]  M. Stoneking,et al.  Genome-wide analysis indicates more Asian than Melanesian ancestry of Polynesians. , 2008, American journal of human genetics.

[23]  Patrick J Biggs,et al.  An approach to transcriptome analysis of non-model organisms using short-read sequences. , 2008, Genome informatics. International Conference on Genome Informatics.

[24]  Alice A. Lin,et al.  Revealing the prehistoric settlement of Australia by Y chromosome and mtDNA analysis , 2007, Proceedings of the National Academy of Sciences.

[25]  Michael W. Scott The Severed Snake: Matrilineages, Making Place, and a Melanesian Christianity in Southeast Solomon Islands , 2007 .

[26]  K. Howe Vaka moana : voyages of the ancestors : the discovery and settlement of the Pacific , 2007 .

[27]  P. Forster,et al.  A mitochondrial stratigraphy for island southeast Asia. , 2007, American journal of human genetics.

[28]  M. Hurles,et al.  Deciphering past human population movements in Oceania: provably optimal trees of 127 mtDNA genomes. , 2006, Molecular biology and evolution.

[29]  Alfredo Coppa,et al.  The Role of Selection in the Evolution of Human Mitochondrial Genomes , 2006, Genetics.

[30]  Hans-Jürgen Bandelt,et al.  A practical guide to mitochondrial DNA error prevention in clinical, forensic, and population genetics. , 2005, Biochemical and biophysical research communications.

[31]  T. Kivisild,et al.  Traces of Archaic Mitochondrial Lineages Persist in Austronesian-Speaking Formosan Populations , 2005, PLoS biology.

[32]  G. Chambers,et al.  Human Evolution in Polynesia , 2005, Human biology.

[33]  Jonathan Scott Friedlaender,et al.  Expanding Southwest Pacific mitochondrial haplogroups P and Q. , 2005, Molecular biology and evolution.

[34]  M. Hurles,et al.  The dual origin of the Malagasy in Island Southeast Asia and East Africa: evidence from maternal and paternal lineages. , 2005, American journal of human genetics.

[35]  H. Bandelt,et al.  Saami and Berbers--an unexpected mitochondrial DNA link. , 2005, American journal of human genetics.

[36]  D Penny,et al.  The MinMax Squeeze: guaranteeing a minimal tree for population data. , 2004, Molecular biology and evolution.

[37]  G. Koki,et al.  Expanding Southwest Pacific mitochondrial haplogroups , 2005 .

[38]  D. Swallow Human Evolutionary Genetics: Origins, Peoples & Disease , 2004, Journal of Medical Genetics.

[39]  Michael P. Cummings,et al.  PAUP* [Phylogenetic Analysis Using Parsimony (and Other Methods)] , 2004 .

[40]  Vincent Moulton,et al.  Using consensus networks to visualize contradictory evidence for species phylogeny. , 2004, Molecular biology and evolution.

[41]  Mike A. Steel,et al.  Two further links between MP and ML under the poisson model , 2004, Appl. Math. Lett..

[42]  P. Hage,et al.  Matrilineality and the Melanesian Origin of Polynesian Y Chromosomes1 , 2003 .

[43]  M. Hurles,et al.  Untangling Oceanic settlement: the edge of the knowable , 2003 .

[44]  U. Gyllensten,et al.  Mitochondrial genome variation and evolutionary history of Australian and New Guinean aborigines. , 2003, Genome research.

[45]  D. Penny,et al.  Estimating the number of females in the founding population of New Zealand: Analysis of mtDNA variation , 2002 .

[46]  J. Diamond Polynesian origins: Slow boat to Melanesia? , 2001, Nature.

[47]  S. Bedford ON THE ROAD OF THE WINDS: AN ARCHAEOLOGICAL HISTORY OF THE PACIFIC ISLANDS BEFORE EUROPEAN CONTACT, by , 2001 .

[48]  S. Pääbo,et al.  Mitochondrial genome variation and the origin of modern humans , 2000, Nature.

[49]  Russell D. Gray,et al.  Language trees support the express-train sequence of Austronesian expansion , 2000, Nature.

[50]  D. Turnbull,et al.  Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA , 1999, Nature Genetics.

[51]  L. Jorde,et al.  Mitochondrial and nuclear genetic relationships among Pacific Island and Asian populations. , 1998, American journal of human genetics.

[52]  D Penny,et al.  Testing migration patterns and estimating founding population size in Polynesia by using human mtDNA sequences. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[53]  M. Rieder,et al.  Automating the identification of DNA variations using quality-based fluorescence re-sequencing: analysis of the human mitochondrial genome. , 1998, Nucleic acids research.

[54]  J. Miles Infectious Diseases: Colonising the Pacific? , 1997 .

[55]  A. Pawley,et al.  Austronesian Historical Linguistics and Culture History , 1993 .

[56]  M. Miyamoto,et al.  Phylogenetic Analysis of DNA Sequences , 1991 .

[57]  L. Foulds,et al.  Identification of phylogenetic trees of minimal length. , 1978, Journal of theoretical biology.

[58]  R. Derrick A history of Fiji , 1952 .