References for mtDNA tree Build 2 (14 Oct 2008)

 

Abu-Amero KK, Gonzalez AM, Larruga JM, Bosley TM, Cabrera VM. 2007. Eurasian and African mitochondrial DNA influences in the Saudi Arabian population. BMC Evol Biol 7:32. http://dx.doi.org/10.1186/1471-2148-7-32

 

Abu-Amero KK, Larruga JM, Cabrera VM, Gonzalez AM. 2008. Mitochondrial DNA structure in the Arabian Peninsula. BMC Evol Biol 8(1):45. http://dx.doi.org/10.1186/1471-2148-8-45

 

Achilli A, Rengo C, Magri C, Battaglia V, Olivieri A, Scozzari R, Cruciani F, Zeviani M, Briem E, Carelli V. 2004. The molecular dissection of mtDNA haplogroup H confirms that the Franco-Cantabrian glacial refuge was a major source for the European gene pool. Am J Hum Genet 75(5):910-918. http://dx.doi.org/10.1086/425590

 

Achilli A, Rengo C, Battaglia V, Pala M, Olivieri A, Fornarino S, Magri C, Scozzari R, Babudri N, Santachiara-Benerecetti AS. 2005. Saami and Berbers—an unexpected mitochondrial DNA link. Am J Hum Genet 76(5):883-886. http://dx.doi.org/10.1086/430073

 

Achilli A, Perego UA, Bravi CM, Coble MD, Kong QP, Woodward SR, Salas A, Torroni A, Bandelt HJ. 2008. The phylogeny of the four pan-American MtDNA haplogroups: implications for evolutionary and disease studies. PLoS ONE 3(3):e1764. http://dx.doi.org/10.1371/journal.pone.0001764

 

Álvarez-Iglesias V, Jaime JC, Carracedo Á, Salas A. 2007. Coding region mitochondrial DNA SNPs: targeting East Asian and Native American haplogroups. Forensic Science International: Genetics 1(1):44-55. http://dx.doi.org/10.1016/j.fsigen.2006.09.001

 

Barik SS, Sahani R, Prasad BV, Endicott P, Metspalu M, Sarkar BN, Bhattacharya S, Annapoorna PC, Sreenath J, Sun D. 2008. Detailed mtDNA genotypes permit a reassessment of the settlement and population structure of the Andaman Islands. Am J Phys Anthropol 136(1):19-27. http://dx.doi.org/10.1002/ajpa.20773

 

Behar DM, Metspalu E, Kivisild T, Achilli A, Hadid Y, Tzur S, Pereira L, Amorim A, Quintana-Murci L, Majamaa K. 2006. The matrilineal ancestry of Ashkenazi Jewry: portrait of a recent founder event. Am J Hum Genet 78(3):487-497. http://dx.doi.org/10.1086/500307

 

Behar DM, Metspalu E, Kivisild T, Rosset S, Tzur S, Hadid Y, Yudkovsky G, Rosengarten D, Pereira L, Amorim A. 2008a. Counting the founders: the matrilineal genetic ancestry of the Jewish Diaspora. PLoS ONE 3(4). http://dx.doi.org/10.1371/journal.pone.0002062

 

Behar DM, Villems R, Soodyall H, Blue-Smith J, Pereira L, Metspalu E, Scozzari R, Makkan H, Tzur S, Comas D. 2008b. The dawn of human matrilineal diversity. Am J Hum Genet 82(5):1130-1140. http://dx.doi.org/10.1016/j.ajhg.2008.04.002

 

Carelli V, Achilli A, Valentino ML, Rengo C, Semino O, Pala M, Olivieri A, Mattiazzi M, Pallotti F, Carrara F. 2006. Haplogroup effects and recombination of mitochondrial DNA: novel clues from the analysis of Leber hereditary optic neuropathy pedigrees. Am J Hum Genet 78(4):564-574. http://dx.doi.org/10.1086/501236

 

Chaubey G, Karmin M, Metspalu E, Metspalu M, Selvi-Rani D, Singh VK, Parik J, Solnik A, Naidu BP, Kumar A, Adarsh N, Mallick CB, Trivedi B, Prakash S, Reddy R, Shukla P, Bhagat S, Verma S, Vasnik S, Khan I, Barwa A, Sahoo D, Sharma A, Rashid M, Chandra V, Reddy AG, Torroni A, Foley RA, Thangaraj K, Singh L, Kivisild T, Villems R. 2008a. Phylogeography of mtDNA haplogroup R7 in the Indian peninsula. BMC Evol Biol 8(1):227. http://dx.doi.org/10.1186/1471-2148-8-227

 

Chaubey G, Metspalu M, Karmin M, Thangaraj K, Rootsi S, Parik J, Solnik A, Rani DS, KumarSingh V, Naidu BP. 2008b. Language shift by indigenous population: a model genetic study in South Asia. International Journal of Human Genetics 8(1-2):41-50. http://www.krepublishers.com/02-Journals/IJHG/IJHG-08-0-000-000-2008-Web/IJHG-08-1-2-001-256-2007-Abst-PDF/IJHG-08-1-2-041-08-337-Chaubey-G/IJHG-08-1&2-041-08-337-Chaubey-G-Tt.pdf

 

Derenko M, Malyarchuk B, Grzybowski T, Denisova G, Dambueva I, Perkova M, Dorzhu C, Luzina F, Lee HK, Vanecek T. 2007. Phylogeographic analysis of mitochondrial DNA in northern Asian populations. Am J Hum Genet 81(5):1025-1041. http://dx.doi.org/10.1086/522933

 

FamilyTreeDNA. Complete mtDNA sequences uploaded to GenBank by FamilyTreeDNA between 2006 and present. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Nucleotide&term=Homo[Organism]+gene_in_mitochondrion[PROP]+family_tree

 

Finnilä S, Lehtonen MS, Majamaa K. 2001. Phylogenetic network for European mtDNA. Am J Hum Genet 68(6):1475-1484. http://dx.doi.org/10.1086/320591

 

Friedlaender J, Schurr T, Gentz F, Koki G, Friedlaender F, Horvat G, Babb P, Cerchio S, Kaestle F, Schanfield M. 2005. Expanding Southwest Pacific mitochondrial haplogroups P and Q. Mol Biol Evol 22(6):1506-1517. http://dx.doi.org/10.1093/molbev/msi142

 

Friedlaender JS, Friedlaender FR, Hodgson JA, Stoltz M, Koki G, Horvat G, Zhadanov S, Schurr TG, Merriwether DA. 2007. Melanesian mtDNA complexity. PLoS ONE 2(2):e248. http://dx.doi.org/10.1371/journal.pone.0000248

 

Gonzalez AM, Garcia O, Larruga JM, Cabrera VM. 2006. The mitochondrial lineage U8a reveals a Paleolithic settlement in the Basque country. BMC Genomics 7:124. http://dx.doi.org/10.1186/1471-2164-7-124

 

Gonzalez AM, Larruga JM, Abu-Amero KK, Shi Y, Pestano J, Cabrera VM. 2007. Mitochondrial lineage M1 traces an early human backflow to Africa. BMC Genomics 8:223. http://dx.doi.org/10.1186/1471-2164-8-223

 

Grzybowski T, Malyarchuk BA, Derenko MV, Perkova MA, Bednarek J, Wozniak M. 2007. Complex interactions of the Eastern and Western Slavic populations with other European groups as revealed by mitochondrial DNA analysis. Forensic Science International: Genetics 1(2):141-147. http://dx.doi.org/10.1016/j.fsigen.2007.01.010

 

Hill C, Soares P, Mormina M, Macaulay V, Meehan W, Blackburn J, Clarke D, Raja JM, Ismail P, Bulbeck D. 2006. Phylogeography and ethnogenesis of aboriginal Southeast Asians. Mol Biol Evol 23(12):2480-2491. http://dx.doi.org/10.1093/molbev/msl124

 

Hill C, Soares P, Mormina M, Macaulay V, Clarke D, Blumbach PB, Vizuete-Forster M, Forster P, Bulbeck D, Oppenheimer S. 2007. A mitochondrial stratigraphy for Island Southeast Asia. Am J Hum Genet 80(1):29-43. http://dx.doi.org/10.1086/510412

 

Hudjashov G, Kivisild T, Underhill PA, Endicott P, Sanchez JJ, Lin AA, Shen P, Oefner P, Renfrew C, Villems R. 2007. Revealing the prehistoric settlement of Australia by Y chromosome and mtDNA analysis. Proc Natl Acad Sci US A 104(21):8726-8730. http://dx.doi.org/10.1073/pnas.0702928104

 

Kivisild T, Shen P, Wall DP, Do B, Sung R, Davis K, Passarino G, Underhill PA, Scharfe C, Torroni A. 2006. The role of selection in the evolution of human mitochondrial genomes. Genetics 172(1):373-387. http://dx.doi.org/10.1534/genetics.105.043901

 

Kong QP, Yao YG, Sun C, Bandelt HJ, Zhu CL, Zhang YP. 2003. Phylogeny of East Asian mitochondrial DNA lineages inferred from complete sequences. Am J Hum Genet 73(3):671-676. http://dx.doi.org/10.1086/377718

 

Kong QP, Yao YG, Sun C, Zhu CL, Zhong L, Wang CY, Cai WW, Xu XM, Xu AL, Zhang YP. 2004. Phylogeographic analysis of mitochondrial DNA haplogroup F2 in China reveals T12338C in the initiation codon of the ND5 gene not to be pathogenic. J Hum Genet 49(8):414-423. http://dx.doi.org/10.1007/s10038-004-0170-3

 

Kong QP, Bandelt HJ, Sun C, Yao YG, Salas A, Achilli A, Wang CY, Zhong L, Zhu CL, Wu SF. 2006. Updating the East Asian mtDNA phylogeny: a prerequisite for the identification of pathogenic mutations. Hum Mol Genet 15(13):2076-2086. http://dx.doi.org/10.1093/hmg/ddl130

 

Kumar S, Padmanabham PB, Ravuri RR, Uttaravalli K, Koneru P, Mukherjee PA, Das B, Kotal M, Xaviour D, Saheb SY, Rao VR. 2008. The earliest settlers' antiquity and evolutionary history of Indian populations: evidence from M2 mtDNA lineage. BMC Evol Biol 8(1):230. http://dx.doi.org/10.1186/1471-2148-8-230

 

Logan J. 2008. The subclades of mtDNA haplogroup J and proposed motifs for assigning control-region sequences into these clades. Journal of Genetic Genealogy 4(1):12-26. http://www.jogg.info/41/Logan.pdf

 

Loogväli EL, Roostalu U, Malyarchuk BA, Derenko MV, Kivisild T, Metspalu E, Tambets K, Reidla M, Tolk HV, Parik J. 2004. Disuniting uniformity: a pied cladistic canvas of mtDNA haplogroup H in Eurasia. Mol Biol Evol 21(11):2012-2021. http://dx.doi.org/10.1093/molbev/msh209

 

Maca-Meyer N, González AM, Pestano J, Flores C, Larruga JM, Cabrera VM. 2003. Mitochondrial DNA transit between West Asia and North Africa inferred from U6 phylogeography. BMC Genet 4:15. http://dx.doi.org/10.1186/1471-2156-4-15

 

Macaulay V, Hill C, Achilli A, Rengo C, Clarke D, Meehan W, Blackburn J, Semino O, Scozzari R, Cruciani F. 2005. Single, rapid coastal settlement of Asia revealed by analysis of complete mitochondrial genomes. Science 308(5724):1034-1036. http://dx.doi.org/10.1126/science.1109792

 

Malyarchuk B, Grzybowski T, Derenko M, Perkova M, Vanecek T, Lazur J, Gomolcak P, Tsybovsky I. 2008a. Mitochondrial DNA phylogeny in Eastern and Western Slavs. Mol Biol Evol 25(8):1651-1658. http://dx.doi.org/10.1093/molbev/msn114

 

Malyarchuk BA, Derenko M, Perkova M, Grzybowski T, Vanecek T, Lazur J. 2008b. Reconstructing the phylogeny of African mitochondrial DNA lineages in Slavs. Eur J Hum Genet 16:1091-1096. http://dx.doi.org/10.1038/ejhg.2008.70

 

Malyarchuk BA, Perkova MA, Derenko MV, Vanecek T, Lazur J, Gomolcak P. 2008c. Mitochondrial DNA variability in Slovaks, with application to the Roma origin. Ann Hum Genet 72(2):228-240. http://dx.doi.org/10.1111/j.1469-1809.2007.00410.x

 

Merriwether DA, Hodgson JA, Friedlaender FR, Allaby R, Cerchio S, Koki G, Friedlaender JS. 2005. Ancient mitochondrial M haplogroups identified in the Southwest Pacific. Proc Natl Acad Sci US A 102(37):13034-13039. http://dx.doi.org/10.1073/pnas.0506195102

 

Metspalu M, Kivisild T, Bandelt HJ, Richards M, Villems R. 2006. The pioneer settlement of modern humans in Asia. In: Bandelt HJ, Macaulay V, Richards M, editors. Human mitochondrial DNA and the Evolution of Homo sapiens. Berlin: Springer-Verlag. p 181–199. http://dx.doi.org/10.1007/3-540-31789-9_8

 

Olivieri A, Achilli A, Pala M, Battaglia V, Fornarino S, Al-Zahery N, Scozzari R, Cruciani F, Behar DM, Dugoujon JM. 2006. The mtDNA legacy of the Levantine early Upper Palaeolithic in Africa. Science 314(5806):1767-1770. http://dx.doi.org/10.1126/science.1135566

 

Palanichamy MG, Sun C, Agrawal S, Bandelt HJ, Kong QP, Khan F, Wang CY, Chaudhuri TK, Palla V, Zhang YP. 2004. Phylogeny of mitochondrial DNA macrohaplogroup N in India, based on complete sequencing: implications for the peopling of South Asia. Am J Hum Genet 75(6):966-978. http://dx.doi.org/10.1086/425871

 

Pierson MJ, Martinez-Arias R, Holland BR, Gemmell NJ, Hurles ME, Penny D. 2006. Deciphering past human population movements in Oceania: provably optimal trees of 127 mtDNA genomes. Mol Biol Evol 23(10):1966-1975. http://dx.doi.org/10.1093/molbev/msl063

 

Rajkumar R, Banerjee J, Gunturi HB, Trivedi R, Kashyap VK. 2005. Phylogeny and antiquity of M macrohaplogroup inferred from complete mt DNA sequence of Indian specific lineages. BMC Evol Biol 5(1):26. http://dx.doi.org/10.1186/1471-2148-5-26

 

Reddy BM, Langstieh BT, Kumar V, Nagaraja T, Reddy AN, Meka A, Reddy AG, Thangaraj K, Singh L. 2007. Austro-Asiatic tribes of Northeast India provide hitherto missing genetic link between South and Southeast Asia. PLoS ONE 2(11):e1141. http://dx.doi.org/10.1371/journal.pone.0001141

 

Reidla M, Kivisild T, Metspalu E, Kaldma K, Tambets K, Tolk HV, Parik J, Loogväli EL, Derenko M, Malyarchuk B. 2003. Origin and diffusion of mtDNA haplogroup X. Am J Hum Genet 73(5):1178-1190. http://dx.doi.org/10.1086/379380

 

Roostalu U, Kutuev I, Loogväli EL, Metspalu E, Tambets K, Reidla M, Khusnutdinova EK, Usanga E, Kivisild T, Villems R. 2007. Origin and expansion of haplogroup H, the dominant human mitochondrial DNA lineage in West Eurasia: the Near Eastern and Caucasian perspective. Mol Biol Evol 24(2):436-448. http://dx.doi.org/10.1093/molbev/msl173

 

Shen P, Lavi T, Kivisild T, Chou V, Sengun D, Gefel D, Shpirer I, Woolf E, Hillel J, Feldman MW. 2004. Reconstruction of patrilineages and matrilineages of Samaritans and other Israeli populations from Y-chromosome and mitochondrial DNA sequence variation. Hum Mutat 24(3):248-260. http://dx.doi.org/10.1002/humu.20077

 

Shlush LI, Behar DM, Yudkovsky G, Templeton A, Hadid Y, Basis F, Hammer M, Itzkovitz S, Skorecki K. 2008. The Druze: a population genetic refugium of the Near East. PLoS ONE 3(5). http://dx.doi.org/10.1371/journal.pone.0002105

 

Soares P, Trejaut JA, Loo JH, Hill C, Mormina M, Lee CL, Chen YM, Hudjashov G, Forster P, Macaulay V. 2008. Climate change and postglacial human dispersals in Southeast Asia. Mol Biol Evol 25(6):1209-1218. http://dx.doi.org/10.1093/molbev/msn068

 

Starikovskaya EB, Sukernik RI, Derbeneva OA, Volodko NV, Ruiz-Pesini E, Torroni A, Brown MD, Lott MT, Hosseini SH, Huoponen K. 2005. Mitochondrial DNA diversity in indigenous populations of the southern extent of Siberia, and the origins of Native American haplogroups. Ann Hum Genet 69(Pt 1):67-89. http://dx.doi.org/10.1046/j.1529-8817.2003.00127.x

 

Sun C, Kong QP, Palanichamy MG, Agrawal S, Bandelt HJ, Yao YG, Khan F, Zhu CL, Chaudhuri TK, Zhang YP. 2006. The dazzling array of basal branches in the mtDNA macrohaplogroup M from India as inferred from complete genomes. Mol Biol Evol 23(3):683-690. http://dx.doi.org/10.1093/molbev/msj078

 

Tamm E, Kivisild T, Reidla M, Metspalu M, Smith DG, Mulligan CJ, Bravi CM, Rickards O, Martinez-Labarga C, Khusnutdinova EK. 2007. Beringian standstill and spread of Native American founders. PLoS ONE 2(9):e829. http://dx.doi.org/10.1371/journal.pone.0000829

 

Tanaka M, Cabrera VM, González AM, Larruga JM, Takeyasu T, Fuku N, Guo LJ, Hirose R, Fujita Y, Kurata M. 2004. Mitochondrial genome variation in eastern Asia and the peopling of Japan. Genome Res 14(10a):1832-1850. http://dx.doi.org/10.1101/gr.2286304

 

Thangaraj K, Chaubey G, Singh VK, Vanniarajan A, Thanseem I, Reddy AG, Singh L. 2006. In situ origin of deep rooting lineages of mitochondrial Macrohaplogroup 'M' in India. BMC Genomics 7:151. http://dx.doi.org/10.1186/1471-2164-7-151

 

Thangaraj K, Chaubey G, Kivisild T, Selvi Rani D, Singh VK, Ismail T, Carvalho-Silva D, Metspalu M, Bhaskar LV, Reddy AG. 2008. Maternal footprints of Southeast Asians in North India. Hum Hered 66(1):1-9. http://dx.doi.org/10.1159/000114160

 

Torroni A, Bandelt HJ, Macaulay V, Richards M, Cruciani F, Rengo C, Martinez-Cabrera V, Villems R, Kivisild T, Metspalu E. 2001. A signal, from human mtDNA, of postglacial recolonization in Europe. Am J Hum Genet 69(4):844-852. http://dx.doi.org/10.1086/323485

 

Torroni A, Achilli A, Macaulay V, Richards M, Bandelt HJ. 2006. Harvesting the fruit of the human mtDNA tree. Trends Genet 22(6):339-345. http://dx.doi.org/10.1016/j.tig.2006.04.001

 

Trejaut JA, Kivisild T, Loo JH, Lee CL, He CL, Hsu CJ, Lee ZY, Lin M. 2005. Traces of archaic mitochondrial lineages persist in Austronesian-speaking Formosan populations. PLoS Biol 3(8). http://dx.doi.org/10.1371/journal.pbio.0030247

 

Volodko NV, Starikovskaya EB, Mazunin IO, Eltsov NP, Naidenko PV, Wallace DC, Sukernik RI. 2008. Mitochondrial genome diversity in arctic Siberians, with particular reference to the evolutionary history of Beringia and Pleistocenic peopling of the Americas. Am J Hum Genet 82(5):1084-1100. http://dx.doi.org/10.1016/j.ajhg.2008.03.019