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Recent Publications

To request a paper (pdf) please contact:

Anett Pechstein
e-mail: pechstn@[>>> Please remove the brackets! <<<]eva.mpg.de
phone: +49 (0) 341 35 50 504

2014

Barbieri, C., M. Vicente, S. Oliveira, K. Bostoen, J. Rocha, M. Stoneking, and B. Pakendorf. 2014. Migration and interaction in a contact zone: mtDNA variation among Bantu-speakers in southern Africa. PLoS One 9:e99117.

Giulani, C., C. Barbieri, M. Li, L. Bucci, D. Monti, G. Passarino, D. Luiselli, C. Franceschi, M. Stoneking, and P. Garagnani. 2014. Transmission from centenarians to their offspring of mtDNA heteroplasmy revealed by ultra-deep sequencing. Aging 6: 454-467.

The Genome of the Netherlands Consortium. 2014. Whole-genome sequence variation, population structure and demographic history of the Dutch population. Nature Genetics 46: 818-825.

Macholdt, E., V. Lede, C. Barbieri, S.W. Mpoloka, H. Chen, M. Slatkin, B. Pakendorf, and M. Stoneking. 2014. Tracing pastoralist migrations to southern Africa with lactase persistence alleles. Current Biology 24:875-879.

Duggan, A.T., B. Evans, F.R. Friedlaender, J.S. Friedlaender, G. Koki, D.A. Merriwether, M. Kayser, and M. Stoneking. 2014. Maternal history of Oceania from complete mtDNA genomes: contrasting ancient diversity with recent homogenization due to the Austronesian expansion. American Journal of Human Genetics 721-733

Barbieri, C., T. Güldemann, C. Naumann, L. Gerlach, F. Berthold, H. Nakagawa, S. W. Mpoloka, M. Stoneking, and B. Pakendorf. 2014. Unraveling the complex maternal history of southern African Khoisan populations.  American Journal of Physical Anthropology 153:435-448.  

Engelken, J., E. Carnero-Montoro, M. Pybus, G.K. Andrews, C. Lalueza-Fox, D. Comas, I. Sekler, M. de la Rasilla, A. Rosas, M. Stoneking, M.A. Valverde, R. Vicente, and E. Bosch.  2014. Extreme population differences in the human zinc transporter ZIP4 (SLC39A4) are explained by positive selection in sub-Saharan Africa.  PLoS Genetics 10:e1004128.

Pickrell, J.K., N. Patterson, P.R. Loh, M. Lipson, B. Berger, M. Stoneking, B. Pakendorf, and D. Reich. 2014. Ancient west Eurasian ancestry in southern and eastern Africa. Proceedings National Academy of Sciences USA 111:2632-2637.

Ko, A.M-S., C-Y. Chen, Q. Fu, F. Delfin, M. Li, H-L. Chiu, M. Stoneking, and Y-C. Ko. 2014. Early Austronesians: Into and out of Taiwan. American Journal of Human Genetics 94:426-436.

Delfin, F., A. Ko, M. Li, E.D. Gunnarsdottir,  K.A. Tabbada, J.M. Salvador, G.C. Calacal, M.S. Sagum, F.A. Datar, S.G. Padilla, M.C.A. De Ungria, and M. Stoneking. 2014. Complete mtDNA genomes of Filipino ethnolinguistic groups: a melting pot of recent and ancient lineages in the Asia-Pacific region. European Journal of Human Genetics 22:228-237.

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2013

Brown, S., P.E. Savage, A. Ko, M. Stoneking, Y.C. Ko, J.H. Loo, and J.A. Trejaut. 2013. Correlations in the population structure of music, genes, and languages. Proceedings of the Royal Society London doi: 10.1098/rspb.2013.2072.

Stoneking, M. 2013. Mitochondrial Genome: Evolution. In: Encyclopedia of the Life Sciences 2013, John Wiley & Sons Ltd: Chichester, http://www.els.net/ [DOI:10.1002/9780470015902.a0005074.pub3]

Grossmann, T., A. Vaish, J. Franz, R. Schroeder, M. Stoneking, and A.D. Friederici. 2013. Emotional voice processing: investigating the role of genetic variation in the serotonin transporter across development. PLoS ONE 8:e68377.

Li, J., I. Nasidze, D. Quinque, M. Li, H.P. Horz, C. Andre, R.M. Garriga, M. Halbwax, A. Fischer, and M. Stoneking. 2013. The saliva microbiome of Pan and Homo. BMC Microbiology 13:204.

Pugach, I., F. Delfin, E. Gunnarsdottir, M. Kayser, and M. Stoneking. 2013. Genome-wide data substantiates Holocene gene flow from India to Australia. Proceedings of the National Academy of Sciences USA 110:1803-1808.

Duggan, A.T. and M. Stoneking. 2013. A highly unstable recent mutation in human mtDNA. American Journal of Human Genetics 92:279-284.

Barbieri, C., M. Vicente, J. Rocha, S. W. Mpoloka, M. Stoneking, and B. Pakendorf. 2013. Ancient substructure in early mtDNA lineages of southern Africa. American Journal of Human Genetics 92:285-292.

Stoneking, M. and K. Harvati. 2013. Early Old World migrations of  Homo sapiens: human biology. In: The Encyclopedia of Global Human Migration, I. Ness (ed.), Blackwell. DOI: 10.1002/9781444351071.wbeghm805.

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2012

Ballantyne, K.N., M. van Oven, A. Ralf, M. Stoneking, R.J. Mitchell, R. A. H. van Oorschot, and M. Kayser. 2012. MtDNA SNP multiplexes for efficient inference of matrilineal genetic ancestry within Oceania. Forensic Science International: Genetics 6:425-436.

de Filippo, C., K. Bostoen, M. Stoneking, and B. Pakendorf. 2012. Bringing together linguistic and genetic evidence to test the Bantu expansion. Proc. Roy. Soc. Lond. B 279:3256-3263.

Delfin, F., S. Myles, Y. Choi, D. Hughes, R. Illek, M. van Oven, B. Pakendorf, M. Kayser, and M. Stoneking. 2012. Bridging Near and Remote Oceania: mtDNA and NRY variation in the Solomon Islands. Molecular Biology and Evolution 29:545-564.

Jinam, T.A., L.C. Hong, M.E. Phipps, M. Stoneking, M. Ameen, J. Edo, The Pan-Asian SNP Consortium, and N. Saitou. 2012. Evolutionary history of continental South East Asians: "early train" hypothesis based on genetic analysis of mitochondrial and autosomal DNA data. Molecular Biology and Evolution 29:3513-3527.

Kenny, E.E., N.J. Timpson, M. Sikora, M.C. Yee, A. Moreno-Estrada, C. Eng, S. Huntsman, E.G. Burchard, M. Stoneking, C.D. Bustamante, and S. Myles. 2012. Melanesian blond hair is caused by an amino acid change in TYRP1. Science 336:554

Li, M. and M. Stoneking. 2012. A new approach for detecting low-level mutations in next-generation sequence data. Genome Biology 13:R34

Li, M., R. Schroeder, A. Ko, and M. Stoneking. 2012. Fidelity of capture-enirchment for mtDNA genome sequencing: influence of NUMTs. Nucleic Acids Research 40:e137.

Li, J., V. Menard, R. L. Benish, R. J. Jurevic, C. Guillemette, M. Stoneking, P.A. Zimmerman, and R.K. Mehlotra. 2012. Worldwide variation in human drug-metabolism enzyme genes CYP2B6 and UGT2B7: implications for HIV/AIDS treatment. Pharmacogenomics 13:555-570.

Pickrell, J.K, N. Patterson, C. Barbieri, F. Berthold, L. Gerlach, T. Güldemann, B. Kure, S.W. Mpoloka, H. Nakagawa, C. Naumann, M. Lipson, P.R. Loh, J. Lachance, J. Mountain, C. Bustamante, B. Berger, S. Tishkoff, B. Henn, M. Stoneking, D. Reich, B. Pakendorf. 2012. The genetic prehistory of southern Africa. Nature Communications 3:1143.

Theunert, C., K. Tang, M. Lachmann, S. Hu, and M. Stoneking. 2012. Inferring the history of population size change from genome-wide SNP data. Molecular Biology and Evolution 29:3653-3667.

Quillen, E.E., M. Bauchet, A.W. Bigham, M.E. Delgado-Burbano, F.X. Faust, Y.C. Klimentidis, X. Mao, M. Stoneking, and M.D. Shriver. 2012. OPRM1 and EGFR contribute to skin pigmentation differences between Indigenous Americans and Europeans. Human Genetics 131:1073-1080.

Xu, S., I. Pugach, M. Stoneking, M. Kayser, L. Jin, and The HUGO Pan-Asian SNP Consortium. 2012. Genetic dating indicates that the Asian-Papuan admixture through Eastern Indonesia corresponds to the Austronesian expansion. Proceedings of the National Academy of Sciences USA 109:4574-4579.

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2011

Delfin, F., J.M. Salvador, G.C. Calcal, H.B. Perdigon, K.A. Tabbada, L.P. Villamor, S.C. Halos, E. Gunnarsdottir, S. Myles, D.A. Hughes, S. Xu, L. Jin, O. Lao, M. Kayser, M. Hurles, M. Stoneking, and M.C.A. De Ungria. 2011. The Y-chromosome landscape of the Philippines: extensive heterogeneity and varying genetic affinities of Negrito and non-Negrito groups. European Journal of Human Genetics 19:224-230.

de Filippo, C., C. Barbieri, M. Whitten, S.W. Mpoloka, E.D. Gunnarsdottir, K. Bostoen, T. Nyambe, K. Beyer, H. Schreiber, P. de Knijff, D. Luiselli, M. Stoneking, and B. Pakendorf. 2011. Y-chromosomal variation insub-Saharan Africa: insights into the history of Niger-Congo groups. Molecular Biology and Evolution 28:1255-1269.

Gross, A., A. Tönjes, P. Kovacs, K. R. Veeramah, P. Ahnert, N. R. Roshyara, C. Gieger, I. Rueckert, M. Loeffler, M. Stoneking, H. Wichmann, J. Novembre, M. Stumvoll, and M. Scholz. 2011. Population-genetic comparison of the Sorbian isolate population in Germany with the German KORA population using genome-wide SNP arrays. BMC Genetics 12:67.

Grossman, T., M.H. Johnson, A. Vaish, D.A. Hughes, D. Quinque, M. Stoneking, and A.D. Friederici. 2011. Genetic and neural dissociation of individual responses to emotional expressions in human infants. Developmental Cognitive Neuroscience 1:57-66.

Gunnarsdóttir, E.D., M. R. Nandineni, M. Li, S. Myles, D. Gil, B.Pakendorf, and M. Stoneking. 2011. Larger mtDNA than Y-chromosome differences between matrilocal and patrilocal groups from Sumatra. Nature Communications 2:228.

Gunnarsdottir, E.D., M. Li, M. Bauchet, K. Finstermeier, and M. Stoneking. 2011. High-throughput sequencing of complete human mtDNA genomes from the Philippines. Genome Research 21:1-11.

Li, J., L. Zhang, H. Zhou, M. Stoneking, and K. Tang. 2011. Global patterns of genetic diversity and signals of natural selection for human drug metabolizing enzyme and transporter genes. Human Molecular Genetics 20:528-540.

Myles, S., R.A. Lea, J. Ohashi, G.K. Chambers, J.G. Weiss, E. Hardouin, J. Engelken, D.P. Macartney-Coxson, D.A. Eccles, I. Naka, R. Kimura, T.a Inaoka, Y. Matsumura, and M. Stoneking. 2011. Testing the thrifty gene hypothesis: the Gly482Ser variant in PPARGC1A is associated with BMI in Tongans. BMC Medical Genetics 12:10.

Nasidze I, Li J, Schroeder R, Creasey JL, Li M, Stoneking M. (2011) High Diversity of the Saliva Microbiome in Batwa Pygmies. PLoS ONE 6(8): e23352.

Nasidze, I. and Stoneking, M. (2011) Microbiome diversity in saliva. In: Handbook of Molecular Microbial Ecology, Volume II: Metagenomics in Different Habitats, First Edition. Editide by Frans J. de Bruijn. pp. 335-339. Wiley-Blackwell. Published 2011 by John Wiley & Sons, Inc.

Pugach, I., R. Matveyev, A. Wollstein, M. Kayser, and M. Stoneking. 2011. Wavelet transform analysis of the admixture signal in genome-wide data. Genome Biology 12:R19.

Reich, D., N. Patterson, M. Kircher, F. Delfin, M.R. Nandineni, I. Pugach, A.M. Ko, Y.C. Ko, T.A. Jinam, M.E. Phipps, N. Saitou, A. Wollstein, M. Kayser, S. Pääbo, and M. Stoneking. 2011. Denisova admixture and the first modern human dispersals into southeast Asia and Oceania. American Journal of Human Genetics 89:516-528.

Schönberg A, Theunert C, Li M, Stoneking M, Nasidze I. (2011) High-throughput sequencing of complete human mtDNA genomes from the Caucasus and West Asia: high diversity and demographic inferences. Eur J Hum Genet. 2011 Sep;19(9):988-994.

Stoneking, M. and J. Krause. 2011. Learning about human population history from ancient and modern genomes. Nature Reviews Genetics 12: 603-614.

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2010

Athanasiadis, G., E. Esteban, M. Gaya-Vidal, J.M. Dugoujon, N. Moschonas, H. Chaabani, N. Bissar-Tadmouri, N. Harich, M. Stoneking, and P. Moral. 2010. Different evolutionary histories of coagulation factor VII gene in human populations? Annals of Human Genetics 74:34-45

Athanasiadis, G., E. Gonzalez-Perez, E. Esteban, J.M. Dugoujon, M. Stoneking, and P. Moral. 2010. The Mediterranean Sea as a barrier to gene flow: evidence from variation in and around the F7 and F12 genomic regions. BMC Evolutionary Biology 10:84.

de Filippo C, Heyn P, Barham L, Stoneking M, Pakendorf B. Genetic perspectives on forager-farmer interaction in the Luangwa Valley of Zambia. Am J Phys Anthropol. 2010 Mar;141(3):382-94.

Li, M., A. Schönberg, M. Schaefer, R. Schroeder, I. Nasidze, and M. Stoneking. 2010. Detecting heteroplasmy from high-throughput sequencing of complete human mitochondrial DNA genomes. American Journal of Human Genetics 87:237-249.

Reich, D., R.E. Green, M. Kircher, J. Krause, N. Patterson, E.Y. Durand, B. Viola, A.W. Briggs, U. Stenzel, P.L.F. Johnson, T. Maricic, J.M. Good, T. Marques-Bonet, C. Alkan, Q. Fu, S. Mallick, H. Li, M. Meyer, E.E. Eichler, M. Stoneking, M.Richards, S. Talamo, M.V. Shunkov, A.P. Derevianko, J.J. Hublin, J. Kelso, M. Slatkin, and S. Pääbo. 2010. Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468:1053-1060.

Stoneking, M. and F. Delfin. 2010. The human genetic history of East Asia: weaving a complex tapestry. Current Biology 20:R188-R193.

Wollstein, A., O. Lao, C. Becker, S. Brauer, R.J. Trent, P. Nürnberg, M. Stoneking, and M. Kayser. 2010. Demographic history of Oceania inferred from genome-wide data. Current Biology 20:1983-1992.

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2009

Balaresque P., Parkin E.J., Roewer L., Carvalho-Silva D.R., Mitchell R.J., van Oorschot R.A.H., Henke J., Stoneking M., Nasidze I., Wetton J., de Knijff P., Tyler-Smith C., Jobling M.A. (2009) Genomic complexity of the Y-STR DYS19: inversions, deletions and founder lineages carrying duplications. International Journal of Legal Medicine. 123:15-23.

Herraez, D.L., M. Bauchet, K. Tang, C. Theunert, I. Pugach, J. Li, M.R. Nandineni, A. Gross, M. Scholz, and M. Stoneking. 2009. Genetic variation and recent positive selection in worldwide human populations: evidence from nearly 1 million SNPs. PLoS ONE 4:e7888

Hillmer, A.M., J. Freudenberg, S. Myles, S. Herms, K. Tang, D.A. Hughes, F.F. Brockschmidt, Y. Ruan, M. Stoneking, and M.M. Nöthen. 2009. Recent positive selection of a human androgen receptor/ectodysplasin A2 receptor haplotype and its relationship to male pattern baldness. Human Genetics 126:255-264

Hughes, D.A., M. Jastroch, M. Stoneking, and M. Klingenspor. 2009. Molecular evolution of UCP1 and the evolutionary history of mammalian non-shivering thermogenesis. BMC Evolutionary Biology 9:4

Hughes, D.A., A. Hinney, H. Brumm, A.K. Wermter, H. Biebermann, J. Hebebrand, and M. Stoneking. 2009. Increased constraints on MC4R during primate and human evolution. Human Genetics 124:633-647.

Mona, S., K.E. Grunz, S. Brauer, B. Pakendorf, L. Castri, H. Sudoyo, S. Marzuki, R.H. Barnes, J. Schmidtke, M. Stoneking, and M. Kayser. 2009. Genetic admixture history of eastern Indonesia as revealed by Y-chromosome and mitochondrial DNA analysis. Molecular Biology and Evolution 26:1865-1877

Moreno-Estrada, A., K. Tang, M. Sikora, T. Marquès-Bonet, F. Casals, A. Navarro, F. Calafell, J. Bertranpetit, M. Stoneking, and E. Bosch. 2009. Interrogating 11 fast-evolving genes for signatures of recent positive selection in worldwide human populations. Molecular Biology and Evolution 26:2285-2297

Myles, S., M. Stoneking, and N. Timpson. 2009. An assessment of the portability of ancestry informative markers between human populations. BMC Medical Genomics 2:45

Nasidze I., Li J., Quinque D., Tang K., and Stoneking M. (2009) Global Diversity in the Human Salivary Microbiome. Genome Research. 19:636-643.

Nasidze I., Quinque D., Li J., Li M., Tang K., and Stoneking M. (2009) Comparative analysis of human saliva microbiome diversity by barcoded pyrosequencing and cloning approaches. Analytical Biochemistry. 391: 64–68.

Nasidze I., Quinque D., Rahmani M.,Ali Alemohamad S., Asadova P., Zhukova O., and Stoneking M. (2009) MtDNA and Y-chromosome Variation in the Talysh of Iran and Azerbaijan. American Journal of Physical Anthropology. 138: 82-89.

Roewer L., Willuweit S., Stoneking M., Nasidze I. (2009) A Y-STR database of Iranian and Azerbaijanian minority populations. Forensic Science International: Genetics. 4:e53–e55.

Ryan, A.W., D. Hughes, K. Tang, D. Kelleher, T. Ryan, R. McManus, and M. Stoneking. 2009. Natural selection and the molecular basis of electrophoretic variation at the coagulation F13B locus. European Journal of Human Genetics 17:219-227.

Stoneking, M. 2009. Humans as second orangutans: sense or nonsense? BioEssays 31:1010-1012.

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2008

Balaresque P., Bowden G.R., Parkin E.J., Omran G.A., Heyer E., Quintana-Murci L., Roewer L., Stoneking ., Nasidze I., Carvalho-Silva D.R., Tyler-Smith C., de Knijff P., Jobling M.A. (2008) Dynamic nature of the proximal /AZFc /region of the human Y chromosome: multiple independent deletion and duplication events revealed by microsatellite analysis. Human mutation. 29:1171-1180.

Bryk, J., E. Hardouin, I. Pugach, D. Hughes, R. Strotmann, M. Stoneking, and S. Myles. 2008. Positive selection in East Asians for an EDAR allele that enhances NF-?B activation. PLoS ONE 3:e2209.

Fechner A., Quinque D., Rychkov S., Morozowa I., Naumova O., Schneider Y., Willuweit S., Zhukova O., Roewer L., Stoneking M., Nasidze I. (2008) Boundaries and clines in the West Eurasian Y-chromosome landscape: Insights from the European part of Russia. American Journal of Physical Anthropology. 137: 41-47.

Güldemann, T. and M. Stoneking. 2008. A historical appraisal of clicks: a linguistic and genetic population perspective. Annual Review of Anthropology 37:93-109

Herráez, D.L. and M. Stoneking. 2008. High fractions of exogenous DNA in human buccal samples reduce the quality of large-scale genotyping. Analytical Biochemistry 383:329-331.

Hughes, D.A., K. Tang, R. Strotmann, T. Schöneberg, J. Prenen, B. Nilius, and M. Stoneking. 2008. Parallel soft sweeps on TRPV6 in human populations. PLoS ONE 3: e1686.

Kayser, M., Y. Choi, M. van Oven, S. Mona, S. Brauer, D. Suarkia, W. Schiefenhövel, and M. Stoneking. 2008. The impact of the Austronesian expansion: evidence from mtDNA and Y-chromosome diversity in the Admiralty Islands of Melanesia. Molecular Biology and Evolution 25:1362-1374.

Kayser, M., O. Lao, and M. Stoneking. 2008. Reply to Hedrick. American Journal of Human Genetics 83: 140-142.

Kayser, M., O. Lao, K. Saar, S. Brauer, X. Wang, P. Nürenberg, R.J. Trent, and M. Stoneking. 2008. Genome-wide analysis indicates more Asian than Melanesian ancestry of Polynesians. American Journal of Human Genetics 82:194-198.

Klingenspor, M. T. Fromme, D. A. Hughes, L. Manzke, E. Polymeropoulos, T. Riemann, M. Trzcionka, V. Hirschberg, and M. Jastroch. 2008. An ancient look at UCP1. Biochimica et Biophysica Acta 1777:637-641

Mehlotra, R.K., G. Mattera, M.J. Bockarie, J.D. Maguire, J.K. Baird, Y.D. Sharma, M. Alifrangis, G. Dorsey, P.J. Rosenthal, D.J. Fryauff, J.W. Kazura, M. Stoneking, and P.A. Zimmerman. 2008. Discordant patterns of genetic variation at two chloroquine-resistant loci in worldwide populations of the malaria parasite Plasmodium falciparum. Antimicrobial Agents and Chemotherapy 52:2212-2222.

Myles S., D. Davison, J. Barrett, M. Stoneking, and N. Timpson. 2008. Worldwide population differentiation at disease-associated SNPs. BMC Medical Genomics 1:22.

Myles, S., K. Tang, M. Somel, R.E. Green, J. Kelso, and M. Stoneking. 2008. Identification and analysis of genomic regions with large between-population differentiation in humans. Annals Human Genetics 72:99-110.

Nasidze I, Quinque D., Rahmani M.,Ali Alemohamad S., Stoneking M. (2008) Close genetic relationship between Semitic-speaking and Indo-European-speaking groups in Iran. Annals of Human Genetics. 72: 241-252. [mtDNA sequences in text format]

Roewer L., Willuweit S., Krüger C., Nagy M., Rychkov S., Morozowa I., Naumova O., Schneider Y., Zhukova O., Stoneking M., Nasidze I. (2008) Analysis of Y chromosome STR haplotypes in the European part of Russia reveals high diversities but non-significant genetic distances between populations. International Journal of Legal Medicine. 122:219–223.

Stoneking, M. 2008. Human origins: the molecular perspective. EMBO Reports 9:S46-S50.

Stoneking, M. 2008. Mitochondrial genome: evolution. In: Encyclopedia of Life Sciences, John Wiley & Sons, Ltd, Chichester, http://www.els.net/ [DOI: 10.1002/9780470015902.a0005074.pub2].

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2007

Cordaux, R., D. Srikanta, J. Lee, M. Stoneking, and M.A. Batzer. 2007. In search of polymorphic Alu insertions with restricted geographic distributions. Genomics 90:154-158.

DaRe, J.T., R.K. Mehlotra, P. Michon, I. Mueller, J. Reeder, Y.D. Sharma, M. Stoneking, and P.A. Zimmerman. 2007. Microsatellite polymorphism within pfcrt provides evidence of continuing evolution of chloroquine-resistant alleles in Papua New Guinea. Malaria Journal 6:34.

Kuch, M., D.R. Gröcke, M.C. Knyf, T.M.P. Gilbert, B. Younghusband, T. Young, I. Marshall, M. Stoneking, and H. Poinar. 2007. A preliminary analysis of the DNA and diet of the extinct Beothuk: a systematic approach to ancient human DNA. American Journal of Physical Anthropology 132:594-604.

Lalueza-Fox, C., H. Römpler, D. Carmelli, C. Stäubert, G. Catalano, D. Hughes, N. Rohland, E. Pilli, L. Longo, S. Condemi, M. de la Rasilla, J. Fortea, A. Rosas, M. Stoneking, T. Schöneberg, J. Bertranpetit, and M. Hofreiter. 2007. A melanocortin 1 receptor allele suggests varying pigmentation among Neanderthals.Science 318:1453-1455.

Myles, S., E. Hradetzky, J. Engelken, O. Lao, P. Nürnberg, R. J. Trent, X. Wang, M. Kayser, and M. Stoneking. 2007. Identification of a candidate genetic variant for the high prevalence of type II diabetes in Polynesians. European Journal of Human Genetics 15:584-589

Myles, S., M. Somel, K. Tang, J. Kelso, and M. Stoneking. 2007. Identifying genes underlying skin pigmentation differences among human populations. Human Genetics 120:613-621.

Nasidze I., Quinque D., Udina I., Kunizhevu S., Stoneking M. (2007) The Gagauz, a linguistic enclave, are not a genetic isolate. Annals of Human Genetics. 71: 379–389.
[mtDNA sequences in text format]

Pakendorf, B.; Novgorodov, I.N.; Osakovskij, V.L.; Stoneking, M. (2007): Mating patterns amongst Siberian reindeer herders: inferences from mtDNA and Y-chromosomal analyses. AJPA. 133: 1013-1027. mtDNA sequences (text file), Y-STR haplotypes (xls file)

Roewer L., Krüger C., Willuweit S., Nagy M., Rodig H., Kokshunova L., Rothämel T., Kravchenko S., Jobling M., Stoneking M., Nasidze I. (2007) Y-chromosomal STR haplotypes in Kalmyk population samples. Forensic Science International. 173: 204-209.

Rootsi, S., L.A. Zhivotovsky, M. Baldovic, M. Kayser, I.A. Kutuev, R. Khusainova, M.A. Bermisheva, M. Gubina, S. Fedorova, A.M. Ilumäe, E.K. Khusnutdinova, L.P. Osipova, M. Stoneking, V. Ferak, J. Parik, T. Kivisild, P.A. Underhill, and R. Villems. 2007. A counter-clockwise northern route of the Y-chromosome haplogroup N from Southeast Asia towards Europe. European Journal of Human Genetics 15:204-211.

Stoneking, M. and M. Kayser.2007. Genealogical markers: mtDNA and the Y-chromosome. In: Genetic Variation: A Laboratory Manual, M. P. Weiner, S. B. Gabriel, J.C. Stephens (eds.), Cold Spring Harbor Laboratory Press, New York, pp. 421-436.

Stoneking, M. and I. Nasidze. (2007) Reply to Parson. Annals Human Genetics 71: 279-280. Supplemental material (pdf)

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2006

Hammer, M.F., T. M. Karafet, H. Park, K. Omoto, S. Harihara, M. Stoneking and S. Horai.  2006.  Dual origins of the Japanese: common ground for hunter-gatherer and farmer Y chromosomes.  Journal of Human Genetics 51:47-58

Kayser, M., S. Brauer, R. Cordaux, A. Casto, O. Lao, L.A. Zhivotovsky, C. Moyse-Faurie, R.B. Rutledge, W. Schiefenhoevel, D. Gil, A.A. Lin, P.A. Underhill, P.J. Oefner, R.J. Trent, and M. Stoneking. 2006. Melanesian and Asian origins of Polynesians: mtDNA and Y-chromosome gradients across the Pacific. Molecular Biology and Evolution 23:2234-2244

Nasidze I., Stoneking M. (2006) Mother tongue: Concomitant replacement of language and mtDNA in South Caspian populations of Iran. In: The Evolution of Language. Eds. A.Cangelosi, A.D.M.Smith and K.Smith. pp. 432-433. World Scientific Co. Pte. Ltd. New Jersey, London, Singapore, Peijing, Shanghai, Hong Kong, Taipei, Chennai.

Nasidze I, Quinque D, Rahmani M, Alemohamad SA, Stoneking M (2006) Concomitant replacement of language and mtDNA in South Caspian populations of Iran. Current Biology. 16: 668-673. MtDNA HVI sequences in the text format

Pakendorf, B.; Novgorodov, I.N.; Osakovskij, V.L.; Danilova, A.P.; Protod’jakonov, A.P.; Stoneking, M. (2006): Investigating the effects of prehistoric migrations in Siberia: genetic variation and the origins of Yakuts. Human Genetics 120/3: 334-353. Sequences (txt files) | Supplementary material MtDNA (doc file) | supplementary material Y-chr (Excel) | Online-Abstract: http://dx.doi.org/10.1007/s00439-006-0213-2

Stoneking, M. 2006. Genetic evidence for our recent African ancestry. In: The Prehistory of Africa, H. Soodyall (ed.), Jonathan Ball Publishers, Johannesburg, South Africa, pp. 24-36

Stoneking, M. 2006. Investigating the health of our ancestors: insights from the evolutionary genetic consequences of prehistoric diseases. In: Integrative Approaches to Human Health and Evolution, T.G. Bromage, A. Vidal, E. Aguirre and A. Perez-Ochoa (eds.), Elsevier B. V., Amsterdam, pp.106-114.

Stoneking M, Nasidze I. (2006) The patient is not dead yet: premature autopsy of an mtDNA data set. Annals of Human Genetics. 70: 327-331.

Quinque D, Kittler R, Kayser M, Stoneking M, Nasidze I. (2006) Evaluation of saliva as a source of human DNA for population and association studies. Analytical Biochemistry. 353: 272-277.

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2005

Hamilton, G., M. Stoneking, and L. Excoffier.  2005.  Molecular analysis reveals tighter social regulation of immigration in patrilocal populations than in matrilocal populations.  Proceedings of the National Academy of Sciences USA 102:7476-7480.

Mehlotra, R.K., G. Mattera, K. Bhatia, J.C. Reeder, M. Stoneking, and P.A. Zimmerman.  2005. Insight into the early spread of chloroquine resistant Plasmodium falciparum in Papua New Guinea.  Journal of Infectious Diseases192:2174-2179

Nasidze I, Quinque D, Dupanloup I, Cordaux R, Kokshunova L, Stoneking M. (2005) Genetic evidence for the Mongolian ancestry of Kalmyks. American Journal of Physical Anthropology. DOI: 10.1002/ajpa.20159 (on-line publication). MtDNA sequences in text format

Nasidze I, Quinque D, Ozturk M, Bendukidze N, Stoneking M. (2005) MtDNA and Y-chromosome variation in Kurdish groups. Annals of Human Genetics. 69: 401-412. MtDNA sequences (txt file)

Oota, H., B. Pakendorf, G. Weiss, A. von Haeseler, S. Pookajorn, W. Settheetham-Ishida, D. Tiwawech, T. Ishida, and M. Stoneking. 2005. Recent Origin and Cultural Reversion of a Hunter–Gatherer Group. PLoS Biology 3:536-542

Pakendorf, B. and M. Stoneking. 2005. Mitochondrial DNA and human evolution. Annual Review of Genomics and Human Genetics 6:165-183

Stoneking, M. 2005. Gene, geographie und Sprache.  In: Gene, Sprachen und ihre Evolution, G. Hauska (ed.), Unversitätsverlag Regensburg GmbH, Regensburg, Germany, pp. 133-140

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2004

Cordaux, R., R. Aunger, G. Bentley, I. Nasidze, S. M. Sirajuddin, and M. Stoneking. 2004. Independent origins of Indian caste and tribal paternal lineages. Current Biology 14:231-235.

Cordaux, R., G. Bentley, R. Aunger, S. M. Sirajuddin, and M. Stoneking. 2004. Y-STR haplotypes from eight south Indian groups based on five loci. Journal of Forensic Sciences 49:847-848.

Cordaux, R., E. Deepa, H. Vishwanathan, and M. Stoneking. 2004. Genetic evidence for the demic diffusion of agriculture to India. Science 304:1125.

Cordaux, R., G. Weiss, N. Saha, and M. Stoneking. 2004. The northeast Indian passageway: a barrier or corridor for human migrations? Molecular Biology and Evolution 21:1525-1533.

Erler, A., M. Stoneking, and M. Kayser. 2004. Development of Y-chromosomal microsatellite markers for non-human primates. Molecular Ecology 13:2921-2930.

Hughes, D.A., R. Cordaux, and M. Stoneking. 2004. Quick guide: humans. Current Biology 14:R367-R369.

Kasperaviciute, D., V. Kucinskas, and M. Stoneking. 2004. Y chromosome and mitochondrial DNA variation in Lithuanians. Annals Human Genetics 68:438-452.

Kayser, M., R. Kittler, A. Erler, M. Hedman, A.C. Lee, A. Mohyuddin, S. Q. Mehdi, Z. Rosser, M. Stoneking, M. A. Jobling, A. Sajantila and C. Tyler-Smith. 2004. A comprehensive survey of human Y-chromosomal microsatellites. American Journal of Human Genetics 74:1183-1197.

Nasidze, I., E. Y.S. Ling, D. Quinque, I. Dupanloup, R. Cordaux, S. Rychkov, O. Naumova, O. Zhukova, N. Sarraf-Zadegan, G. A. Naderi, S. Asgary, S. Sardas, D. D. Farhud, T. Sarkisian, C. Asadov, A. Kerimov, and M. Stoneking. 2004. Mitochondrial DNA and Y-chromosome variation in the Caucasus. Annals Human Genetics 68(3):205-221. MtDNA sequences (txt file)

Nasidze I, Quinque D, Dupanloup I, Rychkov S, Naumova O, Zhukova O, Stoneking M. (2004) Genetic evidence concerning the origins of South and North Ossetians. Annals of Human Genetics. 68: 588-599. MtDNA sequences in text format

Vishwanathan, H., E. Deepa, R. Cordaux, M. Stoneking, M. V. Usha Rani, and P. P. Majumder. 2004. Genetic structure and affinities among tribal populations of southern India: a study of 24 autosomal DNA markers. Annals Human Genetics 68:128-138.

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2003

Cordaux, R., N. Saha, G. R. Bentley, R. Aunger, S. M. Sirajuddin, and M. Stoneking. 2003. Mitochondrial DNA analysis reveals diverse histories of tribal populations of India. European Journal of Human Genetics 11:253-264. MtDNA sequences (txt-file)

Cordaux, R. and M. Stoneking. 2003. South Asia, the Andamanese and the genetic evidence for an “early” human dispersal out of Africa. American Journal of Human Genetics 72:1586-1590.

Kayser, M., S. Brauer, H. Schädlich, M. Prinz, M. A. Batzer, P. A. Zimmerman, B. A. Boatin, and M. Stoneking. 2003. Y chromosome STR haplotypes and the genetic structure of U.S. populations of African, European, and Hispanic ancestry. Genome Research 13:624-634.

Kayser, M., S. Brauer and M. Stoneking. 2003. A genome scan to detect candidate regions influenced by local natural selection in human populations. Molecular Biology and Evolution 20:893-900.

Kayser, M., S. Brauer, G. Weiss, W. Schiefenhövel, P. Underhill, P. Shen, P. Oefner, M. Tommaseo-Ponzetta, and M. Stoneking. 2003. Reduced Y-chromosome, but not mtDNA, diversity in human populations from West New Guinea. American Journal of Human Genetics 72:281-302.

Kittler, R., A. Erler, S. Brauer, M. Stoneking, and M. Kayser. 2003. Apparent intra-chromosomal exchange on the human Y chromosome explained by population history. European Journal of Human Genetics 11:304-314.

Kittler, R., M. Kayser and M. Stoneking: Molecular Evolution of Pediculus humanus and the origin of clothing. Current Biology 13, 1414-1417 (2003). erratum (pdf)

Nasidze, I., T. Sarkisian, A. Kerimov, and M. Stoneking. 2003. Testing hypotheses of language replacement in the Caucasus: evidence from the Y-chromosome. Human Genetics 112:255-261.

Nasidze, I., H. Schädlich, and M. Stoneking. 2003. Haplotypes from the Caucasus, Turkey and Iran for nine Y-STR loci. Forensic Science International 137:85-93.

Pakendorf, B., V. Wiebe, L. A. Tarskaia, V. A. Spitsyn, H. Soodyall, A. Rodewald, and M. Stoneking. 2003. Mitochondrial DNA evidence for admixed origins of central Siberian populations. American Journal of Physical Anthropology 120:211-224.

Stoneking, M. 2003. Mitochondrial genome: evolution. In: Nature Encyclopedia of the Human Genome, D. Cooper (ed.), Nature Publishing Group, London, pp.1019-1023.

Stoneking, M. 2003. Widespread prehistoric human cannibalism: easier to swallow? Trends in Ecology and Evolution 18:489-490.

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2002

Kayser, M., S. Brauer, S. Willuweit, H. Schädlich, M. A. Batzer, J. Zawacki, M. Prinz, L. Roewer, and M. Stoneking. 2002. Online Y-chromosomal short tandem repeat haplotype reference database (YHRD) for U.S. populations. Journal of Forensic Sciences 47:513-519.

Kittler, R., M. Stoneking, and M. Kayser. 2002. A whole genome amplification method to generate long fragments from low quantities of genomic DNA. Analytical Biochemistry 300:237-244.

Nasidze, I. and M. Stoneking. 2002. Genetic variation among human populations from the Caucasus. In: The First Workshop on Information Techologies Application to Problems of Biodiversity and Dynamics, V.K.Shumny, N.A.Kolchanov, and A.M.Fedotov (Eds.), Russian Academy of Sciences, Novosibirsk, Russia, pp.272-278.

Oota, H., T. Kitano, F. Jin, I. Yuasa, L. Wang, S. Ueda, N. Saitou, and M. Stoneking. 2002. Extreme mtDNA homogeneity in continental Asian populations. American Journal of Physical Anthropology 118:146-153.

Pakendorf, B., B. Morar, L. A. Tarskaia, M. Kayser, H. Soodyall, A. Rodewald, and M. Stoneking. 2002. Y-chromosomal evidence for a severe reduction in male population size of Yakuts. Human Genetics 110:198-200.

Romauldi, C., D. Balding, I. S. Nasidze, G. Risch, M. Robichaux, S. Sherry, M. Stoneking, M. A. Batzer, and G. Barbujani. 2002. Patterns of human diversity, within and among continents, inferred from biallelic DNA polymorphisms. Genome Research 12:602-612

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2001

Begovich, A. B., P. V. Moonsamy, S. J. Mack, L. F. Barcellos, L. L. Steiner, S. Grams, V. Suraj-Baker, J. Hollenbach, E. Trachtenberg, L. Louie, P. Zimmerman, A. V. S. Hill, M. Stoneking, T. Sasazuki, V. I. Konenkov, M. L. Sartakova, V. P. K. Titanji, O. Rickards, and W. Klitz. 2001. Genetic variability and linkage disequilibrium within the DP region: analysis of 15 different populations. Tissue Antigens 57:424-439.

Justice, C. M., Z. Den, S. V. Nguyen, M. Stoneking, P. L. Deininger, M. A. Batzer, and B. J. B. Keats. 2001. Phylogenetic analysis of the Friedreich ataxia GAA trinucleotide repeat. Journal of Molecular Evolution 52:232-238.

Kayser, M., S. Brauer, G. Weiss, W. Schiefenhövel, P. A. Underhill, and M. Stoneking. 2001. Independent histories of human Y chromosomes from Melanesia and Australia. American Journal of Human Genetics 68:173-190.

Melton, T., S. Clifford, M. Kayser, I. Nasidze, M. Batzer, and M. Stoneking. 2001. Diversity and heterogeneity in mitochondrial DNA of North American populations. Journal of Forensic Sciences 46:46-52.

Nasidze, I., G. M. Risch, M. Robichaux, S. T. Sherry, M. A. Batzer, and M. Stoneking. 2001. Alu insertion polymorphisms and the genetic structure of human populations from the Caucasus. European Journal of Human Genetics 9:267-272.

Nasidze, I. and M. Stoneking. 2001. Mitochondrial DNA variation and language replacements in the Caucasus. Proceedings Royal Society London B 268:1197-1206.

Oota, H., W. Settheetham-Ishida, D. Tiwawech, T. Ishida, and M. Stoneking. 2001. Human mtDNA and Y-chromosome variation is correlated with matrilocal vs. patrilocal residence. Nature Genetics 29:20-21.

Stone, A. C., J. E. Starrs, and M. Stoneking. 2001. Mitochondrial DNA analysis of the presumptive remains of Jesse James. Journal of Forensic Sciences 46:173-176.

Stoneking, M. 2001. Single nucleotide polymorphisms: from the evolutionary past... Nature 409:821-822.

Stoneking, M., P. L. Deininger, and M. A. Batzer. 2001. Alu insertion polymorphisms in humans: a review. In Genes, Fossils and Behaviour, P. Donnelly and R. Foley (eds.), IOS Press, Amsterdam, The Netherlands, pp.111-121.

Tishkoff, S. A., R. Varkonyi, N. Cahinhinan, S. Abbes, G. Argyropoulos, G. Destro-Bisol, A. Drousiotou, B. Dangerfield, G. Lefranc, J. Loiselet, A. Piro, M. Stoneking, A. Tagarelli, G. Tagarelli, E. H. Touma, S. M. Williams, and A. G. Clark. 2001. Haplotype diversity and linkage disequilibrium at human G6PD: recent origin of alleles that confer malarial resistance. Science 293:455-462.

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2000

Begovich. A.B., W. Klitz, L.L. Steiner, S. Grams, V. Suraj-Baker, J. Hollenbach, E. Trachtenberg, L. Louie, P.A. Zimmerman, A.V.S. Hill, M. Stoneking, T. Sasazuki, O. Rickards, V.P.K. Titanji, V.I. Konenkov, M.L. Sartakova. 2000. HLA-DQ haplotypes in 15 different populations. In The Major Histocompatibility Complex: Evolution, Structure and Function, M Kasahara (Ed.), Springer, New York, NY, pp.412-426.

Clark, V. J., S. Sivendren, N. Saha, G. R. Bentley, R. Aunger, S. M. Sirajuddin, and M. Stoneking. 2000. The 9-bp deletion between the mitochondrial lysine tRNA and COII genes in tribal populations of India. Human Biology 72:273-285.

Comas, D., F. Calafell F, N. Benchemsi, A. Helal, G. Lefranc, M. Stoneking, M. Batzer, J. Bertranpetit, and A. Sajantila. 2000. Alu insertion polymorphisms in Northwest Africa and the Iberian Peninsula: evidence for a strong genetic boundary through the Gibraltar Straits. Human Genetics 107:312-319.

Di Benedetto, G., I. S. Nasidze, M. Stenico, L. Nigro, M. Krings, M. Lanzinger, L. Vigilant, M. Stoneking, S. Pääbo, and G. Barbujani. 2000. Mitochondrial DNA sequences in prehistoric human remains from the Alps. European Journal of Human Genetics 8:669-677.

Kayser, M., L. Roewer, M. Hedman, L. Henke, J. Henke, S. Brauer, C. Kruger, M. Krawczak, M. Nagy, T. Dobosz, R. Szibor, P. de Knijff, M. Stoneking, and A. Sajantila. 2000. Characteristics and frequency of germline mutations at microsatellite loci from the human Y chromosome revealed by direct observation in father/son pairs. American Journal of Human Genetics 66:1580-1588. Kayser, M., S. Brauer, G. Weiss, P. A. Underhill, L. Roewer, W. Schiefenhövel, and M. Stoneking. 2000. Melanesian origin of Polynesian Y chromosomes. Current Biology 10:1237-1246 [Correction: Current Biology 11:I-II, 2001].

Kumar, S., P. W. Hedrick, T. Dowling, and M. Stoneking. 2000. Questioning evidence for recombination in human mitochondrial DNA. Science 288:1931a.

Kumar, S. S., I. Nasidze, S. R. Walimbe, and M. Stoneking. 2000. Discouraging prospects for ancient DNA from India. American Journal of Physical Anthropology 113:129-133.

Mack, S. J., T. L. Bugawan, P. V. Moonsamy, J. A. Erlich, E. A. Trachtenberg, Y. K. Paik, A. B. Begovich, N. Saha, H. P. Beck, M. Stoneking, and H. A. Erlich. 2000. Evolution of Pacific/Asian populations inferred from HLA class II allele frequency distributions. Tissue Antigens 55:383-400.

Sheen, F., S. T. Sherry, G. M. Risch, M. Robichaux, I. Nasidze, M. Stoneking, M. A. Batzer, and G. D. Swergold. 2000. Reading between the LINEs: human genomic variation induced by LINE-1 retrotransposition. Genome Research 10:1496-1508.

Stoneking, M. 2000. Hypervariable sites in the mtDNA control region are mutational hotspots. American Journal of Human Genetics 67:1029-1032.

Tishkoff, S. A., A. J. Pakstis, M. Stoneking, J. R. Kidd, G. Destro-Bisol, A. Sajantila, A. S. Deinard, G. Sirugo, T. Jenkins, K. K. Kidd, and A. G. Clark. 2000. Short tandem-repeat polymorphism/Alu haplotype variation at the PLAT locus: implications for modern human origins. American Journal of Human Genetics 67:901-925.

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