Hela Help, MSc, 2005, juh. Toomas Kivisild. THE SEARCH OF Y-CHROMOSOMAL PENTA- AND HEXANUCLEOTIDE REPEAT LOCI AND THEIR APPLICATION IN PHYLOGENETIC PURPOSES. Tartu

Jana Eensalu, MSc, 2005, juh. Toomas Kivisild. Y kromosoomi haplogruppide E ja R1b fülogeograafia. Tartu

Eva-Liis Loogväli, MSc, 2002, juh. Toomas Kivisild. High-resolution refinement of the phylogenetic tree of the human mitochondrial DNA haplogroup H. Tartu

Mait Metspalu, MSc, 2001, juh. Toomas Kivisild. Common maternal legacy of Indian caste and tribal populations. Tartu

Bandelt, H.-J.; Kivisild, T.; Parik, J.; Villems, R.; Bravi, C.; Yao, Y.-G.; Parson, W. Lab-specific mutation processes. In the Nucleic Acids and Molecular Biology series: Human mitochondrial DNA and the evolution of Homo sapiens. Springer-Verlag. In press.

Kivisild, T.; Metspalu, M.; Bandelt, H.-J.; Richards, M. B.; Villems, R. The world mtDNA phylogeny. In the Nucleic Acids and Molecular Biology series: Human mitochondrial DNA and the evolution of Homo sapiens. Springer-Verlag. In press.

Metspalu, M.; Kivisild, T.; Villems, R. The pioneer settlement of modern humans in Asia. In the Nucleic Acids and Molecular Biology series: Human mitochondrial DNA and the evolution of Homo sapiens. Springer-Verlag. In press.

Richards, M.B.; Bandelt, H.-J.; Kivisild, T.; Oppenheimer, S. A model for the dispersal of modern humans out of Africa. In the Nucleic Acids and Molecular Biology series: Human mitochondrial DNA and the evolution of Homo sapiens. Springer-Verlag. In press.

Shen, P.; Hirsh, A.E.; Kivisild, T.; Do, B.; Song, S.; Sung, R.; Chou, V.; Tang, H.; Zhivotovsky, L.; Underhill, P.A.; Cavalli-Sforza, L.L.; Feldman, M.W.; Oefner, P.J. Population genetic implications from 103 pairs of a globally representative sample of 103 pairs of Y-chromosome and mitochondrial DNA sequences. Am J Hum Genet (in press).

Adojaan, M.; Kivisild, T.; Männik, A.; Krispin, T.; Ustina, V.; Zilmer, K.; Liebert, E.; Jaroslavtsev, N.; Priimägi, L.; Tefanova, V.; Schmidt, J.; Krohn, K.; Villems, R.; Salminen, M.; Ustav, M. Predominance of a rare type of HIV-1 in Estonia. J AIDS. 39(5):598-605

Babalini, C.; Martínez-Labarga, C.; Tolk, H.-V.; Giampaolo, R.; Tarsi, T.; Contini, I.; Barać, L.; Janićijević, B.; Martinović Klarić, I.; Peričić, M.; Sujoldžić, A.; Kivisild, T.; Villems, R.; Biondi, G.; Rudan, P.; Rickards, O. (2005) The genetic history of the Croatian linguistic minority of Molise (southern Italy): a maternal view. Eur J Hum Genet. 13(8):902-12

Bandelt H-J, Kivisild, T. Quality assessment of DNA data: autopsy of a mis-sequenced mtDNA population sample. Annals of Human Genetics (in press).

Bandelt H.-J., Yao Y.-G., Kivisild T. (2004) Mitochondrial genes and schizophrenia. Schizophr Res 28 July 2004

Gonçalves, R.; Freitas, A.; Branco, M.; Rosa, A.; Fernandes, A.; Zhivotovsky, L.; Underhill, P.; Kivisild, T.; Brehm, A. Y-chromosome lineages from Portugal, Madeira and Açores record elements of Sephardim and Berber ancestry. Ann Hum Genet 69(Pt 4):443-54

Kivisild T, Shen P, Wall D, Do B, Sung R, Davis K, Passarino G, Underhill PA, Scharfe C, Torroni A, Scozzari R, Modiano D, Coppa A, de Knijff P, Feldman M, Cavalli-Sforza LL, Oefner PJ. The role of selection in the evolution of human mitochondrial genomes. Genetics (in press)

Leroi AM, Bartke A, Benedictis GD, Franceschi C, Gartner A, Gonos E, Feder ME, Kivisild T, Lee S, Kartal-Ozer N, Schumacher M, Sikora E, Slagboom E, Tatar M, Yashin AI, Vijg J, Zwaan B. What evidence is there for the existence of individual genes with antagonistic pleiotropic effects? Mech Ageing Dev. 2005 126(3):421-9.

Thangaraj K, Chaubey G, Kivisild T, Reddy AG, Singh VK, Rasalkar AA, Singh L (2005) Reconstructing the origin of the enigmatic Andaman Islanders. Science 308(5724):996.

Thangaraj, K.; Sridhar, V.; Kivisild, T.; Reddy, A.; Kaur, S.; Chandra, Y.; Agarawal, P.; Rai, A.; Gupta, J.; Kumar, N.; Velavan, T.; Suganthan, R.; Udaykumar, D.; Pal, R.; Mishra, R.; Khan, A.; Annapurna, C.; Singh, L. India: Source for the Modern South East Asians. Hum Genet 116:507-517

Trejaut, J.; Kivisild, T.; Loo, J.H.; Li, Z.Y.; Lee, H.L.; Chang, H.L.; Chu, C.C.; Lin, M. (2005) Polynesian maternal origins trace back to Taiwan. PLoS Biology. 3(8):e247

Achilli A., Rengo C., Magri C., Battaglia V., Olivieri A., Scozzari R., Cruciani F., Zeviani M., Briem E., Carelli V., Moral P., Dugoujon J.M. Roostalu U., Loogvali E.L., Kivisild T., Bandelt H.J., Richards M., Villems R., Santachiara-Benerecetti A.S., Semino O., Torroni A. (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. 75:910-908.

Cinnioglu, C.; King, R.; Kivisild, T.; Kalfoglu, E.; Atasoy, S.; Cavalleri, G.P.; Lillie, A.S.; Roseman, C.C.; Lin, A.A.; Prince, K.; Oefner, P.J.; Shen, P.; Semino, O.; Cavalli-Sforza, L.L.; Underhill, P.A. (2004) Excavating Y-chromosome haplotype strata in Anatolia. Hum Genet. 114:127-148

Kivisild, T.; Reidla M, Metspalu E, Rosa A, Brehm A, Pennarun E, Parik J, Geberhiwot T, Usanga E, Villems R. (2004) Ethiopian mitochondrial DNA heritage: tracking gene flow across and around the gate of tears. Am J Hum Genet. 75:752-770

Loogvali E.L., Roostalu U., Malyarchuk B.A., Derenko M.V., Kivisild T., Metspalu E., Tambets K., Reidla M., Tolk H.V., Parik J., Pennarun E., Laos S., Lunkina A., Golubenko M., Barac L., Pericic M., Balanovsky O.P., Gusar V., Khusnutdinova E.K., Stepanov V., Puzyrev V., Rudan P., Balanovska E.V., Grechanina E., Richard C., Moisan J.P., Chaventre A., Anagnou N.P., Pappa K.I., Michalodimitrakis E.N., Claustres M., Golge M., Mikerezi I., Usanga E., Villems R. (2004) Disuniting Uniformity: A Pied Cladistic Canvas of mtDNA Haplogroup H in Eurasia. Mol Biol Evol 21:2012-2021

Metspalu M., Kivisild T., Metspalu E., Parik J., Hudjashov G., Kaldma K., Serk P., Karmin M., Behar D.M., Gilbert M.T., Endicott P., Mastana S., Papiha S.S., Skorecki K., Torroni A., Villems R. (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 Genet. 5:26

Rootsi, S.; Magri, C.; Kivisild, T.; Benuzzi, G.; Help, H.; Bermisheva, M.; Kutuev, I.; Barać, L.; Peričić, M.; Balanovsky, O.; Pshenichnov, A.; Dion, D.; Grobei, M.; Zhivotovsky, L.; Battaglia, V.; Achilli, A.; Al-Zahery, N.; Parik, J.; King, R.; Cinnioġlu, C.; Khusnutdinova, E.; Rudan, P.; Balanovska, E.; Scheffrahn, W.; Simonescu, M.; Brehm, A.; Goncalves, R.; Rosa, A.; Moisan, J.-P.; Ferak, V.; Füredi, S.; Oefner, P.; Shen, P.; Beckman, L.; Mikerezi, I.; Terzić, R.; Primorac, D.; Cambon-Thomsen, A.; Krumina, A.; Torroni, A.; Underhill, P.; Santachiara-Benerecetti, A.; Villems, R.; Semino, O. Phylogeography of Y-chromosome haplogroup I reveals distinct domains of prehistoric gene flow in Europe. Am J Hum Genet 75:128-137

Rosa A., Brehm A., Kivisild T., Metspalu E., Villems R. (2004) MtDNA profile of West Africa Guineans: towards a better understanding of the Senegambia region. Ann Hum Genet. 68:340-352

Shen P., Lavi T., Kivisild T., Chou V., Sengun D., Gefel D., Shpirer I., Woolf E., Hillel J., Feldman M.W., Oefner P.J. (2004) Reconstruction of patrilineages and matrilineages of Samaritans and other Israeli populations from Y-chromosome and mitochondrial DNA sequence variation. Hum Mutat.24:248-260.

Zhivotovsky, L.A.; Underhill, P.A.; Cinnioglu, C.; Kayser, M.; Morar, B.; Kivisild, T.; Scozzari, R.; Cruciani, F.; Destro-Bisol, G.; Spedini, G.; Chambers, G.K.; Herrera, R.J.; Yong, K.K.; Gresham, D.; Tournev, I.; Feldman, M.; Kalaydjieva, L. (2004) On the effective mutation rate at Y-chromosome STRs with application to human population divergence time. Am J Hum Genet 74: 50-61

Tambets, K.; Rootsi, S.; Kivisild, T.; Help, H.; Serk, P.; Loogväli, E.-L.; Tolk, H.-V.; Reidla, M.; Metspalu, E.; Pliss, L.; Balanovsky, O.; Pshenichnov, A.; Balanovska, E.; Gubina, M.; Zhadanov, S.; Osipova, L.; Damba, L.; Voevoda, M.; Kutuev, I.; Bermisheva, M.; Khusnutdinova, E.; Gusar, V.; Grechanina, E.; Parik, J.; Pennarun, E.; Chaventre, A.; Moisan, J.-P.; Barać, L.; Peričić, M.; Rudan, P.; Terzić, R.; Mikerezi, I.; Krumina, A.; Baumanis, V.; Koziel, S.; Rickards, O.; De Stefano, G.-F.; Anagnou, N.; Pappa, K.; Michalodimitrakis, E.; Ferák, V.; Füredi, S.; Komel, R.; Beckman, L.; Villems, R. (2004) The western and eastern roots of the Saami – the story of genetic “outliers” told by mtDNA and Y-chromosome. Am J Hum Genet 74:661-682

Bandelt, H.-J.; Herrnstadt, C.; Yao, Y.-G.; Kong, Q.-P.; Kivisild, T.; Rengo, C.; Scozzari, R.; Richards, M.; Villems, R.; Macaulay, V.; Howell, N.; Torroni, A.; Zhang, Y.-P. (2003). Identification of Native American founder mtDNAs through the analysis of complete mtDNA sequences: some caveats. Ann Hum Genet. 67:512-524.

Barac L., Pericic M., Klaric I.M., Rootsi S., Janicijevic B., Kivisild T., Parik J., Rudan I., Villems R., Rudan P. (2003). Y chromosomal heritage of Croatian population and its island isolates. Eur J Hum Genet. 11:535-542.

Brehm A., Pereira L., Kivisild T., Amorim A. (2003). Mitochondrial portraits of the Madeira and Acores archipelagos witness different genetic pools of its settlers. Hum Genet. 114:77-86

Endicott, P.; Macaulay, V.; Kivisild, T.; Stringer, C.; Cooper, A. (2003). Reply to Cordaux and Stoneking. Am J Hum Genet 72: 1590-1593

Goncalves R., Rosa A., Freitas A., Fernandes A., Kivisild T., Villems R. Brehm A. (2003). Y-chromosome lineages in Cabo Verde Islands witness the diverse geographic origin of its first male settlers. Hum Genet. 113:467-472

Kivisild, T., Rootsi, S., Metspalu, M., Mastana, S., Kaldma, K., Parik, J., Metspalu, E., Adojaan, M., Tolk, H.-V., Stepanov, V., Gölge, M., Usanga, E., Papiha, S.S., Cinnioglu, C., King, R., Cavalli-Sforza, L., Underhill, P. A., Villems, R. (2003). The genetic heritage of the earliest settlers persists both in Indian tribal and caste populations. Am J Hum Genet. 72:313-332

Kivisild, T.; Rootsi, S.; Metspalu, M.; Metspalu, E.; Parik, J.; Kaldma, K.; Usanga, E.; Mastana, S.; Papiha, S.; Villems, R. (2003). The genetics of language and Farming spread in India. In the McDonald Insitiute Monographs: Examining the farming/ language dispersal hypothesis. Short Run Press. pp. 215-222

Reidla, M.; Kivisild, T.; Metspalu, E.; Kaldma, K.; Tambets, K.; Tolk, H.-V.; Parik, J.; Loogväli, E.-L.; Derenko, M.; Malyarchuk, B.; Bermisheva, M.; Zhadanov, S.; Pennarun, E.; Gubina, M.; Golubenko, M.; Damba, L.; Fedorova, S.; Gusar, V.; Grechanina, E.; Mikerezi, I.; Moisan, J.-P.; Chaventré, A.; Khusnutdinova, E.; Osipova, L.; Stepanov, V.; Voevoda, M.; Achilli, A.; Rengo, C.; Rickards, O.; De Stefano, G.-F.; Papiha, S.; Beckman, L.; Janicijevic, B.; Rudan, P.; Anagnou, N.; Michalodimitrakis, E.; Koziel, S.; Usanga, E.; Geberhiwot, T.; Herrnstadt, C.; Howell, N.; Torroni, A.; Villems, R. (2003). Origin and Diffusion of mtDNA Haplogroup X. Am J Hum Genet. 73:1178-1190

Tambets, K.; Tolk, H.-V.; Kivisild, T.; Metspalu, E.; Parik, J.; Reidla, M.; Voevoda, M.; Damba, L.; Bermisheva, M.; Khusnutdinova, E.; Golubenko, M.; Stepanov, V.; Puzyrev, V.; Usanga, E.; Rudan, P.; Beckman, L.; Villems, R. (2003). Complex signals for population expansions in Europe and beyond. In the McDonald Insitiute Monographs: Examining the farming/ language dispersal hypothesis. Short Run Press. pp. 449-457.

Yao Y.G., Macauley V., Kivisild T., Zhang Y.P., Bandelt H.-J. (2003). To trust or not to trust an idiosyncratic mitochondrial data set. Am J Hum Genet. 72:1341-1346

Kivisild, T, Tolk, HV, Parik, J, Wang, Y, Papiha, SS, Bandelt, HJ, Villems, R. (2002). The emerging limbs and twigs of the East Asian mtDNA tree. Mol Biol Evol. 19: 1737-1751

Yao, YG, Kong, QP, Bandelt, HJ, Kivisild, T, Zhang YP. Phylogeographic differentiation of mitochondrial DNA in Han Chinese. (2002). Am J Hum Genet. 70: 635-651

Bamshad M, Kivisild T, Watkins WS, Dixon ME, Ricker CE, Rao BB, Naidu JM, Prasad BV, Reddy PG, Rasanayagam A, Papiha SS, Villems R, Redd AJ, Hammer MF, Nguyen SV, Carroll ML, Batzer MA, Jorde LB. (2001). Genetic evidence on the origins of Indian caste populations. Genome Res. 11: 994-1004

Tambets, K., Rootsi, S., Kivisild, T., Villems, R. (2001). The concepts of Richard Indreko about the origin of the Finno-Ugries and the population genetics of the extant North-East European populations. TRAMES 5(55/50), 1:59-74

Tolk, HV, Barac, L, Pericic, M, Klaric, IM, Janicijevic, B, Campbell, H, Rudan, I, Kivisild, T, Villems, R, Rudan, P. (2001). The evidence of mtDNA haplogroup F in a European population and its ethnohistoric implications. Eur J Hum Genet. 9:717-723

Torroni A, Bandelt HJ, Macaulay V, Richards M, Cruciani F, Rengo C, Martinez-Cabrera V, Villems R, Kivisild T, Metspalu E, Parik J, Tolk HV, Tambets K, Forster P, Karger B, Francalacci P, Rudan P, Janicijevic B, Rickards O, Savontaus ML, Huoponen K, Laitinen V, Koivumaki S, Sykes B, Hickey E, Novelletto A, Moral P, Sellitto D, Coppa A, Al-Zaheri N, Santachiara-Benerecetti AS, Semino O, Scozzari R. (2001). A signal, from human mtDNA, of postglacial recolonization in Europe. Am J Hum Genet. 69:844-852

Kivisild, T., Papiha, S.S., Rootsi, S., Parik, J., Kaldma, K., Reidla, M., Laos, S., Metspalu, M., Pielberg, G., Adojaan, M., Metspalu, E., Mastana, S.S., Wang, Y., Gölge, M., Demirtas, H., Schnakenberg, E., De Stefano, G.F., Geberhiwot, T., Claustres, M., Villems, R. (2000). An Indian ancestry: a key for understanding human diversity in Europe and beyond. In Archaeogenetics: DNA and the population prehistory of Europe. Ed. C. Renfrew and K. Boyle. McDonald Institute for Archaeological Research Monograph Series, Cambridge University Press, Cambridge. pp. 267-275

Kivisild, T., Villems, R. (2000). Questioning evidence for recombination in human mitochondrial DNA. Science 288:1931

Richards M, Macaulay V, Hickey E, Vega E, Sykes B, Guida V, Rengo C, Sellitto D, Cruciani F, Kivisild T, Villems R, Thomas M, Rychkov S, Rychkov O, Rychkov Y, Golge M, Dimitrov D, Hill E, Bradley D, Romano V, Cali F, Vona G, Demaine A, Papiha S, Triantaphyllidis C, Stefanescu G, Hatina J, Belledi M, Di Rienzo A, Novelletto A, Oppenheim A, Norby S, Al-Zaheri N, Santachiara-Benerecetti S, Scozari R, Torroni A, Bandelt HJ. (2000). Tracing European founder lineages in the Near Eastern mtDNA pool. Am J Hum Genet 67: 1251-1276

Rootsi, S., Kivisild, T., Tambets, K., Adojaan, M., Parik, J., Reidla, M., Metspalu, E., Laos, S., Tolk, H.-V., Villems, R. On the phylogeographic context of sex-specific genetic markers of Finno-Ugric populations. (2000). In The roots of peoples and languages of northern Eurasia II and III. Societas Historiae Fenno-Ugricae, Turku. 148-165

Rosser ZH, Zerjal T, Hurles ME, Adojaan M, Alavantic D, Amorim A, Amos W, Armenteros M, Arroyo E, Barbujani G, Beckman G, Beckman L, Bertranpetit J, Bosch E, Bradley DG, Brede G, Cooper G, Corte-Real HB, de Knijff P, Decorte R, Dubrova YE, Evgrafov O, Gilissen A, Glisic S, Golge M, Hill EW, Jeziorowska A, Kalaydjieva L, Kayser M, Kivisild T, Kravchenko SA, Krumina A, Kucinskas V, Lavinha J, Livshits LA, Malaspina P, Maria S, McElreavey K, Meitinger TA, Mikelsaar AV, Mitchell RJ, Nafa K, Nicholson J, Norby S, Pandya A, Parik J, Patsalis PC, Pereira L, Peterlin B, Pielberg G, Prata MJ, Previdere C, Roewer L, Rootsi S, Rubinsztein DC, Saillard J, Santos FR, Stefanescu G, Sykes BC, Tolun A, Villems R, Tyler-Smith C, Jobling MA. (2000). Y-Chromosomal diversity in Europe is clinal and influenced primarily by geography, rather than by language. Am J Hum Genet 67: 1526-1543

Tambets, K., Kivisild, T., Metspalu, E., Parik, J., Kaldma, K., Laos, S., Tolk, H.-V., Gölge, M., Demirtas, H., Geberhiwot, T., Papiha, S.S., De Stefano, G.F., Villems, R. (2000). The topology of the maternal lineages of the Anatolian and Trans-Caucasus populations and the peopling of Europe: some preliminary considerations. In Archaeogenetics: DNA and the population prehistory of Europe. Ed. C. Renfrew and K. Boyle. McDonald Institute for Archaeological Research Monograph Series, Cambridge University Press, Cambridge. pp. 219-235

Kivisild, T., Bamshad, M., Kaldma, K., Metspalu, M., Metspalu, E., Reidla, M., Laos, S., Parik, J., Watkins, W.S., Dixon, M. E., Papiha, S.S., Mastana, S.S., Mir, M.R., Ferak, V., Villems, R. (1999). Deep common ancestry of Indian and western Eurasian mitochondrial DNA lineages. Current Biology 9: 1331-1334

Kivisild, T., Kaldma, K., Metspalu, M., Parik, J., Papiha, S.S., Villems, R. (1999). The place of Indian mitochondrial DNA variants in the global network of maternal lineages and the peopling of the Old World. In Genomic Diversity. Kluwer Academic/Plenum Publishers, New York. 135-152

Metspalu, E., Kivisild, T., Kaldma, K., Parik, J., Reidla, M., Tambets, K., Villems, R. (1999). The Trans-Caucasus and the expansion of the caucasoid-specific human mitochondrial DNA. In Genomic Diversity. Kluwer Academic/Plenum Publishers, New York. 121-134

Villems, R., Adojaan, M., Kivisild, T., Metspalu, E., Parik, J., Pielberg, G., Rootsi, S., Tambets, K., Tolk, H.-V. (1998). Reconstruction of maternal lineages of Finno-Ugric speaking people and some remarks on their paternal inheritance. In The roots of peoples and languages of northern Eurasia I. Societas Historiae Fenno-Ugricae, Turku. 180-200

Hela Help, MSc, 2005, superv. Toomas Kivisild. THE SEARCH OF Y-CHROMOSOMAL PENTA- AND HEXANUCLEOTIDE REPEAT LOCI AND THEIR APPLICATION IN PHYLOGENETIC PURPOSES. Tartu

Jana Eensalu, MSc, 2005, superv. Toomas Kivisild. Y kromosoomi haplogruppide E ja R1b fülogeograafia. Tartu

Eva-Liis Loogväli, MSc, 2002, superv. Toomas Kivisild. High-resolution refinement of the phylogenetic tree of the human mitochondrial DNA haplogroup H. Tartu

Mait Metspalu, MSc, 2001, superv. Toomas Kivisild. Common maternal legacy of Indian caste and tribal populations. Tartu

Bandelt, H.-J.; Kivisild, T.; Parik, J.; Villems, R.; Bravi, C.; Yao, Y.-G.; Parson, W. Lab-specific mutation processes. In the Nucleic Acids and Molecular Biology series: Human mitochondrial DNA and the evolution of Homo sapiens. Springer-Verlag. In press.

Kivisild, T.; Metspalu, M.; Bandelt, H.-J.; Richards, M. B.; Villems, R. The world mtDNA phylogeny. In the Nucleic Acids and Molecular Biology series: Human mitochondrial DNA and the evolution of Homo sapiens. Springer-Verlag. In press.

Metspalu, M.; Kivisild, T.; Villems, R. The pioneer settlement of modern humans in Asia. In the Nucleic Acids and Molecular Biology series: Human mitochondrial DNA and the evolution of Homo sapiens. Springer-Verlag. In press.

Richards, M.B.; Bandelt, H.-J.; Kivisild, T.; Oppenheimer, S. A model for the dispersal of modern humans out of Africa. In the Nucleic Acids and Molecular Biology series: Human mitochondrial DNA and the evolution of Homo sapiens. Springer-Verlag. In press.

Shen, P.; Hirsh, A.E.; Kivisild, T.; Do, B.; Song, S.; Sung, R.; Chou, V.; Tang, H.; Zhivotovsky, L.; Underhill, P.A.; Cavalli-Sforza, L.L.; Feldman, M.W.; Oefner, P.J. Population genetic implications from 103 pairs of a globally representative sample of 103 pairs of Y-chromosome and mitochondrial DNA sequences. Am J Hum Genet (in press).

Adojaan, M.; Kivisild, T.; Männik, A.; Krispin, T.; Ustina, V.; Zilmer, K.; Liebert, E.; Jaroslavtsev, N.; Priimägi, L.; Tefanova, V.; Schmidt, J.; Krohn, K.; Villems, R.; Salminen, M.; Ustav, M. Predominance of a rare type of HIV-1 in Estonia. J AIDS. 39(5):598-605

Babalini, C.; Martínez-Labarga, C.; Tolk, H.-V.; Giampaolo, R.; Tarsi, T.; Contini, I.; Barać, L.; Janićijević, B.; Martinović Klarić, I.; Peričić, M.; Sujoldžić, A.; Kivisild, T.; Villems, R.; Biondi, G.; Rudan, P.; Rickards, O. (2005) The genetic history of the Croatian linguistic minority of Molise (southern Italy): a maternal view. Eur J Hum Genet. 13(8):902-12

Bandelt H-J, Kivisild, T. Quality assessment of DNA data: autopsy of a mis-sequenced mtDNA population sample. Annals of Human Genetics (in press).

Bandelt H.-J., Yao Y.-G., Kivisild T. (2004) Mitochondrial genes and schizophrenia. Schizophr Res 28 July 2004

Gonçalves, R.; Freitas, A.; Branco, M.; Rosa, A.; Fernandes, A.; Zhivotovsky, L.; Underhill, P.; Kivisild, T.; Brehm, A. Y-chromosome lineages from Portugal, Madeira and Açores record elements of Sephardim and Berber ancestry. Ann Hum Genet 69(Pt 4):443-54

Kivisild T, Shen P, Wall D, Do B, Sung R, Davis K, Passarino G, Underhill PA, Scharfe C, Torroni A, Scozzari R, Modiano D, Coppa A, de Knijff P, Feldman M, Cavalli-Sforza LL, Oefner PJ. The role of selection in the evolution of human mitochondrial genomes. Genetics (in press)

Leroi AM, Bartke A, Benedictis GD, Franceschi C, Gartner A, Gonos E, Feder ME, Kivisild T, Lee S, Kartal-Ozer N, Schumacher M, Sikora E, Slagboom E, Tatar M, Yashin AI, Vijg J, Zwaan B. What evidence is there for the existence of individual genes with antagonistic pleiotropic effects? Mech Ageing Dev. 2005 126(3):421-9.

Thangaraj K, Chaubey G, Kivisild T, Reddy AG, Singh VK, Rasalkar AA, Singh L (2005) Reconstructing the origin of the enigmatic Andaman Islanders. Science 308(5724):996.

Thangaraj, K.; Sridhar, V.; Kivisild, T.; Reddy, A.; Kaur, S.; Chandra, Y.; Agarawal, P.; Rai, A.; Gupta, J.; Kumar, N.; Velavan, T.; Suganthan, R.; Udaykumar, D.; Pal, R.; Mishra, R.; Khan, A.; Annapurna, C.; Singh, L. India: Source for the Modern South East Asians. Hum Genet 116:507-517

Trejaut, J.; Kivisild, T.; Loo, J.H.; Li, Z.Y.; Lee, H.L.; Chang, H.L.; Chu, C.C.; Lin, M. (2005) Polynesian maternal origins trace back to Taiwan. PLoS Biology. 3(8):e247

Achilli A., Rengo C., Magri C., Battaglia V., Olivieri A., Scozzari R., Cruciani F., Zeviani M., Briem E., Carelli V., Moral P., Dugoujon J.M. Roostalu U., Loogvali E.L., Kivisild T., Bandelt H.J., Richards M., Villems R., Santachiara-Benerecetti A.S., Semino O., Torroni A. (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. 75:910-908.

Cinnioglu, C.; King, R.; Kivisild, T.; Kalfoglu, E.; Atasoy, S.; Cavalleri, G.P.; Lillie, A.S.; Roseman, C.C.; Lin, A.A.; Prince, K.; Oefner, P.J.; Shen, P.; Semino, O.; Cavalli-Sforza, L.L.; Underhill, P.A. (2004) Excavating Y-chromosome haplotype strata in Anatolia. Hum Genet. 114:127-148

Kivisild, T.; Reidla M, Metspalu E, Rosa A, Brehm A, Pennarun E, Parik J, Geberhiwot T, Usanga E, Villems R. (2004) Ethiopian mitochondrial DNA heritage: tracking gene flow across and around the gate of tears. Am J Hum Genet. 75:752-770

Loogvali E.L., Roostalu U., Malyarchuk B.A., Derenko M.V., Kivisild T., Metspalu E., Tambets K., Reidla M., Tolk H.V., Parik J., Pennarun E., Laos S., Lunkina A., Golubenko M., Barac L., Pericic M., Balanovsky O.P., Gusar V., Khusnutdinova E.K., Stepanov V., Puzyrev V., Rudan P., Balanovska E.V., Grechanina E., Richard C., Moisan J.P., Chaventre A., Anagnou N.P., Pappa K.I., Michalodimitrakis E.N., Claustres M., Golge M., Mikerezi I., Usanga E., Villems R. (2004) Disuniting Uniformity: A Pied Cladistic Canvas of mtDNA Haplogroup H in Eurasia. Mol Biol Evol 21:2012-2021

Metspalu M., Kivisild T., Metspalu E., Parik J., Hudjashov G., Kaldma K., Serk P., Karmin M., Behar D.M., Gilbert M.T., Endicott P., Mastana S., Papiha S.S., Skorecki K., Torroni A., Villems R. (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 Genet. 5:26

Rootsi, S.; Magri, C.; Kivisild, T.; Benuzzi, G.; Help, H.; Bermisheva, M.; Kutuev, I.; Barać, L.; Peričić, M.; Balanovsky, O.; Pshenichnov, A.; Dion, D.; Grobei, M.; Zhivotovsky, L.; Battaglia, V.; Achilli, A.; Al-Zahery, N.; Parik, J.; King, R.; Cinnioġlu, C.; Khusnutdinova, E.; Rudan, P.; Balanovska, E.; Scheffrahn, W.; Simonescu, M.; Brehm, A.; Goncalves, R.; Rosa, A.; Moisan, J.-P.; Ferak, V.; Füredi, S.; Oefner, P.; Shen, P.; Beckman, L.; Mikerezi, I.; Terzić, R.; Primorac, D.; Cambon-Thomsen, A.; Krumina, A.; Torroni, A.; Underhill, P.; Santachiara-Benerecetti, A.; Villems, R.; Semino, O. Phylogeography of Y-chromosome haplogroup I reveals distinct domains of prehistoric gene flow in Europe. Am J Hum Genet 75:128-137

Rosa A., Brehm A., Kivisild T., Metspalu E., Villems R. (2004) MtDNA profile of West Africa Guineans: towards a better understanding of the Senegambia region. Ann Hum Genet. 68:340-352

Shen P., Lavi T., Kivisild T., Chou V., Sengun D., Gefel D., Shpirer I., Woolf E., Hillel J., Feldman M.W., Oefner P.J. (2004) Reconstruction of patrilineages and matrilineages of Samaritans and other Israeli populations from Y-chromosome and mitochondrial DNA sequence variation. Hum Mutat.24:248-260.

Zhivotovsky, L.A.; Underhill, P.A.; Cinnioglu, C.; Kayser, M.; Morar, B.; Kivisild, T.; Scozzari, R.; Cruciani, F.; Destro-Bisol, G.; Spedini, G.; Chambers, G.K.; Herrera, R.J.; Yong, K.K.; Gresham, D.; Tournev, I.; Feldman, M.; Kalaydjieva, L. (2004) On the effective mutation rate at Y-chromosome STRs with application to human population divergence time. Am J Hum Genet 74: 50-61

Tambets, K.; Rootsi, S.; Kivisild, T.; Help, H.; Serk, P.; Loogväli, E.-L.; Tolk, H.-V.; Reidla, M.; Metspalu, E.; Pliss, L.; Balanovsky, O.; Pshenichnov, A.; Balanovska, E.; Gubina, M.; Zhadanov, S.; Osipova, L.; Damba, L.; Voevoda, M.; Kutuev, I.; Bermisheva, M.; Khusnutdinova, E.; Gusar, V.; Grechanina, E.; Parik, J.; Pennarun, E.; Chaventre, A.; Moisan, J.-P.; Barać, L.; Peričić, M.; Rudan, P.; Terzić, R.; Mikerezi, I.; Krumina, A.; Baumanis, V.; Koziel, S.; Rickards, O.; De Stefano, G.-F.; Anagnou, N.; Pappa, K.; Michalodimitrakis, E.; Ferák, V.; Füredi, S.; Komel, R.; Beckman, L.; Villems, R. (2004) The western and eastern roots of the Saami – the story of genetic “outliers” told by mtDNA and Y-chromosome. Am J Hum Genet 74:661-682

Bandelt, H.-J.; Herrnstadt, C.; Yao, Y.-G.; Kong, Q.-P.; Kivisild, T.; Rengo, C.; Scozzari, R.; Richards, M.; Villems, R.; Macaulay, V.; Howell, N.; Torroni, A.; Zhang, Y.-P. (2003). Identification of Native American founder mtDNAs through the analysis of complete mtDNA sequences: some caveats. Ann Hum Genet. 67:512-524.

Barac L., Pericic M., Klaric I.M., Rootsi S., Janicijevic B., Kivisild T., Parik J., Rudan I., Villems R., Rudan P. (2003). Y chromosomal heritage of Croatian population and its island isolates. Eur J Hum Genet. 11:535-542.

Brehm A., Pereira L., Kivisild T., Amorim A. (2003). Mitochondrial portraits of the Madeira and Acores archipelagos witness different genetic pools of its settlers. Hum Genet. 114:77-86

Endicott, P.; Macaulay, V.; Kivisild, T.; Stringer, C.; Cooper, A. (2003). Reply to Cordaux and Stoneking. Am J Hum Genet 72: 1590-1593

Goncalves R., Rosa A., Freitas A., Fernandes A., Kivisild T., Villems R. Brehm A. (2003). Y-chromosome lineages in Cabo Verde Islands witness the diverse geographic origin of its first male settlers. Hum Genet. 113:467-472

Kivisild, T., Rootsi, S., Metspalu, M., Mastana, S., Kaldma, K., Parik, J., Metspalu, E., Adojaan, M., Tolk, H.-V., Stepanov, V., Gölge, M., Usanga, E., Papiha, S.S., Cinnioglu, C., King, R., Cavalli-Sforza, L., Underhill, P. A., Villems, R. (2003). The genetic heritage of the earliest settlers persists both in Indian tribal and caste populations. Am J Hum Genet. 72:313-332

Kivisild, T.; Rootsi, S.; Metspalu, M.; Metspalu, E.; Parik, J.; Kaldma, K.; Usanga, E.; Mastana, S.; Papiha, S.; Villems, R. (2003). The genetics of language and Farming spread in India. In the McDonald Insitiute Monographs: Examining the farming/ language dispersal hypothesis. Short Run Press. pp. 215-222

Reidla, M.; Kivisild, T.; Metspalu, E.; Kaldma, K.; Tambets, K.; Tolk, H.-V.; Parik, J.; Loogväli, E.-L.; Derenko, M.; Malyarchuk, B.; Bermisheva, M.; Zhadanov, S.; Pennarun, E.; Gubina, M.; Golubenko, M.; Damba, L.; Fedorova, S.; Gusar, V.; Grechanina, E.; Mikerezi, I.; Moisan, J.-P.; Chaventré, A.; Khusnutdinova, E.; Osipova, L.; Stepanov, V.; Voevoda, M.; Achilli, A.; Rengo, C.; Rickards, O.; De Stefano, G.-F.; Papiha, S.; Beckman, L.; Janicijevic, B.; Rudan, P.; Anagnou, N.; Michalodimitrakis, E.; Koziel, S.; Usanga, E.; Geberhiwot, T.; Herrnstadt, C.; Howell, N.; Torroni, A.; Villems, R. (2003). Origin and Diffusion of mtDNA Haplogroup X. Am J Hum Genet. 73:1178-1190

Tambets, K.; Tolk, H.-V.; Kivisild, T.; Metspalu, E.; Parik, J.; Reidla, M.; Voevoda, M.; Damba, L.; Bermisheva, M.; Khusnutdinova, E.; Golubenko, M.; Stepanov, V.; Puzyrev, V.; Usanga, E.; Rudan, P.; Beckman, L.; Villems, R. (2003). Complex signals for population expansions in Europe and beyond. In the McDonald Insitiute Monographs: Examining the farming/ language dispersal hypothesis. Short Run Press. pp. 449-457.

Yao Y.G., Macauley V., Kivisild T., Zhang Y.P., Bandelt H.-J. (2003). To trust or not to trust an idiosyncratic mitochondrial data set. Am J Hum Genet. 72:1341-1346

Kivisild, T, Tolk, HV, Parik, J, Wang, Y, Papiha, SS, Bandelt, HJ, Villems, R. (2002). The emerging limbs and twigs of the East Asian mtDNA tree. Mol Biol Evol. 19: 1737-1751

Yao, YG, Kong, QP, Bandelt, HJ, Kivisild, T, Zhang YP. Phylogeographic differentiation of mitochondrial DNA in Han Chinese. (2002). Am J Hum Genet. 70: 635-651

Bamshad M, Kivisild T, Watkins WS, Dixon ME, Ricker CE, Rao BB, Naidu JM, Prasad BV, Reddy PG, Rasanayagam A, Papiha SS, Villems R, Redd AJ, Hammer MF, Nguyen SV, Carroll ML, Batzer MA, Jorde LB. (2001). Genetic evidence on the origins of Indian caste populations. Genome Res. 11: 994-1004

Tambets, K., Rootsi, S., Kivisild, T., Villems, R. (2001). The concepts of Richard Indreko about the origin of the Finno-Ugries and the population genetics of the extant North-East European populations. TRAMES 5(55/50), 1:59-74

Tolk, HV, Barac, L, Pericic, M, Klaric, IM, Janicijevic, B, Campbell, H, Rudan, I, Kivisild, T, Villems, R, Rudan, P. (2001). The evidence of mtDNA haplogroup F in a European population and its ethnohistoric implications. Eur J Hum Genet. 9:717-723

Torroni A, Bandelt HJ, Macaulay V, Richards M, Cruciani F, Rengo C, Martinez-Cabrera V, Villems R, Kivisild T, Metspalu E, Parik J, Tolk HV, Tambets K, Forster P, Karger B, Francalacci P, Rudan P, Janicijevic B, Rickards O, Savontaus ML, Huoponen K, Laitinen V, Koivumaki S, Sykes B, Hickey E, Novelletto A, Moral P, Sellitto D, Coppa A, Al-Zaheri N, Santachiara-Benerecetti AS, Semino O, Scozzari R. (2001). A signal, from human mtDNA, of postglacial recolonization in Europe. Am J Hum Genet. 69:844-852

Kivisild, T., Papiha, S.S., Rootsi, S., Parik, J., Kaldma, K., Reidla, M., Laos, S., Metspalu, M., Pielberg, G., Adojaan, M., Metspalu, E., Mastana, S.S., Wang, Y., Gölge, M., Demirtas, H., Schnakenberg, E., De Stefano, G.F., Geberhiwot, T., Claustres, M., Villems, R. (2000). An Indian ancestry: a key for understanding human diversity in Europe and beyond. In Archaeogenetics: DNA and the population prehistory of Europe. Ed. C. Renfrew and K. Boyle. McDonald Institute for Archaeological Research Monograph Series, Cambridge University Press, Cambridge. pp. 267-275

Kivisild, T., Villems, R. (2000). Questioning evidence for recombination in human mitochondrial DNA. Science 288:1931

Richards M, Macaulay V, Hickey E, Vega E, Sykes B, Guida V, Rengo C, Sellitto D, Cruciani F, Kivisild T, Villems R, Thomas M, Rychkov S, Rychkov O, Rychkov Y, Golge M, Dimitrov D, Hill E, Bradley D, Romano V, Cali F, Vona G, Demaine A, Papiha S, Triantaphyllidis C, Stefanescu G, Hatina J, Belledi M, Di Rienzo A, Novelletto A, Oppenheim A, Norby S, Al-Zaheri N, Santachiara-Benerecetti S, Scozari R, Torroni A, Bandelt HJ. (2000). Tracing European founder lineages in the Near Eastern mtDNA pool. Am J Hum Genet 67: 1251-1276

Rootsi, S., Kivisild, T., Tambets, K., Adojaan, M., Parik, J., Reidla, M., Metspalu, E., Laos, S., Tolk, H.-V., Villems, R. On the phylogeographic context of sex-specific genetic markers of Finno-Ugric populations. (2000). In The roots of peoples and languages of northern Eurasia II and III. Societas Historiae Fenno-Ugricae, Turku. 148-165

Rosser ZH, Zerjal T, Hurles ME, Adojaan M, Alavantic D, Amorim A, Amos W, Armenteros M, Arroyo E, Barbujani G, Beckman G, Beckman L, Bertranpetit J, Bosch E, Bradley DG, Brede G, Cooper G, Corte-Real HB, de Knijff P, Decorte R, Dubrova YE, Evgrafov O, Gilissen A, Glisic S, Golge M, Hill EW, Jeziorowska A, Kalaydjieva L, Kayser M, Kivisild T, Kravchenko SA, Krumina A, Kucinskas V, Lavinha J, Livshits LA, Malaspina P, Maria S, McElreavey K, Meitinger TA, Mikelsaar AV, Mitchell RJ, Nafa K, Nicholson J, Norby S, Pandya A, Parik J, Patsalis PC, Pereira L, Peterlin B, Pielberg G, Prata MJ, Previdere C, Roewer L, Rootsi S, Rubinsztein DC, Saillard J, Santos FR, Stefanescu G, Sykes BC, Tolun A, Villems R, Tyler-Smith C, Jobling MA. (2000). Y-Chromosomal diversity in Europe is clinal and influenced primarily by geography, rather than by language. Am J Hum Genet 67: 1526-1543

Tambets, K., Kivisild, T., Metspalu, E., Parik, J., Kaldma, K., Laos, S., Tolk, H.-V., Gölge, M., Demirtas, H., Geberhiwot, T., Papiha, S.S., De Stefano, G.F., Villems, R. (2000). The topology of the maternal lineages of the Anatolian and Trans-Caucasus populations and the peopling of Europe: some preliminary considerations. In Archaeogenetics: DNA and the population prehistory of Europe. Ed. C. Renfrew and K. Boyle. McDonald Institute for Archaeological Research Monograph Series, Cambridge University Press, Cambridge. pp. 219-235

Kivisild, T., Bamshad, M., Kaldma, K., Metspalu, M., Metspalu, E., Reidla, M., Laos, S., Parik, J., Watkins, W.S., Dixon, M. E., Papiha, S.S., Mastana, S.S., Mir, M.R., Ferak, V., Villems, R. (1999). Deep common ancestry of Indian and western Eurasian mitochondrial DNA lineages. Current Biology 9: 1331-1334

Kivisild, T., Kaldma, K., Metspalu, M., Parik, J., Papiha, S.S., Villems, R. (1999). The place of Indian mitochondrial DNA variants in the global network of maternal lineages and the peopling of the Old World. In Genomic Diversity. Kluwer Academic/Plenum Publishers, New York. 135-152

Metspalu, E., Kivisild, T., Kaldma, K., Parik, J., Reidla, M., Tambets, K., Villems, R. (1999). The Trans-Caucasus and the expansion of the caucasoid-specific human mitochondrial DNA. In Genomic Diversity. Kluwer Academic/Plenum Publishers, New York. 121-134

Villems, R., Adojaan, M., Kivisild, T., Metspalu, E., Parik, J., Pielberg, G., Rootsi, S., Tambets, K., Tolk, H.-V. (1998). Reconstruction of maternal lineages of Finno-Ugric speaking people and some remarks on their paternal inheritance. In The roots of peoples and languages of northern Eurasia I. Societas Historiae Fenno-Ugricae, Turku. 180-200