Y-DNA Papers Cited - 2015

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Contact Person for Papers/Presentations Cited: Bob May or Dave Dowell

Disclaimer: The papers included here do not necessarily represent the first publication of some discoveries. In some cases, authors may be including the work of others. In this document ISOGG in no way is trying to assign credit to researchers. Some of the earlier research papers have been omitted because they use older naming conventions that would require further explanation.

Author, Year, Paper, Journal Haplogroup(s)
Adams S.M., King T.E., Bosch E., Jobling M.A. (2006).
The Case of the Unreliable SNP: Recurrent Back-mutation of Y-chromosomal Marker P25 Through Gene Conversion. (abstract) Forensic Science International 159:14-20.
Adams S., Bosch E., Balaresque P., Ballereau S., Lee A., Arroyo E., Lopez-Parra A., Aler M., Grifo M., Brion M., Carracedo A., Lavinha J., Martinez-Jarreta B., Quintana-Murci Ll., Picornell A., Ramon M., SKorecki K., Behar D., Calafell F. Jobling M. (2008),
The Genetic Legacy of Religious Diversity and Intolerance: Paternal Lineages of Christians, Jews, and Muslims in the Iberian Peninsula. American Journal of Human Genetics, 83(6): 725-36.
E, G, J, R
Alonso S, Flores C., Cabrera, V. Alonso, A., Martin P, Albarran C., Izagirre, N, de la Rua C, Garcia O, (2005).
The Place of the Basques in the European Y-chromosome Diversity Landscape. (available by subscription) European Journal of Human Genetics, 13:1293-1302.
E, F, G, J, K, R, T
Athey T W, Schrack B E (2008-1).
A New Subclade of Y Haplogroup J2b. (pdf) Journal of Genetic Genealogy, 4(1):27-34.
Athey T W, Wilson J F (2008-2).
Y-SNP rs34134567 Defines a Large Subgroup of Haplogroup G2a-P15. (pdf) Journal of Genetic Genealogy, 4(2):149-150.
Athey T W, Nordtvedt K (2005).
Resolving the Placement of Haplogroup I-M223 in the Y-chromosome Phylogenetic Tree. (pdf) Journal of Genetic Genealogy, 1:54-55.
Balanovsky O, Zhabagin M, Agdzhoyan A, Chukhryaeva M, Zaporozhchenko V, Utevska O, Highnam G, Sabitov Z, Greenspan E, Dibirova K, Skhalyakho R, Kuznetsova M, Koshel S, Yusupov Y, Nymadawa P, Zhumadilov Z, Pocheshkhova E, Haber M, Zalloua P A, Yepiskoposyan L, Dybo A, Tyler-Smith C, Balanovska E. (2015).
Deep Phylogenetic Analysis of Haplogroup G1 Provides Estimates of SNP and STR Mutation Rates on the Human Y-Chromosome and Reveals Migrations of Iranic Speakers. PLoS ONE 10(4): e0122968. doi:10.1371/journal.pone.0122968.
Balanovsky O, Dibirova K, Dybo A, Mudrak O, Frolova S, Pocheshkhova E, Haber M, Platt D, Schurr T, Haak W, Kuznetsova M, Radzhabov M, Balaganskaya O, Romanov A, Zakharova T, Soria Hernanz DF, Zalloua P, Koshel S, Ruhlen M, Renfrew C, Wells RS, Tyler-Smith C, Balanovska E; The Genographic Consortium. (2011).
Parallel Evolution of Genes and Languages in the Caucasus Region. Molecular Biology and Evolution, 2011 May 13. [Epub ahead of print].
G, J, L, R
Balanovsky O, Rootsi S, Pshenichnov A, Kivisild T, Churnosov M, Evseeva I, Pocheshkhova E, Boldyreva M, Yankovsky N, Balanovska E, and Villems R (2008).
Two Sources of the Russian Patrilineal Heritage in Their Eurasian Context. American Journal of Human Genetics, 82(1):236-250.
Balaresque P, Bowden G R, Adams S M, Leung H-Y, King T E. Rosser Z H, Goodwin J,Moisan J-P, Richard C, Millward A, Demaine A G, Barbujani G, Previderè C, Wilson I J, Tyler-Smith C, Jobling M A. (2010).
A Predominantly Neolithic Origin for European Paternal Lineages. PLoS biology. 2010;8(1):e1000285.
Batini C, Hallast P, Zadik D, Delser P D, Benazzo A, Ghirotto S, Arroyo-Pardo E, Cavalleri G L, de Knijff P, Dupuy B M, Eriksen H A, King T E, López de Munain A, López-Parra A, Loutradis A, Milasin J, Novelletto A, Pamjav H, Sajantila A, Tolun A, Winney B, Jobling M A, (2015).
Large-scale Recent Expansion of European Patrilineages Shown by Population Resequencing. Nature Communications, 19 May 2015.
Tree Trunk
Batini C, Ferri G, Destro-Bisol G, Brisighelli F, Luiselli C, Sánchez-Diz P, Rocha J, Simonson T, Brehm A, Montano V, Elwali N E, Spedini G, D’Amato M E, Myres N, Ebbesen P, Comas D, Capelli D, (2011).
Signatures of the Preagricultural Peopling Processes in Sub-Saharan Africa as Revealed by the Phylogeography of Early Y Chromosome Lineages. (abstract) Molecular Biology and Evolution. 28 (9): 2603-2613.
A, B
Battaglia V, Fornarino S, Al-Zahery N, Olivieri A, Pala M, Myres N M, King R J, Rootsi S, Marjanovic D, Primorac D, Hadziselimovic R, Vidovic S, Drobnic K, Durmishi11 N, Torroni1 A, Santachiara-Benerecetti A S, Underhill P A, Semino O, (2008).
Y-chromosomal Evidence of the Cultural Diffusion of Agriculture in Southeast Europe European Journal of Human Genetics, 249.
E, I
Behar D M, Garrigan D, Kaplan M E, Mobasher Z, Rosengarten D, Karafet T M, Quintana-Murci L, Ostrer H, Skorecki K, Hammer M F, (2004).
Contrasting Patterns of Y chromosome Variation in Ashkenazi Jewish and Host Non-Jewish European Populations. (pdf) Hum Genet 114:354-365.
E, F, G, J, K, L, N, P, Q, R
Behar D M, Yunusbayev B, Metspalu M, Metspalu E, Rosset S, Parik J, Rootsi S, Chaubey G, Kutuev I, Yudkovsky G, Khusnutdinova E K, Balanovsky O, Semino O, Pereira L, Comas D, Gurwitz D, Bonne-Tamir B, Parfitt T, Hammer M F, Skorecki K, Villems R, (2010).
Genome-Wide Structure of the Jewish People. Nature, 446:238-42.
A, C, E, F, G, H, I, J, K, L, N, P, Q, R
Berger B, Niederstatter H, Erhart D, Gassner C, Schennach H, Parson W. (2013).
High Resolution Mapping of Y haplogroup G in Tyrol (Austria). Forensic Science International: Genetics, 7(5), 529-36, 2013.
Bertoncini S, Bulayeva K, Ferri G, Pagani L, Caciagli L, Taglioli L, Semyonov I, Bulayev O, Paoli G, Tofanelli S. (2012).
The Dual Origin of Tati-speakers from Dagestan as Written in the Genealogy of Uniparental Variants. (abstract) American Journal of Human Biology, Volume 24, Issue 4, pages 391-399, July/August 2012.
G, J
Biro A, Zalan A, Volgyi A, Pamjav H. (2009).
A Y-Chromosomal Comparison of the Madjars (Kazakhstan) and the Magyars (Hungary). American Journal of Physical Anthropology, 139:305-310. (abstract)
F, G, J, K
Bortolini M-C, Salzano FM, Thomas MG, Stuart S, Nasanen SPK, Bau CHD, Hutz MH, Layrisse Z, Petzl-Erler ML, Tsuneto LT, Hill K, Hurtado AM, Castro-de-Guerra D, Torres MM, Groot H, Michalski R, Nymadawa P, Bedoya G, Bradman N, Labuda D, and Ruiz-Linares A, (2003).
Y-Chromosome Evidence for Differing Ancient Demographic Histories in the Americas. American Journal of Human Genetics, 73:524-539.
C, E, K, P, Q, T
Bosch E, (2006).
Paternal and Maternal Lineages in the Balkans Show a Homogeneous Landscape over Linguistis Barriers except for the Isolated Aromuns. Annals of Human Genetics, 70:459-87.
C, E, G, H, I, J, K, R
Butler J M, (2003)
Recent Developments in Y-Short Tandem Repeat and Y-Single Nucleotide Polymorphism Analysis. (pdf) Forensic Science Review, Vol. 15, No. 2, 100-111.
Main Tree; also refers to SNPs on A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R
Cadenas A M, Zhivotovsky L A, Cavalli-Sforza L L, Underhill P A, HerreraR J, (2008).
Y-chromosome Diversity Characterizes the Gulf of Oman. European Journal of Human Genetics, 16:374-386.
C, E
Capelli C, Redhead, N, Romano V, Cali F, Lefranc, G, Delague V, Megarbane A, Felice A E, Pascali V L, Neophytou P I, Poulli Z, Novelletto A, Malaspina P, Terrenato L, Berebbi A, Fellous M, Thomas M G, Goldstein D B, (2005).
Population Structure in the Mediterranean Basin: A Y Chromosome Perspective. (pdf) Annals of Human Genetics.
C, E, J, P, R
Capredon M, Brucato N, Tonasso L, Chosemel-Cadmuro V, Ricaut F-X, Razafindrazaka H, Rakotondrabe A B, Ratolojanahary M A, Randriamarolaza L-P, Champion B, Dugoujon J-M, (2013).
Tracing Arab-Islamic Inheritance in Madagascar: Study of the Y-chromosome and Mitochondrial DNA in the Antemoro. PLoS ONE 8(11): e80932. doi:10.1371/journal.pone.0080932.
O, T
Chandrasekar A, Saheb, S Y, Gangopadyaya P, Gangopayaya S, Mukherjee A, Basu D, Lakshmi G R, Sahani A K, Cas B, Battacharya S, Kumar S, Xavior D, Sun D, Rao V R, (2007).
YAP Insertion Signature in South Asia. Annals of Human Biology, 34(5);582-6.
Main Tree
Charoni J, Underhill P, Cavalli-Sforza L L, (2009).
Y Chromosome Diversity, Human Expansion, Drift, and Cultural Evolution. PNAS, 106 (48); 20174-20179.
Main Tree
Chen J,Li H, Qin Z D, Liu W H, Lin W X, Yin R X, Jin L, Pan S L, (2006).
Y Chromosome Genotyping and Genetic Structure of Zhuang Populations. (abstract) Acta Genetica Sinica, 33(12), 1060-72.
C, O
Cinnioglu C, King R, Kivisild T, Kalfoglu E, Atasoy S, Cavalleri G L, 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. (pdf) Human Genetics, 114:127-148.
A, C, E, G, H, I, J, K, L, N, O, Q, R, T
Cox M P, Lahr M M (2006).
Y-Chromosome Diversity Is Inversely Associated with Language Affiliation in Paired Austronesian- and Papuan-Speaking Communities from Solomon Islands. (pdf) American Journal of Human Biology, 18:35-50.
K, M, O, S
Cristofaro J D, Pennarun E, Mazieres S, Myres N M, Lin A A, Temori S A, Metspalu M, Metspalu E, Witzel M, King R J, Underhill P A, Villems R, Chiaroni J (2013).
Afghan Hindu Kush: Where Eurasian Sub-Continent Gene Flows Converge. PLoS ONE 8(10): e76748. doi:10.1371/journal.pone.0076748.
C, D
Cruciani F, Santolamazza P, Shen P, Macaulay V., Moral P, Olckers A, Modiano D, Holmes S, Destro-Bisol G, Coia V, Wallace D C, Oefner P J, Torroni A, Cavalli-Sforza L L, Scozarri R, Underhill P A, (2002).
A Back Migration from Asia to Sub-Saharan Africa Is Supported by High-Resolution Analysis of Human Y-Chromosome Haplotypes. American Journal of Human Genetics, 70:1197-1214.
A, B, D, E, F, G, J, K, L, O, R, T
Cruciani F, Trombetta B, Sellitto D, Massaia A, Destro=Bisol G, Watson E, Colomb E B, Dugoujon J-M, Moral P, Scozzari R (2010a).
Human Y Chromosome Haplogroup R-V88: A Paternal Genetic Record of Early Mid Holocene Trans-Saharan Connections and the Spread of Chadic Languages. (abstract) (Epub ahead of print) European Journal of Human Genetics, January 6, 2010.
Cruciani F, La Fratta R, Santolamazza P, Sellito D, Pascone R, Moral P, Watson E, Guida V, Beraud Colomb E, Zaharova B, Lavinha J, Vona G, Aman R, Cali F, Akar N, Richards M, Torroni A, Novelletto A, Scozzari R, (2004).
Phylogeographic Analysis of Haplogroup E3b (E-M215) Y Chromosomes Reveals Multiple Migratory Events Within and Out of Africa. (pdf) American Journal of Human Genetics, 74:1014-1022.
D, E
Cruciani F, La Fratta R, Torroni A, Underhill P A, Scozzari R, (2006).
Molecular Dissection of the Y Chromosome Haplogroup E-M78 (E3b1a): A Posteriori Evaluation of a Microsatellite-Networked-Based Approach Through Six New Biallelic Markers. Human Mutation: Mutation in Brief #916.
Cruciani F, Trombetta1 B, Massaia A, Destro-Bisol G, Sellitto D, ScozzariR, (2011).
A Revised Root for the Human Y Chromosomal Phylogenetic Tree--The Origin of Patrilineal Diversity in Africa. The American Journal of Human Genetics, doi:10.1016/j.ajhg.2011.05.002.
Y-DNA Tree Trunk, A, C
Cruciani F, Trombetta B, Antonelli C, Pascone R, Valesini G, Scalzi V, Vona G, Melegh B, Zagradisnik B, Assum G, Efremov G D, Sellitto D, Scozzari R. (2010b)
Strong Intra- and Inter-continental Differentiation Revealed by Y chromosome SNPs M269, U106 and U152. Forensic Science International. Genetics. 2010:7-10.
Cruciani F, La Fratta R, Trombetta B, Santolamazza P, Sellitto D, Colomb E B, Dugoujon J-M, Crivellaro F, Benincasa T, Pascone R, Moral P, Watson E, Melegh B, Barbujani G, Fusselli S, Vona G, Zagradisnik B, Assum G, Brdicka R, Kozlov A I, Efremov G D, Coppa A, Novelletto A, Scozzari R, (2007).
Tracing Past Human Male Movements in Northern/Eastern Africa and Western Eurasia: New Clues from Y-Chromosomal Haplogroups E-M78 and J-M12. (pdf) Molecular Biology and Evolution 24(6):1300-1311.
E, J
Cruciani F, Trombetta B, Novelletto A, Scozzari R, (2008).
Recurrent Mutation in SNPs within Y chromosome E3b (E-M215) Haplogroup: A Rebuttal. (abstract) American Journal of Human Biolology. Sep-Oct; 20(5):614-6.
Delfin F, Salvador J M, Calacal G C, Perdigon H B, Tabbada K A, Villamor L P, Halos S C, Gunnarsdóttir E, Myles S, Hughes D A, Xu S, Jin L, Lao O, Kayser M, Hurles M E, Stoneking M, De Ungria M C A, (2011).
The Y Chromosome Landscape of the Philippines: Extensive Heterogeneity and Varying Genetic Affinities of Negrito and Non-Negrito Groups. (abstract) European Journal of Human Genetics, 19:224-30.
C, K, O, P
Deng W, Shi B, He X, Zhang Z, Xu J, Li B, Yang J, Ling L, Dai C, Qiang B, Shen Y, Chen R, (2004).
Evolution and Migration History of the Chinese Population Inferred from the Chinese Y-chromosome Evidence. (pdf) Journal of Human Genetics, 49:339-348.
A, C, D, E, K, L, O, P, Q, R
Derenko M, Malyarchuk B, Denisova GA, Wozniak M, Dambueva I, Dorzhu C, Luzina F, Danuta Miscicka-Sliwka D, Zakharov I, (2006).
Contrasting Patterns of Y-Chromosome Variation in South Siberian Populations from Baikal and Altai-Sayan Regions, Human Genetics, 118:591-604.
C, P
Di Giacomo F, Luca F, Popa L O, Akar N, Anagnou N, Banyko J, Brdicka R, Barbujani G, Papola F, Ciavarella G, Cucci F, Di Stasi L, Gavrila L, Kerimova M G, Kovatchev D, Kozlov A I, Loutradis A, Mandarino V, Mammi C, Michalodimitrakis E N, Paoli G, Pappa K I, Pedicini G, Terrenato L, Tofanelli A, Mapaspina P, Novelletto A, (2004).
Y Chromosomal Haplogroup J as a Signature of the Post-Neolithic Colonization of Europe. (pdf) Human Genetics, 115:357-371.
Dulik M C, Zhadanov S I, Osipova L P, Askapuli A, Gau L, Gokcumen O, Rubenstein S, Schurr T G, (2012a).
Mitochondrial DNA and Y Chromosome Variation Provides Evidence for a Recent Common Ancestry between Native Americans and Indigenous Altaians. (pdf) The American Journal of Human Genetics (2012), doi: 10.1016/ajhg.2011.12.014, 2012(a).
C, Q, R
Dulik M C, Owings A C, Gaieski J B, Vilar M G, Andre A, Lennie C, Mackenzie M A, Kritsch I, Snowshoe S, Wright R, Martin J, Gibson N, Andrews T D, Schurr T G; Genographic Consortium,(2012b).
Y-chromosome Analysis Reveals Genetic Divergence and New Founding Native Lineages in Athapaskan- and Eskimoan-speaking Populations. (pdf) Proc Natl Acad Sci U S A. 2012 May 29;109(22):8471-6. doi: 10.1073/pnas.1118760109. Epub May 14, 2012(b).
Dulik M C, Osipova L P, Schurr T G, (2011).
Y-Chromosome Variation in Altaian Kazakhs Reveals a Common Paternal Gene Pool for Kazakhs and the Influence of Mongolian Expansions. (pdf) PLoS ONE, Vol. 6, Issue 3, e17548.
C, O
Eaaswarkhanth M, Haque I, Ravesh I, Gomero I G, Meganathan P R, Dubey B, Khan F A, Chaubey G, Kivisild T, Tyler-Smith C, Singh L, Thangaraj K, (2010).
Traces of Sub-Saharan and Middle Eastern Lineages in Indian Muslim Populations. European Journal of Human Genetics, 18, 354-363.
C, F, K
El Sibai M, Platt D, Haber M, Xue Y, Youhanna S, Wells R, Izaabel H, Anyoura M, Harmanani H, Bonab M, Behbehani J, Hashwa F, Tyler-Smith C, Zalloua P, The Genographic Consortium, (2009).
Geographical Structure of the Y-Chromosomal Genetic Landscape of the Levant: A Coastal Inland Contrast, Annals of Human Genetics, 73:568-81. (abstract)
E, G. I, J
Firasat S, Khaliq S, Mohyuddin A, Papaioannou M, Tyler-Smith C, Underhill P, Ayub Q, (2007).
Y-chromosomal Evidence for a Limited Greek Contribution to the Pathan Population of Pakistan, European Journal Human Genetics, 15:121+126.
Flores G, Maca-Meyer N, Gonzalez A M, Oefner P J, Shen P, Perez, J A, Rojas A, Larruga J M, Underhill, P A, (2004).
Reduced Genetic Structure of the Iberian Peninsula Revealed by Y-chromosome Analysis: Implications for population demography. (pdf) European Journal of Human Genetics, 12:855-863.
E F, K, N, P, R, T
Fornarino S, Pala M, Battaglia V, Maranta R, Achilli A, Modiano G, Torroni A, Semino O, Santachiara-Benerecetti SA, (2009).
Mitochondrial and Y-chromosome Diversity of the Tharus (Nepal): A Reservoir of Genetic Variation. BMC Evol Biol. 2009; 9: 154. Published online 2009 July 2. doi: 10.1186/1471-2148-9-154.
C, F
Francalacci P, Morelli L, Angius A, Berutti R, Reinier F, Atzeni R, Pilu R, Busonero F, Maschio A, Zara I, Sanna D, Useli A, Urru M F, Marcelli M, Cusano R, Oppo M, Zoledziewska M, Pitzalis M, Deidda F, Porcu E, Poddie F, Kang H M, Lyons R, Tarrier B, Gresham J B, Li B, Tofanelli S, Alonso S, Dei M, Lai S, Mulas A, Whalen M B, Uzzau S, Jones C, Schlessinger D, Abecasis G R, Sanna S, Sidore D, Cucca F, (2013).
Low-Pass DNA Sequencing of 1200 Sardinians Reconstructs European Y-Chromosome Phylogeny. Science 2 August 2013: Vol. 341 no. 6145, pp. 565-569, DOI: 10.1126/science.1237947.
A, E, F, G, I, J, L, Q, R, T
Gayden T, Cadenas A M, Regueiro M, Singh N B, Zhivotovsky L A, Underhill P A, Cavalli-Sforza L L, and Herrera R J (2007)
The Himalayas as a Directional Barrier to Gene Flow. American Journal of Human Genetics, 80(5):884-894, 2007.
C, D, N
Gebremeskel E I, Ibrahim M E (2014)
Y-chromosome E haplogroups: Their Distribution and Implication to the Origin of Afro-Asiatic Languages and Pastoralism. European Journal of Human Genetics; doi: 10.1038/ejhg.2014.41.
Geppert M, Baetab M, Núñez C, Martínez-Jarreta B, Zweynert S, Vacas Cruz O W, González-Andrade F, González-Solorzano J, Nagya M and Roewer L (2010)
Hierarchical Y-SNP Assay to Study the Hidden Diversity and Phylogenetic Relationship of Native Populations in South America, Forensic Science International: Genetics, 6 Oct 2010. [Epub ahead of print]
C, Q
Ghiani M, Mameli A, Piras G, Berti A, Calo C, Vona G. (2009).
Population Data for Y-chromosome Haplotypes Defined by AmpFlSTR YFiler PCR Amplification Kit in North Sardinia (Italy). Collegium Antropologicum, 33 (2): 643-51.
G, I
Gomes V, Sánchez-Diz P, Amorim A, Carracedo A, Gusmão L. (2010).
Digging Deeper into East African Human Y Chromosone Lineages, Human Genetics, 2010 Mar;127(5):603-13.
B, E
Gurianov V, Kull L, Sychev R, Tagankin V, Ursin V. (2014a).
Phylogenetic Structure of Q-M378 Subclade Based on Full Y-Chromosome Sequencing, The Russian Journal of Genetic Genealogy, Rom 5, No 1., 2014 Jan:84-102.
Gurianov V, Kull L, Sychev R, Tagankin V, Ursin V. (2014b).
The update of Phylogenetic Structure of Q-M378 Subclade Based on Full Y-Chromosome Sequencing, The Russian Journal of Genetic Genealogy, Vol 6, No 1.
Haber M, Platt D, Badro D, Xue Y, El-Sibai M, Bonab M, Youhanna S, Saade S, Soria-Hernanz D, Rowuru A, Wells R, Tyler-Smith C, Zalloua P, Genographic Consortium (2010)
Influences of History, Geography, and Religion on Genetic Structure: the Maronites in Lebanon, European Journal of Human Genetics, 19(3): 334-40.
Hallast P, Batini C, Zadik D, Delser P M, Wetton J H, Arroyo-Pardo E, Cavalleri G L, de Knijft P, Bisol G D, Dupuy B M, Eriksen H A, Jorde L B, King T E, Larmuseau M H, de Munain A L, Lopez-Parra A M, Loutradis A, Milasin J, Novelletto A, Pamjav H, Sajantila A, Schempp W, Sears M, Tolun A, Tyler-Smith C, Van Guystelen A, Watkins S, Winney B, Jobling M A (2014)
The Y-chromosome Tree Bursts into Leaf: 13,000 High-confidence SNPs Covering the Majority of Known Clades, Molecular Biology and Evolution, doi: 10.1093/molbev/msu327.
Y-DNA Tree Trunk
Hammer M F, Krafet T M, Park H, Omoto K, Harihara S, Stoneking M, Harai S, (2006).
Dual Origins of the Japanese: Common Ground for Hunter-gatherer and Farmer Y Chromosomes. (abstract) Journal of Human Genetics, 51:47-58.
C, D, N, O
Hammer M F, Karafet T M, Redd A J, Jarjanazi H, Santachiara-Benerecetti A S, Soodyall H, Zegura S L, (2001).
Hierarchical Patterns of Global Human Y-Chromosome Diversity. (pdf) Molecular Biology and Evolution, 18:1189-1203.
Main Tree; also refers to SNPs on A, B, C, D, I, J, K, M, N, O, Q, R
Hammer M F, Chamberlain V F, Kearney V F, Stover D, Zhang G, Karafet T, Walsh B, Redd A J, (2005).
Population Structure of Y Chromosome SNP Haplogroups in the United States and Forensic Implications for Constructing Y Chromosome STR Databases. (in press) Forensic Science International.
Main Tree; also refers to SNPs on
Henn B M, Gignoux D, Lin A A, Oefner P J, Shen P, Scozzari R, Cruciani F, Tishkoff S A, Mountain J L, Underhill P A, (2008).
Y-chromosomal Evidence of a Pastoralist Migration through Tanzania to Southern Africa. PNAS, vol. 105 no. 31 10693-10698.
Herrera K J, Lowery R K, Hadden L, Calderon S, Chiou C, Yepiskoposyan L, Regueiro M, Underhill P A, Herrera R J, (2011).
Neolithic Patrilineal Signals Indicate that the Armenian Plateau was Repopulated by Agriculturalists. European Journal of Human Genetics, 10.1038/ejhg.2011.192, 2011.
G, J, R, T
Hinds D A, Stuve L L, Nilsen G B, Haperin E, Eskin E, Ballinger D G, Frazer K A, Cox D R. (2005).
Whole-genome Patterns of Common DNA Variation in Three Human Populations. Science, 307:1072-1079.
Hudjashov G, Kivisild T, Underhill P A, Endiott P, Sanchez J, Lin A A, Shed P, Oefner P, Renfew C, Villems R, Forster P, (2007).
Revealing the Prehistoric Settlement of Australia by Y chromosome and mtDNA Analysis. PNAS, 104:21.
C, F
Hurles M E, Irven C, Nicholson J, Taylor P G, Santos F R, Loughlin J, Jobling M A, Sykes B C, (1998).
European Y-Chromosomal Lineages in Polynesians: A Contrast to the Population Structure Revealed by mtDNA. American Journal of Human Genetics, 63:1793-1806.
Hurles M E, Nicholson J, Bosch E, Renfew C, Sykes B C, Jobling M A, (2002).
Y Chromosomal Evidence for the Origins of Oceanic-Speaking Peoples. Genetics, 160:289-303.
Jin H-J, Kim K-C, Kim W, (2010).
Genetic Diversity of Two Haploid Markers in the Udegey Population from Southeastern Siberia. (abstract) American Journal of Physical Anthropology, 142:303-313.
C, O
Jin H-J, Tyler-Smith C, Wook.K, (2009).
The Peopling of Korea Revealed by Analyses of Mitochondrial DNA and Y-Chromosomal Markers. PLoS One, vol 4(1):ed4210.
C, O
Jobling M A, Tyler-Smith C, (2003).
The Human Y Chromosome: An Evolutionary Marker Comes of Age. Nature/Reviews/Genetics, 4:598-612.
Main Tree; also refers to SNPs on A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R
Jota M S, Lacerda D R, Sandoval J R, Vieira P P, Santos-Lopes S S, Bisso-Machado R, Paixão-Cortes V R, Revollo S, Paz-Y-Miño C, Fujita R, Salzano F M, Bonatto S L, Bortolini M C, Santos F R; Genographic Consortium, (2011).
A New Subhaplogroup of Native American Y-Chromosomes from the Andes. Abstract. Am J Phys Anthropol. 2011 Dec;146(4):553-9. doi: 10.1002/ajpa.21519. Epub Sep 13, 2011.
Karafet T M, Mendez F L, Sudoyo H, Lansing J S, Hammer M F (2014).
Improved Phylogenetic Resolution and Rapid Diversification of Y-chromosome Haplogroup K-M526 in Southeast Asia. European Journal of Human Genetics, 1-5.
Main Tree, K, P
Karafet T M, Hallmark B, Cox M P, Sudoyo H, Downey S, Lansing J S, Hammer M, (2010).
Major East-West Division Underlies Y Chromosome Stratification Across Indonesia. Abstract. Molecular Biology and Evolution, doi:10.1093/molbev/msq063.
Main Tree
Karafet T M, Mendez F L, Meilerman M B, Underhill P A, Zegura S L, Hammer M F, (2008).
New Binary Polymorphisms Reshape and Increase Resolution of the Human Y-Chromosomal Haplogroup Tree. Abstract. Genome Research, published online April 2, 2008. Supplementary Material.
Main Tree; also refers to SNPs on A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R S T
Karafet T, Xu L, Du R, Wang W, Feng S, Wells R S, Redd A J, Zegura S L, Hammer M F, (2001).
Paternal Population History of East Asia: Sources, Patterns, and Microevolutionary Processes. (pdf) American Journal of Human Genetics, 69:615-628.
C, D, J, L, O, R
Karlsson A O, Wallerstrom T, Gotherstrom A, Holmlund G, (2006)
Y-chromosome Diversity in Sweden - A Long-time Perspective. (pdf) European Journal of Human Genetics, 4:963-970
N, R
Karmin M, Saag L, Vicente M, Sayres M A W, Järve M, Talas U G, Rootsi S, Ilumäe A-M, Mägi R, Mitt M, Pagani L, Puurand T, Faltyskova A, Clemente F, Cardona A, Metspalu E, Sahakyan H, Yunusbayev B, Hudjashov G, DeGiorgio M, Loogväli E-L, Eichstaedt C, Eelmets M, Chaubey G, Tambets K, Litvinov S, Mormina M, Xue Y, Ayub Q, Zoraqi G, Korneliussen T S, Akhatova F, Lachance J, Tishkoff S, Momynaliev K, Ricaut F-X, Kusuma P, Razafindrazaka H, Pierron D, Cox M P, Sultana G N N, Willerslev R, Muller C, Westaway M, Lambert D, Skaro V, Kovačević L, Turdikulova S, Dalimova D, Khusainova1 R, Trofimova N, Akhmetova V, Khidiyatova I, Lichman D V, Isakova J, Pocheshkhova E, Sabitov Z, Barashkov N A, Nymadawa P, Mihailov E, Seng J W T, Evseeva I, Migliano A B, Abdullah S, Andriadze G, Primorac D, Atramentova L, Utevska O, Yepiskoposyan L, Marjanović D, Kushniarevich A, Behar D M, Gilissen C, Vissers L, Veltman J A, Balanovska E, Derenko M, Malyarchuk B, Metspalu A, Fedorova S, Eriksson A, Manica A, Mendez F L, Karafet T M, Veeramah K R, Bradman N, Hammer M F, Osipova L P, Balanovsky O, Khusnutdinova E K, Johnsen K, Remm M, Thomas M G, Tyler-Smith C, Underhill P A, Willerslev E, Nielsen R, Metspalu M, Villems R, Kivisild T, (2015).
A Recent Bottleneck of Y chromosome Diversity Coincides with a Global Change in Culture. Genome Research, doi: 10.1101/gr.186684.114
C, D, G Y-DNA Tree Trunk
Kayser M, Choi Y, van Oven M, Mona S, Brauer S, Trent R J, Swarkia, D, Schiefenhovel W, Stoneking M, (2008).
The Impact of the Austronesian Expansion: Evidence from mtDNa and Y Chromosome Diversity in the Admiralty Islands of Melanesia. Molecular Biology Evolution, 25(7):1362-1374.
C, K, M, O
Kayser M, Brauer S, Weiss G, Schiefenhovel W, Underhill P A, Stoneking M, (2001).
Independent Histories of Human Y Chromosomes from Melanesia and Australia. American Journal of Human Genetics, 68:173-190.
C, K, M, O, S
Kayser M, Brauer S, Cordaux R, Casto A, Lao O, Zhivotovsky L A, Moyse-Faurie C, Rutledge R B, Schiefenhovel W, Gil D, Lin A A, Underhill P A, Oefner P J, Trent R J, Stoneking M. (2006).
Melanesian and Asian Origins of Polynesians: mtDNA and Y-Chromosome Gradients across the Pacific. MBE Advance Access published August 21, 2006.
C, K, M, NO, O, S
Kayser M, Brauer S, Weiss G, Underhill P A, Roewer L, Schiefenhovel W, Stoneking M, (2000).
Melanesian Origin of Polynesian Y Chromosomes. Current Biology, Vol. 10, No. 20.
Kayser M. Brauer S., Weiss G., Schiefenhovel W, Underhill P, Shen P, Oefner P, Tommaseo-Ponzetta M, Stoneking M. (2003).
Reduced Y-Chromosome, but Not Mitochondrial DNA, Diversity in Human Populations from West New Guinea. American Journal of Human Genetics, 72:281-302.
C, F, K, M, O, P, R, S
Keller A, Graefen A, Ball M, Matzas M, Boisguerin V, Maixner F, Leidinger P, Backes C, Khairat R, Forster M, Stade B, Franke A, Mayer J, Spangler J, McLaughlin S, Shah M, Lee C, Harkins T T, Sartori A, Moreno-Estrada A, Henn B, Sikora M, Semino O, Chiaroni1 J, Rootsi S, Myres N M, Cabrera V M, Underhill P A, Bustamante C A, Egarter Vigl E, Samadelli M, Cipollini G, Haas J, Katus H, O’Connor B D, Carlson M R J, Meder B, Blin N, Meese E, Pusch C M, Zink A (2012)
New Insights into the Tyrolean Iceman’s Origin and Phenotype as Inferred by Whole-genome Sequencing. Nature Communications, DOI: 10.1038/ncomms1701, 2023.
King R, DiCristofaro J, Kouvatsi A, Triantaphyllidis C, Scheidel W, Myres N, Lin A, Eissautier A, Mitchell M, Binder D, Semino O, Novelletto A, Underhill P, and Chiaroni J. (2011).
The Coming of the Greeks to Provence and Corsica: Y-Chromosome Models of Archaic Greek Colonization of the Western Mediterranean. BMC Evolutionary Biology, 11:69.
E; G; J
King RJ, Ozcan SS, Carter T, Kalfoglu E, Atasoy S, Triantaphyllidis C, Kouvatsi A, Lin AA, Chow CET, Zhivotovsky LA, M. Michalodimitrakis M, Underhill PA (2008).
Differential Y-chromosome Anatolian Influences on the Greek and Cretan Neolithic. (abstract) Annals of Human Genetics 72:205-214.
E; G; J
Kivisild T, Rootsi S, Metspalu M, Mastana S, Kaldma K, Parik J, Metspalu E, Adojaan M, Tolk HV, Stepanov V, Golge 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 in Both Indian Tribal and Caste Populations. (pdf) American Journal of Human Genetics, 72:313-332.
C, F, G, H, J, K, L, P, R, T
Li H, Wen B, Chen S-J, Su B, Pramoonjago P, Liu Y, Pan S, Qin Z, Liu W, Cheng X, Yang N, Li X, Tran D, Lu D, Hsu M-T, Deka R, Marzuki S, T C-C, Jim L, (2008).
Paternal Genetic Affinity between Western Austronesians and Daic Populations BMC Evolutionary Biology, Vo. 15(8), p. 146.
C, D, F, K, O
Magoon G R , Banks R H, Rottensteiner C, Schrack B E, Tilroe V O, Robb T, Grierson A J, (2013).
Generation of High-resolution a priori Y-chromosome Phylogenies Using "Next-generation" Sequencing Data bioRxiv, doi: 10.1101/000802, December 13, 2013.
E, Tree Trunk
Malhi R S, Gonzalez-Oliver A, Schroeder K B, Kemp B M, Greenberg J A, Dobrowski S Z, Smith D G, Resendez A, Karafet T, Hammer M, Zegura S, Brovko T, (2008).
Distribution of Y Chromosomes among Native North Americans: A Study of Athapaskan Population History American Journal of Physical Anthropology, 137:412-24.
C, Q, R
Malyarchuk B, Derenko M, Denisova G. (2012).
On the Y-chromosome Haplogroup C3c Classification. (abstract) Journal of Human Genetics. Epub ahead of print, 2012 Jul 19.
Malyarchuk B, Derenko M, Denisova G, Wozniak M, Grzybowski T, Dambueva I, Zakharov I, (2010).
Phylogeography of the Y-Chromosome Haplogroup C in Northern Eurasia. (abstract) Annals of Human Genetics, 74:539-46.
McEvoy B, Bradley D G, (2006).
Y-chromosomes and the Extent of Patrilineal Ancestry in Irish Surnames (abstract) Human Genetics 2006 Jan 12;:1-8 (Epub ahead of print).
Mendez F L, Krahn T, Schrack B, Krahn A-M, Veeramah1 K R, Woerner1 A E, Fomine F L M, Bradman N, Thomas M G, Karafet T M, Hammer M H. (2013).
An African American Paternal Lineage Adds an Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree. (abstract) American Journal of Human Genetics 28 February 2013.
A, Y-DNA Tree Trunk
Mendez F L, Karafet T M, Krahn T, Ostrer H, Soodyall H, Hammer M H. (2011).
Increased Resolution of Y Chromosome Haplogroup T Defines Relationships among Populations of the Near East, Europe, and Africa. Human Biology 83(1):39-53, 2011.
Mohyuddin A., Ayub Q, Underhill P A, Tyler-Smith C, Mehdi S Q, (Feb. 10 2006).
Detection of Novel Y SNPs Provides Further Insights into Y Chromosomal Variation in Pakistan. (abstract) Journal of Human Genetics.
A, C, L, O, R
Moore L T, McEvoy B, Cape E, Simms K, Bradley D G, (2006).
A Y-chromosome Signature of Hegemony in Gaelic Ireland. American Journal of Human Genetics, 78(2):334-338.
Mona S, Tommaseo-Ponzetta M, Brauer S, Sudoyo H, Marzuki S, Kayser M. (2007).
Patterns of Y-chromosome Diversity Intersect with the Trans-New Guinea Hypothesis. Mol Biol Evol. 2007 Sep 10; [Epub ahead of print]
C, K, M, O, S
Myres N M, Rootsi S, Lin A A, Järve M, King R J, Kutuev I, Cabrera V M, Khusnutdinova E K, Pshenichnov A, Yunusbayev B, Balanovsky O, Balanovska E, Rudan P, Baldovic M, Herrera R J, Chiaroni J, Di Cristofaro J, Villems R, Kivisild T, Underhill P A. (2010).
A Major Y-chromosome Haplogroup R1b Holocene Era Founder Effect in Central and Western Europe. European journal of human genetics : EJHG. 2010;(July):1-7.
Myres N M, Elkins J E, Lin A A, Cavalli-Sforza, L L, Woodward S R, Underhill P A. (2007).
Y-chromosome Short Tandem Repeat DYS458.2 Non-concensus Alleles Occur Independently in Both Binary Haplogroups J1-M267 and R1b3-M405. Croatian Medical Journal, 48.
J, R
Naitoh S, Kasahara-Nonaka I, Minaguchi K, Nambiar P. (2013).
Assignment of Y-chromosomal SNPs Found in Japanese Population to Y-chromosomal Haplogroup tree. Journal of Human Genetics, 2013 Feb 7. doi: 10.1038/jhg.2012.159.
C, D, O
Nasidze I, Quinque D, Dupanloup I, Rychkov S, Naumova O, Zoukova O, Stoneking M, (2004).
Genetic Evidence Concerning the Origins of the South and North Ossetians. (abstract) Annals of Human Genetics, 68:588-599.
E, F, G, J, P, R
Nasidze I, Quinque D, Ozturk M, Bendukidze N, and Stoneking M, (2005).
MtDNA and Y-chromosome Variation in Kurdish Groups. (abstract) Annals of Human Genetics, 69:401-412.
C, E, F, G, J, K, P, R
Nasidze I, Sarkisian T, Kerimov A, Stoneking M. (2003).
Testing Hypotheses of Language Replacement in the Caucasus: Evidence from the Y-chromosome. Human Genetics 112(3): 255-61.
F, G, J
Nonaka I, Minaguchi K, and Takezaki N. (2007).
Y Chromosomal Binary Haplogroups in the Japanese Population and their Relationship to 16 Y-STR Polymorphisms. (abstract) Annals of Human Genetics, 71:480-495.
C, D, O
Olalde I, Sánchez-Quinto F, Datta D, Marigorta U M, Chiang C W K, Rodríguez J A, Fernández-Callejo M, González I, Montfort M, Matas-Lalueza L, Civit S, Luiselli D, Charlier P, Pettener D, Ramírez O, Navarro A, Himmelbauer H, Marquès-Bonet T, Lalueza-Fox C. (2014).
Genomic Analysis of the Blood Attributed to Louis XVI (1754–1793), King of France. Scientific Reports, 4, Article number: 4666, doi:10.1038/srep04666.
Pakendorf B, Novgorodov I N, Osakovskij V L, Danilova A P, Protod’jakonov A P, and Stoneking M. (2006).
Investigating the Effects of Prehistoric Migrations in Siberia: Genetic Variation and the Origins of Yakuts, Human Genetics, Volume 120, Number 3, 334-353.
Poznik G D, Henn B M, Yee M-C, Sliwerska E, Euskirchen G M, Lin A A, Snyder M, Quintana-Murci L, Kidd J M, Underhill P A, Bustamante C D. (2013).
Sequencing Y Chromosomes Resolves Discrepancy in Time to Common Ancestor of Males Versus Females. (abstract) Science, 341 (6145): 562-5. 2013.
G, Tree Trunk
Regueiro M, Cardenas A M, Gayden T, Underhill P A, Herrera T J, (2006).
Iran: Tricontinental Nexus for Y-Chromosome Driven Migration. (abstract) Human Heredity, Vol. 61, No 3., 132-143.
B, C, E, F, G, H, J, K, L, N, O, Q, R, T
Repping S, van Daalen S K M, Brown L G, Korver C M, Lange J, Marszalek J D, Pyntikova T, van der Veen F, Skaletsky H, Page D C, Rozen S. (2006) High Mutation Rates Have Driven Extensive Structural Polymorphism among Human Y Chromosomes. (pdf) National Genetics, 38: 463-467. E, R
Rocca R A, Magoon G, Reynolds D F, Krahn T, Tilroe V O, Op den Velde Boots P M, Grierson A J. (2012).
Discovery of Western European R1b1a2 Y Chromosome Variants in 1000 Genomes Project Data: An Online Community Approach. (pdf) PLoS ONE 7(7): e41634. doi:10.1371/journal.pone.0041634, 2012.
Rootsi S, Zhivotovsky LA, Baldovic M, Kayser M, Kutuev I A, Khusainova1 R, Bermisheva1 M A, Gubina M, Fedorova1 S A, Ilumae1 A, Khusnutdinova E K, Voevoda M I, Osipova L P, Stoneking M, Lin A A, Ferak V, Parik J, Kivisild T, Underhill P A and Villems R. (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.
Rootsi S, Myres N M, Lin A A, Järve M, King R J, Kutuev I, Cabrera V M, Khusnutdinova E K, Varendi K, Sahakyan J, Behar D M, Khusainova R, Balanovsky O, Balanovska E, Rudan P, Yepiskoposyan L, Bahmanimehr A, Farjadian S, Kushniarevich A, Herrera R J, Grugni V, Battaglia V, Nici C, Crobu F, Karachanak S, Kashani B H, Houshmand M, Sanati M H, Toncheva D, Lisa A ,Semino O, Chiaroni J, Di Cristofaro J, Villems R, Kivisild T and Underhill, P A. (2012).
Distinguishing the Co-Ancestries of Haplogroup G Y-Chromosomes in the Populations of Europe and the Caucasus. Abstract. European Journal of Human Genetics, (e-pub 16 May 2012 ahead of print), pp 1-8.
Rootsi S, (Oct 2004).
Human Y Chromosomal Variations in European Populations. (dissertation) Council of the Institute of Molecular and Cell Biology, University of Tartu.
Main Tree; also significant reference to SNPs on N, O
Rootsi S, Behar D M, Järve M, Lin A A, Myres N M, Passarelli B, Poznik G D, Tzur S, Sahakyan H, Pathak A K, Rosset S, Metspalu M, Grugni V, Semino O, Metspalu E, Bustamante C D, Skorecki K, Villems R, Kivisild T, Underhill P A, (2013).
Phylogenetic Applications of Whole Y-chromosome Sequences and the Near Eastern Origin of Ashkenazi Levites. Nature Communications 4, Article number: 2928, doi:10.1038/ncomms3928.
P, R
Rootsi S, Magri C, Kisivild T, Benuzzi G, Help H, Bermisheva M, Kutuev I, Barac L, Pericic M, Balanovsky O, Pshenichnov A, Dion D, Grobei M, Zhivotovsky L A, Battaglia V, Achilli A, Al-Zahery N, Parik J, King R, Cinnioglu C, Kushnutdinova E, Rudan P, Balanovska E, Scheffrahn W, Simonescu M, Brehm A, Goncalves R, Rosa A, Joisan J-P, Chaventre A, Ferak V, Furedi S, Oefner P J, Shen P, Beckman L, Mikerezi I, Terzic R, Primorac D, Cambon-Thomsen A, Krumina A, Torroni A, Underhill P A, Santachiara-Benerecetti A S, Villems R, Semino O, (2004).
Phylogeography of Y-Chromosome Haplogroup I Reveals Distinct Domains of Prehistoric Gene Flow In Europe. American Journal of Human Genetics, 75:128-137.
Rozen S, Marszalek J D, Alagappan R K, Skaletsky H, and Page D C (2009).
Remarkably Little Variation in Proteins Encoded by the Y Chromosome's Single-Copy Genes, Implying Effective Purifying Selection. American Journal of Human Genetics. 2009 December 11; 85(6): 923-928.
Main Tree, A, B, C, D, E, I, M, N, O, P, R, T
Scheinfeldt L. Friedlaender F, Friedlaender J, Latham K, Koki G, Karafet T, Hammer M, Lorenz J, (2006).
Unexpected NRY Chromosome Variation in Northern Island Melanesia. Society for Molecular Biology, 2006.
C, I, K, M, O, S
Schuster S C, Miller W, Ratan A, Tomsho L P, Giardine B, Kasson L R, Harris R S, Petersen D C, Zhao F, Qi J, Alkan C, Kidd J M, Sun Y, Drautz D I, Bouffard P, Muzny D M, Reid J G, Nazareth L V, Wang Q, Burhans R, Riemer C, Wittekindt N E, Moorjani P, Tindall E A, Danko C G, Teo W S, Buboltz A M, Zhang A, Ma Q, Oosthuysen A, Steenkamp A W, Oostuisen H, Venter P, Gajewski J, Zhang Y, Pugh B F, Makova K D, Nekrutenko A, Mardis E R, Patterson N, Pringle T H, Chiaromonte F, Mullikin J C, Eichler E E, Hardison R C, Gibbs R A, Harkins T T, Hayes V M. (2010).
Complete Khoisan and Bantu Genomes from Southern Africa. (abstract) Nature 463, 943-947 (18 February 2010).
A, B, E
Scozzari R, Massaia A, D’Atanasio E, Myres N M, Perego U A, Trombetta B, Cruciani F, (2012).
Molecular Dissection of the Basal Clades in the Human Y Chromosome Phylogenetic Tree, PLoS ONE, Vol. 7, Issue 11, e4917.
B, C
Scozzari R, Massaia A, Trombetta B, Bellusci G, Myres N M, Novelletto A, Cruciani F, (2014).
An Unbiased Resource of Novel SNP Markers Provides a New Chronology for the Human Y Chromosome and Reveals a Deep Phylogenetic Structure in Africa, Genome Research, Vol. doi:10.1101/gr.160788.113.
A, B
Semino O, Santachiara-Benerecetti A S, Falaschi F, Cavalli-Sforza L L, Underhill P A, (2002).
Ethiopians and Khoisan Share the Deepest Clades of the Human Y-Chromosome Phylogeny. (pdf) American Journal of Human Genetics, 70:265-268.
A, B, E, F, G, J, K, R
Semino O, Magri C, Benuzzi G, Lin A A, Al-Zahery N, Battaglia V, Maccioni L, Triantaphyllidis C, Shen P, Oefner P J, Zhivotovsky L A, King R, Torroni A, Cavalli-Sforza L L, Underhill P A, Santachiara-Benerecetti A S, (2004).
Origin, Diffusion, and Differentiation of Y-Chromosome Haplogroups E and J: Inferences on the Neolithization of Europe and Later Migratory Events in the Mediterranean Area. (pdf) American Journal of Human Genetics, 74:1023-1034.
E, J
Sengupta S, Zhivotovsky L A, King R, Mehdi S Q, Edmonds C A, Chow C-A T, Lin A A Mitra M, Sil S K, Ramesh A, Rani M V U, Thakur C M, Cavalli-Sforza L L, Majumder P P, Underhill P A, (2006).
Polarity and Temporality of High Resolution Y-chromosome Distributions in India Identify Both Indigenous and Exogenous Expansions and Reveal Minor Genetic Influence of Central Asian Pastoralists. (pdf) American Journal of Human Genetics, 78:202-221.
C, D, E, F, G, H, J, K, L, N, O, R, T
Sharma S, Rai E, Sharma P, Jena M, Singh W, Darvishi K, Bhat A K, Bhanwer A J S, Tiwari P K, Bamezai R N K, (2009).
The Indian Origin of Paternal Haplogroup R1a1 Substantiates the Autochthonous Origin of Brahmins and the Caste SystemOrigin of Paternal Haplogroup R1a1. (abstract) Journal of Human Genetics, 54:47-55.
C, R
Shen P, Lavi T, Kisivild 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. (pdf) Human Mutation, 24:248-260.
A, E, F, G, J, K, L, O, P, Q, R, T
Shi H, Zhong H, Peng Y, Dong Y-L, Qi X-B. Zhang F, Liu L-F, Tan S-J, Ma R Z, Xiao C-J, Wells R S, Jin L, Su B (2008).
Y-Chromosome Evidence of Earliest Modern Human Settlement in East Asia and Multiple Origins of Tibetan and Japanese Populations. (abstract) BMC Biology 2008, 6:45.
Shi H, Dong Y, Wen B, Xiao C, Underhill P, Shen P, Chakraborty R, Jin L, Su B, (2005).
Y-Chromosome Evidence of Southern Origin of the East Asian-Specific Haplogroup O3-M122. (aabstract) American Journal of Human Genetics. 77:408-419.
Shi Yan, Chuan-Chao Wang, Hui Li, Shi-Lin Li, Li Jin and The Genographic Consortium, (2011).
An Updated Tree of Y-chromosome Haplogroup O and Revised Phylogenetic Positions of Mutations P164 and PK4. European Journal of Human Genetics advance online publication 20 April 2011; doi: 10.1038/ejhg.2011.64.
Shou W-H, Qiao E-F, Wei C-Y, Dong Y-L, Tan S-J, Shi H, Tang W R, Xiao C-J, (2010).
Y-Chromosome Distributions among Populations in Northwest China Identify Significant Contribution from Central Asian Pastoralists and Lesser Influence of Western Eurasians. (abstract) Journal of Human Genetics, 55: 314-22.
C, J
Sims L M, Garvey D, Ballantyne J (2006).
Differentiation of sub-populations within Y-SNP haplogroup G, (poster citation- not available online) Forensic Science Society, Autumn Conference, Wyboston, UK, November 3-5, 2006.
Sims L M, Garvey D, Ballantyne J (2009).
Improved Resolution Haplogroup G Phylogeny in the Y Chromosome, Revealed by a Set of Newly Characterized SNPs. (pdf) PLoS One, 4:6, e5792, 2009.
Sims L M, Garvey D, Ballantyne J (2007).
Sub-Populations Within the Major European and African Derived Haplogroups R1b3 and E3a Are Differentiated by Previously Phylogenetically Undefined Y-SNPs. Human Mutation: Mutation in Brief #940 (2007) Online.
E, I, R
Su B, Xiao J, Underhill P, Deka R, Zhang W, Akey J, Huang W, Shen D, Lu D, Luo J, Chu J, Tan J, Shen P, Davis R, Cavalli-Sforza L L, Chakraborty R, Xiong M, Du R, Oefner P, Chen Z, Jim L, (1999).
Y-chromosome Evidence for a Northward Migration of Modern Humans into Eastern Asia during the Last Ice Age. (pdf) American Journal of Human Genetics, 65:1718-1724.
D, F, K, O, P, Q, R, T
Tan S, Yang M, Yu H, Dong Y, Shou W, Zou J, Tang W, Guo Y, Xiao C, (2007).
Y-chromosome Polymorphisms Define the Origin of the Mang, an Isolated Population in China. Annals of Human Biology, Sep;34(5):573-581.
Thangaraj K, Singh L, Reddy A G, Rao V R, Sehgal S C, Underhill P A, Pierson M, Frame I G, Hagelberg E, (2003).
Genetic Affinities of the Andaman Islanders, a Vanishing Human Population. (pdf) Current Biology, 13:86-93.
D, K, L, O, P, T
Trombetta B, Cruciani F, Sellitto D, Scozzari R, (2011)
A New Topology of the Human Y Chromosome Haplogroup E1b1 (E-P2) Revealed through the Use of Newly Characterized Binary Polymorphisms. PLoS ONE 6(1), Online.
Underhill P A, Myres N M, Rootsi S, Chow C T, Lin A A, Otillar R P, King R, Zhivotovsky L A, Balanovsky O, Pshenichnov A, Ritchie K H, Cavalli-Sforza L L, Kivisild T, Villems R, Woodward S R, (2007b).
New Phylogenetic Relationships for Y-chromosome Haplogroup I: Reappraising its Phylogeography and Prehistory. in Rethinking the Human Evolution, Mellars P, Boyle K, Bar-Yosef O, Stringer C, Eds. McDonald Institute for Archaeological Research, Cambridge, UK, 2007, pp. 33-42. (not available online)
Underhill P A, Poznik G D, Rootsi S, Järve M, Lin A A, Wang J, Passarelli B, Kanbar J, Myres N M, King R J, Di Cristofaro J, Sahakyan H, Behar D M, Kushniarevich A, Šarac J, Šaric T, Rudan P, Pathak A K, Chaubey G, Grugni V, Semino O, Yepiskoposyan L, Bahmanimehr A, Farjadian S, Balanovsky O, Khusnutdinova E K, Herrera R J, Chiaroni J, Bustamante C D, Quake S R, Kivisild T, Villems R, (2014).
The Phylogenetic and Geographic Structure of Y-chromosome Haplogroup R1a. European Journal of Human Genetics, doi:10.1038/ejhg.2014.50.
Underhill P A, Passarino G, Lin A A, Shen P, Mirazon Lahr M, Foley R A, Oefner P J, Cavalli-Sforza, L L, (2001).
The Phylogeography of Y Chromosome Binary Haplotypes and the Origins of Modern Human Populations. (pdf) Annals of Human Genetics, 65:43-62.
Main Tree; also refers to SNPs on B, C, D, E, F, H, I, J, K, L, M, N, O, P, Q, R
Underhill P A, Myres N M, Rootsi S, Metspalu M, Zhivotovsky L A, King R J, Lin A A, Chow C-E T, Semino O, Battaglia V, Kutuev I, Jarve M, Chaubey G, Ayub Q, Mohyuddin A, Mehdi S Q, Sengupta S, Rogaev E I, Khusnutdinova E K. Pshenichnov A, Balanovsky O, Balanovka E, Jeran N, Augustin D H, Baldovid M, Herrera R J, Thangaraj K, Singh V, Singh L, Majumder P, Rudan P, Primorac D, Villems S, Kivisild T. (2009).
Separating the Post-Glacial Coancestry of European and Asian Y Chromosomes within Haplogroup R1a. (abstract) European Journal of Human Genetics, 1-6.
Underhill P A, Kisivild T, (2007a).
Use of Y Chromosome and Mitochondrial DNA Population Structure in Tracing Human Migrations. (abstract) Annual Review Genetics 2007 Dec 1;41:539-564.
Main Tree, C, F
Underhill P A, Shen P, Lin A A, Passarino G, Yang W H, Karuffman E, Bonne-Tamir B, Bertranpetit J, Francalacci P, Ibrahim M, Jenkins T, Kidd J R, Mehdi S Q, Seielstad M T, Wells R S, Piazza A, Davis R W, Feldman M W, Cavalli-Sforza L L, Oerner P J, (2000).
Y Chromosome Sequence Variation and the History of Human Populations. (pdf) Nature Genetics, 26: 358-361.
Main Tree; also refers to SNPs on
Valone P M, Butler, J M, (2004)
Y SNP Typing of African-American and Caucasian Samples Using Allele-Specific Hybridization and Primer Extension. (pdf) Journal of Forensic Science, 49:4.
A, B, E, G, R
Wang C-C, Yan S, Qin Z-D, Lu Y, Ding Q-L, Wei L-H, Li S-L, Yang Y-J, Jin L, Li H, The Genographic Consortium (2003)
Late Neolithic Expansion of Ancient Chinese Revealed by Y chromosome Haplogroup O3a1c-002611. (abstract) Journal of Systematics and Evolution, 51:3.
Wang C-C, Li H, (2013)
Discovery of Phylogenetic Relevant Y-chromosome Variants in 1000 Genomes Project Data. Quantitative Biology, arXiv:1310.6590.
Y-DNA Tree Trunk
Wang C-C, Li H, (2014)
Inferring Human History in East Asia from Y Chromosomes. Investigative Genetics, doi: 10.1186/2041-2223-4-11.
N, O
Wei W, Ayub Q, Chen Y, McCarthy S, Hou Y, Carbone I, Xue Y, Tyler-Smith C. (2013).
A Calibrated Human Y-Chromosomal Phylogeny Based on Resequencing. Genome Research, 23(2): 388-95, 2013.
Xue F, Wang Y, Xu S, Zhang F, Wen B, Wu X, Lu M, Deka R, Quian J, Jin L, (2008)
A Spatial Analysis of Genetic Structure of Human Populations in China Reveals Distinct Difference between Maternal and Paternal Lineages. European Journal of Human Genetics, 16:705-17.
C, D, F, K, O, P
Xue Y, Zerjal T, Bao W, Zhu S, Shu Q, Xu J, Du R, Fu S, Li P, Hurles M, Yang H and Tyler-Smith C. (2006)
Male Demography in East Asia: A North-South Contrast in Human Population Expansion Times. (abstract) Genetics, 172:2431-2439.
Y Chromosome Consortium (YCC), (2002).
A Nomenclature System for the Tree of Human Y-Chromosomal Binary Haplogroups. Genome Research, 12:339-348.
Main Tree; also refers to SNPs on A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R
Zalloua P, Platt D, El Sibai M, Khalife J, Makhoul N, Haber M, Xue Y, Izaabel H, Bosch E, Adams S, Arroy E, Lopez-Parra A, Aler M, Picornell A, Ramon M, Jobling M, Comas D, Bertranpetit J, Wells R, Tyler-Smith C, Genographic Consortium. (2008).
Identifying Genetic Traces of Historic Expansions: Phoenician Footprints in the Mediterranean, American Journal of Human Genetics, 83: 633-42.
G, J
Zalloua P A, Xue Y, Khalife1 J, Makhoul1 N, Debiane1 L, Platt D E , Royyuru A K, Herrera R J, Hernanz D F S, Blue-Smith J, Wells R S, Comas D, Bertranpetit J, Tyler-Smith C. (2008)
Y Chromosome Diversity in Lebanon is Structured by Recent Historical Events. (abstract) The American Journal of Human Genetics, Volume 82, Issue 4, 873-882, 28 March 2008.
J, R
Zhao Z, Khan F, Borkar M, Herrera R, Agrawal S, (2009)
Presence of Three Different Paternal Lineages among North Indians: A Study of 560 Y Chromosomes. (abstract) Annals of Human Biology, 36(1):46-59.
C, E, F, G, H, J, L, O, R
Zhong H, Shi H, Qi X-B, Duan Z-Y, Tan P-P, Jim L, Su B, Ma R Z, (2011)
Extended Y-chromosome Investigation Suggests Post-Glacial Migrations of Modern Humans into East Asia via the Northern Route. Molecular Biology, 28(1):717-727.
C, D, N, O
Zhong H, Shi H, Qi X-B, Xiao C-J, Jin L, Ma R Z, Su B, (2010)
Global Distribution of Y-Chromosome Haplogroup C Reveals the Prehistoric Migration Routes of African Exodus and Early Settlement in East Asia. (abstract) Journal of Human Genetics, 55(7):428-35.
Zhou R, (2008)
Origin and Evolution of Two Yuger Sub-Clans in Northwest China: A Case Study in Paternal Genetic Landscape. (abstract) Annals of Human Biology, 35(2):198-211.

Additional Older Papers: Haplogroup(s)
Hurles ME, Veitia R, Arroyo E, Armenteros M, Bertranpetit J, Perez-Lezaun A, Bosch E, Shlumukova M, Cambon-Thomsen A, McElreavey K, Lopez De Munain A, Rohl A, Wilson IJ, Singh L, Pandya A, Santos FR, Tyler-Smith C, Jobling MA, (1999).
Recent Male-mediated Gene Flow over a Linguistic Barrier in Iberia, Suggested by Analysis of a Y-chromosomal DNA Polymorphism. American Journal of Human Genetics, Nov;65(5):1437-48.
Jobling M, Samara, V, Pandya A, Fretwell N, Bernasconi B, Mitchell R J, Gerelsaikhan T, Dashnyam B, Sajamtila A, Salo P J, Nakahori Y, Disteche C M, Thangaraj K, Singh L, Crawford M H, Tyler Smith C, (1996).
Recurrent Duplication and Deletion Polymorphisms on the Long Arm of the Y Chromosome in Normal Males. Human Molecular Genetics, Vol 5, No. 11, 1767-1775.
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. American Journal of Human Genetics, 2000 Dec;67(6):1526-43.
Semino O, Passarino G, Oefner P J, Lin A A, Abruzova S, Beckman L E, De Benedictis G, Francalacci P, Kouvatsi A, Limborska S, Marcikiae M, Mika A, Mika B, Primorac D, Santachiara-Benerecetti A S, Cavalli-Sforza L L, Underhill P. (2000).
The Genetic Legacy of Paleolithic Homo Sapiens Sapiens in Extant Europeans. (pdf) Science, V290:1155-1159.
Underhill PA, Jin L, Lin AA, Mehdi SQ, Jenkins T, Vollrath D, Davis RW, Cavalli-Sforza LL, Oefner PJ. (1997).
Detection of Numerous Y Chromosome Biallelic Polymorphisms by Denaturing High-performance Liquid Chromatography. (Abstract) Genome Research, 7(10):996-1005.
Wells R S, Yuldasheva N, Ruzibakiev R, Underhill P A, Evseeva I, Blue-Smith J, Jim L, Su B, Pitchappan R, Shanmuglakshmi S, Balakrisnan K, Read M, Pearson N M, Zerjal T, Webster M T, Zholoshvili I, Jamarjashvili E. Gambarov S, Nikbin B, Dostiev A, Aknazarov O, Zalloua P, Tsoy I, Kitaev M, Mirrakhimov M, Chariev A, Bodmer W, F. (2001).
The Eurasian Heartland: A Continental Perspective on Y-chromosome Diversity. PNAS, Vol. 98; 18:10244-10249.
Zerjal Zerjal T, Dashnyam B, Pandya A, Kayser M, Roewer L, Santos FR, Schiefenhovel W, Fretwell N, Jobling MA, Harihara S, Shimizu K, Semjidmaa D, Sajantila A, Salo P, Crawford MH, Ginter EK, Evgrafov OV, Tyler-Smith C, (1997).
Genetic Relationships of Asians and Northern Europeans, Revealed by Y-chromosomal DNA Analysis. American Journal of Human Genetics, 1997 May;60(5):1174-83.

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