Haplogroup R (Y-DNA) - Wikipedia, the Free Encyclopedia Page 1 of 9

Total Page:16

File Type:pdf, Size:1020Kb

Haplogroup R (Y-DNA) - Wikipedia, the Free Encyclopedia Page 1 of 9 Haplogroup R (Y-DNA) - Wikipedia, the free encyclopedia Page 1 of 9 Haplogroup R (Y-DNA) From Wikipedia, the free encyclopedia In human genetics, haplogroup R is a Y- Haplogroup R chromosome DNA haplogroup common throughout West Eurasia. It is a subgroup of haplogroup P and is defined by the M207 mutation. Contents ■ 1 Origins ■ 2 Subclades ■ 3 Distribution ■ 4 Subclades ■ 4.1 Paragroup R* ■ 4.2 R1 ■ 4.2.1 R1* ■ 4.2.2 R1a Possible time of 35,000-40,000 ago years [1] [2] ■ 4.2.3 R1b origin ■ 4.3 R2 ■ 4.3.1 R2* Possible place of Central Asia or Middle east ■ 4.3.2 R2a origin ■ 5 Tree Ancestor P which origin is belived to be in west ■ 6 Notes central Asia ■ 7 See also ■ 8 References Descendants R*, R1, R2 ■ 9 External links Defining R = M207 (UTY2), P224, P227, P229, mutations P232, P280, P285, S4, S8, S9 and V45. [3] Origins :R1 = M173 ::R1a = L62, L63 This haplogroup is believed to have arisen ::R1b = M342 around in the Upper Paleolithic period :R2 = M479 [4] (35,000-40,000 years ago), suggests that ::R2a = L266, M124, P249, and P267. central and western Asia might be the source of this haplogroup: "Given the geographic spread and STR diversities of sister clades R1 and R2, the latter of which is restricted to India, Pakistan, Iran, and southern central Asia, it is possible that western Asia were the source for R1 and R1a differentiation." Subclades Haplogroup R Paragroup R* http://en.wikipedia.org/wiki/Haplogroup_R_(Y-DNA) 5/23/2011 Haplogroup R (Y-DNA) - Wikipedia, the free encyclopedia Page 2 of 9 Paragroup R1* Paragroup R1a* Haplogroup R1a Haplogroup R1 Haplogroup R1a1 Paragroup R1b* Haplogroup R1b Haplogroup R1b1 Paragroup R2* Haplogroup R2 Paragroup R2a* Haplogroup R2a Haplogroup R2a1 Distribution Y-haplogroup R is found throughout all continents, but is fairly common throughout Europe, South Asia and Central Asia. In these regions the distribution is markedly different for the two major subclades R1a and R1b. It is important in Native Americans and it also occurs in Caucasus, Near East, West China, Siberia and some parts of Africa. Small frequencies are found in Malaysia, Indonesia, Philippines, Korea and Indigenous Australians.[5] Subclades Paragroup R* Y-chromosomes which possess the marker M207 (which defines Haplogroup R), but neither of the markers for its subgroups, are categorised as belonging to group R*. However, R* is exceedingly rare. According to Firasat et al. (2007), R* has been found in 10.3% (10/97) of a sample of Burusho, 6.8% (3/44) of a sample of Kalash, and 1.0% (1/96) of a sample of Pashtuns from northern Pakistan in addition to 0.63% (4/638) of an ethnically mixed Pakistani sample[.6] Kivisild et al. (2003) have reported finding R* in 3.4% (1/29) of a sample of Indians from Gujarat.[7] There is also a significant sample of RxR1 from Chad [8]. R1 http://en.wikipedia.org/wiki/Haplogroup_R_(Y-DNA) 5/23/2011 Haplogroup R (Y-DNA) - Wikipedia, the free encyclopedia Page 3 of 9 Main article: Haplogroup R1 (Y-DNA) The majority of members of haplogroup R belong to its subgroup R1, defined by marker M173. R1 is very common throughout Europe and western Eurasia in the form of its subclades R1a1a-M17 and R1b1b2-M269.[11][12] R1 is the second most important haplogroup in Indigenous peoples of the Americas following haplogroup Q, and spreads Spread of Haplogroup R in Native populations. The presence specially in Algonquian peoples from United of R1 in the American continent is still uncertain and it is [9] States and Canada. probably the result of recent European admixture[9] or came from Siberia.[10] R1* The Haplogroup R1* is very rare. Examples have been found in Turkey, Pakistan and India, but the highest frequency so far discovered is in Iran.[13] R1a R1a is typical in populations of Eastern Europe, Indian Subcontinent and parts of Central Asia. It has a significant presence in Northern Europe , Central Europe, Iran, Altaians and Xinjiang (China) as well as in Siberia. R1a can be found in low frequencies in the Middle East, mostly in Indo-European speakers or their descendants.[14] Main article: Haplogroup R1a (Y-DNA) The highest levels of R1a (>50%) are found across the Eurasian Steppe: West Bengal Brahmins (72%), and Uttar Pradesh Brahmins, (67%) , the Ishkashimi (68%), the Tajik population of Khojant (64%), Kyrgyz (63.5%), Sorbs (63.39%), Poles (56.4%), Ukrainians (50%) and Russians (50%)[15][11][16][17]. R1a has been variously associated with: Distribution of R1a (purple) and R1b (red). ■ the re-colonization of Eurasia during the Late Glacial Maximum.[11][18] ■ the expansion of the Kurgan people from the Pontic-Caspian steppe, which is associated with the spread of the Indo-European languages.[15][11] The Modern studies for R1a1 (M17) suggest that it could have originated in South Asia.[citation needed ] It could have found its way initially from WesternI ndia (Gujarat) through Pakistan and Kashmir, then via Central Asia and Russia, before finally coming to Europe"..."as part of an archaeologically dated Paleolithic movement from east to west 30,000 years ago.[19] http://en.wikipedia.org/wiki/Haplogroup_R_(Y-DNA) 5/23/2011 Haplogroup R (Y-DNA) - Wikipedia, the free encyclopedia Page 4 of 9 R1b Main article: Haplogroup R1b (Y-DNA) Haplogroup R1b predominates in Western Europe. It can be found at high frequency in Bashkortostan (Russia).[20] Low frequency in Central Asia, Middle East, South Asia as well as North Africa. There is an isolated pocket of R1b in Sub Saharan Africa.[21] In Europe, R1b coincides with areas of Italic and Celtic influence. R1b is thought to have originated in Central Asia, the Middle East, or Anatolia. It is prolific in Western Europe, where frequencies of 70% or more have been found in populations from Ireland,[12] Spain,[11] and the Netherlands,[11] according to the Genographic Project conducted by the National Geographic Society.[22] It is also found in Bashkortostan where its frequency surpasses 84%.[20] It is also present at lower frequencies throughout Eastern Europe. [23] Although it is rare in South Asia, some populations show relatively high percentages for R1b. These include Lambadi (Andhra Pradesh) showing 37%,[24] Hazara 32%[25] and Agharia (East India) at 30%. [25] Besides these, R1b has appeared in Balochi (8%), Chenchu (2%), Makrani (5%), Newars (Nepal) (10.6%), Pallan (3.5%), Pathan (10%), Punjabi (7.6%) and West Bengalis (6.5%).[24][25][26] It is also found in North Africa where its frequency surpasses 10% in some parts of Algeria.[27] R2 Main article: Haplogroup R2 (Y-DNA) Haplogroup R2 is defined by the presence of the marker M479. R2* Paragroup is a term used in population genetics to describe lineages within a haplogroup that are not defined by any additional unique markers. They are typically represented by a nasterisk (*) placed after the main haplogroup. Y-chromosomes which are positive to the M479 SNP and negative to the M124, L266, P249, P267, and PAGES00004 SNPs, are categorized as belonging to Paragroup R2*. Paragroup R2* (M124-) is found in Pakistan North, Lisbon (Portugal), Sevilla (Andalusia, Spain), Tatars (Bashkortostan, Russia), Italy North, and Osetins South (South Caucasus). [28] R2a Main article: Haplogroup R2a (Y-DNA) http://en.wikipedia.org/wiki/Haplogroup_R_(Y-DNA) 5/23/2011 Haplogroup R (Y-DNA) - Wikipedia, the free encyclopedia Page 5 of 9 Haplogroup R2a is a subgroup of haplogroup R2. Haplogroup R2a is defined by the presence of the markers M124, L266, P249, P267, & PAGES00004. At least 90% of R2a individuals are located in the Indian sub-continent.[29] It is also reported in Caucasus and Central Asia. R2a may have arisen in southern Central Asia, and its members migrated southward as part of the second major wave of human migration into India.[30] Tree The subclades of haplogroup R with their defining mutation, according to the stratification chart published by the 2010 International Society of Genetic Genealogy (ISOGG)[3]: ■ R (M207/UTY2, P224, P227, P229, P232, P280, P285, S4, S8, S9, V45) ■ R* Found with low frequency in Iran Pakistan and Gujarat (India) ■ R1 (M173/P241, M306/S1,P225, P231, P233, P234, P236, P238, P242, P245, P286, P294) Fairly common throughout Europe, South Asia and Central Asia. It also occurs in Africa, Near East and Native americans from North America. Low frecuencies in Siberia, Malay Archipelago and Indigenous Australians ■ R1* Found at low frequency in Middle East and South Asia ■ R1a (L62/M513, L63/M511, L145/M449, L146/M420) ■ R1a* ■ R1a1 (SRY1532.2/SRY10831.2, L120/M516, L122/M448, M459) ■ R1a1* ■ R1a1a (M17, M198, M417, M512, M514, M515) Is typical in parts of Eastern Europe, Central Europe, South Asia and Central Asia. R1a1a also has a significant presence in the rest of Europe, Siberia, and the Middle East. ■ R1b (M343) ■ R1b* ■ R1b1 (P25, L278) ■ R1b1* ■ R1b1a (V88) The majority was found in northern and central Africa ■ R1b1b (P297) Spread in Europe, Caucasus and Near East ■ R1b1b1 (M73) Typical of Bashkortostan (Russia) and Hazaras (Pakistan) ■ R1b1b2 (M269, S3, S10, S13, S17, L265) Typical of populations of Western Europe and Perm region, with a moderate distribution throughout Eurasia ■ R1b1c (M335) ■ R2 (M479) ■ R2* Found in Pakistan North, Lisbon (Portugal), Sevilla (Andalusia, Spain), Tatars (Bashkortostan, Russia), Italy North, and Osetins South (South Caucasus). ■ R2a (L266, M124, P249, P267) Typical of populations of South Asia, with a moderate distribution in Central Asia and the Caucasus. Notes 1. ^ http://www.rootsweb.ancestry.com/~wellsfam/dnaproje/haplogroupR.html http://en.wikipedia.org/wiki/Haplogroup_R_(Y-DNA) 5/23/2011 Haplogroup R (Y-DNA) - Wikipedia, the free encyclopedia Page 6 of 9 2.
Recommended publications
  • Y-Chromosome and Surname Analyses for Reconstructing Past Population Structures: the Sardinian Population As a Test Case
    International Journal of Molecular Sciences Article Y-chromosome and Surname Analyses for Reconstructing Past Population Structures: The Sardinian Population as a Test Case Viola Grugni 1, Alessandro Raveane 1, Giulia Colombo 1, Carmen Nici 1, Francesca Crobu 1,2, Linda Ongaro 1,3,4, Vincenza Battaglia 1, Daria Sanna 1,5, Nadia Al-Zahery 1, Ornella Fiorani 6, Antonella Lisa 6, Luca Ferretti 1 , Alessandro Achilli 1, Anna Olivieri 1, Paolo Francalacci 7, Alberto Piazza 8, Antonio Torroni 1 and Ornella Semino 1,* 1 Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; [email protected] (V.G.); [email protected] (A.R.); [email protected] (G.C.); [email protected] (C.N.); [email protected] (F.C.); [email protected] (L.O.); [email protected] (V.B.); [email protected] (D.S.); [email protected] (N.A.-Z.); [email protected] (L.F.); [email protected] (A.A.); [email protected] (A.O.); [email protected] (A.T.) 2 Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), 09042 Monserrato, Italy 3 Estonian Biocentre, Institute of Genomics, Riia 23, 51010 Tartu, Estonia 4 Department of Evolutionary Biology, Institute of Molecular and Cell Biology, Riia 23, 51010 Tartu, Estonia 5 Dipartimento di Scienze Biomediche, Università di Sassari, 07100 Sassari, Italy 6 Istituto di Genetica Molecolare “L.L. Cavalli-Sforza”, Consiglio Nazionale delle Ricerche (CNR), 27100 Pavia, Italy; fi[email protected]
    [Show full text]
  • Germanic Origins from the Perspective of the Y-Chromosome
    Germanic Origins from the Perspective of the Y-Chromosome By Michael Robert St. Clair A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor in Philosophy in German in the Graduate Division of the University of California, Berkeley Committee in charge: Irmengard Rauch, Chair Thomas F. Shannon Montgomery Slatkin Spring 2012 Abstract Germanic Origins from the Perspective of the Y-Chromosome by Michael Robert St. Clair Doctor of Philosophy in German University of California, Berkeley Irmengard Rauch, Chair This dissertation holds that genetic data are a useful tool for evaluating contemporary models of Germanic origins. The Germanic languages are a branch of the Indo-European language family and include among their major contemporary representatives English, German, Dutch, Danish, Swedish, Norwegian and Icelandic. Historically, the search for Germanic origins has sought to determine where the Germanic languages evolved, and why the Germanic languages are similar to and different from other European languages. Both archaeological and linguist approaches have been employed in this research direction. The linguistic approach to Germanic origins is split among those who favor the Stammbaum theory and those favoring language contact theory. Stammbaum theory posits that Proto-Germanic separated from an ancestral Indo-European parent language. This theoretical approach accounts for similarities between Germanic and other Indo- European languages by posting a period of mutual development. Germanic innovations, on the other hand, occurred in isolation after separation from the parent language. Language contact theory posits that Proto-Germanic was the product of language convergence and this convergence explains features that Germanic shares with other Indo-European languages.
    [Show full text]
  • Y-Chromosome Marker S28 / U152 Haplogroup R-U152 Resource Page
    Y-Chromosome Marker S28 / U152 Haplogroup R-U152 Resource Page David K. Faux To use this page as a resource tool, click on the blue highlighted words, which will take the reader to a relevant link. How was this marker discovered? In 2005 Hinds et al. published a paper outlining the discovery of almost 1.6 million SNPs in 71 Americans by Perlegen.com, and which were deposited in the online dbSNP database. Gareth Henson noticed three SNPs that appeared to be associated with M269, what was then known as haplogroup R1b1c. Dr. James F. Wilson of EthnoAncestry developed primers for these Single Nucleotide Polymorphism (SNP) markers on the Y-chromosome, one of which was given the name of S28 (part of the S-series of SNPs developed by Dr. Wilson). Who were the first to be identified with this SNP? In testing the DNA of a number of R- M269 males (customers or officers of EthnoAncestry), two were found to be positive for S28 (U152). These were Charles Kerchner (of German descent) and David K. Faux, co- founder of EthnoAncestry (of English descent). How is this marker classified? In 2006 the International Society of Genetic Genealogists (ISOGG) developed a phylogenetic tree since the academic grouping (the Y Chromosome Consortium – YCC) set up to do this task had lapsed in 2002. They determined, with the assistance of Dr. Wilson, that the proper placement would be R1b1c10, in other words downstream of M269 the defining marker for R1b1c. Karafet et al. (2008) (including Dr. Michael Hammer of the original YCC group) published a new phylogenetic tree in the journal Genome Research.
    [Show full text]
  • Y-Chromosome Phylogeographic Analysis Of
    Y-chromosome phylogeographic analysis of the Greek-Cypriot population reveals elements consistent with Neolithic and Bronze Age settlements Konstantinos Voskarides, Stéphane Mazières, Despina Hadjipanagi, Julie Di Cristofaro, Anastasia Ignatiou, Charalambos Stefanou, Roy King, Peter Underhill, Jacques Chiaroni, Constantinos Deltas To cite this version: Konstantinos Voskarides, Stéphane Mazières, Despina Hadjipanagi, Julie Di Cristofaro, Anastasia Ignatiou, et al.. Y-chromosome phylogeographic analysis of the Greek-Cypriot population reveals ele- ments consistent with Neolithic and Bronze Age settlements. Investigative Genetics, BioMed Central, 2016, 7 (1), 10.1186/s13323-016-0032-8. hal-01273302 HAL Id: hal-01273302 https://hal.archives-ouvertes.fr/hal-01273302 Submitted on 12 Feb 2016 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Voskarides et al. Investigative Genetics (2016) 7:1 DOI 10.1186/s13323-016-0032-8 RESEARCH Open Access Y-chromosome phylogeographic analysis of the Greek-Cypriot population reveals elements consistent with Neolithic and Bronze Age settlements Konstantinos Voskarides1†, Stéphane Mazières2†, Despina Hadjipanagi1, Julie Di Cristofaro2, Anastasia Ignatiou1, Charalambos Stefanou1, Roy J. King3, Peter A. Underhill4, Jacques Chiaroni2* and Constantinos Deltas1* Abstract Background: The archeological record indicates that the permanent settlement of Cyprus began with pioneering agriculturalists circa 11,000 years before present, (ca.
    [Show full text]
  • Genetic History of Haplogroup
    Genetic History of Haplogroup R1b The genetic markers that define the ancestral history of those of us in the R1b haplogroup reach back roughly 60,000 years to the first common marker of all non-African men, M168, and follow their lineage to present day, ending with M343, the defining marker of haplogroup R1b. The migration map for R1b highlights our ancestors’ route and shows that members of this haplogroup carry the following Y-chromosome markers: M168 > M89 > M9 > M45 > M207 > M173 > M343 Today, roughly 70 percent of the men in southern England belong to haplogroup R1b. In parts of Spain and Ireland, that number exceeds 90 percent. Our Genetic Sequence Type: Y-Chromosome Haplogroup: R1b (M343) STRs DYS393: 13 DYS439: 12 DYS388: 12 DYS385a: 11 DYS19: 14 DYS389-1: 13 DYS390: 25 DYS385b: 14 DYS391: 11 DYS389-2: 16 DYS426: 12 DYS392: 13 How to Interpret Your Results Above are results from the laboratory analysis of your Y-chromosome. Your DNA was analyzed for Short Tandem Repeats (STRs), which are repeating segments of your genome that have a high mutation rate. The location on the Y chromosome of each of these markers is depicted in the image, with the number of repeats for each of your STRs presented to the right of the marker. For example, DYS19 is a repeat of TAGA, so if your DNA repeated that sequence 12 times at that location, it would appear: DYS19 12. Studying the combination of these STR lengths in your Y Chromosome allows researchers to place you in a haplogroup, which reveals the complex migratory journeys of your ancestors.
    [Show full text]
  • Admixture and Population Structure in Mexican-Mestizos Based on Paternal Lineages
    Journal of Human Genetics (2012) 57, 568–574 & 2012 The Japan Society of Human Genetics All rights reserved 1434-5161/12 $32.00 www.nature.com/jhg ORIGINAL ARTICLE Admixture and population structure in Mexican-Mestizos based on paternal lineages Gabriela Martı´nez-Corte´s1,5, Joel Salazar-Flores1, Laura Gabriela Ferna´ndez-Rodrı´guez1, Rodrigo Rubi-Castellanos1, Carmen Rodrı´guez-Loya1, Jesu´s Salvador Velarde-Fe´lix2, Jose´ Franciso Mun˜oz-Valle3, Isela Parra-Rojas4 and He´ctor Rangel-Villalobos1,5 In the nonrecombining region of the Y-chromosome, there are single-nucleotide polymorphisms (Y-SNPs) that establish haplogroups with particular geographical origins (European, African, Native American, etc.). The complex process of admixture that gave rise to the majority of the current Mexican population (B93%), known as Mestizos, can be examined with Y-SNPs to establish their paternal ancestry and population structure. We analyzed 18 Y-SNPs in 659 individuals from 10 Mexican-Mestizo populations from different regions of the country. In the total population sample, paternal ancestry was predominately European (64.9%), followed by Native American (30.8%) and African (4.2%). However, the European ancestry was prevalent in the north and west (66.7–95%) and, conversely, Native American ancestry increased in the center and southeast (37–50%), whereas the African ancestry was low and relatively homogeneous (0–8.8%). Although this paternal landscape concurs with previous studies based on genome-wide SNPs and autosomal short tandem repeats (STRs), this pattern contrasts with the maternal ancestry, mainly of Native American origin, based on maternal lineages haplogroups. In agreement with historical records, these results confirm a strong gender-biased admixture history between European males and Native American females that gave rise to Mexican-Mestizos.
    [Show full text]
  • Carriers of Mitochondrial DNA Macrohaplogroup L3 Basal Lineages Migrated Back to Africa from Asia Around 70,000 Years Ago Vicente M
    Cabrera et al. BMC Evolutionary Biology (2018) 18:98 https://doi.org/10.1186/s12862-018-1211-4 RESEARCHARTICLE Open Access Carriers of mitochondrial DNA macrohaplogroup L3 basal lineages migrated back to Africa from Asia around 70,000 years ago Vicente M. Cabrera1* , Patricia Marrero2, Khaled K. Abu-Amero3,4 and Jose M. Larruga1 Abstract Background: The main unequivocal conclusion after three decades of phylogeographic mtDNA studies is the African origin of all extant modern humans. In addition, a southern coastal route has been argued for to explain the Eurasian colonization of these African pioneers. Based on the age of macrohaplogroup L3, from which all maternal Eurasian and the majority of African lineages originated, the out-of-Africa event has been dated around 60-70 kya. On the opposite side, we have proposed a northern route through Central Asia across the Levant for that expansion and, consistent with the fossil record, we have dated it around 125 kya. To help bridge differences between the molecular and fossil record ages, in this article we assess the possibility that mtDNA macrohaplogroup L3 matured in Eurasia and returned to Africa as basal L3 lineages around 70 kya. Results: The coalescence ages of all Eurasian (M,N) and African (L3 ) lineages, both around 71 kya, are not significantly different. The oldest M and N Eurasian clades are found in southeastern Asia instead near of Africa as expected by the southern route hypothesis. The split of the Y-chromosome composite DE haplogroup is very similar to the age of mtDNA L3. An Eurasian origin and back migration to Africa has been proposed for the African Y-chromosome haplogroup E.
    [Show full text]
  • A Genetic Chronology of African Y-Chromosomes R
    Indian Journal of Fundamental and Applied Life Sciences ISSN: 2231– 6345 (Online) An Open Access, Online International Journal Available at http://www.cibtech.org/jls.htm 2017 Vol. 7 (2) April-June, pp. 24-37/Winters Research Article A GENETIC CHRONOLOGY OF AFRICAN Y-CHROMOSOMES R-V88 AND R-M269 IN AFRICA AND EURASIA *Clyde Winters Department of Archaeogenetics, Uthman dan Fodio Institute, Chicago, Illinois 60643 *Author for Correspondence ABSTRACT There is a global distribution of Y-Chromosome R-M343 subclades across the African continent. The major subclades are R-M269 and R-V88. The V88 subclade is the oldest clade to separate from R-M343. The V88 sub-clade, had relatives in Early Neolithic samples from across a wide geographic area from Iberia, eastward to Germany and Samara. This would place carriers of relatives of V88 among the Yamnaya and Bell Beaker people. Given the wide distribution of V88 and M269 in Africa and Neolithic Europe suggest that, the Bell Beaker and Yamnaya people were Africans, not Indo-Europeans, because these cultural complexes and the people who practiced these cultures originated in Africa. Keywords: Haplogroup (hg), Bell Beaker, Iberia, Yamnaya, Subclades, Megalithic INTRODUCTION The Bell Beaker culture spread from Iberia to the rest of Europe (Haak et al., 2015). The eastern Corded Ware and even earlier Yamnaya ceramic decorations are characteristic of the African “Maritime Beaker complex” that was carried from Morocco to Iberia (Turek, 2012; Winters, 2017). Because the Bell Beaker cultural complex was also present in North Africa, makes it clear Africans took R-V88 and R-M269 to Iberia and across Europe.
    [Show full text]
  • Mitochondrial DNA Diversity of Present-Day Aboriginal Australians and Implications for Human Evolution in Oceania
    Journal of Human Genetics (2016), 1–11 & 2016 The Japan Society of Human Genetics All rights reserved 1434-5161/16 www.nature.com/jhg ORIGINAL ARTICLE Mitochondrial DNA diversity of present-day Aboriginal Australians and implications for human evolution in Oceania Nano Nagle1, Kaye N Ballantyne2,3, Mannis van Oven3, Chris Tyler-Smith4, Yali Xue4, Stephen Wilcox5, Leah Wilcox1, Rust Turkalov5, Roland AH van Oorschot2, Sheila van Holst Pellekaan6,7, Theodore G Schurr8, Peter McAllister9, Lesley Williams10, Manfred Kayser3, R John Mitchell1 and The Genographic Consortium27 Aboriginal Australians are one of the more poorly studied populations from the standpoint of human evolution and genetic diversity. Thus, to investigate their genetic diversity, the possible date of their ancestors’ arrival and their relationships with neighboring populations, we analyzed mitochondrial DNA (mtDNA) diversity in a large sample of Aboriginal Australians. Selected mtDNA single-nucleotide polymorphisms and the hypervariable segment haplotypes were analyzed in 594 Aboriginal Australians drawn from locations across the continent, chiefly from regions not previously sampled. Most (~78%) samples could be assigned to mtDNA haplogroups indigenous to Australia. The indigenous haplogroups were all ancient (with estimated ages 440 000 years) and geographically widespread across the continent. The most common haplogroup was P (44%) followed by S (23%) and M42a (9%). There was some geographic structure at the haplotype level. The estimated ages of the indigenous haplogroups range from 39 000 to 55 000 years, dates that fit well with the estimated date of colonization of Australia based on archeological evidence (~47 000 years ago). The distribution of mtDNA haplogroups in Australia and New Guinea supports the hypothesis that the ancestors of Aboriginal Australians entered Sahul through at least two entry points.
    [Show full text]
  • The Enigmatic Origin of Bovine Mtdna Haplogroup R: Sporadic Interbreeding Or an Independent Event of Bos Primigenius Domestication in Italy?
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by PubMed Central The Enigmatic Origin of Bovine mtDNA Haplogroup R: Sporadic Interbreeding or an Independent Event of Bos primigenius Domestication in Italy? Silvia Bonfiglio1, Alessandro Achilli1,2, Anna Olivieri1, Riccardo Negrini3, Licia Colli3, Luigi Liotta4, Paolo Ajmone-Marsan3, Antonio Torroni1, Luca Ferretti1* 1 Dipartimento di Genetica e Microbiologia, Universita` di Pavia, Pavia, Italy, 2 Dipartimento di Biologia Cellulare e Ambientale, Universita` di Perugia, Perugia, Italy, 3 Istituto di Zootecnica, Universita` Cattolica del Sacro Cuore, Piacenza, Italy, 4 Dipartimento di Morfologia, Biochimica, Fisiologia e Produzioni Animali, Universita` di Messina, Messina, Italy Abstract Background: When domestic taurine cattle diffused from the Fertile Crescent, local wild aurochsen (Bos primigenius) were still numerous. Moreover, aurochsen and introduced cattle often coexisted for millennia, thus providing potential conditions not only for spontaneous interbreeding, but also for pastoralists to create secondary domestication centers involving local aurochs populations. Recent mitochondrial genomes analyses revealed that not all modern taurine mtDNAs belong to the shallow macro-haplogroup T of Near Eastern origin, as demonstrated by the detection of three branches (P, Q and R) radiating prior to the T node in the bovine phylogeny. These uncommon haplogroups represent excellent tools to evaluate if sporadic interbreeding or even additional events of cattle domestication occurred. Methodology: The survey of the mitochondrial DNA (mtDNA) control-region variation of 1,747 bovine samples (1,128 new and 619 from previous studies) belonging to 37 European breeds allowed the identification of 16 novel non-T mtDNAs, which after complete genome sequencing were confirmed as members of haplogroups Q and R.
    [Show full text]
  • Y-Chromosome Phylogeographic Analysis of the Greek-Cypriot
    Voskarides et al. Investigative Genetics (2016) 7:1 DOI 10.1186/s13323-016-0032-8 RESEARCH Open Access Y-chromosome phylogeographic analysis of the Greek-Cypriot population reveals elements consistent with Neolithic and Bronze Age settlements Konstantinos Voskarides1†, Stéphane Mazières2†, Despina Hadjipanagi1, Julie Di Cristofaro2, Anastasia Ignatiou1, Charalambos Stefanou1, Roy J. King3, Peter A. Underhill4, Jacques Chiaroni2* and Constantinos Deltas1* Abstract Background: The archeological record indicates that the permanent settlement of Cyprus began with pioneering agriculturalists circa 11,000 years before present, (ca. 11,000 y BP). Subsequent colonization events followed, some recognized regionally. Here, we assess the Y-chromosome structure of Cyprus in context to regional populations and correlate it to phases of prehistoric colonization. Results: Analysis of haplotypes from 574 samples showed that island-wide substructure was barely significant in a spatial analysis of molecular variance (SAMOVA). However, analyses of molecular variance (AMOVA) of haplogroups using 92 binary markers genotyped in 629 Cypriots revealed that the proportion of variance among the districts was irregularly distributed. Principal component analysis (PCA) revealed potential genetic associations of Greek-Cypriots with neighbor populations. Contrasting haplogroups in the PCA were used as surrogates of parental populations. Admixture analyses suggested that the majority of G2a-P15 and R1b-M269 components were contributed by Anatolia and Levant sources, respectively, while Greece Balkans supplied the majority of E-V13 and J2a-M67. Haplotype-based expansion times were at historical levels suggestive of recent demography. Conclusions: Analyses of Cypriot haplogroup data are consistent with two stages of prehistoric settlement. E-V13 and E-M34 are widespread, and PCA suggests sourcing them to the Balkans and Levant/Anatolia, respectively.
    [Show full text]
  • Cattle Mitogenome Variation Reveals a Post-Glacial Expansion Of
    www.nature.com/scientificreports OPEN Cattle mitogenome variation reveals a post‑glacial expansion of haplogroup P and an early incorporation into northeast Asian domestic herds Hideyuki Mannen1,4*, Takahiro Yonezawa2,4, Kako Murata1, Aoi Noda1, Fuki Kawaguchi1, Shinji Sasazaki1, Anna Olivieri3, Alessandro Achilli3 & Antonio Torroni3 Surveys of mitochondrial DNA (mtDNA) variation have shown that worldwide domestic cattle are characterized by just a few major haplogroups. Two, T and I, are common and characterize Bos taurus and Bos indicus, respectively, while the other three, P, Q and R, are rare and are found only in taurine breeds. Haplogroup P is typical of extinct European aurochs, while intriguingly modern P mtDNAs have only been found in northeast Asian cattle. These Asian P mtDNAs are extremely rare with the exception of the Japanese Shorthorn breed, where they reach a frequency of 45.9%. To shed light on the origin of this haplogroup in northeast Asian cattle, we completely sequenced 14 Japanese Shorthorn mitogenomes belonging to haplogroup P. Phylogenetic and Bayesian analyses revealed: (1) a post‑glacial expansion of aurochs carrying haplogroup P from Europe to Asia; (2) that all Asian P mtDNAs belong to a single sub‑haplogroup (P1a), so far never detected in either European or Asian aurochs remains, which was incorporated into domestic cattle of continental northeastern Asia possibly ~ 3700 years ago; and (3) that haplogroup P1a mtDNAs found in the Japanese Shorthorn breed probably reached Japan about 650 years ago from Mongolia/Russia, in agreement with historical evidence. All modern cattle derive from wild ancestral aurochs (Bos primigenius), which were distributed throughout large parts of Eurasia and Northern Africa during the Pleistocene and the early Holocene1,2.
    [Show full text]