Haplogroup R1a (Y-DNA)

Infobox haplogroup
name =R1a


origin-date =15,000 years BP
origin-place =East Iran or Pakistan or North India or Western Caucasus or Ukraine
ancestor =Haplogroup R1
descendants =
mutations =SRY-1532, M17
members =Ishkashimi 68%, Tajik/Khojant 64%, Sorbs 63%, Kyrgyz 63%, Hungarians 20.4%-60%, Poles 56%, Ukrainians 41.5%-54%, Altayans 38%-53%, Russians 47%, Pashtuns 45%, Iranians 35%, Belorussians 39%-46%, North Indians 40%-72%
FTDNA = http://www.familytreedna.com/public/R1aY%2DHaplogroup/A subclade of R1, R1a is a Y-chromosome haplogroup found at high frequency in the extreme north of India among the Kashmiri Pandits (72%) [The Autochthonous Origin and a Tribal Link of Indian Brahmins: Evaluation Through Molecular Genetic Markers, by S. Sharma (1,2), E. Rai (1,2), S. Singh (1,2), P.R. Sharma (1,3), A.K. Bhat (1), K. Darvishi (1), A.J.S. Bhanwer (2), P.K. Tiwari (3), R.N.K. Bamezai (1) 1) NCAHG, SLS, JNU, New delhi; 2) Department of Human Genetics, GNDU, Amritsar; 3) Centre for Genomics, SOS zoology, JU, Gwalior, Page 273 (1344/T), Published in THE AMERICAN SOCIETY OF HUMAN GENETICS 57th Annual Meeting, October 23–27, 2007, San Diego, California] , and more than 40% from the Czech Republic across to the Altai Mountains in Siberia and south throughout Central Asia.Harvcoltxt|Wells|2002]

R1a arose 15,000 years ago in the vicinity of Ukraine, expanding from either the Ukrainian LGM refuge following the end of the last ice age, or from the Pontic-Caspian steppe as a result of the Kurgan migrations.Harvcoltxt|Semino et al.|2000] Harvcoltxt|Wells et al.|2001] Harvcoltxt|Passarino et al.|2002] . But some studies question these earlier findings and claim that R1a lineages may have their origins in North India [Sengupta et al. (2006) Am J Hum Genet. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1380230&rendertype=abstract] [ Sahoo et al. (2006) Proc. Natl. Acad. Sci, USA. http://www.pnas.org/cgi/content/abstract/103/4/843] [ S. Sharma et al. (2007) American Society of Human Genetics meeting. http://www.ashg.org/genetics/ashg/annmeet/2007/call/abstractbook.pdf ] . The expansion of R1a, R2 and J2 has been associated with the spread of the Indo-European languages.

Origins

Although in south east Europe the R1a haplogroup occurs at just 16% frequency, high-resolution Y chromosome analysis by Harvcoltxt|Pericic et al.|2005 shows a maximum diversity of R1a STR variance among mainland Croatians and Bosnians. At the current resolution level the influence of gene flow to this effect is not fully understood:quote|At least three major episodes of gene flow might have enhanced R1a variance in the region: early post-LGM recolonizations expanding from the refugium in Ukraine, migrations from northern Pontic steppe between 3000 and 1000 B.C., as well as possibly massive Slavic migration from A.D. 5th to 7th centuries. The gene reach maximum distribution frequencies in Poland and in the Ukraine.

Kivisild et al. (2003) suggested that southern and western Asia might be the source of R1 and R1a differentiation. [http://www.ebc.ee/EVOLUTSIOON/publications/Kivisild2003b.pdf] The Genetic Heritage of the Earliest Settlers Persists Both in Indian Tribal and Caste Populations - Kivisild et al., Am. J. Hum. Genet. 72:p.313–332, 2003]

Earlier, Spencer Wells, director of the Genographic Project at the National Geographic Society, identified southern Russia/Ukraine as the likely origin of R1a (as identified by genetic marker M17) on the basis of both microsatellite diversity "and" frequency distribution.

Microsatellite diversity is greatest in southern Russia and Ukraine, suggesting that it arose there.

The current distribution of the M17 haplotype is likely to represent traces of an ancient population migration originating in southern Russia/Ukraine, where M17 is found at high frequency(>50%).

Harvcoltxt|Wells et al.|2001 support spread of R1a with the expansion of the Kurgan people around 3,000 B.C., which may have been driven by the domestication of the horse, which also took place in southern Russia/Ukraine at about the same time:

Harvcoltxt|Passarino et al.|2002 support the Ukrainian LGM refuge scenario, that R1a expanded from the area of the Dniepr-Don Valley in Ukraine between 13 000 and 7600 years ago, after the Last Glacial Maximum receded.

Harvcoltxt|Semino et al.|2000 propose a synthesis of these two explanations, suggesting that the spread of R1a from a point of origin in Ukraine following the Last Glacial Maximum may have been magnified by the expansion of males from the Kurgan culture area of present-day southern Ukraine, where according to Gimbutas proposals [M. Gimbutas, in Indo-European and Indo-Europeans, G. Cardona, H. M. Hoenigswald, A. M. Senn, Eds. (Univ. of Pennsylvania Press, Philadelphia, PA, 1970),pp. 155-195.] Indo-European languages spread from. Within this context, the study also reminds the existence of an alternative hypothesis proposed on the basis of archeological data, [C. Renfrew, Archaeology and Language; the Puzzle of Indo-European Origin (Jonathan Cape, London, 1987).] pointing to a Middle Eastern origin of the language family instead (see Urheimat hypotheses).

Investigation of SNP and STR markers in the Czech Republic, however, that focus on frequently related to diversity occurring within subgroup R1a1 (and two other prominent YDNA groupings), confirmed that the results are compatible with a presence of the gene "during or soon after the LGM". Without any reference to Kurgan invasions, the Czech population appears to be influenced though, to a very moderate extent, by genetic inputs (E3b, J2) from outside Europe in the post-Neolithic and historical times. Population growth beginning in the first millennium B.C. was detected and found characteristic for a gene pool that already contained R1a1, next to I-M170 and P*(xR1a1). [Quote: "On the whole, in this scheme Hg P-DYS257*(xR1a) is relatively ill-defined"] The overall diversity suggests a rapid demographic expansion beginning about 60 to 80 generations ago, which would equate to about 1500 years ago (approx. 500 AD) to 2000 years ago (approx. 1 AD) with a generation time of 25 years. Similar results have been found in Lithuania. [http://vetinari.sitesled.com/czech.pdf] F. Luca et al. - Y-chromosomal variation in the Czech Republic, 2006, American Journal of Physical Anthropology]

ubclades

*R1a (SRY1532)
**R1a1 (M17, M198) "Typical of Eastern Europeans, Central Asians, and South Asians"
***R1a1a (M56) "Found in a significant minority of people of Eastern Europe"
***R1a1b (M157) "Found at low frequency in Scotland, Ireland and France"
***R1a1c (M64.2, M87, M204) "Found at low frequency in Scotland and Ireland"
***R1a1*
**R1a*

Distribution

R1a is "present at high frequency (40 per cent plus) from the Czech Republic across to the Altai Mountains in Siberia and south throughout Central Asia." To the east, this gene found its way as far as Eastern Siberia, with considerable concentrations in Kamchatka and Chukotka, and it is possible that the gene even entered the Americas by this route. [The Dual Origin and Siberian Affinities of Native American - Jeffrey T. Lell et al [http://hpgl.stanford.edu/publications/AJHG_2002_v70_p192-206.pdf] ]

The modern population of Ukraine has the highest level of diversity of the gene making it the likeliest location of its origin. [Harvcoltxt|Passarino et al.|2001] [http://mbe.oxfordjournals.org/content/vol22/issue10/images/large/molbiolevolmsi185f05_ht.jpeg this map] Harvcoltxt|Pericic et al.|2005 Haplogroup frequency data in [http://mbe.oxfordjournals.org/cgi/content/full/22/10/1964/TBL1 table 1] ] Even in South Eastern Europe (not a major concentration of R1a1) microsatellite networks of major Y chromosomal lineages show high diveristy of R1a1 [http://mbe.oxfordjournals.org/content/vol22/issue10/images/large/molbiolevolmsi185f08_ht.jpeg (graph C)] . The variance cluster in South Eastern Europe (SEE) is located in the Republic of Macedonia.Fact|date=June 2008

Europe

In Europe, R1a is found primarily in the eastern part of the continent, with the highest frequencies among the Sorbs (63.39%), Poles (56.4%), , Russians (50.0%) [ [http://www.ajhg.org/AJHG/fulltext/S0002-9297(07)00025-0 Oleg Balanovsky. Two Sources of the Russian Patrilineal Heritage in Their Eurasian Context] ] and Ukrainians (54.0%). Harvcoltxt|Behar et al.|2003] An early study reported an R1a frequency of 60.0% among a sample of 45 Hungarians, but a more recent study found haplogroup R1a Y-DNA in only 20.4% of a sample of 113 Hungarians. [Kristiina Tambets et al., "The Western and Eastern Roots of the Saami—the Story of Genetic 'Outliers' Told by Mitochondrial DNA and Y Chromosomes," "American Journal of Human Genetics" 74:661–682, 2004.] The two main directional components of the spread are consistent with an East to West migration as well as a radial spread from the Balkans.Fact|date=March 2008

Harvcoltxt|Pericic et al.|2005 suggest three possible explanations for the distribution of R1a variation:

It is likely that Vikings settling in Britain and Ireland carried the the R1a lineage, which accounts for the presence of the haplogroup on those islands.Citation | author=Capelli et al. | year=2003 | title=A Y chromosome census of the British Isles | periodical=Current Biology | volume=13 | issue=11 | pages=979–84 | id=PMID 12781138 | url=http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRT-48PV5SH-12&_user=10&_coverDate=05%2F27%2F2003&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=0eb0c8ff85bde2ebc2ef136619f57e7a. ] cite web | last = Garvey | first = D | title = Y Haplogroup R1a1 | url = http://freepages.genealogy.rootsweb.com/%7Edgarvey/DNA/hg/YCC_R1a1.html | accessdate = 2007-04-23]

Central Asia

Exceptionally high frequencies of M17 are found among the Ishkashimi (68%), the Tajik population of Khojant (64%), and the Kyrgyz (63%), but are likely "due to drift, as these populations are less diverse, and are characterized by relatively small numbers of individuals living in isolated mountain valleys." (The frequency of the Tajik/Dushanbe population is, at 19%, far lower than the 64% frequency of the Tajik/Khojant population.)

Haplogroup R1a is also common among Mongolic- and Turkic-speaking populations of Northwestern China, such as the Bonan, Dongxiang, Salar, and Uyghur peoples. [Wei Wang, Cheryl Wise, Tom Baric, Michael L. Black and Alan H. Bittles, "The origins and genetic structure of three co-resident Chinese Muslim populations: the Salar, Bo'an and Dongxiang," "Human Genetics" (2003)] [Ruixia Zhou, Lizhe An, Xunling Wang, Wei Shao, Gonghua Lin, Weiping Yu, Lin Yi, Shijian Xu, Jiujin Xu and Xiaodong Xie, "Testing the hypothesis of an ancient Roman soldier origin of the Liqian people in northwest China: a Y-chromosome perspective," "Journal of Human Genetics", Volume 52, Number 7 / July, 2007 [http://www.springerlink.com/content/h715lv1315473n16/] ]

Iran

The gene has proven to be a "diagnostic Indo-Iranian marker," and "it is possible to represent traces of an ancient population migration originating in southern Russia/Ukraine," where it may have been driven by the domestication of the horse around 3,000 B.C.; its distribution and age are "consistent with the inferred movements of these people, who left a clear pattern of archaeological remains known as the Kurgan culture, and are thought to have spoken an early Indo-European language".

The frequency of R1a1 in western Iran, as in the Middle East, is only 5% to 10%, but in eastern Iran, the frequency of R1a1 is around 35%.cite web|url= https://www3.nationalgeographic.com/genographic/atlas.html|title= The Genographic Project|accessdate= 2008-03-10|publisher= National Geographic Society|quote= In India, around 35 percent of the men in Hindi-speaking populations carry the "M17" marker, whereas the frequency in neighboring communities of Dravidian speakers is only about ten percent. This distribution adds weight to linguistic and archaeological evidence that a large migration from the Asian steppes into India occurred within the last 10,000 years

The "M17" marker is found in only five to ten percent of Middle Eastern men. This is true even in (some) Iranian populations where Persian, a major Indo-European language, is spoken. Despite the low frequency, the distribution of men carrying the "M17" marker in Iran provides a striking example of how climate conditions, the spread of language, and the ability to identify specific markers can combine to tell the story of the migration patterns of individual genetic lineages. In the western part of the country, descendants of the Indo-European clan are few, encompassing perhaps five to ten percent of the men. However, on the eastern side, around 35 percent of the men carry the "M17" marker. This distribution suggests that the great Iranian deserts presented a formidable barrier and prevented much interaction between the two groups.] Harvcoltxt|Wells et al.|2001 suggest that the deserts of central Iran acted as "significant barriers to gene flow," and propose two possibilities:

Harvcoltxt|Kivisild et al.|2003 on the other hand "suggests that southern and western Asia might be the source of this haplogroup":

India

:"Further information: Genetics and archaeogenetics of South Asia

In a seminal work titled The Real Eve: Modern Man's Journey out of Africa (New York: Carroll and Graf Publishers, 2003), the prominent Oxford University scholar Stephen Oppenheimer concludes that South Asia is logically the ultimate origin of M17 and his ancestors.He observes:

In the "Peopling of South Asia: investigating the caste-tribe continuum in India", Chaubey G, Metspalu M, Kivisild T. et al arrive at the conclusion that both caste and tribal populations are autochthonous to India:"Molecular studies and archaeological record are both largely consistent with autochthonous differentiation of the genetic structure of the caste and tribal populations in South Asia. High level of endogamy created by numerous social boundaries within and between castes and tribes, along with the influence of several evolutionary forces such as genetic drift, fragmentation and long-term isolation, has kept the Indian populations diverse and distant from each other as well as from other continental populations."(Bioessays Jan 2007)

Recent studies suggest that R1a*, ancestral clade to Hg R1a1 arose in India. A study by S.Sharma et al published in the ASHG Abstracts 2007 screened 621 Y-chromosomes (of Brahmins, occupying upper most caste position and Dalits and Tribals with the lower most positions in the Indian caste hierarchical system) with fifty-five Y-chromosomal binary markers and Y-microsatellite markers and compiled a data set of 2809 Y-chromosomes (681 Bamins, 2128 Tribals and Dalits) for conclusions. Overall, no consistent difference was observed in Y-haplogroups distribution between Bamins, Dalits and Tribals, except for some differences confined to a given geographical region. The widespread distribution and high frequency across Eurasia and Central Asia of R1a1* as well as scanty representation of its ancestral (R*, R1* and R1a*) and derived lineages across the region has kept the origin of this haplogroup unresolved. The analyses of a pooled dataset of 530 Indians, 224 Pakistanis and 276 Central Asians and Eurasians,bearing R1a1* haplogroup resolved the controversy of origin of R1a1*. The conclusion was drawn on the basis of: i) presence of this haplogroup in many of the tribal populations such as, Saharia (present study) and Chenchu tribe in high frequency, ii) the highest ever reported presence of R1a* (ancestral haplogroup of R1a1*) in Kashmiri Pandits and Saharia tribe, and iii) associated averaged phylogenetic ages of R1a* (~18,478 years) and R1a1* (~13,768 years) in India.

However, Studies of India scholars showed the R1a lineage forms around 35–45% among all the castes in North Indian population (Namita Mukherjee et al. 2001) and the Badagas of the Nilgiris making the association with the Brahmin caste more vague. A further study (Saha et al 2005)cite journal | last = Saha | first = A | coauthors = Sharma S, Bhat A, Pandit A, Bamezai R | title = Genetic affinity among five different population groups in India reflecting a Y-chromosome gene flow | journal = J. Hum. Genet. | year = 2005 | volume = 50 | issue = 1 | pages = 49–51 | id = PMID 15611834] examined R1a1 in South Indian tribals and Dravidian population groups more closely, and questioned the concept of its Indo-Iranian origin. Most recently Sengupta et al. (2006)cite journal | last = Sengupta | first = S | coauthors = Zhivotovsky LA, King R, Mehdi SQ, Edmonds CA, Chow CE, Lin AA, Mitra M, Sil SK, Ramesh A, Usha Rani MV, Thakur CM, Cavalli-Sforza LL, Majumder PP, Underhill PA | title = 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 | url = http://www.journals.uchicago.edu/AJHG/journal/issues/v78n2/42812/42812.html | journal = Am. J. Hum. Genet. | year = 2006 | volume = 78 | issue = 2 | pages = 202–21 | id = PMID 16400607] have confirmed R1a's diverse presence including even Indian tribal and lower castes (the so-called untouchables) and populations not part of the caste system. From the diversity and distinctiveness of microsatellite Y-STR variation they conclude that there must have been an independent R1a1 population in India dating back to a much earlier expansion than the Indo-Aryan migration. Sengupta concludes saying North India including the Indus Valley contributed R1a1-M17 chromosomes to both the Central Asian and South Asian tribes much before the Indo-European event.

The pattern of clustering does not support the model that the primary source of the R1a1-M17 chromosomes in India was Central Asia or the Indus Valley via Indo-European speakers. [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 - Sanghamitra Sengupta et al [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1380230] 2005, by The American Society of Human Genetics]

According to Sengupta et al. (table 5), R1* is virtually absent in Southeast and East Asia.

Haplotypes

Modal

The "Eastern European" Y-DNA-R1a Modal Haplotype can be found in Poland, Lithuania, Belarus and Ukraine. It has spread westwards into Germany, Bohemia, Moravia, Slovakia and Hungary. Ysearch: [http://www.ysearch.org/search_results.asp?uid=ANJNY&min_markers=12&mismatch_type=absolute&mismatches_max=2&mismatches_sliding_starting_marker=8 ANJNY]

Ysearch: [http://www.ysearch.org/search_results.asp?uid=YS495&min_markers=12&mismatch_type=absolute&mismatches_max=2&mismatches_sliding_starting_marker=8 YS495]

* Tõnu Trubetsky the descendant of Nikita Trubetskoy

Ysearch: [http://www.ysearch.org/search_results.asp?uid=WUZG2&min_markers=12&mismatch_type=absolute&mismatches_max=2&mismatches_sliding_starting_marker=8 WUZG2]

* Anderson Cooper also belongs to Y-DNA haplogroup Haplogroup R1a. [http://www.isogg.org/famoushg.htm] , ISOGG]

Frequency

R1a frequency is expressed as percentage of population samples.

Europe