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Haplogroup R1a
Possible time of origin	probably more recent than 18,500 years BP
Possible place of origin	Asia, probably South Asia. Other possibilities include Central Asia, Middle East, and Eastern Europe.
Ancestor	R1 (R-M173)
Descendants	R1a1a1 to R1a1a8. R-M458 being the most significant (R1a1a7 in Underhill et al. (2009)).
Defining mutations	1. M420 now defines R1a in the broadest sense. 2. Within R1a, SRY1532.2 also known as SRY10831.2, now defines R1a1, previously R1a. 3. M17 and M198 (equivalent to one another) now define R1a1a, previously R1a1, and often referred to as if equal to R1a.
Highest frequencies	Parts of Eastern Europe, Scandinavia, Central Asia, Siberia and South Asia. (See List of R1a frequency by population)

Haplogroup R1a is the phylogenetic name of a major clade of human Y-chromosome lineages. In other words, it is a way of grouping a significant part of all modern men according to a shared male-line ancestor. It is common in many parts of Eurasia and is frequently discussed in human population genetics and genetic genealogy. One sub-clade (branch) of R1a, currently designated R1a1a, is much more common than the others in all major geographical regions. R1a1a, defined by the SNP mutation M17, is particularly common in a large region extending from South Asia and Southern Siberia to Central Europe and Scandinavia.

Currently, the R1a family is defined most broadly by the SNP mutation M420. The recent discovery of M420 resulted in a reorganization of the known family tree of R1a, in particular establishing a new paragroup (designated R1a*) for lineages which are not in the R1a1 branch leading to R1a1a.

R1a and R1a1a are believed to have originated somewhere within Eurasia, most likely in the area from Eastern Europe to South Asia. The most recent studies indicate that South Asia is a more likely region of origin than Europe.

Different meanings of "R1a"

The naming system commonly used for R1a remains inconsistent in different published sources, and requires some explanation.

In 2002, the Y chromosome consortium (YCC) proposed a new naming system for haplogroups, which has now become standard. In this system, names with the format "R1" and "R1a" are "phylogenetic" names, aimed at marking positions in a family tree. Names of SNP mutations can also be used to name clades or haplogroups. For example, as M173 is currently the defining mutation of R1, R1 is also R-M173, a "mutational" clade name. When a new branching in a tree is discovered, some phylogenetic names will change, but by definition all mutational names will remain the same.

The widely occurring haplogroup defined by mutation M17 was known by various names, such as "Eu19", in the older naming systems. The 2002 YCC proposal assigned the name R1a to the haplogroup defined by mutation SRY1532.2. This included Eu19 (i.e. R-M17) as a subclade, so Eu19 was named R1a1. The discovery of M420 in 2009 has caused a reassignment of these phylogenetic names. R1a is now defined by the M420 mutation: in this updated tree, the subclade defined by SRY1532.2 has moved from R1a to R1a1, and Eu19 (R-M17) from R1a1 to R1a1a.

Phylogeny (Family Tree)

The R1a family tree now has three major levels of branching, with the largest number of defined subclades within the dominant and best known branch, R1a1a (which, as has been noted, will be found with various names; in particular, as "R1a1" in relatively recent but not the latest literature.)

Roots of R1a

R1a, distinguished by several unique markers including the M420 mutation, is a subclade of haplogroup R1, which is defined by SNP mutation M173. Besides R1a, R1 also has the subclades R1b, defined by the M343 mutation, and the paragroup R1*. There is no simple consensus concerning the places in Eurasia where R1, R1a or R1b evolved.

R1a (R-M420)

R1a, defined by the mutation M420, has two branches: R1a1, defined by the mutation SRY1532.2, which makes up the vast majority; and R1a*, the paragroup, defined as M420 positive but SRY1532.2 negative. (In the 2002 scheme, this SRY1532.2 negative minority was one part of the relatively rare group classified as the paragroup R1*.) Mutations understood to be equivalent to M420 include M449, M511, M513, L62, and L63.

Only isolated samples of the new paragroup R1a* have been found by Underhill et al., mostly in the Middle East and Caucasus: 1/121 Omanis, 2/150 Iranians, 1/164 in the United Arab Emirates, and 3/612 in Turkey. Testing of 7224 more males in 73 other Eurasian populations showed no sign of this category.

R1a1 (R-SRY1532.2)

R1a1 is currently defined by SRY1532.2, also referred to as SRY10831.2. SNP mutations understood to be always occurring with SRY1532.2 include M448, M459, and M516. This family of lineages is dominated by the very large and well-defined R1a1a branch, which is positive for M17 and M198. The paragroup R1a1* (old R1a*) is positive for the SRY1532.2 marker but lacks either the M17 or M198 markers.

The R1a1* paragroup is apparently less rare than R1* but still relatively unusual, though it has been tested in more than one survey. Underhill et al. for example report 1/51 in Norway, 3/305 in Sweden, 1/57 Greek Macedonians, 1/150 Iranians, 2/734 Ethnic Armenians, and 1/141 Kabardians. Sharma et al. (2009) also report the presence of this paraclade in India.

R1a1a (R-M17 or R-M198)

R1a1a (old R1a1) makes up the vast majority of all R1a over its entire geographic range. It is defined by SNP mutations M17 or M198, which have always appeared together in the same men so far. SNP mutations understood to be always occurring with M17 and M198 include M417, M512, M514, M515.

Currently, R1a1a has eight subclades of its own defined by mutations, but the vast majority of the incidence has not yet been categorized and is therefore in the paragroup R1a1a*.

R1a1a subclades

Currently, of the eight SNP-defined subclades of R1a1a only R1a1a7 has significant frequencies. R1a1a7 is defined by M458 and was found almost entirely in Europe, and with low frequency in Turkey and parts of the Caucasus. Its highest frequencies were found in Central and Southern Poland, particularly near the river valleys flowing northwards to the Baltic sea.

R1a1a7 has its own SNP-defined subclade, defined by the M334 marker. However this mutation was found only in one Estonian man and may define a very recently founded and small clade.

R1a1a3, defined by the M64.2, M87, and M204 SNP mutations, is apparently rare: it was found in 1 of 117 males typed in southern Iran.

R1a1a6, defined by M434, was detected in 14 people (out of 3667 people tested) all in a restricted geographical range from Pakistan to Oman. This likely reflects a recent mutation event in Pakistan.

R1a STR clusters

Genetic genealogists looking at high accuracy STR (microsattelite)haplotypes (as used in genealogy) have also identified clusters of similar within R1a1a. Such clusters equate to groups with probable common ancestry, but with no known SNP defining them yet.

Gwozdz (2009) has identified two clusters within R1a1a7 ("P" and "N"). Cluster P was originally identified by Pawlowski (2002) and apparently accounts for about 8% of Polish men, making it the most common clearly identifiable haplotype cluster in Poland. Outside of Poland it is less common. Cluster N is not concentrated in Poland, but is apparently common in many Slavic areas. Gwozdz also identified at least one large cluster of R1a1a* (not having M458), referred to as cluster K. This cluster is common in Poland but not only there.

Klyosov (2009) notes a potential clade identified by a mutation on the relatively stable STR marker DYS388 (to an unusual repeat value of 10, instead of the more common 12), noting that this "is observed in northern and western Europe, mainly in England, Ireland, Norway, and to a much lesser degree in Sweden, Denmark, Netherlands and Germany. In areas further east and south that mutation is practically absent".

Both Gwozdz and Klyosov also note frequent close STR matching between part of the Indian R1a1a population, and part of the Russian and Slavic R1a1a population, indicating apparent links between these populations in a time-frame more recent than the age of R1a1a overall.

Distribution of R1a1a (R-M17 or R-M198)

R1a has been found in high frequency at both the eastern and western ends of its core range, for example in some parts of India and Tajikistan on the one hand, and Poland on the other. Throughout all of these regions, R1a is dominated by the R1a1a (R-M17 or R-M198) sub-clade.

South Asia

In South Asia R1a1a has been observed, often with high frequency, in a number of demographic groups, in India such as the Khatri (67%); Hindus in Nepal/India (69%) and in Punjab (47%); and the Mohanna (Punjab) (71%) and Sindhi (49%) in Pakistan. It has also been found in several South Indian Dravidian-speaking tribes including the Chenchu and Valmikis of Andhra Pradesh and the Kallar of Tamil Nadu suggesting that M17 is widespread in tribal southern Indians. To the south of India, it has also been found in >10% of Sinhalese in Sri Lanka.

Europe

In Europe, R1a, again almost entirely in the R1a1a sub-clade, is found at highest levels among peoples of Eastern European descent (Sorbs, Poles, Russians and Ukrainians; 50 to 65%). In the Baltic countries R1a frequencies decrease from Lithuania (45%) to Estonia (around 30%). Levels in Hungarians have been noted between 20 and 60%

There is a significant presence in peoples of Scandinavian descent, with highest levels in Norway and Iceland, where between 20 and 30% of men are in R1a1a. Vikings and Normans may have also carried the R1a1a lineage westward; accounting for at least part of the small presence in the British Isles.

In Southern Europe R1a1a is not normally common but it is widespread. Significant levels have been found in pockets, such as in the Pas Valley in Northern Spain, areas of Venice, and Calabria in Italy. The Balkans shows lower frequencies, and significant variation between areas, for example >30% in Slovenia, Croatia and Greek Macedonia, but <10% in Albania, Kosovo and parts of Greece.

The remains of three individuals, from an archaeological site discovered in 2005 near Eulau (in Saxony-Anhalt, Germany) and dated to about 2600 BCE, tested positive for the Y-SNP marker SRY10831.2. The R1a1 clade was thus present in Europe at least 4600 years ago, and appears associated with the Corded Ware culture.

Central and Northern Asia

R1a1a frequencies vary widely between populations within central and northern parts of Eurasia, but it is found in areas including Western China and Eastern Siberia. This big variation is possibly a consequence of population bottlenecks in isolated areas and the large movements of Turco-Mongols during the historic period. For example, exceptionally high frequencies of R1a1a (R-M17 or R-M198; 50 to 70%) are found among the Ishkashimis, Khojant Tajiks, Kyrgyzs, and in several peoples of Russia's Altai Republic. Although levels are comparatively low amongst some Turkic-speaking groups (e.g. Turks, Azeris, Kazakhs, Yakuts), levels are very high in certain Turkic or Mongolic-speaking groups of Northwestern China, such as the Bonan, Dongxiang, Salar, and Uyghurs. R1a1a is also found among certain indigenous Eastern Siberians, including:Kamchatkans and Chukotkans, and peaking in Itel'man at 22%.

Middle East and Caucasus

R1a has been found in various forms, in most parts of Western Asia, in widely varying concentrations, from almost no presence in areas such as Jordan, to much higher levels in parts of Turkey and Iran.

Wells et al. (2001), noted that in the western part of the country, Iranians show low R1a1a levels, while males of eastern parts of Iran carried up to 35% R1a. Nasidze et al. (2004) found R1a in approximately 20% of Iranian males from the cities of Tehran and Isfahan. Regueiro et al. (2006), in a study of Iran, noted much higher frequencies in the south than the north.

Turkey also shows high but unevenly distributed R1a levels amongst some sub-populations. For example Nasidze et al. (2005) found relatively high levels amongst Kurds (12%) and Zazas (26%).

Further to the north of these Middle Eastern regions on the other hand, R1a levels start to increase in the Caucasus, once again in an uneven way. Several populations studied have shown no sign of R1a, while highest levels so far discovered in the region appears to belong to speakers of the Karachay-Balkar language amongst whom about one quarter of men tested so far are in haplogroup R1a1a.

Origins and hypothesized migrations of R1a1a

Most discussions purportedly of R1a origins are actually about the origins of the dominant R1a1a (R-M17 or R-M198) sub-clade. Data so far collected indicates that there two widely separated areas of high frequency, one in South Asia, around North India, and the other in Eastern Europe, around Poland and the Ukraine. The historical and prehistoric possible reasons for this are the subject of on-going discussion and attention amongst population geneticists and genetic genealogists, and are considered to be of potential interest to linguists and archaeologists also.

In 2009, several large studies of both old and new STR data concluded that while these two separate "poles of the expansion" are of similar age, South Asian R1a1a is apparently older than Eastern European R1a1a, suggesting that South Asia is the more likely locus of origin.

South Asian origin hypothesis

An increasing number of studies have found South Asia to have the highest level of diversity of Y-STR haplotype variation within R1a1a. On this basis, while several studies have concluded that the data is at least consistent with South Asia as the likely original point of dispersal, a few have actively argued for this scenario. A survey study as of December 2009, including a collation of retested Y-DNA from previous studies, makes a South Asian R1a1a origin the strongest proposal amongst the various possibilities.

Eastern European migration hypotheses

A widely cited theory proposed in 2000 that there may have been two expansions: first, R1a1a originally spreading from a Ukrainian refugium during the Late Glacial Maximum; and then, the spread being magnified by the expansion of males from the Kurgan culture. A recent survey argues that R1a1a could be old enough for this scenario, but find it more likely that it was initially in Asia even if it was in parts of Europe by approximately 11,000 years ago.

Most age estimates for R1a1a having such an early presence in Europe come from papers using the "evolutionarily effective" methodology. Researchers using this dating method therefore conclude that any Neolithic or more recent dispersals of R1a1a do not represent the initial spread of the whole clade, and might be more visible in the distribution of a subclade or subclades. Underhill et al. (2009) remark on the "geographic concordance of the R1a1a7-M458 distribution with the Chalcolithic and Early Bronze Age Corded Ware (CW) cultures of Europe". However they also note evidence contrary to a connection: Corded Ware period human remains at Eulau from which Y-DNA was extracted of R1a haplogroup appear to be R1a1a*(xM458) (which they found most similar to the modern German R1a1a* haplotype.) An earlier paper speculated that "R1a might represent the spread of the Corded Ware and Battle-Axe cultures from central and east Europe."

Steppe cultures

Archaeologists recognize a complex of inter-related and relatively mobile cultures living on the Eurasian steppe, part of which protrudes into Europe as far west as the Ukraine. These cultures from the late Neolithic and into the Iron Age, with specific traits such as Kurgan burials and horse domestication, have been associated with the dispersal of Indo-European languages across Eurasia.

Geneticists believing that they see evidence of R1a1a gene-flow from the Eurasian Steppe to India have frequently proposed the involvement of these Steppe cultures in the process. Such a Steppe origin for all or part R1a1a continues to be argued on the basis of DNA results from ancient remains from several South Siberian late Kurgan sites, including some from the Andronovo culture. However, in recent discussions of this theory it is considered only to apply to a part of R1a1a, making this theory no longer incompatible with other origins theories for R1a more broadly defined.

Central Asia

Cordaux et al. (2004) argued, citing data from 3 earlier publications, that R-M17 (R1a1a) Y chromosomes most probably have a central Asian origin. Central Asia is still considered a possible place of origin by Mirabal et al. (2009) after their larger analysis of more recent data. However these authors also consider other parts of Asia, particularly South Asia, to likely places of origin.

Middle East

As mentioned above, R1a haplotypes are less common in most of the Middle East than they are in either South Asia or Eastern Europe or much of Central Asia. It has nevertheless been mentioned in speculation about the origins of the clade. This is both because there are above-described pockets of high frequency and diversity, for example in some parts of Iran and amongst some Kurdish populations. A Middle Eastern origin for R1a has long been considered a possibility, and is still considered to be consistent with known data.

Popular science

Bryan Sykes in his book Blood of the Isles gives imaginative names to the founders or "clan patriarchs" of major British Y haplogroups, much as he did for mitochondrial haplogroups in his work The Seven Daughters of Eve. He named R1a1a in Europe the "clan" of a "patriarch" Sigurd, reflecting the theory that R1a1a in the British Isles has Norse origins. It should be noted that this does not mean that there ever was any clan or other large grouping of people, which was dominated by R1a1a or any other major haplogroup. Real clans and ethnic groups are made up of men in many Y Haplogroups.

See also

• List of R1a frequency by population
• Human Y-chromosome DNA haplogroups
• Genetic history of Europe
• Genetics and Archaeogenetics of South Asia
• Y-DNA haplogroups by ethnic groups
• Nordic R1a Y-DNA Project
• Somerled

v t e Phylogenetic tree of human Y-chromosome DNA haplogroups
This article needs to be updated. Please help update this article to reflect recent events or newly available information. (February 2021)
"Y-chromosomal Adam" A00 A0-T  A0 A1  A1a A1b A1b1 BT B CT DE CF D E C F F1  F-Y27277   F3  GHIJK G HIJK IJK H IJ K I   J     LT        K2  I1   I2  J1   J2  L     T  K2e K2d K2c K2b   K2a K2b1    P  K-M2313  S   M     P1   NO1 P1c P1b P1a N O R Q
Y-DNA by population Y-DNA haplogroups of historic people Footnotes Van Oven M, Van Geystelen A, Kayser M, Decorte R, Larmuseau HD (2014). "Seeing the wood for the trees: a minimal reference phylogeny for the human Y chromosome". Human Mutation. 35 (2): 187–91. doi:10.1002/humu.22468. PMID 24166809. S2CID 23291764. International Society of Genetic Genealogy (ISOGG; 2015), Y-DNA Haplogroup Tree 2015. (Access date: 1 February 2015.) Haplogroup A0-T is also known as A-L1085 (and previously as A0'1'2'3'4). Haplogroup A1 is also known as A1'2'3'4. F-Y27277, sometimes known as F2'4, is both the parent clade of F2 and F4 and a child of F-M89. Haplogroup LT (L298/P326) is also known as Haplogroup K1. Between 2002 and 2008, Haplogroup T-M184 was known as "Haplogroup K2". That name has since been re-assigned to K-M526, the sibling of Haplogroup LT. Haplogroup K2b (M1221/P331/PF5911) is also known as Haplogroup MPS. Haplogroup K2b1 (P397/P399) is also known as Haplogroup MS, but has a broader and more complex internal structure. Haplogroup P (P295) is also klnown as K2b2. K-M2313*, which as yet has no phylogenetic name, has been documented in two living individuals, who have ethnic ties to India and South East Asia. In addition, K-Y28299, which appears to be a primary branch of K-M2313, has been found in three living individuals from India. See: Poznik op. cit.; YFull YTree v5.08, 2017, "K-M2335", and; PhyloTree, 2017, "Details of the Y-SNP markers included in the minimal Y tree" (Access date of these pages: 9 December 2017) Haplogroup S, as of 2017, is also known as K2b1a. (Previously the name Haplogroup S was assigned to K2b1a4.) Haplogroup M, as of 2017, is also known as K2b1b. (Previously the name Haplogroup M was assigned to K2b1d.)

Notes

1. Karafet et al. (2008). See Table 2, giving age of parent clade R1.
2. ^ Underhill et al. (2009)
3. YCC (2002) harvcoltxt error: no target: CITEREFYCC2002 (help)
4. as used in Semino et al. (2000)
5. SRY1532.2 is also known as SRY10831.2
6. ^ ISOGG phylogenetic tree
7. Identified by the authors with the standardized SNP reference rs34351054.
8. ^ Regueiro et al. (2006)
9. Sengupta et al. (2005)
10. Sahoo et al. (2006)
11. Underhill et al. (2009)
12. Fornarino et al. (2009)
13. ^ Kivisild et al. (2003)
14. Balanovsky et al. (2008)
15. Behar et al. (2003)
16. ^ Semino et al. (2000)
17. Kasperaviciūte et al. (2005)
18. Semino et al. (2000) found a level of 60% but a later study, Tambets et al. (2004), found haplogroup R1a Y-DNA in only 20.4% of a sample of 113 Hungarians. Rosser et al. (2000) found SRY1532b positive lineages in approximately 22% (8/36) of a Hungarian sample. Battaglia et al. (2008) found haplogroup R1a1a-M17 in approximately 57% of a sample of 53 Hungarians.
19. Bowden et al. (2008)
20. ^ Dupuy et al. (2005)
21. Irish Heritage DNA Project, R1 and R1a
22. Passarino et al. (2002)
23. Capelli et al. (2003)
24. Garvey, D. "Y Haplogroup R1a1". Retrieved 2007-04-23.
25. Scozzari et al. (2001)
26. Rosser et al. (2000)
27. Pericic et al. (2005)
28. The Ysearch number for the Eulau remains is 2C46S.
29. Haak et al. (2008)
30. ^ Wells et al. (2001)
31. Kharkov et al. (2007)
32. Tambets et al. (2004)
33. Wang et al. (2003)
34. Zhou et al. (2007)
35. Lell et al. (2002)
36. Nasidze et al. (2004)
37. Nasidze et al. (2005)
38. see Mirabal et al. (2009) and Underhill et al. (2009)
39. Mirabal et al. (2009) additionally felt the data to be consistent with central Asian, while Underhill et al. (2009) took to the data to be consistent with Western Asian origins.
40. see: Kivisild et al. (2003), Mirabal et al. (2009) and Underhill et all. (2009) harvcoltxt error: no target: CITEREFUnderhill_et_all.2009 (help)
41. see, e.g.: Sengupta et al. (2005), Sahoo et al. (2006), Sharma et al. (2009)
42. described by Zhivotovsky et al. (2004), the latest such example being Mirabal et al. (2009) and Underhill et al. (2009)
43. For several examples from 2002, see Semino et al. (2000), Passarino et al. (2001), Passarino et al. (2002) and Wells (2002)
44. See Keyser et al. (2009): 9 out of 10 male specimens were found to be in R1a1a, evidence felt by the authors to suggest that the Steppes Kurgan culture spread from Europe to Siberia.
45. Kloyosov et al. (2009) harvcoltxt error: no target: CITEREFKloyosov_et_al.2009 (help)
46. Wells et al. (2001), Semino et al. (2000), and Quintana-Murci et al. (2001)

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Projects

• FTDNA R1a Y-chromosome Haplogroup Project
• Danish Demes Regional DNA Project: Y-DNA Haplogroup R1a

• Human Y-DNA haplogroups
• Human genetic history