Haplogroup R1a

Haplogroup R-M420
Possible time of origin	Less than 18,500 YBP
Possible place of origin	Eurasia, most probably South Asia, Central Eurasia or Southwest Asia
Ancestor	R1 (R-M173)
Descendants	R1a1a1 to R1a1a8
Defining mutations	M420 (also includes M17, M198, SRY1532.2 and SRY10831.2)
Highest frequencies	South Asia, Eastern Europe, Central Asia, Central Europe, Scandinavia and Siberia (See List of R1a frequency by population)

Haplogroup R-M420 is an Eurasian lineage. It is common in many parts of Eurasia and is frequently discussed in human population genetics and genetic genealogy. One sub-clade (branch) of R-M420, 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 R-M420 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 the relatively rare lineages which are not in the R1a1 branch leading to R1a1a.

R-M420 and R1a1a are believed to have originated somewhere within Eurasia, most likely in the area from Eastern Europe to South Asia. Several recent studies have proposed that South Asia is the most likely region of origin. But on the other hand, as will be discussed below, some researchers continue to treat modern Indian R-M420 as being largely due to immigration from the Central Eurasian steppes or Southwestern Asia.

Phylogeny

The R-M420 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 R-M420

Haplogroup R family tree    Haplogroup R     Haplogroup R1   M173   M420    R1a   M343   R1b ? R1*  Haplogroup R2

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.

R-M420

R-M420, defined by the mutation M420, has two branches: R-SRY1532.2, defined by the mutation SRY1532.2, which makes up the vast majority; and R-M420*, 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 R-M420* 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.

R-SRY1532.2

R-SRY1532.2 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 R-M17 branch, which is positive for M17 and M198. The paragroup R-SRY1532.2* (old R1a*) is positive for the SRY1532.2 marker but lacks either the M17 or M198 markers.

The R-SRY1532.2* 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. While Sahoo et al. reported R1a*(new R-SRY1532.2*) for 1/15 Himachal Pradesh Rajput samples.

R-M17 (aka R-M198)

R-M17 makes up the vast majority of all R-M420 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, R-M17 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 R-M17*.

R1a1a subclades

Currently, of the eight SNP-defined subclades of R1a1a only R1a1a7 (now R1a1a1g) has significant frequencies. R1a1a7 (now R1a1a1g) 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 (now R1a1a1g) has its own SNP-defined R1a1a7a 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.

Relative frequency of R1a1a6 (R-M434) to R1a1a (R-M17)

Region	People	N	R1a1a-M17		R1a1a6-M434
			Number	Freq. (%)	Number	Freq. (%)
Pakistan	Baloch	60	9	15%	5	8%
Pakistan	Makrani	60	15	25%	4	7%
Middle East	Oman	121	11	9%	3	2.5%
Pakistan	Sindhi	134	65	49%	2	1%
Table only shows positive sets from N = 3667 derived from 60 Eurasian populations sample, Underhill et al. (2009)

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.

R1a1a STR clusters

Frequency distribution of R1a1a7 (now R1a1a1g) (R-M458)

Genetic genealogists looking at high accuracy STR (microsatellite) 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.

Western Slavic cluster (L260 - R1a1a1g2 )

Gwozdz (2009) has identified two clusters within R1a1a7 (now R1a1a1g) ("P" and "N"). Western Slavic cluster (L260 - R1a1a1g2 ) 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.

Central European cluster (M458 - R1a1a1g)

Cluster N is not concentrated in Poland, but is apparently common in many Slavic areas i.e. Czech republic, Slovakia, Poland, Eastern Germany - Lusatia, Bavaria, Western Ukraine. Archeologically M458 was found in the 14th century graves discovered on Usedom (eastern Germany).

There is also M334 - R1a1a1g1 - one person in Estonia. 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. Northern European cluster (L265 - R1a1a1i2) Example is cluster G or L365 - R1a1a1i2 (also called Pomeranian) popular in Pomerania, Baltic coast of Germany (former Abodrite and Veleti areas), former Eastern Prussia, Lithuania.

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.

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.

Historic meanings of "R1a"

Further information: Conversion table for Y chromosome haplogroups

The historic naming system commonly used for R1a was inconsistent in different published sources, because it changed often, this 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.

More recent updates recorded at the ISOGG reference webpage involve branches of R-M17, including one major branch, R-M417.

Contrasting family trees for R1a, showing the evolution of understanding of this clade

2002 Scheme proposed in YCC (2002)	2009 Scheme as per Underhill et al. (2009)	Latest ISOGG tree as per January 2011
As M420 went undetected, M420 lineages were classified as either R1* or R1a (SRY1532.2, also known as SRY10831.2) R1  M173   R1*  All cases without M343 or SRY1532.2 (including a minority M420+ cases) R1a  SRY1532.2    (SRY10831.2)   R1a*    R1a1  M17, M198   R1a1*  M56   R1a1a  M157   R1a1b  M87, M204 M64.2    R1a1c R1b M343  sibling clade to R1a	After 2009, a new layer was inserted covering all old R1a, plus its closest known relatives R1  M173   R1*  All cases without M343 or M420 (smaller than old "R1a*") R1a  M420    R1a* All cases with M420 but without SRY1532.2 R1a1  SRY1532.2    R1a1*(Old R1a*)  R1a1a   M17, M198  R1a1a* M56   R1a1a1 M157   R1a1a2  M64.2,..   R1a1a3 P98   R1a1a4 PK5   R1a1a5 M434   R1a1a6  M458     R1a1a7*   M334     R1a1a7a  Page68   R1a1a8 R1b M343  Sibling clade to R1a (same as before)	Latest information R1 M173 R1* (As before) M420 R1a* (As before) SRY1532.2 R1a1* (As before) M17 R1a1a* (As before) R1a1a1 M417,Page7 R1a1a1* M56   R1a1a1a  Z280     R1a1a1g2*   P278.2     R1a1a1g2a L365     R1a1a1g2b L366     R1a1a1g2c Z92     R1a1a1g2d  Z284     R1a1a1g3*   P278.2     R1a1a1g3a P98   R1a1a1d PK5   R1a1a1e M434   R1a1a1f  Z283     R1a1a1g*  M458     R1a1a1g1*   M334     R1a1a1g1a L260     R1a1a1g1b  Z93  R1a1a1h*   L342.2     R1a1a1h1*   L657     R1a1a1h1a R1b M343 Sibling clade to R1a (same as before)

See also

• List of R1a frequency by population
• Human Y-chromosome DNA haplogroups
• Genetic history of Europe
• Genetics and Archaeogenetics of South Asia
• Y-chromosome haplogroups by populations
• Nordic R1a Y-DNA Project
• Somerled
• Haplogroup Q (Y-DNA)

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• Y Chromosome Consortium "YCC" (2002). "A Nomenclature System for the Tree of Human Y-Chromosomal Binary Haplogroups". Genome Research. 12 (2): 339–348. doi:10.1101/gr.217602. PMC 155271. PMID 11827954.

• Zerjal, T; Beckman, L; Beckman, G; Mikelsaar, AV; Krumina, A; Kucinskas, V; Hurles, ME; Tyler-Smith, C (2001). "Geographical, linguistic, and cultural influences on genetic diversity: Y-chromosomal distribution in Northern European populations". Mol Biol Evol. 18 (6): 1077–1087. PMID 11371596.

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• Zhou, Ruixia; An, Lizhe; Wang, Xunling; Shao, Wei; Lin, Gonghua; Yu, Weiping; Yi, Lin; Xu, Shijian; Xu, Jiujin (2007). "Testing the hypothesis of an ancient Roman soldier origin of the Liqian people in northwest China: a Y-chromosome perspective". Journal of Human Genetics,. 52 (7): 584. doi:10.1007/s10038-007-0155-0. PMID 17579807. {{cite journal}}: Invalid |ref=harv (help)CS1 maint: extra punctuation (link)

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• Zhivotovsky, L; Underhill, PA; Cinnioğlu, C; Kayser, M; Morar, B; Kivisild, T; Scozzari, R; Cruciani, F; Destro-Bisol, G (2004). "The effective mutation rate at Y chromosome short tandem repeats, with application to human population-divergence time". Am J Hum Genet. 74 (1): 50–61. doi:10.1086/380911. PMC 1181912. PMID 14691732.

Projects

• FTDNA R1a Y-chromosome Haplogroup Project
• R1a1a1 and Subclades Y-DNA Project - Background Family Tree DNA R1a1a1
• Danish Demes Regional DNA Project: Y-DNA Haplogroup R1a