Haplogroup R1a1

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Haplogroup R1a1
R1a1a distribution.png
Possible place of origin Eurasia
Ancestor R-M448
Defining mutations M17, M198, M512, M514, M515, L168, L449, L457, L566

Haplogroup R1a1, also referred to as haplogroup R-M17 or R-M198, is a Y-DNA haplogroup defining one of the most common human male lines found in modern Eurasia. It is defined by the SNP mutation M17, and is particularly common in a large region extending from South Asia and Southern Siberia to Central Europe and Scandinavia (Underhill 2009).

The R1a1 is the most common subclade within the family of the Y-DNA Haplogroup R1a, which share in common the M420 SNP mutation, and before the discovery of M420, R1a1 was itself referred to as R1a.


The modern distribution of R1a1 has two widely separated areas of high frequency, one in South Asia, and the other in Eastern Europe. The demographic reasons for this are the subject of on-going discussion and attention among population geneticists and genetic genealogists.

Geographic origin[edit]

Until 2012, there was extensive scholarly debate as to the origins of haplogroup R1a1. Some researchers found that Indian, or more generally, South Asian populations, had the highest STR diversity.[1] Other studies variously proposed Eastern European, Central Asian and even Western Asian origins for the R1a1.[2]

Coalescent time estimates for R-M17(xM458) STR from (Underhill 2009)
Location TD
W. India 15,800
Pakistan 15,000
Nepal 14,200
India 14,000
Oman 12,500
N. India 12,400
S. India 12,400
Caucasus 12,200
E. India 11,800
Poland 11,300
Slovakia 11,200
Crete 11,200
Germany 9,900
Denmark 9,700
UAE 9,700

Ancient DNA and archaeological correlates[edit]

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 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. Nearly all samples from Bronze and Iron Age graves in the Krasnoyarsk area in south Siberia belonged to R1a1 and appeared to represent an eastward migration from Europe.[3] In central Europe, Corded Ware period human remains at Eulau from which Y-DNA was extracted appear to be R-M17(xM458) (which they found most similar to the modern German R-M17* haplotype.[4]

Frequency distribution of R1a1 adapted from (Underhill 2009).



Central Asia[edit]

In Afghanistan, R1a1 is found at 51.02% among the Pashtuns who are the largest ethnic group in Afghanistan and 30.36% among the Tajiks. It is less frequent among the Hazaras (6.67%) and the Turkic-speaking Uzbeks (17.65%) (Haber 2012).

South Asia[edit]

In South Asia, R1a1 has often been observed with high frequency in a number of demographic groups. (Sahoo 2006 and Sengupta 2005)

In India, high frequencies of this haplogroup is observed in West Bengal Brahmins (72%)(Sengupta 2005) to the east, Konkanastha Brahmins (48%) (Sengupta 2005) to the west, Khatris (67%)(Underhill 2009) in the north and Iyenger Brahmins (31%)(Sengupta 2005) in the south. It has also been found in several South Indian Dravidian-speaking Adivasis including the Chenchu (26%) and the Valmikis of Andhra Pradesh and the Kallar of Tamil Nadu suggesting that R1a1 is widespread in Tribal Southern Indians (Kivisild 2003).

Besides these, studies show high percentages in regionally diverse groups such as Manipuris (50%)(Underhill 2009) to the extreme North East and in Punjab (47%)(Kivisild 2003) to the extreme North West.

In Pakistan it is found at 71% among the Mohanna tribe in Sindh province to the south and 46% among the Baltis of Gilgit-Baltistan to the north (Underhill 2009). Among the Sinhalese of Sri Lanka, 13% were found to be R1a1 positive (Kivisild 2003).

Hindus of Terai region of Nepal show it at 69% (Fornarino 2009).

East Asia[edit]

The frequency of R1a1 is comparatively low among some Turkic-speaking groups including Turks, Azeris, Kazakhs, and Yakuts, yet levels are higher (19 to 28%) in certain Turkic or Mongolic-speaking groups of Northwestern China, such as the Bonan, Dongxiang, Salar, and Uyghurs.(Wells 2001, Wang 2003, and Zhou 2007)

In Eastern Siberia, R1a1 is found among certain indigenous ethnic groups including Kamchatkans and Chukotkans, and peaking in Itel'man at 22% (Lell 2002).

West Asia[edit]

R1a1 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 Kuwait, Turkey and Iran. The Shimar (Shammar) Bedouin tribe in Kuwait show the highest frequency in the Middle East at 43%.(Mohammad 2009,Nasidze 2004, and Nasidze 2005)

Wells 2001, noted that in the western part of the country, Iranians show low R1a1 levels, while males of eastern parts of Iran carried up to 35% R1a1. Nasidze 2004 found R1a1 in approximately 20% of Iranian males from the cities of Tehran and Isfahan. Regueiro 2006 in a study of Iran, noted much higher frequencies in the south than the north.

A newer Study has found 20.3% R-M17* among Kurdish samples which were taken in the Kurdistan Province in western Iran, 9.7% among Mazandaranis in North Iran in the province of Mazandaran, 9.4% among Gilaks in province of Gilan, 12.8% among Persian and 17.6% among Zoroastrians in Yazd, 18.2% among Persians in Isfahan, 20.3% among Persians in Khorasan, 16.7% Afro-Iranians, 18.4% Qeshmi "Gheshmi", 21.4% among Persian Speaking Bandari people in Hormozgan and 25% among the Baloch people in Sistan and Baluchestan Province (Grugni 2012).

Further to the north of these Middle Eastern regions on the other hand, R1a1 levels start to increase in the Caucasus, once again in an uneven way. Several populations studied have shown no sign of R1a1, while highest levels so far discovered in the region appears to belong to speakers of the Karachay-Balkar language among whom about one quarter of men tested so far are in haplogroup R1a1 (Underhill 2009).


R1a1 among other European haplogroups

In Europe, the R1a1 sub-clade, is found at highest levels among peoples of Eastern European descent (Sorbs, Poles, Russians and Ukrainians; 50 to 65%) (Balanovsky 2008, Behar 2003, and Semino 2000). In the Baltic countries R1a1 frequencies decrease from Lithuania (45%) to Estonia (around 30%) (Kasperaviciūte 2005). Levels in Hungarians have been noted between 20 and 60% (Battaglia 2008, Rosser 2000, Semino 2000, and Tambets 2004).

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 R1a1 (Bowden 2008 and (Dupuy 2005)). Vikings and Normans may have also carried the R1a1 lineage westward; accounting for at least part of the small presence in the British Isles (Passarino 2002 and Capelli 2003). In East Germany, where Haplogroup R1a1 reaches a peak frequency in Rostock at a percentage of 31.3%, it averages between 20%-30% (Kayser 2005).

Haplogroup R1a1 was found at elevated levels among a sample of the Israeli population who self-designated themselves as Levites and Ashkenazi Jews (Levites comprise approximately 4% of Jews). Behar reported R1a1 to be the dominant haplogroup in Ashkenazi Levites (52%), although rare in Ashkenazi Cohanim (1.3%). (Behar 2003).

In Southern Europe R1a1 is not common, but significant levels have been found in pockets, such as in the Pas Valley in Northern Spain, areas of Venice, and Calabria in Italy (Scozzari 2001). 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 (Pericić 2005, Rosser 2000, and Semino 2000).

The remains of a father and his two sons, 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 Ysearch number for the Eulau remains is 2C46S. The ancestral clade was thus present in Europe at least 4600 years ago, in association with one site of the widespread Corded Ware culture (Haak 2008).

Subclade distribution[edit]

R-M458 This branch is 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 (Underhill 2009).

R-M334 is 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 (Underhill 2009).

Relative frequency of R-M434 to R-M17
Region People N R-M17 R-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 2009)

R-M87 (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 (Regueiro 2006).

R-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 (Underhill 2009).

Associated SNPs[edit]

SNP Mutation Y-position (NCBI36) Y-position (GRCh37) RefSNP ID
M17 INS G 20192556 21733168 rs3908
M198 C->T 13540146 15030752 rs2020857
M512 C->T 14824547 16315153 rs17222146
M514 C->T 17884688 19375294 rs17315926
M515 T->A 12564623 14054623 rs17221601
L168 A->G 14711571 16202177 -
L449 C->T 21376144 22966756 -
L457 G->A 14946266 16436872 rs113195541
L566 C->T - - -


Thomas Krahn's draft tree[edit]

This is Thomas Krahn at the Genomic Research Center's Draft tree Proposed Tree for haplogroup R-M17.

  • R-M17 M17, M198, M512, M514, M515, L168, L449, L457, L566
    • R-M417 M417, PAGES7, Z85
      • R-M56 M56
      • R-M157.1 M157.1
      • R-M204 M64.2, M87, M204
      • R-P98 P98
      • R-PK5 PK5
      • R-M434 M434
      • R-L12 L12
      • R-PAGES68 PAGES68
      • R-L450 L450
      • R-L451 L451
      • R-L579 L579
      • R-L664 L664
        • R-L872 L872, L873, L874
      • R-Z93 Z93
        • R-Z94 L342.2, L319.4, L348.3, L349.2, Z94
      • R-Z283 Z283
        • R-M458 M458
        • R-Z280 Z280
        • R-Z284 Z284

R1a1 subclades and STR clusters[edit]

Frequency distribution of R-M458


R-M458 is a mainly Slavic SNP, characterized by its own mutation, and was first called cluster N. Underhill et al. (2009) found it to be present in modern European populations roughly between the Rhine catchment and the Ural Mountains and traced it to "a founder effect that [...] falls into the early Holocene period, 7.9±2.6 KYA."[5] M458 was found in one skeleton from a 14th-century grave field in Usedom, Mecklenburg-Vorpommern, Germany.[6] The paper by Underhill et al. (2009) also reports a surprisingly high frequency of M458 in some Northern Caucasian populations (for example 27.5% among Karachays and 23.5% among Balkars, 7.8% among Karanogays and 3.4% among Abazas).


The R-L260 lineage, commonly referred to as West Slavic or Polish, is a subclade of the larger parent group R-M458, and was first identified as an STR cluster by Pawlowski 2002 and then by Gwozdz 2009. Thus, R-L260 was what Gwozdz 2009 called cluster "P." In 2010 it was verified to be a haplogroup identified by its own mutation (SNP).[7] It apparently accounts for about 8% of Polish men, making it the most common subclade in Poland. Outside of Poland it is less common (Pawlowski 2002). In addition to Poland, it is mainly found in the Czech Republic and Slovakia, and is considered "clearly West Slavic."[8] The founding ancestor of R-L260 is estimated to have lived between 2000 and 3000 years ago, i.e. during the Iron Age, with significant population expansion less than 1,500 years ago (Gwozdz 2009).


The R-M334 was identified in an Estonian population sample (Underhill 2009).



R-L365 was early called Cluster G.

Gwozdz's Cluster K[edit]

This is an STR based group that is R-M17(xM458). This cluster is common in Poland but not exclusive to Poland (Gwozdz 2009).

See also[edit]

Y-DNA R-M207 Subclades[edit]

Y-DNA backbone tree[edit]

Evolutionary tree of human Y-chromosome DNA haplogroups [χ 1][χ 2]
"Y-chromosomal Adam"
A00 A0-T [χ 3]
A0 A1[χ 4]
A1a A1b
A1b1 BT
I J LT [χ 5]  K2
L T NO [χ 6] K2b [χ 7]   K2c K2d K2e [χ 8]
N O K2b1 [χ 9]    P
M S [χ 10] Q R
  1. ^ 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. 
  2. ^ International Society of Genetic Genealogy (ISOGG; 2015), Y-DNA Haplogroup Tree 2015. (Access date: 1 February 2015.)
  3. ^ Haplogroup A0-T is also known as A0'1'2'3'4.
  4. ^ Haplogroup A1 is also known as A1'2'3'4.
  5. ^ Haplogroup LT (L298/P326) is also known as Haplogroup K1.
  6. ^ Haplogroup NO (M214) is also known as Haplogroup K2a (although the present Haplogroup K2e was also previously known as "K2a").
  7. ^ Haplogroup K2b (M1221/P331/PF5911) is also known as Haplogroup MPS.
  8. ^ Haplogroup K2e (K-M147) was previously known as "Haplogroup X" and "K2a" (but is a sibling subclade of the present K2a, also known as Haplogroup NO).
  9. ^ Haplogroup K2b1 (P397/P399) is similiar to the former Haplogroup MS, but has a broader and more complex internal structure.
  10. ^ Haplogroup S (S-M230) was previously known as Haplogroup K5.



Conference posters[edit]



Further reading[edit]

External links[edit]


  1. ^ (Kivisild 2003,Mirabal 2009,Underhill 2009, (Sengupta 2005,Sahoo 2006,Sharma 2009,Thangaraj 2010),Sharma 2012)
  2. ^ (Underhill 2009Regueiro 2006Kivisild 2003Semino 2000)(Zhao 2009)(Semino 2000)
  3. ^ (Keyser 2009)
  4. ^ Underhill 2009
  5. ^ Underhill PA, et al. (2010). "Separating the post-Glacial coancestry of European and Asian Y chromosomes within haplogroup R1a". European Journal of Human Genetics 18 (4): 479–484. doi:10.1038/ejhg.2009.194. PMC 2987245. PMID 19888303. 
  6. ^ J. Freder, Die mittelalterlichen Skelette von Usedom [The mediaeval skeletons of Usedom], Berlin 2010, p. 86 (Dissertation Free University Berlin 2010).
  7. ^ Peter Gwozdw. M458, L260, CTS11962
  8. ^ Haplogroup R1a (Y-DNA)