Haplogroup R1a

Haplogroup R1a
Possible time of origin 22,000 YBP [1] to 25,000[2] years ago
Possible place of origin Eurasia (see text).
Ancestor Haplogroup R1
Descendants Haplogroup R1a-Z282 (Europe), R1a-Z93 (Asia)
Defining mutations R1a: L62, L63, L120, M420, M449, M511, M513
R1a1a: M17, M198, M512, M514, M515, L168, L449, L457, L566
Highest frequencies See List of R1a frequency by population

Haplogroup R1a, or haplogroup R-M420, is a human Y-chromosome DNA haplogroup which is distributed in a large region in Eurasia, extending from Scandinavia and Central Europe to southern Siberia and South Asia.[3][2]

While R1a originated ca. 22,000[1] to 25,000[2] years ago, its subclade M417 (R1a1a1) diversified ca. 5,800 years ago.[4] The distribution of M417-subclades R1a-Z282 (including R1a-Z280)[5] in Central and Eastern Europe and R1a-Z93 in Asia[5][2] suggests that R1a1a diversified within the Eurasian Steppes or the Middle East and Caucasus region.[5] The place of origin of these subclades plays a role in the debate about the origins of Proto-Indo-Europeans.

The SNP mutation R-M420 was discovered after R-M17 (R1a1a), which resulted in a reorganization of the lineage in particular establishing a new paragroup (designated R-M420*) for the relatively rare lineages which are not in the R-SRY10831.2 (R1a1) branch leading to R-M17.

Origins

R1a origins

Tatiana et al. (2014) "rapid diversification process of K-M526 likely occurred in Southeast Asia, with subsequent westward expansions of the ancestors of haplogroups R and Q." [6]

The split of R1a (M420) is computed to ca. 22,000,[1] or 25,000[2] years ago, which is the time of the last glacial maximum. A large, 2014 study by Peter A. Underhill et al., using 16,244 individuals from over 126 populations from across Eurasia, concluded that there was compelling evidence that "the initial episodes of haplogroup R1a diversification likely occurred in the vicinity of present-day Iran."[2]

Diversification of R1a1a1 (M417) and ancient migrations

R1a origins (Underhill 2010;[7] R1a1a origins (Pamjav 2012); possible migration R1a to Baltic coast; and R1a1a oldest expansion and highest frequency (Underhill 2014)

According to Underhill (2014), the downstream R1a-M417 subclade diversified into Z282 and Z93 circa 5,800 years ago.[4][note 1] Even though R1a occurs as the most frequent Y-chromosome haplogroup among populations speaking a wide variety of languages such as Slavic, Indo-Iranian, Dravidian, Turkic and Finno-Ugric, the question of the origins of R1a1a is relevant to the ongoing debate concerning the urheimat of the Proto-Indo-European people, and may also be relevant to the origins of the Indus Valley Civilisation. R1a shows a strong correlation with Indo-European languages of Southern and Western Asia and Central and Eastern Europe,[9][3] being most prevalent in Eastern Europe, West Asia, South Asia and Central Asia. In Europe, Z282 is prevalent particularly while in Asia Z93 dominates. The connection between Y-DNA R-M17 and the spread of Indo-European languages was first noted by T. Zerjal and colleagues in 1999.[10]

Steppe origins

Proposed steppe dispersal of R1a1a

Kivisild et al. (2003) have proposed either south or west Asia,[11][note 2] while Mirabal et al. (2009) see support for both south and central Asia.[9] Other studies suggest Ukrainian,[12] Central Asian[13] and West Asian origins for R1a1a.[14][3][15][5][2]

Ornella Semino et al. (2000) proposed Ukrainian origins, and a postglacial spread of the R1a1 gene during the Late Glacial Maximum, subsequently magnified by the expansion of the Kurgan culture into Europe and eastward.[16] Spencer Wells proposes central Asian origins, suggesting that the distribution and age of R1a1 points to an ancient migration corresponding to the spread by the Kurgan people in their expansion from the Eurasian steppe.[13] According to Pamjav et al. (2012), R1a1a diversified in the Eurasian Steppes or the Middle East and Caucasus region:

Inner and Central Asia is an overlap zone for the R1a1-Z280 and R1a1-Z93 lineages [which] implies that an early differentiation zone of R1a1-M198 conceivably occurred somewhere within the Eurasian Steppes or the Middle East and Caucasus region as they lie between South Asia and Central- and Eastern Europe."[5]

Three genetic studies in 2015 gave support to the Kurgan theory of Gimbutas regarding the Indo-European Urheimat. According to those studies, haplogroups R1b and R1a, now the most common in Europe (R1a is also common in South Asia) would have expanded from the Russian steppes, along with the Indo-European languages; they also detected an autosomal component present in modern Europeans which was not present in Neolithic Europeans, which would have been introduced with paternal lineages R1b and R1a, as well as Indo-European languages.[17][18][19]

Source of R1a1a1 in Corded Ware culture
European middle-Neolithic period. Comb Ware culture ca. 4200 BCE – ca. 2000 BCE
Corded Ware culture (ca. 2900 BCE – ca. 2350 BCE
Cucuteni Trypillian culture boundaries

David Anthony considers the Yamna culture to be the Indo-European Urheimat.[20][21] According to Haak et al. (2015), a massive migration from the Yamna culture northwards took place ca. 2,500 BCE, accounting for 75% of the genetic ancestry of the Corded Ware culture, noting that R1a and R1b may have "spread into Europe from the East after 3,000 BCE".[22] Yet, all their seven Yamna samples belonged to the R1b-M269 subclade,[22] but no R1a1a has been found in their Yamna samples. This raises the question where the R1a1a in the Corded Ware culture came from, if it was not from the Yamna culture.[23]

Semenov and Bulat do argue for such an origin of R1a1a in the Corded ware culture, noting that several publications point to the presence of R1a1 in the Comb Ware culture.[24][note 3]

Haak et al. (2015) found that part of the Yamna ancestry derived from the Middle East, and that neolithic techniques probably arrived at the Yamna culture from the Balkans.[note 4] The Rossen culture (4,600–4,300 BC), which was situated on Germany and predates the Corded Ware culture, an old subclade of R1a, namely L664, can still be found.[note 5] Some speculate that R1a arrived in the Balkans via Anatolia, and from there spread first north-west to the Rossen culture, and then east from the Cucuteni culture to the Yamna and Afanasevo cultures, despite the absence of R1a from intermediate cultures between the Near East, Anatolia and the Balkans.[note 6]

Transcaucasia & West Asian origins and possible influence on Indus Valley Civilisation

Part of the South Asian genetic ancestry derives from west Eurasian populations, and some researchers have implied that Z93 may have come to India via Iran[27] and expanded there during the Indus Valley Civilisation.[2][28]

Mascarenhas et al. (2015) note that the roots of Z93 lie in West Asia, and propose that "Z93 and L342.2 expanded in a southeasterly direction from Transcaucasia into South Asia,"[27] noting that such an expansion is compatible with "the archeological records of eastward expansion of West Asian populations in the 4th millennium BCE culminating in the so-called Kura-Araxes migrations in the post-Uruk IV period."[27] Yet, Lazaridis noted that sample I1635 of Lazaridis et al. (2016), their Armenian Kura-Araxes sample, carried Y-haplogroup R1b1-M415(xM269)[note 7] (also called R1b1a1b-CTS3187).[29]

According to Underhill et al. (2014/2015) the diversification of Z93 and the "early urbanization within the Indus Valley [...] occurred at [5,600 years ago] and the geographic distribution of R1a-M780 (Figure 3d[note 8]) may reflect this."[2][note 9] Poznik et al. (2016) note that 'striking expansions' occurred within R1a-Z93 at ~4,500–4,000 years ago, which "predates by a few centuries the collapse of the Indus Valley Civilisation."[31][note 10]

Yet, according to Narasimhan et al. (2018), steppe pastoralists are a likely source for R1a in India.[32][note 11]

Proposed South Asian origins

Kivisild et al. (2003) have proposed either South or West Asia,[11][note 2] while Mirabal et al. (2009) see support for both South and Central Asia.[9]

South Asian populations have the highest STR diversity within R1a1a,[33][34][9][3][1][35] and subsequent older TMRCA datings, and R1a1a is present among both higher (Brahmin) castes and lower castes, although the presence is substantially higher among Brahmin castes.[1][35] From these findings some researchers have concluded that R1a1a originated in South Asia,[34][1][note 12] excluding a substantial genetic influx from Indo-European migrants.[34][33][3]

However, this diversity, and the subsequent older TMRCA-datings, can also be explained by the historically high population numbers, which increases the likelihood of diversification and microsatellite variation.[37][38] According to Sengupta et al. (2006), "[R1a1 and R2] could have actually arrived in southern India from a southwestern Asian source region multiple times."[33][note 13] Silva et al. (2017) noted that R1a in South Asia most "likely spread from a single Central Asian source pool, there do seem to be at least three and probably more R1a founder clades within the Subcontinent, consistent with multiple waves of arrival."[38]

Phylogeny

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 will be found with various names; in particular, as "R1a1" in relatively recent but not the latest literature.)

Topology

The topology of R1a is as follows (codes [in brackets] non-isogg codes):[39][8][40][41][42] Tatiana et al. (2014) "rapid diversification process of K-M526 likely occurred in Southeast Asia, with subsequent westward expansions of the ancestors of haplogroups R and Q." [6]

  • P P295/PF5866/S8 (also known as K2b2).
  • R (R-M207)[39][8]
    • R*
    • R1 (R-M173)
      • R1*[39]
      • R1a (M420)[39] (Eastern Europe, Asia)[41]
        • R1a*[8]
        • R1a1[39] (M459/PF6235,[39] SRY1532.2/SRY10831.2[39])
          • R1a1 (M459)[39][8]
          • R1a1a (M17, M198)[39]
            • R1a1a1 (M417, page7)[39]
              • R1a1a1a (CTS7083/L664/S298)[39]
              • R1a1a1b (S224/Z645, S441/Z647)[39]
                • R1a1a1b1 (PF6217/S339/Z283)[39]
                  • R1a1a1b1a (Z282)[39] [R1a1a1a*] (Z282) (Europe)[43]
                    • R1a1a1b1a1[39] [The old topological code is R1a1a1b*，which is outdated and might lead to some confusion.][43] (M458)[39][43] [R1a1a1g] (M458)[42]
                    • R1a1a1b1a2[39] (S466/Z280, S204/Z91)[39]
                      • R1a1a1b1a2a[39]
                      • R1a1a1b1a2b (CTS1211)[39] [R1a1a1c*] (M558)[43] [R-CTS1211] (V2803/CTS3607/S3363/M558, CTS1211/S3357, Y34/FGC36457)[8]
                        • R1a1a1b1a2b3* (M417+, Z645+, Z283+, Z282+, Z280+, CTS1211+, CTS3402, Y33+, CTS3318+, Y2613+) (Gwozdz's Cluster K)[40]
                        • R1a1a1b1a2b3a (L365/S468)[39]
                    • R1a1a1b1a3 (Z284)[39] [R1a1a1a1] (Z284)[43]
                • R1a1a1b2 (F992/S202/Z93)[39] [R1a1a2*] (Z93, M746)(Asia)[43]
                  • R1a1a1b2a (F3105/S340/Z94, L342.2/S278.2)[39] [R1a1b2a*] (Z95)[43] R-Z94 (Z94/F3105/S340, Z95/F3568)[8]
                    • R-Z2124 (Z2121/S3410, Z2124)[8]
                      • [R1a1b2a*] (Z2125)[43]
                        • [R1a1b2a*] (M434)[43] [R1a1a1f] (M434)[42]
                        • [R1a1b2a*] (M204)[43]
                    • [R1a1b2a1*] (M560)[43]
                    • [R1a1b2a2*] (M780, L657)[43] (India)[41]
                    • [R1a1b2a3*] (Z2122, M582)[43]
              • [R1a1a1c] (M64.2, M87, M204)[42]
              • [R1a1a1d] (P98)[42]
              • [R1a1a1e] (PK5)[42]
      • R1b (M343) (Western Europe)
    • R2

Haplogroup R

Haplogroup R phylogeny

 
R  (M207)   

 R1   (M173)   

  M420 

 R1a

 
  M343 

 R1b

 
 M173(xM420, M343) 

 R1*

 
 
 

R2 (M479)    

 
 

R* M207(xM173, M479)

 
 

R-M173 (R1)

R1a is distinguished by several unique markers, including the M420 mutation. It is a subclade of Haplogroup R-M173 (previously called R1). R1a has the sister-subclades Haplogroup R1b-M343, and the paragroup R-M173*.

R-M420 (R1a)

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.[3][45]

Only isolated samples of the new paragroup R-M420* were found by Underhill 2009, 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.[3]

R-SRY1532.2 (R1a1)

R1a1 is defined by SRY1532.2 or SRY10831.2 (understood to always include SRY10831.2, M448, L122, M459, and M516[3][46]). This family of lineages is dominated by M17 and M198. In contrast, paragroup R-SRY1532.2* 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 all. (2009) reported 1/51 in Norway, 3/305 in Sweden, 1/57 Greek Macedonians, 1/150 Iranians, 2/734 ethnic Armenians, and 1/141 Kabardians.[3] Sahoo et al. (2006) reported R-SRY1532.2* for 1/15 Himachal Pradesh Rajput samples.[34]

R-M17/M198 (R1a1a)

The following SNPs are associated with R1a1a:

SNP Mutation Y-position (NCBI36) Y-position (GRCh37) RefSNP ID
M17INS G2019255621733168rs3908
M198C->T1354014615030752rs2020857
M512C->T1482454716315153rs17222146
M514C->T1788468819375294rs17315926
M515T->A1256462314054623rs17221601
L168A->G1471157116202177-
L449C->T2137614422966756-
L457G->A1494626616436872rs113195541
L566C->T---

R-M417 (R1a1a1)

R1a1a1 (R-M417) is the most widely found subclade, in two variations which are found respectively in Europe (R1a1a1b1 (R-Z282) ([R1a1a1a*] (R-Z282) (Underhill 2014/2015)[41]) and Central and South Asia (R1a1a1b2 (R-Z93) ([R1a1a2*] (R-Z93) Underhill 2014/2015)[41]).

R-Z282 (R1a1a1b1a) (Eastern Europe)

This large subclade appears to encompass most of the R1a1a found in Europe.[47]

  • R1a1a1b1a [R1a1a1a* (Underhill (2014))] (R-Z282*) occurs in northern Ukraine, Belarus, and Russia at a frequency of ~20%. (Underhill et al. 2014)
  • R1a1a1b1a3 [R1a1a1a1 (Underhill (2014))] (R-Z284) occurs in Northwest Europe and peaks at ~20% in Norway. (Underhill et al. 2014)
  • R1a1a1c (M64.2, M87, M204) is apparently rare: it was found in 1 of 117 males typed in southern Iran.[14]
R-M458 (R1a1a1b1a1)
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."[48] M458 was found in one skeleton from a 14th-century grave field in Usedom, Mecklenburg-Vorpommern, Germany.[49] 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).

R-L260 (R1a1a1b1a1a) (Gwozdz's cluster P)

R1a1a1b1a1a (R-L260), 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).[50] 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."[51] 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.[52]

R-M334

R-M334 ([R1a1a1g1],[42] a subclade of [R1a1a1g] (M458)[42] c.q. R1a1a1b1a1 (M458)[39]) was found by Underhill et al. (2009) only in one Estonian man and may define a very recently founded and small clade.[3]

R1a1a1b1a2 (S466/Z280, S204/Z91)
R1a1a1b1a2b3* (Gwozdz's Cluster K)

R1a1a1b1a2b3* (M417+, Z645+, Z283+, Z282+, Z280+, CTS1211+, CTS3402, Y33+, CTS3318+, Y2613+) (Gwozdz's Cluster K)[40] is a STR based group that is R-M17(xM458). This cluster is common in Poland but not exclusive to Poland.[52]

R1a1a1b1a2b3a (R-L365)

R1a1a1b1a2b3a (R-L365)[39] was early called Cluster G.

R1a1a1b2 (R-Z93) (Asia)

Relative frequency of R-M434 to R-M17
Region People N R-M17 R-M434
Number Freq. (%) Number Freq. (%)
 Pakistan Baloch60915%58%
 Pakistan Makrani601525%47%
 Middle East Oman121119%32.5%
 Pakistan Sindhi1346549%21.5%
Table only shows positive sets from N = 3667 derived from 60 Eurasian populations sample.[3]

This large subclade appears to encompass most of the R1a1a found in Asia.[47]

  • R-Z93* or R1a1a1b2* (R1a1a2* in Underhill (2014)) is most common (>30%) in the South Siberian Altai region of Russia, cropping up in Kyrgyzstan (6%) and in all Iranian populations (1–8%).[53]
  • R-Z2125 occurs at highest frequencies in Kyrgyzstan and in Afghan Pashtuns (>40%). At a frequency of >10%, it is also observed in other Afghan ethnic groups and in some populations in the Caucasus and Iran.[53]
    • R-M434 is a subclade of Z2125. It 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.[54]
  • R-M560 is very rare and was only observed in four samples: two Burushaski speakers (north Pakistan), one Hazara (Afghanistan), and one Iranian Azerbaijani.[53]
  • R-M780 occurs at high frequency in South Asia: India, Pakistan, Afghanistan, and the Himalayas. The group also occurs at >3% in some Iranian populations and is present at >30% in Roma from Croatia and Hungary.[53]

Geographic distribution of R1a1a

R1a among other European haplogroups
Distribution of R1a in Europe
Distribution of R1a (purple) and R1b (red).

Historical

Haplogroup R1a has been found in ancient fossils associated with the Corded Ware culture[55][56] and Urnfield culture;[57] as well as the burial of the remains of the Sintashta culture,[58] Andronovo culture,[59] the Pazyryk culture,[60] Tagar culture[59] and Tashtyk culture,[59] the inhabitants of ancient Tanais,[61] in the Tarim mummies,[62] the aristocracy Xiongnu,[63] in two ancient Khazar fossils. The skeletal 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.[64]

Europe

In Europe, the R1a1 sub-clade is found at highest levels among peoples of Central and Eastern European descent, with results ranging from 35-65% among Czechs, Hungarians, Poles, Slovaks, western Ukrainians (particularly Rusyns), Belarusians, Moldovans, and Russians.[65][66][12] In the Baltics, R1a1a frequencies decrease from Lithuania (45%) to Estonia (around 30%).[67][68][69][12][70].

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.[71][72] Vikings and Normans may have also carried the R1a1a lineage westward; accounting for at least part of the small presence in the British Isles.[73][74] In East Germany, where Haplogroup R1a1a reaches a peak frequency in Rostock at a percentage of 31.3%, it averages between 20 and 30%.[75]

In Southern Europe R1a1a 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.[76] The Balkans shows lower frequencies, and significant variation between areas, for example more than 30% in Slovenia, Croatia and Greek Macedonia, but less than 10% in Albania, Kosovo and parts of Greece.[77][69][12]

R1a is virtually composed only of the Z284 subclade in Scandinavia, which is only found in single sample of a Slovenian in Eastern Europe, where the main subclade is Z282 (Z280 and M458) and there is a negligible representation of Z93 in each region other than Turkey.[41] The West Slavs and Hungarians are characterized by a high frequency of the subclade M458 and a low Z92, a subclade of Z280. Hundreds of samples of each Slovenians, and Czechs lack the Z92 subclade of Z280, while Poles, Slovaks, Croats and Hungarians only show a very low frequency of Z92.[41] The Balts, East Slavs, Serbs, Macedonians, Bulgarians and Romanians demonstrate a ratio Z280>M458 and a high, up to a prevailing share of Z92.[41] Balts and East Slavs have the same subclades and similar frequencies in a more detailed phylogeny of the subclades.[78][79] The Russian geneticist Oleg Balanovsky speculated that there is a predominance of the assimilated pre-Slavic substrate in the genetics of East and West Slavic populations, according to him the common genetic structure which contrasts East Slavs and Balts from other populations may suggest the explanation that the pre-Slavic substrate of the East Slavs consisted most significantly of Baltic-speakers, which at one point predated the Slavs in the cultures of the Eurasian steppe according to archaeological and toponymic references.[80]

Asia

Central Asia

In Afghanistan, R1a1a is found at 51% among the Pashtuns - and 30% among the Tajiks. It is less frequent among the Hazaras (7%) and the Uzbeks (18%).[81]

South Asia

In South Asia, R1a1a has often been observed with high frequency in a number of demographic groups.[34][33]

In India, high frequencies of this haplogroup is observed in West Bengal Brahmins (72%)[33] and Bihar Paswan (40.74%)[1] to the east, Gurajat Lohanas (60%) [3] to the west, Khatris (67%)[3] in the north and Iyengar Brahmins (31%)[33] 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, Kota (22.58%)[82] and the Kallar of Tamil Nadu suggesting that R1a1a is widespread in Tribal Southern Indians.[11]

Besides these, studies show high percentages in regionally diverse groups such as Manipuris (50%)[3] to the extreme North East and among Punjabis (47%)[11] 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.[3] Among the Sinhalese of Sri Lanka, 23% were found to be R1a1a (R-SRY1532) positive.[83] Hindus of Chitwan District in the Terai region Nepal show it at 69%.[84]

East Asia

The frequency of R1a1a 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.[13][85][86]

A Chinese paper published in 2018 found R1a-Z94 in 38.5% (15/39) of a sample of Keriyalik Uyghurs from Darya Boyi/Darya Boye Village, Yutian/Keriya County, Xinjiang (于田县达里雅布依乡), R1a-Z93 in 28.9% (22/76) of a sample of Dolan Uyghurs from Horiqol township, Awat County, Xinjiang (阿瓦提县乌鲁却勒镇), and R1a-Z93 in 6.3% (4/64) of a sample of Loplik Uyghurs from Karquga/Qarchugha Village, Yuli/Lopnur County, Xinjiang (尉犁县喀尔曲尕乡). R1a(xZ93) was observed only in one of 76 Dolan Uyghurs.[87] Note that Darya Boyi Village is located in a remote oasis formed by the Keriya River in the Taklamakan Desert.

In Eastern Siberia, R1a1a is found among certain indigenous ethnic groups including Kamchatkans and Chukotkans, and peaking in Itel'man at 22%.[88]

West Asia

R1a1a 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%.[89][90][91])

Wells 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% R1a1a. Nasidze 2004 found R1a1a 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.[92]

Haplogroup R1a1a 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 R1a1a to be the dominant haplogroup in Ashkenazi Levites (52%), although rare in Ashkenazi Cohanim (1.3%).[66]

Further to the north of these Middle Eastern regions on the other hand, R1a1a levels start to increase in the Caucasus, once again in an uneven way. Several populations studied have shown no sign of R1a1a, 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 R1a1a.[3]

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 naming of "R1a"

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 (YCC 2002), 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", as used in (Semino 2000) 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. Note, SRY1532.2 is also known as SRY10831.2 The discovery of M420 in 2009 has caused a reassignment of these phylogenetic names.(Underhill 2009 and ISOGG 2012) 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 (2009) 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)

 
R1a
M420

 

R1a* (As before)

 
R1a1
SRY1532.2

 

R1a1* (As before)

 
R1a1a
M17

 

 

R1a1a* (As before)

 
 
R1a1a1
M417, Page7

 

R1a1a1*

 
M56
 

R1a1a1a

 
M157
 

R1a1a1b

 
 M64.2,..
 

R1a1a1c

 
P98
 

R1a1a1d

 
PK5
 

R1a1a1e

 
M434
 

R1a1a1f

 
 Z283 
 

 

 R1a1a1g*

 
 M458 
 

 

 R1a1a1g1*

 
 
M334 
 

 R1a1a1g1a

 

L260 
 

 R1a1a1g1b

 
 
 Z280 
 

 

 R1a1a1g2*

 
 
P278.2 
 

 R1a1a1g2a

 

L365 
 

 R1a1a1g2b

 

L366 
 

 R1a1a1g2c

 

Z92 
 

 R1a1a1g2d

 
 
 Z284 
 

 

 R1a1a1g3*

 
 
P278.2 
 

 R1a1a1g3a

 
 
 
 Z93

 

 R1a1a1h*

 
 
L342.2 
 

 

 R1a1a1h1*

 
 
L657 
 

 R1a1a1h1a

 
 
 
 
 
 
 
R1b
M343

Sibling clade to R1a (same as before)

 
 

See also

Y-DNA R-M207 subclades

Y-DNA backbone tree

Phylogenetic 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
B CT
DE CF
D E C F
F1  F2  F3  GHIJK
G HIJK
IJK H
IJ K
I   J     LT [χ 5]       K2 [χ 6]
L     T    K2a [χ 7]        K2b [χ 8]     K2c     K2d K2e [χ 9]  
K-M2313 [χ 10]     K2b1 [χ 11] P [χ 12]
NO   S [χ 13]  M [χ 14]    P1     P2
N O Q R

Notes

  1. ↑ According to Family Tree, they diversified ca. 5,000 years ago.[8]
  2. 1 2 Kivisild et al. (2003): "Haplogroup R1a, previously associated with the putative Indo-Aryan invasion, was found at its highest frequency in Punjab but also at a relatively high frequency (26%) in the Chenchu tribe. This finding, together with the higher R1a-associated short tandem repeat diversity in India and Iran compared with Europe and central Asia, suggests that southern and western Asia might be the source of this haplogroup."[11]
  3. ↑ Semenov and Bulat refer to the following publications:
    5. Haak W. et al. Massive migration from the steppe is a source for Indo-European languages in Europe. doi:10.1101/013433.
    6. Mathieson I et al. Eight thousand years of natural selection in Europe. doi:10.1101/016477
    8. Chekunova Е.М., Yartseva N.V., Chekunov М.К., Мazurkevich А.N. The First Results of the Genotyping of the Aboriginals and Human Bone Remains of the Archeological Memorials of the Upper Podvin’e. // Archeology of the lake settlements of IV—II Thousands BC: The chronology of cultures and natural environment and climatic rhythms. Proceedings of the International Conference, Devoted to the 50-year Research of the Pile Settlements on the North-West of Russia. St. Petersburg, 13–15 November 2014.
    9. Eppie R. Jones et al. Upper Palaeolithic genomes reveal deep roots of modern Eurasians. Nature Communications. doi:10.1038/ncomms9912 PMID 26567969
  4. ↑ Yet, Haak et al. also explicitly state: "...a type of Near Eastern ancestry different from that which was introduced by early farmers."[25]
  5. ↑ According to Family Tree DNA, L664 formed 4,700 ybp, that is, 2,700 BCE.[8]
  6. ↑ Asko Parpola (2015) proposes the Cucuteni-Trypolye culture as the carrier of late Proto-Indo-European. He notes that the Cucuteni-Trypolye culture may have been the birthplace of wheeled vehicles, giving the words related to these vehicles. Parpola further notes that the Cucuteni-Trypolye culture was taken over by PIE speakers at circa 4,000 BCE, and expanded to the Pontic steppe ca. 3,400 BCE, eventually giving rise to the Yamna culture.[26]
  7. ↑ Lazaridis, Twitter, 18 juni 2016: "I1635 (Armenia_EBA) is R1b1-M415(xM269). We'll be sure to include in the revision. Thanks to the person who noticed! #ILovePreprints."
    See also Eurogenes Blog, Big deal of 2016: the territory of present-day Iran cannot be the Indo-European homeland, for a discussion of the same topic.
  8. ↑ See map for M780 distribution at Dieneke's Anthropology Blog, Major new article on the deep origins of Y-haplogroup R1a (Underhill et al. 2014)[30]
  9. ↑ According to Family Tree DNA, M780 formed 4700 ybp.[8] This dating coincides with the eastward movement between 2800 and 2600 BCE of the Yamna culture into the region of the Poltavka culture, a predecessor of the Sintashta culture, from which the Indo-Iranians originated. M780 is concentrated in the Ganges Vally, the locus of the classic Vedic society.
  10. ↑ Poznik et al. (2026) calculate with a generation time of 30 years; a generation time of 20 years yields other results.
  11. ↑ "The evidence that the Steppe_MLBA [Middle to Late Bronze Age] cluster is a plausible source for the Steppe ancestry in South Asia is also supported by Y chromosome evidence, as haplogroup R1a which is of the Z93 subtype common in South Asia today [Underhill et al 2015, M. Silva et al 2017] was of high frequency in Steppe_MLBA (68%) (16), but rare in Steppe_EMBA [Early to Middle Bronze Age] (absent in our data)."[32]
  12. ↑ Qutes:
    • Sahoo et al. (2006): "... one should expect to observe dramatically lower genetic variation among Indian Rla lineages. In fact, the opposite is true: the STR haplotype diversity on the background of R1a in Central Asia (and also in Eastern Europe) has already been shown to be lower than that in India (6). Rather, the high incidence of R1* and Rla throughout Central Asian European populations (without R2 and R* in most cases) is more parsimoniously explained by gene flow in the opposite direction, possibly with an early founder effect in South or West Asia.[36]
    • Sharma et al. (2009): "A peculiar observation of the highest frequency (up to 72.22%) of Y-haplogroup R1a1* in Brahmins hinted at its presence as a founder lineage for this caste group. Further, observation of R1a1* in different tribal population groups, existence of Y-haplogroup R1a* in ancestors and extended phylogenetic analyses of the pooled dataset of 530 Indians, 224 Pakistanis and 276 Central Asians and Eurasians bearing the R1a1* haplogroup supported the autochthonous origin of R1a1 lineage in India and a tribal link to Indian Brahmins. However, it is important to discover novel Y-chromosomal binary marker(s) for a higher resolution of R1a1* and confirm the present conclusions."[1]
  13. ↑ Sengupta et al. (2006): "The widespread geographic distribution of HG R1a1-M17 across Eurasia and the current absence of informative subdivisions defined by binary markers leave uncertain the geographic origin of HG R1a1-M17. However, the contour map of R1a1-M17 variance shows the highest variance in the northwestern region of India [...] The question remains of how distinctive is the history of L1 relative to some or all of R1a1 and R2 representatives. This uncertainty neutralizes previous conclusions that the intrusion of HGs R1a1 and R2 from the northwest in Dravidian-speaking southern tribes is attributable to a single recent event. [R1a1 and R2] could have actually arrived in southern India from a southwestern Asian source region multiple times, with some episodes considerably earlier than others. Considerable archeological evidence exists regarding the presence of Mesolithic peoples in India (Kennedy 2000), some of whom could have entered the subcontinent from the northwest during the late Pleistocene epoch. The high variance of R1a1 in India (table 12), the spatial frequency distribution of R1a1 microsatellite variance clines (fig. 4), and expansion time (table 11) support this view."[33]

References

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  3. 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 Underhill 2009.
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  5. 1 2 3 4 5 Pamjav 2012.
  6. 1 2 Karafet, Tatiana; Mendez, Fernando; Sudoyo, Herawati (2014). "Improved phylogenetic resolution and rapid diversification of Y-chromosome haplogroup K-M526 in Southeast Asia". Nature. 23 (3): 369–373. doi:10.1038/ejhg.2014.106. PMC 4326703. PMID 24896152.
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  18. ↑ Population genomics of Bronze Age Eurasia, Allentoft et al, 2015
  19. ↑ Eight thousand years of natural selection in Europe, Mathieson et al, 2015
  20. ↑ Anthony 2007.
  21. ↑ Anthony & Ringe 2015.
  22. 1 2 Haak 2015, p. 5.
  23. ↑ Semenov & Bulat 2016.
  24. ↑ Semenov & Bulat 2016, p. 41.
  25. ↑ Haak 2015, p. 4.
  26. ↑ Parpola 2015, p. 43-47.
  27. 1 2 3 Mascarenhas 2015, p. 9.
  28. ↑ Pozink 2016, p. 5.
  29. ↑ Arame's English blog, Y DNA from ancient Near East
  30. ↑ Major new article on the deep origins of Y-haplogroup R1a (Underhill et al. 2014)
  31. ↑ Poznik 2016, p. 5.
  32. 1 2 Narasimhan 2018.
  33. 1 2 3 4 5 6 7 Sengupta 2006.
  34. 1 2 3 4 5 Sahoo 2006.
  35. 1 2 Thangaraj 2010.
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  37. ↑ Joseph 2017.
  38. 1 2 Silva 2017.
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  65. ↑ Balanovsky 2008.
  66. 1 2 Behar 2003.
  67. ↑ Kasperaviciūte 2005.
  68. ↑ Battaglia 2008.
  69. 1 2 Rosser 2000.
  70. ↑ Tambets 2004.
  71. ↑ Bowden 2008.
  72. ↑ Dupuy 2005.
  73. ↑ Passarino 2002.
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  75. ↑ Kayser 2005.
  76. ↑ Scozzari 2001.
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  78. ↑ http://pereformat.ru/wp-content/uploads/2015/02/russian-plain-01.jpg. Missing or empty |title= (help)
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  80. ↑ П, Балановский О. (2015-11-30). Генофонд Европы (in Russian). KMK Scientific Press. ISBN 9785990715707. Прежде всего, это преобладание в славянских популяциях дославянского субстрата — двух ассимилированных ими генетических компонентов – восточноевропейского для западных и восточных славян и южноевропейского для южных славян...Можно с осторожностью предположить, что ассимилированный субстратмог быть представлен по преимуществу балтоязычными популяциями. Действительно, археологические данные указыва ют на очень широкое распространение балтских групп перед началом расселения славян. Балтскийсубстрату славян (правда, наряду с финно-угорским) выявляли и антропологи. Полученные нами генетические данные — и на графиках генетических взаимоотношений, и по доле общих фрагментов генома — указывают, что современные балтские народы являются ближайшими генетически ми соседями восточных славян. При этом балты являются и лингвистически ближайшими род ственниками славян. И можно полагать, что к моменту ассимиляции их генофонд не так сильно отличался от генофонда начавших свое широкое расселение славян. Поэтому если предположить,что расселяющиеся на восток славяне ассимилировали по преимуществу балтов, это может объяснить и сходство современных славянских и балтских народов друг с другом, и их отличия от окружающих их не балто-славянских групп Европы...В работе высказывается осторожное предположение, что ассимилированный субстрат мог быть представлен по преимуществу балтоязычными популяциями. Действительно, археологические данные указывают на очень широкое распространение балтских групп перед началом расселения славян. Балтский субстрат у славян (правда, наряду с финно-угорским) выявляли и антропологи. Полученные в этой работе генетические данные — и на графиках генетических взаимоотношений, и по доле общих фрагментов генома — указывают, что современные балтские народы являются ближайшими генетическими соседями восточных славян.
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  82. ↑ Arunkumar 2012.
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Extended content
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DNA Tree
TMRCA
Various
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