Haplogroup R1a
Possible time of origin	22,000[1] to 25,000[2] years ago
Possible place of origin	Eurasia
Ancestor	Haplogroup R1
Descendants	R1a-Z282, R1a-Z93
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 Central Asia, southern Siberia and South Asia.^[3][2]

While one genetic study indicates that R1a originated 25,000^[2] years ago, its subclade M417 (R1a1a1) diversified c. 5,800 years ago.^[4] The place of origin of the subclade 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

The genetic divergence of R1a (M420) is estimated to have occurred 25,000^[2] years ago, which is the time of the last glacial maximum. A 2014 study by Peter A. Underhill et al., using 16,244 individuals from over 126 populations from across Eurasia, concluded that there was "a compelling case for the Middle East, possibly near present-day Iran, as the geographic origin of hg R1a".^[2] The ancient DNA record has shown the first R1a during the Mesolithic in Eastern Hunter-Gatherers (from Eastern Europe, c. 13,000 years ago),^[5][6] and the earliest case of R* among Upper Paleolithic Ancient North Eurasians,^[7] from which the Eastern Hunter-Gatherers predominantly derive their ancestry.^[8]

Diversification of R1a1a1 (M417) and ancient migrations

According to Underhill et al. (2014), the downstream R1a-M417 subclade diversified into Z282 and Z93 circa 5,800 years ago "in the vicinity of Iran and Eastern Turkey".^{[4][note 1]} Even though R1a occurs as a Y-chromosome haplogroup among various languages such as Slavic and Indo-Iranian, 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 civilization. R1a shows a strong correlation with Indo-European languages of Southern and Western Asia, Central and Eastern Europe and to Scandinavia^[10][3] being most prevalent in Eastern Europe, West Asia, and South 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.^[11]

Proposed steppe dispersal of R1a1a

Semino et al. (2000) proposed Ukrainian origins, and a postglacial spread of the R1a1 haplogroup during the Late Glacial Maximum, subsequently magnified by the expansion of the Kurgan culture into Europe and eastward.^[12] 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 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.^[14]

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 Pontic–Caspian 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.^[15][16][17]

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 Indian subcontinent, consistent with multiple waves of arrival."^[18] According to Martin P. Richards, co-author of Silva et al. (2017), the prevalence of R1a in India was "very powerful evidence for a substantial Bronze Age migration from central Asia that most likely brought Indo-European speakers to India."^{[19][note 2]}

Proposed South Asian origins

Kivisild et al. (2003) have proposed either South or West Asia,^{[20][note 3]} while Mirabal et al. (2009) see support for both South and Central Asia.^[10] Sengupta et al. (2006) have proposed Indian origins.^[21] Thanseem et al. (2006) have proposed either South or Central Asia.^[22] Sahoo et al. (2006) have proposed either South or West Asia.^[23] Thangaraj et al. (2010) have also proposed a South Asian origin.^[24] Sharma et al.(2009) theorizes the existence of R1a in India beyond 18,000 years to possibly 44,000 years in origin.^[1]

South Asian populations have the highest STR diversity within R1a1a,^{[25][26][10][3][1][27]} and subsequent older TMRCA datings,^{[citation needed]} and R1a1a is present among both higher (Brahmin) castes and lower castes, although the frequency is higher among Brahmin castes. Nevertheless, the oldest TMRCA datings of the R1a haplogroup occur in the Saharia tribe, a scheduled caste of the Bundelkhand region of Central India.^[1][27] From these findings some researchers have concluded that R1a1a originated in South Asia,^{[26][1][note 4][note 5]} excluding a more recent, yet minor, genetic influx from Indo-European migrants in northwestern regions such as Afghanistan, Balochistan, Punjab, and Kashmir.^[26][25][3]

However, this diversity, and the subsequent older TMRCA-datings, can also be explained by the historically high population numbers,^{[note 6]} which increases the likelihood of diversification and microsatellite variation.^[19][18] According to Sengupta et al. (2006), " could have actually arrived in southern India from a southwestern Asian source region multiple times."^{[25][note 7]} However, Sengupta also described in this article:

We found that the influence of Central Asia on the pre-existing gene pool was minor. The ages of accumulated microsatellite variation in the majority of Indian haplogroups exceed 10,000–15,000 years, which attests to the antiquity of regional differentiation. Therefore, our data do not support models that invoke a pronounced recent genetic input from Central Asia to explain the observed genetic variation in South Asia.

In the MIT publishing, "Inequality a genetic Theory", it is stated "the phylogenetic reconstruction of R1a does not support a South Asian origin." Despite the source (i.e. MIT) bearing credibility, the phylogenetic reconstruction the author is referring to is not cited, also excluding the fact that phylogenetic reconstructions have large margins of error mainly attributing to "Model Uncertainty" since assumptions are made on the evolutionary/Mutation process beforehand (Here it would refer to Different models of evolution may produce different phylogenetic trees, leading to uncertainty in the inferred relationships.), also excluding errors generated due to sampling, measurement and of course statistical uncertainty. The mainstream position among geneticists is that haplogroup R1a did not originate in South Asia, and that the bearers of haplogroup R1a moved from West Asia to South Asia some time after the establishment of the Indus Valley Civilization.^[29][30]

Proposed Yamnaya origins

David Anthony considers the Yamnaya culture to be the Indo-European Urheimat.^[31][32] According to Haak et al. (2015), a massive migration from the Yamnaya culture northwards took place c. 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".^[33] Yet, all their seven Yamnaya samples belonged to the R1b-M269 subclade,^[33] but no R1a1a has been found in their Yamnaya samples. This raises the question where the R1a1a in the Corded Ware culture came from, if it was not from the Yamnaya culture.^[34]

According to Marc Haber, the absence of haplogroup R1a-M458 in Afghanistan does not support a Pontic-Caspian steppe origin for the R1a lineages in modern Central Asian populations.^[35]

According to Leo Klejn, the absence of haplogroup R1a in Yamnaya remains (despite its presence in Eneolithic Samara and Eastern Hunter Gatherer populations) makes it unlikely that Europeans inherited haplogroup R1a from Yamnaya.^[36]

Archaeologist Barry Cunliffe has said that the absence of haplogroup R1a in Yamnaya specimens is a major weakness in Haak's proposal that R1a has a Yamnaya origin.^[37]

Semenov & Bulat (2016) do argue for a Yamnaya origin of R1a1a in the Corded Ware culture, noting that several publications point to the presence of R1a1 in the Comb Ware culture.^{[38][note 8]}

Proposed Transcaucasia and West Asian origins and possible influence on Indus Valley Civilization

Haak et al. (2015) found that part of the Yamnaya ancestry derived from the Middle East and that neolithic techniques probably arrived at the Yamnaya culture from the Balkans.^{[note 9]} The Rössen 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 10]}

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^[40] and expanded there during the Indus Valley civilization.^[2][41]

Mascarenhas et al. (2015) proposed that the roots of Z93 lie in West Asia, and proposed that "Z93 and L342.2 expanded in a southeasterly direction from Transcaucasia into South Asia",^[40] 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."^[40] Yet, Lazaridis noted that sample I1635 of Lazaridis et al. (2016), their Armenian Kura-Araxes sample, carried Y-haplogroup R1b1-M415(xM269)^{[note 11]} (also called R1b1a1b-CTS3187).^{[42][unreliable source?]}

According to Underhill et al. (2014) the diversification of Z93 and the "early urbanization within the Indus Valley ... occurred at and the geographic distribution of R1a-M780 (Figure 3d^{[note 12]}) may reflect this."^{[2][note 13]} Poznik et al. (2016) note that "striking expansions" occurred within R1a-Z93 at c. 4,500–4,000 years ago, which "predates by a few centuries the collapse of the Indus Valley Civilisation."^{[41][note 14]}

However, according to Narasimhan et al. (2018), steppe pastoralists are a likely source for R1a in India.^{[44][note 15]}

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 such as "R1a1" in relatively recent but not the latest literature).

Topology

The topology of R1a is as follows (codes non-isogg codes):^{[9][45][verification needed][46][2][47]} 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."^[48]

Haplogroup Redit

R-M173 (R1)edit

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)edit

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][51]

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]

This paragroup is now known as R1a2 (R-YP4141). It then has two branches R1a2a (R-YP5018) and R1a2b (R-YP4132).

R-SRY1532.2 (R1a1)edit

R1a1 is defined by SRY1532.2 or SRY10831.2 (understood to always include SRY10831.2, M448, L122, M459, and M516^[3][52]). 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 al. (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.^[26]

R-M17/M198 (R1a1a)edit

The following SNPs are associated with R1a1a:

R-M417 (R1a1a1)edit

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)^[2]) and Central and South Asia (R1a1a1b2 (R-Z93) (R1a1a2* (R-Z93) Underhill 2014)^[2]).

R-Z282 (R1a1a1b1a) (Eastern Europe)edit

This large subclade appears to encompass most of the R1a1a found in Europe.^[14]

• R1a1a1b1a R1a1a1a* (Underhill (2014)) (R-Z282*) occurs in northern Ukraine, Belarus, and Russia at a frequency of c. 20%.^[2]
• R1a1a1b1a3 R1a1a1a1 (Underhill (2014)) (R-Z284) occurs in Northwest Europe and peaks at c. 20% in Norway.^[2]
• R1a1a1c (M64.2, M87, M204) is apparently rare: it was found in 1 of 117 males typed in southern Iran.^[53]

R-M458 (R1a1a1b1a1)edit

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." (Zhivotovsky speeds, 3x overvalued)^[3] M458 was found in one skeleton from a 14th-century grave field in Usedom, Mecklenburg-Vorpommern, Germany.^[54] The paper by Underhill et al. (2009) also reports a surprisingly high frequency of M458 in some Northern Caucasian populations (18% among Ak Nogai,^[55] 7.8% among Qara Nogai and 3.4% among Abazas).^[56]

R-L260 (R1a1a1b1a1a)edit

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 et al. 2002. In 2010 it was verified to be a haplogroup identified by its own mutation (SNP).^[57] It apparently accounts for about 8% of Polish men, making it the most common subclade in Poland. Outside of Poland it is less common.^[58] In addition to Poland, it is mainly found in the Czech Republic and Slovakia, and is considered "clearly West Slavic". 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.^[59]

R-M334edit

R-M334 (R1a1a1g1,^[47] a subclade of R1a1a1g (M458)^[47] c.q. R1a1a1b1a1 (M458)^[46]) 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)edit

R1a1a1b1a2b3* (Gwozdz's Cluster K)edit

R1a1a1b1a2b3* (M417+, Z645+, Z283+, Z282+, Z280+, CTS1211+, CTS3402, Y33+, CTS3318+, Y2613+) (Gwozdz's Cluster K)^{[45][verification needed]} is a STR based group that is R-M17(xM458). This cluster is common in Poland but not exclusive to Poland.^[59]

R1a1a1b1a2b3a (R-L365)edit

R1a1a1b1a2b3a (R-L365)^[46] was early called Cluster G.^{[citation needed]}

R1a1a1b2 (R-Z93) (Asia)edit

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