Haplogroup R1a
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. While R1a originated ca. 22,000 to 25,000 years ago, its subclade M417 (R1a1a1) diversified ca. 5,800 years ago. 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 split of R1a (M420) is computed to ca. 22,000 or 25,000 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." The ancient DNA record has shown the first R1a during the Mesolithic  in Eastern Hunter-Gatherers (from Eastern Europe), and the earliest case of R* among Upper Paleolithic Ancient North Eurasians, from which the Eastern Hunter-Gatherers predominantly derive their ancestry. No early samples of R1a have so far been found in Iran. Diversification of R1a1a1 (M417) and ancient migrations. According to , the downstream R1a-M417 subclade diversified into Z282 and Z93 circa 5,800 years ago "in the vicinity of Iran and Eastern Turkey." 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 some extent Scandinavia 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. Steppe origins. Proposed steppe dispersal of  R1a1a. 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. 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. According to , R1a1a diversified in the Eurasian Steppes or the Middle East and Caucasus region: 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. Source of R1a1a1 in Corded Ware culture. David Anthony considers the Yamnaya culture to be the Indo-European Urheimat. According to , a massive migration from the Yamnaya 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". Yet, all their seven Yamnaya samples belonged to the R1b-M269 subclade, 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. Transcaucasia & West Asian origins and possible influence on Indus Valley Civilization. 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 and expanded there during the Indus Valley Civilization. According to 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) may reflect this." 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." However, according to , steppe pastoralists are a likely source for R1a in India. Proposed South Asian origins. Kivisild et al. (2003) have proposed either South or West  Asia, while see support for both South and Central Asia. Sharma et al.(2009) showcased the existence of R1a in India beyond 18,000 years to possibly 44,000 years in origin. South Asian populations have the highest STR diversity within R1a1a, and subsequent older TMRCA datings, and R1a1a is present among both higher (Brahmin) castes and lower castes, although the frequency is higher among Brahmin castes. From these findings some researchers have concluded that R1a1a originated in South Asia, excluding a substantial genetic influx from Indo-European migrants. 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. According to Sengupta et al. (2006), "[R1a1 and R2] could have actually arrived in southern India from a southwestern Asian source region multiple times." 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." According to Martin P. Richards, co-author of , "[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." 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 [in brackets] non-isogg codes): 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." 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. 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. 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). R1a1 is defined by SRY1532.2 or SRY10831.2 (understood to always include SRY10831.2, M448, L122, M459 , and M516). 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. reported R-SRY1532.2* for 1/15 Himachal Pradesh Rajput samples. R-M17/M198 (R1a1a). The following SNPs are associated with R1a1a: 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)) and Central and South Asia (R1a1a1b2 (R-Z93) ([R1a1a2*] (R-Z93) Underhill 2014)). R-Z282 (R1a1a1b1a) (Eastern Europe). This large subclade appears to encompass most of the R1a1a found in Europe. R-M458 (R1a1a1b1a1). 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."" M458 was found in one skeleton from a 14th-century grave field in Usedom, Mecklenburg-Vorpommern, Germany. 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). 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 . In 2010 it was verified  to be a haplogroup identified by its own mutation (SNP). It apparently accounts for about 8% of Polish men, making it the most common subclade in Poland. Outside of Poland it is less common. 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. R-M334. R-M334 ([R1a1a1g1], a subclade of [R1a1a1g] (M458) c.q. R1a1a1b1a1 (M458)) was  found by Underhill et al. (2009) only in one Estonian man and may define a very recently founded and small clade. 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) is a STR based group that is R-M17(xM458). This cluster is common in Poland but not exclusive to Poland. R1a1a1b1a2b3a (R-L365). R1a1a1b1a2b3a (R-L365) was early called "Cluster G". R1a1a1b2 (R-Z93) (Asia). This large subclade appears to encompass most of the R1a1a  found in Asia. Geographic distribution of R1a1a. Historical. In Mesolithic Europe, R1a is characteristic of Eastern Hunter-Gatherers (EHGs). A male EHG of the Veretye culture buried at Peschanitsa near Lake Lacha in Arkhangelsk Oblast, Russia ca. 10,700 BCE was found to be a carrier of the paternal haplogroup R1a5-YP1301 and the maternal haplogroup U4a. A Mesolithic male from Karelia ca. 8,800 BCE to 7950 BCE has been found to be carrying haplogroup R1a. A Mesolithic male buried at Deriivka ca. 7000 BCE to 6700 BCE carried the paternal haplogroup R1a and the maternal U5a2a. Another male from Karelia  from ca. 5,500 to 5,000 BC, who was considered an EHG, carried haplogroup R1a. A male from the Comb Ceramic culture in Kudruküla ca. 5,900 BCE to 3,800 BCE has been determined to be a carrier of R1a and the maternal U2e1. According to archaeologist David Anthony, the paternal R1a-Z93 was found at Alexandria, Ukraine ca. 4000 BCE, Sredny Stog culture, "the earliest known sample to show the genetic adaptation to lactase persistence (I3910-T)." R1a has been found in the Corded Ware culture, in which it is predominant. Examined males of the Bronze Age Fatyanovo culture belong entirely  to R1a, specifically subclade R1a-Z93. Haplogroup R1a has later been found in ancient fossils associated with the Urnfield culture; as well as the burial of the remains of the Sintashta, Andronovo, the Pazyryk, Tagar, Tashtyk, and Srubnaya cultures, the inhabitants of ancient Tanais, in the Tarim mummies, and the aristocracy Xiongnu. 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. 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. In the Baltics, R1a1a frequencies decrease from Lithuania (45%) to Estonia (around 30%). 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 further out; accounting for at least part of the small presence in the British Isles, the Canary Islands, and Sicily. In East Germany, where Haplogroup R1a1a reaches a peak frequency in Rostock at a percentage of 31.3%, it averages between 20 and 30%. 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. The Balkans shows wide variation between areas with significant levels of R1a1a, for example 36–39 % in Slovenia, 27%-34% in Croatia, and over 30% in Greek Macedonia, but less than 10% in Albania, Kosovo and parts of Greece south of Olympus gorge. R1a is virtually composed only of the Z284 subclade in Scandinavia. In Slovenia, the main subclade is Z282 (Z280 and M458), although the Z284 subclade was found in one sample of a Slovenian. There is a negligible representation of Z93 in each region other than Turkey. West Slavs and Hungarians are characterized by a high frequency of the subclade M458 and a low Z92, a subclade of Z280. Hundreds of Slovenian samples and Czechs  lack the Z92 subclade of Z280, while Poles, Slovaks, Croats and Hungarians only show a very low frequency of Z92. The Balts, East Slavs, Serbs, Macedonians, Bulgarians and Romanians demonstrate a ratio Z280>M458 and a high, up to a prevailing share of Z92. Balts and East Slavs have the same subclades and similar frequencies in a more detailed phylogeny of the subclades. 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. Asia. Central Asia. found R1a1a in 64% of a sample of the Tajiks of Tajikistan and 63% of a sample of the Kyrgyz of Kyrgyzstan. South Asia. In South Asia, R1a1a has often been observed in a number of demographic groups. In India, high frequencies of this haplogroup is observed in West Bengal Brahmins (72 %) to the east, Gujarat Lohanas (60%) to the west, Khatris (67%) in the north and Iyengar Brahmins (31%) 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%) and the Kallar of Tamil Nadu suggesting that R1a1a is widespread in Tribal Southern Indians. Besides these, studies show high percentages in regionally diverse groups such as Manipuris (50%) to the extreme North East and among Punjabis (47%) 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. Among the Sinhalese of Sri Lanka, 23% were found to be R1a1a (R-SRY1532) positive. Hindus of Chitwan District in the Terai region Nepal show it at 69%. East Asia. The frequency of R1a1a is comparatively low among some Turkic-speaking groups like 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. 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 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 County, Xinjiang (尉犁县喀尔曲尕乡). R1a(xZ93) was observed only in one of 76 Dolan Uyghurs. Note that Darya Boyi Village is located in a remote oasis formed by the Keriya River in the Taklamakan Desert. A 2011 Y-dna study found Y-dna R1a1 in 10% of a sample of southern Hui people  from Yunnan, 1.6% of a sample of Tibetan people from Xizang (Tibet Autonomous Region), 1.6% of a sample of Xibe people from Xinjiang, 3.2% of a sample of northern Hui from Ningxia, 9.4% of a sample of Hazak (Kazakhs) from Xinjiang, and rates of 24.0%, 22.2%, 35.2%, 29.2% in 4 different samples of Uyghurs from Xinjiang, 9.1% in a sample of Mongols from Inner Mongolia, 10% of a sample of Northern Han Chinese from Gansu and 8.9% of a sample of Northern Han from western Henan. A different subclade of R1 was also found in 1.5% of a sample of  northern Hui from Ningxia. in the same study there were no cases of R1a detected at all in 6 samples of Han Chinese in Yunnan, 1 sample of Han in Guangxi, 5 samples of Han in Guizhou, 2 samples of Han in Guangdong, 2 samples of Han in Fujian, 2 samples of Han in Zhejiang, 1 sample of Han in Shanghai, 1 samples of Han in Jiangxi, 2 samples of Han in Hunan, 1 sample of Han in Hubei, 2 samples of Han in Sichuan, 1 sample of Han in Chongqing, 3 samples of Han in Shandong, 5 samples of  Han in Gansu, 3 samples of Han in Jilin and 2 samples of Han in Heilongjiang. T-M70, R-M207 (a subclade of R1a), Q-M242, L-M20, J-P209, I-M170, H-M69, G-M201, C5-M356 and E-SRY4064 collectively make up only 6.79% of the total male population of East Asia (from samples in North Korea and China). The vast majority of East Asia is N-M231, C-M130 except C5-M356, D-M174 and O-M175 which is 92.87% of the population and are all East Eurasian male haplogroups. R-M207 (a subclade of R1a) came  into East Asia via the north from the Central South Asia region (CSA) during paleolithic times in the post glacial period, especially R1a1a. R1a1a in East Asia is an extremely ancient subclade from the Central Asia-South Asia region and is older than the Western Eurasian (European_ and Central Asian-South Asian (CSA) R1a1*-M17, rivaling the R1a1*-M17 of IWest India in age from testing on variations in STR. The Europe and West Asian R1a1*-M17 split into 7 subbranches only after R1a1 came to North East Asia, indicating R1a1 in East Asia is an extremely ancient one dating  back 15,370 years ago juding from variation in STR (predating the more recent Aryan and Indo-European expansions). In a 2014 paper, R1a1a has been detected in 1.8% (2/110) of Chinese samples. These two samples (R-M17, R-M198, R-M434, R-M458 for both) belonged to Han individuals from Fujian and Shanxi provinces. 40% of Salars, 45.2% of Tajiks of Xinjiang, 54.3% of Dongxiang, 60.6% of Tatars and 68.9% of Kyrgyz in Xinjiang in northwestern China tested in one sample had R1a1-M17. Bao'an (Bonan) had the most haplogroup diversity of 0.8946±0.0305 while the other ethnic minorities in northwestern  China had a high haplogroup diversity like Central Asians, of 0.7602±0.0546. . In Eastern Siberia, R1a1a is found among certain indigenous ethnic groups including Kamchatkans and Chukotkans, and peaking in Itel'man at 22%. 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 and Iran. The Shimar (Shammar) Bedouin tribe in Kuwait show the highest frequency in the Middle East at 43%. , 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. found R1a1a in approximately 20% of Iranian males from the cities of Tehran and Isfahan. 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, 19% among Azerbaijanis in West Azerbaijan, 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 Bandari people in Hormozgan and 25% among the Baloch people in Sistan and Baluchestan Province. Further to the north of these Western Asian 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 . 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 , 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 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.( and ) 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.