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Haplogroup R (Y-DNA)

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For the mitochondrial DNA haplogroup, see Haplogroup R (mtDNA).

Haplogroup R
Possible time of originabout 27,000 years BP[1][2]
Possible place of originNorth Asia[3], Indian subcontinent,[4] Central Asia, or Middle East
AncestorP-M45 (P1c, formerly P1), one of the three primary clades of P* (P-F5850)
DescendantsR1 (R-M173), R2 (R-M479) (R2)
Defining mutationsM207/Page37/UTY2, CTS207/M600/PF5992, CTS2426/M661/PF6033, CTS2913/M667, CTS3229/M672/PF6036/YSC0001265, CTS3622/PF6037, CTS5815/M696, CTS6417/Y480, CTS7876/PF6052, CTS7880/M725/PF6053, CTS8311/M732, CTS9005/M741, CTS10663/M788, CTS11075/M795/P6078, CTS11647/Y369, F33/M603/PF6013, F63/M614/PF6016, F82/M620, F154/M636, F295/M685, F356/M703/PF5919, F370/M708/Y479, F459/Y482, F652/M805, F765, FGC1168, L248.3/M705.3, L747/M702/PF5918/YSC0000287, L760/M642/PF5877/YSC0000286, L1225/M789/YSC0000232, L1347/M792/PF6077/YSC0000233, M613, M628/PF5868, M651/Y296, M718, M734/PF6057/S4/YSC0000201, M760/Y506, M764/PF5953, M799, P224/PF6050, P227, P229/PF6019, P232, P280, P285, PF5938, PF6014/S9[1]

Haplogroup R, or R-M207, is a Y-chromosome DNA haplogroup. It is both numerous and widespread among modern populations.

Some descendant subclades have been found since pre-history in Europe, Central Asia and South Asia. Others have long been present, at lower levels, in parts of West Asia and Africa. Some authorities have also suggested, more controversially, that R-M207 has long been present among Native Americans in North America – a theory that has not yet been widely accepted.[5]

According to geneticist Spencer Wells, haplogroup K originated in the Middle East or Central Asia.[6] However, Karafet et al. (2014) proposed that "rapid diversification ... of K-M526", also known as K2, likely occurred in Southeast Asia (near Indonesia) and later expanded to mainland Asia, although they could not rule out that it might have arisen in Eurasia and later went extinct there, and that either of these scenarios are "equally parsimonious".[7] According to Bergstorm et al, haplogroup K2b1 (Y-haplogroup S/M) found in Indigenous Australians and ancestors of haplogroup R and Q (Y-haplogroup K2b2/root P) split in Southeast Asia near Sahul.[8]

Structure

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Human Y-DNA Phylogenetic Tree
Haplogroup R
M207 (R)
M173 (R1)
M420 (R1a)
M459

(R1a1)

(R1a*)

M343 (R1b)
L278

(R1b1)

(R1b*)

M479 (R2)
M124 (R2a)
L263

(R2a1)

F1092

(R2a2)

Y12100

(R2a3)

(R2*)

Origins

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Geneticist Spencer Wells suggests that haplogroup K likely originated in the Middle East or Central Asia, perhaps in the region of Iran or Pakistan.[6] According to Bergstorm et al, deep-rooted haplogroup K2b1 (Y-haplogroup S/M) found in Indigenous Australians and ancestors of haplogroup R and Q (Y-haplogroup K2b2/root P) split in Southeast Asia near Sahul.[8] Haplogroup P1 may have emerged in Southeast Asia, however according to Karafet, et al. this hypothesis is "parsimonious" and it is just as likely that it originated elsewhere in Eurasia.[7] The SNP M207, which defines Haplogroup R, is believed to have arisen during the Upper Paleolithic era, about 27,000 years ago.[2][1]

Remains of the Mal'ta boy (MA-1) with tomb artifacts, Hermitage Museum, Saint-Petersburg.[9]

Only one confirmed example of basal R* has been found, in 24,000-year-old remains, known as MA1, found at Mal'ta–Buret' culture near Lake Baikal in Siberia.[2] (While a living example of R-M207(xM17,M124) was reported in 2012, it was not tested for the SNP M478; the male concerned – among a sample of 158 ethnic Tajik males from Badakshan, Afghanistan – may therefore belong to R2.)

It is possible that neither of the primary branches of R-M207, namely R1 (R-M173) and R2 (R-M479) still exist in their basal, original forms, i.e. R1* and R2*. No confirmed case, either living or dead, has been reported in scientific literature. (Although in the case of R2*, relatively little research has been completed.)

Despite the rarity of R* and R1*, the relatively rapid expansion – geographically and numerically – of subclades from R1 in particular, has often been noted: "both R1a and R1b comprise young, star-like expansions" (Karafet 2008).

The wide geographical distribution of R1b, in particular, has also been noted. Hallast et al. (2014) mentioned that living examples found in Central Asia included:

  • the "deepest subclade" of R-M269 (R1b1a1a2) – the most numerous branch of R1b in Western Europe, and;
  • the rare subclade R-PH155 (R1b1b) found only in one Bhutanese individual and one Tajik.

(While Hallast et al. suggested that R-PH155 was "almost as old as the R1a/R1b split", R-PH155 was later discovered to be a subclade of R-L278 (R1b1) and has been given the phylogenetic name R1b1b.)

Distribution

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Y-haplogroup R-M207 is common throughout Europe, South Asia and Central Asia (Kayser 2003). It also occurs in the Caucasus and Siberia. Some minorities in Africa also carry subclades of R-M207 at high frequencies.

Proposed migration routes of Haplogroup P among others.[10]

While some indigenous peoples of The Americas and Australasia also feature high levels of R-M207, it is unclear whether these are deep-rooted, or an effect of European colonisation during the early modern era.

R (R-M207)

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Haplogroup R* Y-DNA (xR1,R2) was found in 24,000-year-old remains from Mal'ta in Siberia near Lake Baikal.[11] In 2013, R-M207 was found in one out of 132 males from the Kyrgyz people of East Kyrgyzstan.[12]

R1 (R-M173)

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Main article: Haplogroup R1

There are many downstream mutations of haplogroup R (Semino 2000 and Rosser 2000).

Initially, there was debate about the origin of haplogroup R1b in Native Americans. Two early studies suggested that this haplogroup could have been one of the founding Siberian lineages of Native Americans, however this is now considered unlikely, because the R1b lineages commonly found in Native Americans are in most cases identical to those in western Europeans, and its highest concentration is found among a variety of culturally unaffiliated tribes, in eastern North America.[13]

Thus, according to several authors, R1b was most likely introduced through admixture during the post-1492 European settlement of North America.[14][15][16]

R2 (R-M479)

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Main article: Haplogroup R2

Haplogroup R-M479 is defined by the presence of the marker M479. The paragroup for the R-M479 lineage is found predominantly in South Asia, although deep-rooted examples have also been found among Portuguese, Spanish, Tatar (Bashkortostan, Russia), and Ossetian (Caucasus) populations (Myres 2010).

One rare subclade may occur only among Ashkenazi Jews, possibly as a result of a founder effect.

See also

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Genetics

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Y-DNA R-M207 subclades

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Y-DNA backbone tree

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References

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  1. ^ a b c ISOGG, Y-DNA Haplogroup R and its Subclades – 2016 (12 December 2016).
  2. ^ a b c Raghavan, M. et al. 2014. Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans, Nature, 505, 87–91.
  3. ^ Mahal, David G.; Matsoukas, Ianis G. (2018). "The Geographic Origins of Ethnic Groups in the Indian Subcontinent: Exploring Ancient Footprints with Y-DNA Haplogroups". Frontiers in Genetics. 9: 4. doi:10.3389/fgene.2018.00004. ISSN 1664-8021. PMC 5787057. PMID 29410676. This is one of the largest haplogroups in India and Pakistan. This is also the largest haplogroup in the dataset used in this study. It originated in north Asia about 27,000 years ago (ISOGG, 2016). It is one of the most common haplogroups in Europe, with its branches reaching 80 percent of the population in some regions (Eupedia, 2017). From somewhere in central Asia, some descendants of the man carrying the M207 mutation on the Y chromosome headed south to arrive in India about 10,000 years ago (Wells, 2007).
  4. ^ Driem, George L. van (25 May 2021). Ethnolinguistic Prehistory: The Peopling of the World from the Perspective of Language, Genes and Material Culture. BRILL. p. 204. ISBN 978-90-04-44837-7.
  5. ^ Zhao, Zhongming; Khan, Faisal; Borkar, Minal; Herrera, Rene; Agrawal, Suraksha (2009). "Presence of three different paternal lineages among North Indians: A study of 560 Y chromosomes". Annals of Human Biology. 36 (1): 46–59. doi:10.1080/03014460802558522. ISSN 0301-4460. PMC 2755252. PMID 19058044. Figure 3
  6. ^ a b Wells, Spencer (20 November 2007). Deep Ancestry: The Landmark DNA Quest to Decipher Our Distant Past. National Geographic Books. p. 79. ISBN 978-1-4262-0211-7. "Given the widespread distribution of K, it probably arose somewhere in the Middle East or Central Asia, perhaps in the region of Iran or Pakistan."
  7. ^ a b Karafet TM, Mendez FL, Sudoyo H, Lansing JS, Hammer MF (March 2015). "Improved phylogenetic resolution and rapid diversification of Y-chromosome haplogroup K-M526 in Southeast Asia". European Journal of Human Genetics. 23 (3): 369–73. doi:10.1038/ejhg.2014.106. PMC 4326703. PMID 24896152. "This pattern leads us to hypothesize a southeastern Asian origin for P-P295 and a later expansion of the ancestor of subhaplogroups R and Q into mainland Asia. An alternative explanation would involve an extinction event of ancestral P-P295* chromosomes everywhere in Asia. These scenarios are equally parsimonious. They involve either a migration event (P* chromosomes from Indonesia to mainland Asia) or an extinction event of P-P295* paragroup in Eurasia."
  8. ^ a b Bergström, Anders; Nagle, Nano; Chen, Yuan; McCarthy, Shane; Pollard, Martin O.; Ayub, Qasim; Wilcox, Stephen; Wilcox, Leah; van Oorschot, Roland A.H.; McAllister, Peter; Williams, Lesley; Xue, Yali; Mitchell, R. John; Tyler-Smith, Chris (March 2016). "Deep Roots for Aboriginal Australian Y Chromosomes". Current Biology. 26 (6): 809–813. Bibcode:2016CBio...26..809B. doi:10.1016/j.cub.2016.01.028. PMC 4819516. PMID 26923783."Applying a point mutation rate of 0.76 × 10−9 per site per year inferred from the number of missing mutations on the Y chromosome of a ~45-ky-old radiocarbon-dated Eurasian sample [18], we infer a divergence time of 54.3 ky (95% confidence interval [CI]: 48.0–61.6 ky) between K∗/M chromosomes in Sahul and their closest relatives in the R and Q haplogroups (Figure 1B)" - (Figure 1B):"The phylogeny of Y chromosomes in haplogroups K∗ and M. This detailed view of a part of the larger tree displayed in (A) focuses on chromosomes in haplogroups K∗ and M. Haplogroups Q and R, which are the closest relatives to K∗ and M in the phylogeny, are represented schematically because they contain very large numbers of samples. Aboriginal Australian and Papuan samples are colored in two different shades of red for easier visual separation."
  9. ^ Lbova, Liudmila (2021). "The Siberian Paleolithic site of Mal'ta: a unique source for the study of childhood archaeology". Evolutionary Human Sciences. 3: 8, Fig. 6-1. doi:10.1017/ehs.2021.5. PMC 10427291. PMID 37588521.
  10. ^ Wang CC, Li H (June 2013). "Inferring human history in East Asia from Y chromosomes". Investigative Genetics. 4 (1): 11. doi:10.1186/2041-2223-4-11. PMC 3687582. PMID 23731529.
  11. ^ Raghavan M, Skoglund P, Graf KE, Metspalu M, Albrechtsen A, Moltke I, et al. (January 2014). "Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans". Nature. 505 (7481): 87–91. Bibcode:2014Natur.505...87R. doi:10.1038/nature12736. PMC 4105016. PMID 24256729.
  12. ^ Di Cristofaro J, Pennarun E, Mazières S, Myres NM, Lin AA, Temori SA, et al. (18 October 2013). "Afghan Hindu Kush: where Eurasian sub-continent gene flows converge". PLOS ONE. 8 (10): e76748. Bibcode:2013PLoSO...876748D. doi:10.1371/journal.pone.0076748. PMC 3799995. PMID 24204668.
  13. ^ Bolnick, Deborah; Bolnick, Daniel; Smith, David (2006). "Asymmetric Male and Female Genetic Histories among Native Americans from Eastern North America". Molecular Biology and Evolution. 23 (11): 2161–2174. doi:10.1093/molbev/msl088. PMID 16916941. "In most cases, there is widespread agreement about whether a particular haplogroup represents an ancient Native American lineage or post-1492 admixture, but the status of haplogroup R-M173 has recently been subject to some debate. Some authors have argued that this haplogroup represents a founding Native American lineage (Lell et al. 2002; Bortolini et al. 2003), whereas others suggest that it instead reflects recent European admixture (Tarazona-Santos and Santos 2002; Bosch et al. 2003; Zegura et al. 2004). In eastern North America, the pattern of haplotype variation within this haplogroup supports the latter hypothesis: R-M173 haplotypes do not cluster by population or culture area, as haplotypes in the other founding haplogroups do, and most match or are closely related to R-M173 haplotypes that are common in Europe but rare in Asia. This pattern is opposite than expected if the Native American R-M173 haplotypes were descended from Asian haplotypes and suggests that recent European admixture is responsible for the presence of haplogroup R-M173 in eastern North America."
  14. ^ Bolnick, Deborah Ann (2005). The Genetic Prehistory of Eastern North America: Evidence from Ancient and Modern DNA. University of California, Davis. p. 83. "Haplogroup R - M173 likely represents recent (post 1492) European admixture, as may P-M45* (Tarazona-Santos and Santos 2002; Bosch et al. 2003..."
  15. ^ Raff, Jennifer (8 February 2022). Origin: A Genetic History of the Americas. Grand Central Publishing. pp. 59–60. ISBN 978-1-5387-4970-8. "Y chromosome founder haplogroups in Native Americans include Q-M3 (and its sub-haplogroups, Q-CTS1780), and C3-MPB373 (potentially C- P39-Z30536). Other haplogroups found [sic] Native American populations, like R1b, were likely the result of post-European contact admixture (44)."
  16. ^ Malhi, Ripan Singh; Gonzalez-Oliver, Angelica; Schroeder, Kari Britt; et al. (December 2008). "Distribution of Y chromosomes among Native North Americans: A study of Athapaskan population history". American Journal of Physical Anthropology. 137 (4): 412–424. doi:10.1002/ajpa.20883. PMC 2584155. PMID 18618732. "All individuals that did not belong to haplogroup Q and C were excluded from the Haplotype data set because these haplotypes are likely the result of non-native admixture (Tarazona-Santos and Santos, 2002; Zegura et al., 2004; Bolnick et al, 2006)...The frequency of haplogroup C is highest in Northwestern North America and the frequency of haplogroup R, the presence of which is attributed to European admixture, reaches its maximum in Northeastern North America."

Further reading

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