Haplogroup R (Y-DNA)

Haplogroup R
Possible time of origin	about 27,000 years BP[1][2]
Possible place of origin	possibly Central Asia[3], Siberia[4], or South Asia[5]
Ancestor	P1 (P-M45), the only primary clade of P* (P-P295)
Descendants	R1 (R-M173), R2 (R-M479) (R2)
Defining mutations	M207/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 (ISOGG 2016)

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

Karafet et al. (2014) and other researchers state that a "rapid diversification ... of K-M526", also known as K2, into K2a and K2b , followed by K2b1 and P (also known as K2b2) "likely occurred in Southeast Asia". This was followed by the relatively rapid "westward expansion" of P1 – the immediate ancestor of both Haplogroups Q and R.[6][7]

Structure

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

Haplogroup P1 (P-M45), the immediate ancestor of Haplogroup R, likely emerged in Southeast Asia.[6] The SNP M207, which defines Haplogroup R, is believed to have arisen during the Upper Paleolithic era, about 27,000 years ago.[2][1]

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, undivergent 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",[6] R-PH155 was later discovered to be a subclade of R-L278 (R1b1) and has been given the phylogenetic name R1b1b.)

Distribution

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.

While some indigenous peoples of The Americas 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)

Haplogroup R* Y-DNA (xR1,R2) was found in 24,000-year-old remains from Mal'ta in Siberia near Lake Baikal.[4] In 2013, R-M207 was found in one out of 132 males from the Kyrgyz people of East Kyrgyzstan.[8]

R1 (R-M173)

R-M173, also known as R1, has been common throughout Europe and South Asia since pre-history. It has many branches (Semino 2000 and Rosser 2000).

It is the second most common haplogroup in Indigenous peoples of the Americas following haplogroup Q-M242, especially in the Algonquian peoples of Canada and the United States (Malhi 2008). The reasons for high levels of R-M173 among Native Americans are a matter of controversy:

some scholars claim that this is partly or wholly the result of colonial-era immigration from Europe (see e.g. Malhi 2008), whereas;
other authorities point to the greater similarity of many R-M173 subclades found in North America to those found in Siberia (e.g. Lell 2002 and Raghavan 2013), suggesting prehistoric immigration from Asia and/or Beringia.

R2 (R-M479)

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.

References

ISOGG, Y-DNA Haplogroup R and its Subclades – 2016 (12 December 2016).
Raghavan, M. et al. 2014. Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans, Nature, 505, 87–91.
karafet et al 2014.
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.
Hallast2014.
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.
See also: Tumonggor MK, Karafet TM, Downey S, Lansing JS, Norquest P, Sudoyo H, Hammer MF, Cox MP (September 2014). "Isolation, contact and social behavior shaped genetic diversity in West Timor". Journal of Human Genetics. 59 (9): 494–503. doi:10.1038/jhg.2014.62. PMC 4521296. PMID 25078354., and Heyer E, Georges M, Pachner M, Endicott P (2013). "Genetic diversity of four Filipino negrito populations from Luzon: comparison of male and female effective population sizes and differential integration of immigrants into Aeta and Agta communities". Human Biology. 85 (1–3): 189–208. doi:10.3378/027.085.0310. PMID 24297226.
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.

External links

Discussion and projects

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[vanOven2014-9] Van Oven M, Van Geystelen A, Kayser M, Decorte R, Larmuseau HD (2014). "Seeing the wood for the trees: a minimal reference phylogeny for the human Y chromosome". Human Mutation. 35 (2): 187–91. doi:10.1002/humu.22468. PMID 24166809.

[ISOGG2015-10] International Society of Genetic Genealogy (ISOGG; 2015), Y-DNA Haplogroup Tree 2015. (Access date: 1 February 2015.)

[A0-T-11] Haplogroup A0-T is also known as A-L1085 (and previously as A0'1'2'3'4).

[A1-12] Haplogroup A1 is also known as A1'2'3'4.

[LT-13] Haplogroup LT (L298/P326) is also known as Haplogroup K1.

[K2-14] Between 2002 and 2008, Haplogroup T-M184 was known as "Haplogroup K2". That name has since been re-assigned to K-M526, the sibling of Haplogroup LT.

[K2a-15] Haplogroup K2a (M2308) and its primary subclade K-M2313 were separated from Haplogroup NO (F549) in 2016. (This followed the publication of: Poznik GD, Xue Y, Mendez FL, et al. (2016). "Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences". Nature Genetics. 48 (6): 593–9. doi:10.1038/ng.3559. PMC 4884158. PMID 27111036. In the past, other haplogroups, including NO (M214) and K2e had also been identified with the name "K2a".

[K2b-16] Haplogroup K2b (M1221/P331/PF5911) is also known as Haplogroup MPS.

[K2e-17] Haplogroup K2e (K-M147) was previously known as "Haplogroup X" and "K2a" (but is a sibling subclade of the present K2a).

[K-M2313-18] K-M2313*, which as yet has no phylogenetic name, has been documented in two living individuals, who have ethnic ties to India and South East Asia. In addition, K-Y28299, which appears to be a primary branch of K-M2313, has been found in three living individuals from India. See: Poznik op. cit.; YFull YTree v5.08, 2017, "K-M2335", and; PhyloTree, 2017, "Details of the Y-SNP markers included in the minimal Y tree" (Access date of these pages: 9 December 2017)

[K2b1-19] Haplogroup K2b1 (P397/P399) is also known as Haplogroup MS, but has a broader and more complex internal structure.

[P-20] Haplogroup P (P295) is also klnown as K2b2.

[S-21] Haplogroup S, as of 2017, is also known as K2b1a. (Previously the name Haplogroup S was assigned to K2b1a4.)

[M-22] Haplogroup M, as of 2017, is also known as K2b1b. (Previously the name Haplogroup M was assigned to K2b1d.)

[isogg2016-1] ISOGG, Y-DNA Haplogroup R and its Subclades – 2016 (12 December 2016).

[Raghavan-2] Raghavan, M. et al. 2014. Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans, Nature, 505, 87–91.

[FOOTNOTEkarafet_et_al_2014-3] rafet et al 2014.

[Mal'ta_boy-4] 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.

[FOOTNOTEHallast2014-5] Hallast2014.

[Hallast2014-6] 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.

[tumonggor-7] See also: Tumonggor MK, Karafet TM, Downey S, Lansing JS, Norquest P, Sudoyo H, Hammer MF, Cox MP (September 2014). "Isolation, contact and social behavior shaped genetic diversity in West Timor". Journal of Human Genetics. 59 (9): 494–503. doi:10.1038/jhg.2014.62. PMC 4521296. PMID 25078354., and Heyer E, Georges M, Pachner M, Endicott P (2013). "Genetic diversity of four Filipino negrito populations from Luzon: comparison of male and female effective population sizes and differential integration of immigrants into Aeta and Agta communities". Human Biology. 85 (1–3): 189–208. doi:10.3378/027.085.0310. PMID 24297226.

[Cristofaro-8] 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.

Haplogroup R (Y-DNA)

Structure

Origins

Distribution

R (R-M207)

R1 (R-M173)

R2 (R-M479)

See also

Genetics

Y-DNA R-M207 subclades

Y-DNA backbone tree

References

Further reading

External links