Haplogroup P1 (Y-DNA)

Haplogroup P1, also known as P-M45 and K2b2a, is a Y-chromosome DNA haplogroup in human genetics. Defined by the SNPs M45 and PF5962, P1 is a primary branch (subclade) of P* (P-P295; K2b2).

Haplogroup P1 (P-M45; K2b2a)
Possible place of origin	Southeast Asia or East Asia [1][2][3]
Ancestor	P* (P-P295)[4]
Descendants	Q (Q-M242) and R (R-M207).
Defining mutations	M45/PF5962

The only primary subclades of P1 are Haplogroup Q (Q-M242) and Haplogroup R (R-M207). These haplogroups now comprise most of the male lineages among Native Americans, Europeans, Central Asia and South Asia, among other parts of the world.

P1 (M45) likely originated in East Asia or Southeast Asia,[2][1] even though basal P1* (P1xQ,R) is now most common among individuals in Eastern Siberia and Central Asia.[5] Both P* and its precursor, K2b, reach their highest rates among members of the Aeta (or Agta) people of Luzon in the Philippines,[3][1] and; Luzon is also the only location where P*, P1 and haplogroup P2 (P-B253; K2b2b), the only other primary subclade of P*, have been found together.[6][1][2] A 2018 study found basal P1* in two Siberian individuals dated to the Upper Paleolithic (~31,630 cal BP) from a Yana river archaeological site.[7]

Structure

The subclades of Haplogroup P1 with their defining mutation, according to the 2016 ISOGG tree:[6]

• P1 (M45/PF5962)
  • Q (M242)
    • Q1 (L232/S432)
  • R (M207, P224, P227, P229, P232, P280, P285, L248.2, V45)
    • R1 (M173/P241/Page29)
    • R2 (M479/PF6107)

Modern distribution

P1*

The modern populations with high frequencies of P1* (or P1xQ,R) are located in Central Asia and Eastern Siberia:

• 35.4% among Tuvan males;
• 35% among Nivkh and;
• 28.3% among Altai-Kizhi.[5]

Modern South Asian populations also feature P1 (M45) at low to moderate frequencies.[8] In South Asia, P-M45 is most frequent among the Muslims of Manipur (Pangal, 33%), but this may be due to a very small sample size (nine individuals).

A levels of 14% P-M45* on the island of Korčula in Dalmatia (modern Croatia) and 6% on the neighbouring island of Hvar, may be linked to immigration during the early medieval period, by Central Asian peoples such as the Avars.[9]

It is possible that many cases of haplogroup P1 reported in Central Asia, South Asia and/or West Asia are members of rare or less-researched subclades of haplogroups R2 and Q, rather than P1* per se.

Population group	Language family	Citation	Sample size	Percentage	Comments
Tuvinian	Turkic	Darenko 2005	113	35.40	P-M45
Nivkh	Nivkh	Lell 2001	17	35	P-M45
Altai-Kizhi	Turkic	Darenko 2005	92	28.3	P-M45
Todjin	Turkic	Darenko 2005	36	22.2	P-M45
Chukchi	Chukotko-Kamchatkan	Lell 2001	24	20.8	P-M45
Koryak	Chukotko-Kamchatkan	Lell 2001	27	18.5	P-M45
Yupik	Eskimo-Aleut languages	Lell 2001	33	18.2	P-M45
Uighur	Turkic	Xue 2006	70	17.1	P-M45
Kalmyk	Mongolic	Darenko 2005	68	11.8	P-M45
Turkmen	Turkic	Wells 2001	30	10	P-M45
Soyot	Turkic	Darenko 2005	34	8.8	P-M45
Uriankhai	Mongolic	Katoh 2004	60	8.3	P-M45
Khakas	Turkic	Darenko 2005	53	7.6	P-M45
Kazakh	Turkic	Wells 2001	54	5.6	P-M45
Uzbek	Turkic	Wells 2001	366	5.5	P-M45
Khasi-Khmuic	Austroasiatic	Reddy 2009	353	5.40	P-M45(xM173)^§
Munda	Austroasiatic	Reddy 2009	64	10.90	P-M45(xM173)^§
Nicobarese	Mon-Khmer	Reddy 2009	11	0.00	P-M45(xM173)^§
South-East Asia	Austroasiatic	Reddy 2009	257	1.60	P-M45(xM173)^§
Garo	Tibeto-Burman	Reddy 2009	71	1.40	P-M45(xM173)^§
North-east India	Tibeto-Burman	Reddy 2009	226	3.10	P-M45(xM173)^§
East Asia	Tibeto-Burman	Reddy 2009	214	0.00	P-M45(xM173)^§
Eastern India	various/unknown	Reddy 2009	54	18.50	P-M45(xM173)^§
Southern Talysh (Iran)	Iranian	Nasidze 2009	50	4.00	P-M45(xM124,xM173)
Northern Talysh (Azerbaijan)	Iranian	Nasidze 2009	40	5.00	P-M45(xM124,xM173)
Mazandarani	Iranian	Nasidze 2009	50	4.00	P-M45(xM124,xM173)
Gilaki	Iranian	Nasidze 2009	50	0.00	P-M45(xM124,xM173)
Tehran	Iranian	Nasidze 2004	80	4.00	P-M45(xM124,xM173)
Isfahan	Iranian	Nasidze 2004	50	6.00	P-M45(xM124,xM173)
Bakhtiari	Iranian	Nasidze 2008	53	2.00	P-M45(xM124,xM173)
Iranian Arabs	Arabic	Nasidze 2008	47	2.00	P-M45(xM124,xM173)
North Iran	Iranian	Regueiro 2006	33	9.00	P-M45(xM124,xM173)
South Iran	Iranian	Regueiro 2006	117	3.00	P-M45(xM124,xM173)
South Caucacus	Georgian	Nasidze and Stoneking 2001	77	3.00	P-M45(xM124,xM173)
South Caucacus	Armenian	Nasidze and Stoneking 2001	100	2.00	P-M45(xM124,xM173)
Sherpas from Nepal	Tibeto-Burman	Bhandari et al. 2015	582	1.67	P1(M45) or P(xQ,R1a1,R1b,R2)^†
Sherpas from Tibet	Tibeto-Burman	Bhandari et al. 2015	582	0.64	P1(M45) or P(xQ,R1a1,R1b,R2)^†
Hvar (Dalmatian Islands)	Croatian	Barać et al. 2003 harvnb error: no target: CITEREFBarać_et_al.2003 (help)		14	Possible link to medieval Avar settlers.[9]
Korčula (Dalmatian Islands)	Croatian	Barać et al. 2003 harvnb error: no target: CITEREFBarać_et_al.2003 (help)		6	Possible link to medieval Avar settlers.[9]

^§ May include members of haplogroup R2.
^† May include members of haplogroup R1*/R1a*

Population group	N	P (xQ,xR)		Q		R		Paper
		Count	%	Count	%	Count	%
Gope	16	1	6.4					Sahoo 2006
Oriya Brahmin	24	1	4.2					Sahoo 2006
Mahishya	17	3	17.6					Sahoo 2006
Bhumij	15	2	13.3					Sahoo 2006
Saora	13	3	23.1					Sahoo 2006
Nepali	7	2	28.6					Sahoo 2006
Muslims of Manipur	9	3	33.3					Sahoo 2006
Himachal Pradesh Rajput	15	1	6.7					Sahoo 2006
Lambadi	18	4	22.2					Sahoo 2006
Gujarati Patel	9	2	22.2					Sahoo 2006
Katkari	19	1	5.3					Sahoo 2006
Madia Gond	14	1	7.1					Sahoo 2006
Kamma Chowdary	15	0	0	1	6.7	12	80	Sahoo 2006

Q

Near universal in the Kets (95%) of Siberia. Very common in pre-modern Native American populations, except for the Na-Dene peoples, where it reaches 50-90%.

Also common, at 25-50%, in modern Siberian populations such as the Nivkhs, Selkups, Tuvans, Chukchi, Siberian Eskimos, Northern Altaians, and in 30% of Turkmens.

R

The only discovered case of basal R* (i.e. one that does not belong to R1 or R2) is the Mal'ta Boy.

Subclades of R1b, R1a and R2 are now dominant in various populations from Europe to South Asia.

References

1. Tumonggor, Karafet et al., 2014, "Isolation, contact and social behavior shaped genetic diversity in West Timor", Journal of Human Genetics Vol. 59, No. 9 (September), pp. 494–503.
2. E. Heyer et al., 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, Vol. 85, Iss. 1, p. 201.
3. Tatiana M Karafet; et al. (2015). "Improved phylogenetic resolution and rapid diversification of Y-chromosome haplogroup K-M526 in Southeast Asia" (PDF). European Journal of Human Genetics. 23 (3): 369–373. doi:10.1038/ejhg.2014.106. PMC 4326703. PMID 24896152.
4. Gregory R Magoon; et al. (2013-11-22). "Generation of high-resolution a priori Y-chromosome phylogenies using "next-generation" sequencing data". bioRxiv 10.1101/000802.
5. Miroslava Derenko et al 2005, Contrasting patterns of Y-chromosome variation in South Siberian populations from Baikal and Altai-Sayan regions Zgms.cm.umk.pl
6. ISOGG (2016). "Y-DNA Haplogroup P". Retrieved 2016-12-11.
7. Sikora, Martin; Pitulko, Vladimir; Sousa, Vitor; Allentoft, Morten E.; Vinner, Lasse; Rasmussen, Simon; Margaryan, Ashot; Damgaard, Peter de Barros; Castro, Constanza de la Fuente (2018-10-22). "The population history of northeastern Siberia since the Pleistocene". bioRxiv: 448829. doi:10.1101/448829.
8. Sahoo, S. (2006). "A prehistory of Indian Y chromosomes: Evaluating demic diffusion scenarios". Proceedings of the National Academy of Sciences. 103 (4): 843–8. Bibcode:2006PNAS..103..843S. doi:10.1073/pnas.0507714103. PMC 1347984. PMID 16415161.
9. Paolo Francalacci & Daria Sanna, "History and geography of human Y-chromosome in Europe: a SNP perspective", Journal of Anthropological Sciences, vol. 86 (2008), pp. 59-89. [Access: Aug 24, 2017].)

Sources

• Barać; et al. (2003). "Y chromosomal heritage of Croatian population and its island isolates" (PDF). European Journal of Human Genetics. 11 (7): 535–542. doi:10.1038/sj.ejhg.5200992. PMID 12825075.CS1 maint: ref=harv (link)

External links

• Spread of Haplogroup P, from The Genographic Project, National Geographic

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
Y-DNA by population Y-DNA haplogroups of historic people Footnotes  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. International Society of Genetic Genealogy (ISOGG; 2015), Y-DNA Haplogroup Tree 2015. (Access date: 1 February 2015.) Haplogroup A0-T is also known as A-L1085 (and previously as A0'1'2'3'4). Haplogroup A1 is also known as A1'2'3'4. Haplogroup LT (L298/P326) is also known as Haplogroup K1. 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. 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". Haplogroup K2b (M1221/P331/PF5911) is also known as Haplogroup MPS. Haplogroup K2e (K-M147) was previously known as "Haplogroup X" and "K2a" (but is a sibling subclade of the present K2a). 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) Haplogroup K2b1 (P397/P399) is also known as Haplogroup MS, but has a broader and more complex internal structure. Haplogroup P (P295) is also klnown as K2b2. Haplogroup S, as of 2017, is also known as K2b1a. (Previously the name Haplogroup S was assigned to K2b1a4.) Haplogroup M, as of 2017, is also known as K2b1b. (Previously the name Haplogroup M was assigned to K2b1d.)