Haplogroup F-M89

Haplogroup F-M89
Possible time of origin 57,500–62,500;(Raghavan 2014);[1]
45,000–55,700 BP (Karafet 2008);[2]
43,000–56,800 BP (Hammer & Zegura 2002).[3]
Possible place of origin South Asia[4][5][6][7]
Ancestor CF
Descendants F1, F2, F3, GHIJK
Defining mutations M89/PF2746, L132.1, M213/P137/Page38, M235/Page80, P14, P133, P134, P135, P136, P138, P139, P140, P141,P142, P145, P146, P148, P149, P151, P157, P158, P159, P160, P161, P163, P166, P187, P316

Haplogroup F, also known as F-M89 and previously as Haplogroup FT is a very common Y-chromosome haplogroup. The clade and its subclades constitute over 90% of paternal lineages outside of Africa. It is primarily found throughout South Asia, Southeast Asia and parts of East Asia.

The vast majority of individual males with F-M89 fall into its direct descendant Haplogroup GHIJK (F1329/M3658/PF2622/YSC0001299).[8] Apart from GHIJK, haplogroup F has four other immediate descendant subclades, all of which are rare in modern populations: the basal paragroup F-M89* (M89/PF2746), F1 (P91/P104), F2 (M427/M428), and F3 (M481).

Haplogroup GHIJK branches subsequently into two direct descendants: G (M201/PF2957) and HIJK (F929/M578/PF3494/S6397). HIJK in turn splits into H (L901/M2939) and IJK (F-L15). The descendants of Haplogroup IJK include haplogroups I, J, K, and, ultimately, several major haplogroups descended from Haplogroup K, namely: haplogroups M, N, O, P, Q, R, S, L, and T.

Origins

The diversion of Haplogroup F and its descendants.

This megahaplogroup contains mainly lineages that are not typically found in sub-Saharan Africa, suggesting that its immediate ancestor haplogroup CF may have been carried out of Africa very early in the modern human diaspora, suggesting that F-M89 appeared 38,700-55,700 years ago, probably in South Asia.[2][9]

The descendants of Basal F-M89* are found mostly in populations of South Asia, Southeast Asia and parts of East Asia.[10]

Other sources suggest that this ancient haplogroup may have first appeared in North Africa, the Levant, or the Arabian Peninsula, as much as 50,000 years ago (50,300±6500).[3] It is sometimes believed to represent a "second-wave" of expansion out of Africa. However, the location of this lineage's first expansion and rise to prevalence appears to have been in South Asia or somewhere close to it within the extended Middle East. Most of F's descendant haplogroups appear to radiate outward from South Asia and/or the Middle East.

Some lineages derived from Haplogroup F-M89 appear to have migrated into Africa from Southwest Asia, during prehistory. Y-chromosome haplogroups associated with this hypothetical "Back to Africa" migration include J, R1b, and T.

Distribution

The vast majority of living individuals carrying F-M89 belong to subclades of GHIJK. By comparison, cases of F xG,H,I,J,K – that is, either basal F* (M89) or the primary subclades F1 (P91; P104), F2 (M427; M428) and F3 (M481) – are relatively rare worldwide.

F xG,H,I,J,K

A lack of precise, high resolution testing in the past makes it difficult to discuss F*, F1, F2* and F3* separately. ISOGG states that F xG,H,I,J,K has not been well studied, occurs "infrequently" in modern populations and peaks in South Asia, especially Sri Lanka.[8] It also appears to have long been present in South East Asia. However, the possibility of misidentification is considered to be relatively high and some cases may in fact belong to misidentified subclades of Haplogroup GHIJK. This was, for instance, the case with the original subclade F3 (M96), which has since been renamed Haplogroup H2.

F* (F xF1,F2,F3) has been reported among 10% of males in Sri Lanka, 5.2% of males across India (including up to 10% of males in South India), 5% in Pakistan, as well as lower levels among the Tamang people (Nepal), and in Iran. Men originating in Indonesia have also been reported to carry F xG,H,I,J,K – especially F* – at relatively significant levels. It has been reported at rates of 4-5% in Sulawesi and Lembata. One study, which did not comprehensively screen for other subclades of F-M89 (including some subclades of GHIJK), found that Indonesian men with the SNP P14/PF2704 (which is equivalent to M89), comprise 1.8% of men in West Timor, 1.5% of Flores 5.4% of Lembata 2.3% of Sulawesi and 0.2% in Sumatra.[11] [12] F1 (P91), F2 (M427) and F3 (M481; previously F5) are all highly rare and virtually exclusive to regions/ethnic minorities in Sri Lanka, India, Nepal, South China, Thailand, Burma, and Vietnam.

In Central Asia, examples of F xG,H,I,J,K have been reported, in individuals from Turkmenistan and Uzbekistan.[13]

There is also evidence of significant westward Paleolithic back-migration of F xG,H,I,J,K from South Asia, to Iran, Arabia and Northeast Africa,[14] [15] as well as South-East Europe.[16] An individual known to scholars as "Oase 1", who lived circa 37,800 years BP in Romania falls into F xG,H,I,J,K.[16]

Neolithic migration into Europe from Southwest Asia, by first wave of farmers in Europe has been put forward as the source of F(xGHIJK) and G2a found in European Neolithic remains, dating from circa 4000 BCE. These remains, according to Herrerra et al. (2012) showed a "greater genetic similarity" to "individuals from the modern Near East" than to modern Europeans.[17] F xG,H,I,J,K has also apparently been found in Bronze Age remains from Europe:

Some cases reported amongst modern populations of Europeans, Native Americans and Pacific Islanders may be due to migration and admixture of F xG,H,I,J,K as a result of contact with South and South East Asia during the early modern era (16th–19th Century).[8] Such examples include:

F* (M89*)

Basal F-M89* has been reported among 5.2% of males in India.[9] A regional breakdown was provided by Chiaroni et al (2009): 10% in South India; 8% in Central India; about 1.0% in North India and Western India, as well as 5% in Pakistan; 10% in Sri Lanka; >4% among the Tamang people of Nepal; 2% in Borneo and Java; 4-5% in Sulawesi and Lembata.[11]

In Iran, 2.3% of Bandari males from Hormozgan Province have been found to carry basal F-M89.[14]

Haplogroup F-M89 has also been observed in Northeast Africa among two Christian period individuals, who were excavated on the Nile's Fourth Cataract and on Meroe Island.[21]

F1 (P91)

This subclade is defined by the SNP P91. It is most common in Sri Lanka.[2][22]

F2 (M427)

F2 Y-chromosomes have been reported among minorities from the borderlands of South China (Yunnan and Guizhou), Thailand, Burma, and Vietnam, namely the Yi and Kucong or Lahu Shi ("Yellow Lahu"), a subgroup of the Lahu.[23]

F3 (M481)

The newly defined and rare subclade F3 (M481; previously F5) has been found in India and Nepal, among the Tharu people and in Andhra Pradesh.[24] F-M481 should not be confused with Haplogroup H2 (L279, L281, L284, L285, L286, M282, P96), which was previously misclassified under F-M89, as "F3".

Haplogroup GHIJK

Main article: Haplogroup GHIJK

Basal GHIJK has never been found, either in living males or ancient remains.

Subclades – including some major haplogroups – are widespread in modern populations of the Caucasus, Middle East, South Asia, Europe South East Asia, Pacific Islands and Native Americans.

Phylogenetics

In Y-chromosome phylogenetics, subclades are the branches of haplogroups. These subclades are also defined by single nucleotide polymorphisms (SNPs) or unique event polymorphisms (UEPs).

Phylogenetic trees

There are several confirmed and proposed phylogenetic trees available for haplogroup F-M89. The scientifically accepted one is the Y-Chromosome Consortium (YCC) one published in Karafet 2008[2] and subsequently updated. A draft tree that shows emerging science is provided by Thomas Krahn at the Genomic Research Center in Houston, Texas. The International Society of Genetic Genealogy (ISOGG) also provides an amateur tree.

The Genomic Research Center draft tree

he Genomic Research Center's draft tree for haplogroup F-M89 is as follows.[25] (Only the first three levels of subclades are shown.)

YCC/ISOGG tree

This is the official scientific tree produced by the Y-Chromosome Consortium (YCC). The last major update was in 2008.[2] Subsequent updates have been quarterly and biannual. The current version is a revision of the 2010 update.

Phylogenetic history

Prior to 2002, there were in academic literature at least seven naming systems for the Y-Chromosome Phylogenetic tree. This led to considerable confusion. In 2002, the major research groups came together and formed the Y-Chromosome Consortium (YCC). They published a joint paper that created a single new tree that all agreed to use. Later, a group of citizen scientists with an interest in population genetics and genetic genealogy formed a working group to create an amateur tree aiming at being above all timely. The table below brings together all of these works at the point of the landmark 2002 YCC Tree. This allows a researcher reviewing older published literature to quickly move between nomenclatures.

YCC 2002/2008 (Shorthand) (α) (β) (γ) (δ) (ε) (ζ) (η) YCC 2002 (Longhand) YCC 2005 (Longhand) YCC 2008 (Longhand) YCC 2010r (Longhand) ISOGG 2006 ISOGG 2007 ISOGG 2008 ISOGG 2009 ISOGG 2010 ISOGG 2011 ISOGG 2012
F-M892VI1R20Eu10H4BF*FFFFFFFFFF
F-APT/H-APT15VI1R20Eu10H4BF1H2H2H2H2H2H2H2H2H2H2

See also

Genetics

Backbone Tree

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
L T [χ 6] NO [χ 7] K2b [χ 8]     K2c  K2d  K2e [χ 9]
N   O   K2b1 [χ 10]     P
K2b1a[χ 11]     K2b1b K2b1c      M     P1 P2
K2b1a1   K2b1a2   K2b1a3 S [χ 12] Q   R
  1. ↑ 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.
  2. ↑ International Society of Genetic Genealogy (ISOGG; 2015), Y-DNA Haplogroup Tree 2015. (Access date: 1 February 2015.)
  3. ↑ Haplogroup A0-T is also known as A0'1'2'3'4.
  4. ↑ Haplogroup A1 is also known as A1'2'3'4.
  5. ↑ Haplogroup LT (L298/P326) is also known as Haplogroup K1.
  6. ↑ 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.
  7. ↑ Haplogroup NO (M214) is also known as Haplogroup K2a (although the present Haplogroup K2e was also previously known as "K2a").
  8. ↑ Haplogroup K2b (M1221/P331/PF5911) is also known as Haplogroup MPS.
  9. ↑ Haplogroup K2e (K-M147) was previously known as "Haplogroup X" and "K2a" (but is a sibling subclade of the present K2a, also known as Haplogroup NO).
  10. ↑ Haplogroup K2b1 (P397/P399) is similar to the former Haplogroup MS, but has a broader and more complex internal structure.
  11. ↑ Haplogroup K2b1a has also been known as Haplogroup S-P405.
  12. ↑ Haplogroup S (S-M230), also known as K2b1a4, was previously known as Haplogroup K5.

References

  1. ↑ Estimated time that F split from C = 70,000–75,000 BP; estimated time when G split from HIJK = 45,000-50,000 M. Raghavan et. al., 2014, "Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans", Nature, no. 505 (2 January), pp. 87–91.
  2. 1 2 3 4 5 6 Karafet, Tatiana; et al. (2008). "New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree". Genome Research. 18 (5): 830–8. doi:10.1101/gr.7172008. PMC 2336805Freely accessible. PMID 18385274.
  3. 1 2 Hammer, M.F.; Zegura, S.L. (2002). "The human Y chromosome haplogroup tree: Nomenclature and phylogeography of its major divisions". Annual Review of Anthropology. 31: 303–321. doi:10.1146/annurev.anthro.31.040402.085413. (subscription required (help)).
  4. ↑ Kivisild et al 2003, The Genetic Heritage of the Earliest Settlers Persists Both in Indian Tribal and Caste Populations
  5. ↑ Sengupta et al 2005, Polarity and Temporality of High-Resolution Y-Chromosome Distributions in India Identify Both Indigenous and Exogenous Expansions and Reveal Minor Genetic Influence of Central Asian Pastoralists
  6. ↑ Sanghamitra Sahoo et al 2006, A prehistory of Indian Y chromosomes: Evaluating demic diffusion scenarios
  7. ↑ Arunkumar et al 2012
  8. 1 2 3 4 ISOGG, 2015, Y-DNA Haplogroup F and its Subclades - 2015 (8 September 2015).
  9. 1 2 Sengupta, Sanghamitra; et al. (2006). "Polarity and Temporality of High-Resolution Y-Chromosome Distributions in India Identify Both Indigenous and Exogenous Expansions and Reveal Minor Genetic Influence of Central Asian Pastoralists". The American Journal of Human Genetics. 78 (2): 202–21. doi:10.1086/499411. PMC 1380230Freely accessible. PMID 16400607.
  10. ↑ Zhong et al, (2011) Extended Y Chromosome Investigation Suggests Postglacial Migrations of Modern Humans into East Asia via the Northern Route, Mol Biol Evol January 1, 2011 vol. 28 no. 1 717-727, See Tables.
  11. 1 2 Chiaroni, Jacques; Underhill, Peter A.; Cavalli-Sforza, Luca L. (1 December 2009). "Y chromosome diversity, human expansion, drift, and cultural evolution". Proceedings of the National Academy of Sciences of the United States of America. 106 (48): 20174–9. doi:10.1073/pnas.0910803106. PMC 2787129Freely accessible. PMID 19920170.
  12. ↑ "Nature Publishing Group: Error Page" (PDF). nature.com.
  13. ↑ Balaresque et al (2015), Y-chromosome descent clusters and male differential reproductive success: young lineage expansions dominate Asian pastoral nomadic populations, Supplementary Table 2
  14. 1 2 Viola Grugni etal., 2012, "Ancient Migratory Events in the Middle East: New Clues from the Y-Chromosome Variation of Modern Iranians" (5 August 2016).
  15. ↑ Yousif, Hisham; Eltayeb, Muntaser. "Genetic Patterns of Y-chromosome and Mitochondrial DNA Variation, with Implications to the Peopling of the Sudan" (PDF). University of Khartoum. Retrieved 17 July 2016.
  16. 1 2 Qiaomei Fu, Mateja Hajdinjak, Oana Teodora Moldovan, Silviu Constantin, Swapan Mallick, Pontus Skoglund, Nick Patterson, Nadin Rohland, Iosif Lazaridis, Birgit Nickel, Bence Viola, Kay Prüfer, Matthias Meyer, Janet Kelso, David Reich, Svante Pääbo (13 August 2015). "An early modern human from Romania with a recent Neanderthal ancestor". Nature. 524: 216–219. doi:10.1038/nature14558. Retrieved 10 June 2016.
  17. ↑ {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3286660/ Herrera KJ, Lowery RK, Hadden L, Calderon S, Chiou C, Yepiskoposyan L, et al. 2010, "Neolithic patrilineal signals indicate that the Armenian plateau was repopulated by agriculturalists", PLoS Biology, vol. 8 (Nov.), no. 11].
  18. 1 2 3 4 Jean Manco, 2016, DNA from the European Neolithic (1 March 2016).
  19. ↑ "Melanesian and Asian Origins of Polynesians: mtDNA and Y Chromosome Gradients Across the Pacific".
  20. ↑ Phillip Edward Melton, 2008, Genetic History and Pre-Columbian Diaspora of Chibchan Speaking Populations: Molecular Genetic Evidence; Ann Arbor, Michigan; ProQuest, p. 29.
  21. ↑ Mohamed, Hisham Yousif Hassan. "Genetic Patterns of Y-chromosome and Mitochondrial DNA Variation, with Implications to the Peopling of the Sudan" (PDF). University of Khartoum. p. 76. Retrieved 22 August 2016.
  22. ↑ http://www.phylotree.org/Y/tree/index.htm
  23. ↑ Black, M.L.; Wise, C.A.; Wang, W.; Bittles, A.H. (June 2006). "Combining Genetics and Population History in the Study of Ethnic Diversity in the People's Republic of China". Human Biology. 78 (3): 277–293. doi:10.1353/hub.2006.0041. PMID 17216801. (subscription required (help)).
  24. ↑ S. Fornarino et al., "Mitochondrial and Y-chromosome diversity of the Tharus (Nepal): a reservoir of genetic variation", BMC Evol Biol 2009; no. 9: p. 154. (15 September 2015).
  25. ↑ http://ytree.ftdna.com/index.php?name=Draft&parent=92331011
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