Haplogroup F-M89

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This article is about the human Y-DNA haplogroup. For the human mtDNA haplogroup, see Haplogroup F (mtDNA).
Haplogroup F-M89
Haplogroup F (Y-DNA).PNG
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 Primary: 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] in addition to GHIJK, haplogroup F has three other immediate descendant subclades: F1 (P91/P104), F2 (M427/M428), and F3 (M481). These three, with F* (M89*), constitute the paragroup F(xGHIJK).

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[edit]

F-M89 is a megahaplogroup of lineages that are not typically found in Sub-Saharan Africa. The paragroup constituted by basal F*, F2 and F3 is now found mostly in populations within South Asia, South East Asia and parts of East Asia.[9] This suggests that haplogroup CF, its immediate ancestor, was carried out of Africa with an early wave of modern humans.

It is estimated that the SNP M89 appeared 38,700–55,700 years ago, most likely in South Asia.[2][10] This theory has all but superseded previous research, which suggested that F-M89 first appeared in the Arabian Peninsula, Levant or North Africa, about 43,800–56,800 years ago,[3] and may, therefore, have represented a "second wave" of expansion out of Africa. The location of this lineage's first expansion and rise to prevalence appears to have been in the Indian Subcontinent, or somewhere close to it, and most of the descendant subclades and haplogroups appear to have radiated outward from South Asia and/or neighbouring parts of the Middle East and South East Asia.

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

Distribution[edit]

The vast majority of living individuals carrying F-M89 belong to subclades of GHIJK. By comparison, cases of the paragroup 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)[edit]

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 subclade Haplogroup H2, (H-M96), which was originally named "F3", i.e – a name that has since been reassigned to F-M481.

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-M89* – 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 North East 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:

  • two individuals, known as BAM 17 and BAM 26, who lived 7,850 – 7,675 years BP and were found at Alsónyék Bátaszék in Hungary,[18] and
  • DEB 20 and DEB 38, who lived about 7,000 – 7,210 years BP, and were found at the Derenburg Meerenstieg II site in Germany;[18]
  • TOLM 3, and individual who lived about 7,030 – 7,230 years BP, in the Tolna-Mözs area of Hungary,[18] and;
  • an individual known as I0411/Troc 4, who lived 7,195 – 7,080 years BP and whose remains were found in the Els Trocs cave, near Bisaurri, in the Spanish Pyrenees – haplogroups G, I1, I2a, J, L1b2, T, O2b, Q1a2a, Q1b1, R1a1a and R1b1c2 were ruled out.[18]

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/or South East Asia, during the early modern era (16th–19th Century).[8] Such examples include:

F* (M89*)[edit]

Basal F-M89* has been reported among 5.2% of males in India.[10] 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)[edit]

Main article: Haplogroup F1 (Y-DNA)

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

F2 (M427)[edit]

Main article: Haplogroup F2 (Y-DNA)

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)[edit]

Main article: Haplogroup F3 (Y-DNA)

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[edit]

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[edit]

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[edit]

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[edit]

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

  • F-M89 P14, M89, M213, P133, P134, P135, P136, P138, P139, P140, P141, P142, P145, P146, P148, P149, P151, P157, P158, P159, P160, P161, P163, P166, P187, P316, L132.1, L313, L498
    • F-P91 P91, P104
    • F-M427 M427, M428
    • F-P96 P96, M282, L279, L281, L284, L285, L286
      • F-L280 L280
    • G-M201 M201, P257, L116, L154, L204, L240, L269, L402, L605, L769, L770, L836, L837, L1258, U2, U3, U6, U7, U12, U17, U20, U21, U23, U33
    • H-M69 M69, M370, PAGES00049
    • IJK L15, L16

YCC/ISOGG tree[edit]

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.[citation needed]

  • CF
    • F (L132.1, M89/PF2746).
      • F1 (P91, P104)
      • F2 (M427, M428)
      • F3 (M481)
      • Macrohaplogroup GHIJK (F1329/M3658/PF2622/YSC0001299).

Phylogenetic history[edit]

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-M89 2 VI 1R 20 Eu10 H4 B F* F F F F F F F F F F
F-APT/H-APT 15 VI 1R 20 Eu10 H4 B F1 H2 H2 H2 H2 H2 H2 H2 H2 H2 H2

See also[edit]

Genetics[edit]

Backbone Tree[edit]

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] K2a [χ 7] K2b [χ 8]     K2c  K2d  K2e [χ 9]
NO  K2a1 K2b1 [χ 10]     P [χ 11]
NO1   S [χ 12]   M [χ 13] P1 P2
N   O 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 K2a (M2308) and the new subclade K2a1 (M2313) were separated from Haplogroup NO (F549) in 2016. (This followed the publication of: G. David Poznik et al., 2016, "Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences" Nature Genetics], no. 48, pp. 593–599.) In the past, other haplogroups, including NO1 (M214) and K2e had also been identified with the name "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).
  10. ^ Haplogroup K2b1 (P397/P399) is similar to the former Haplogroup MS, but has a broader and more complex internal structure.
  11. ^ Haplogroup P (P295) is also klnown as K2b2.
  12. ^ The name Haplogroup S, as of 2017 also known as K2b1a, was previously assigned to K2b1a4.
  13. ^ The name Haplogroup M, as of 2017 also known as K2b1b, was previously assigned to K2b1d.

References[edit]

  1. ^ Estimated time that F split from C = 70,000–75,000 BP; estimated time when G split from HIJK = 45,000-50,000 Raghavan, M.; et al. (2014). "Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans". Nature. 505: 87–91. doi:10.1038/nature12736. 
  2. ^ a b c d e f 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. ^ a b 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. ^ a b c d ISOGG, 2015, Y-DNA Haplogroup F and its Subclades - 2015 (8 September 2015).
  9. ^ 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.
  10. ^ a b 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. 
  11. ^ a b 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. ^ "Isolation, contact and social behavior shaped genetic diversity in West Timor". Journal of Human Genetics. 59: 494–503. doi:10.1038/jhg.2014.62. 
  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. ^ a b 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. ^ a b 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. PMC 4537386Freely accessible. PMID 26098372. Retrieved 10 June 2016. 
  17. ^ Herrera, KJ; Lowery, RK; Hadden, L; et al. (March 2012). "Neolithic patrilineal signals indicate that the Armenian plateau was repopulated by agriculturalists". Eur. J. Hum. Genet. 20: 313–20. doi:10.1038/ejhg.2011.192. PMC 3286660Freely accessible. PMID 22085901. 
  18. ^ a b c d 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. ^ Fornarino, S; Pala, M; Battaglia, V; et al. (2009). "Mitochondrial and Y-chromosome diversity of the Tharus (Nepal): a reservoir of genetic variation". BMC Evol. Biol. 9: 154. doi:10.1186/1471-2148-9-154. PMC 2720951Freely accessible. PMID 19573232. 
  25. ^ http://ytree.ftdna.com/index.php?name=Draft&parent=92331011

External links[edit]