Haplogroup F-M89

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Haplogroup F-M89
Possible time of origin 48,000 years BP (45,000-55,700) [1] 50,300±6500[2] Estimated time that F split from C (70,000-75,000) estimated time when G split from HIJK (45,000-50,000) [3]
Possible place of origin Most probably South Asia, Southwest Asia or Middle East[4]
Ancestor CF
Descendants (G, HIJK) Vietnam F* singleton, F2?,F*-Indonesia?
Defining mutations L132.1, M89, 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

In human genetics, haplogroup F is a very common Y-chromosome haplogroup spanning all the continents. This haplogroup and its subclades contain more than 90% of the world's existing non-African male population. Sometimes it is referred to as haplogroup FT to distinguish the part of it which is referred to in standard nomenclature as haplogroup (or paragroup) F-M89* (the branches of haplogroup F-M89 which have not yet been designated as defining a major haplogroup of their own).

This haplogroup is ancestral to, and contains, Y-chromosome haplogroups G (M201), H (M69), and IJK (L15/S137, L16/S138, L69.1(=G)/S163.1) along with their descendant haplogroups.

Origins[edit]

This megahaplogroup contains mainly lineages that are not typically found in sub-Saharan Africa, suggesting that its ancestral haplogroup CF may have been carried out of Africa very early in the modern human diaspora, and F-M89 may have appeared 48,000 (38,700-55,700) years ago, probably in Eurasia.[1]

According to the phylogeographic distribution of haplotypes observed among South Asian populations defined by social and linguistic criteria, the possibility arose of haplogroup F might have originated in or near India, and F-M89* might share a common demographic history with H-M69, C5, R2 and L1.[5] The presence of several subclusters of F-M89 and K that are largely restricted to the Indian subcontinent is consistent with the scenario that a coastal (southern route) of early human migration out of Africa carried ancestral Eurasian lineages first to the coast of the Indian subcontinent, or that some of them originated there.[6]

Other sources mention 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).[2] 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. All of Haplogroup F's descendant haplogroups also show a pattern of radiation from South Asia (haplogroups H, F* and K) or the Middle East (haplogroups G and IJ).

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

Distribution[edit]

F(xGHIJK)[edit]

Haplogroups belonging to FxGHIJK are rare in most regions. Only one verified case of FxGHIK has been found in Vietnam out of a sample of 46. This sample may have been F2 or the same as the Indonesian F*. Or it may be local and mostly found in the Vietnam area. In other words, no one knows for sure whether the F2 and the Indonesian F* belong to GHIJK because they never had a high resolution test.However one case of FxGHIJK has been verified in Vietnam and it proves that at least one new branch of F* exists although it may be part of a larger (but still small) branch which may or may not be centered on Vietnam.[7]

F-P14* has been found in 1.8% of West Timor, 1.5% of Flores 5.4% of Lembata 2.3% of Sulawesi and 0.2% of Sumatra. This strongly suggests a new branch (or branchs) of F in Indonesia.This Nature article studied for all main branchs of F including G and H however they did not study for F2 or the most divergent types of H, meaning this F in Indonesia may be F2 or H.[8]

It may be found in two north Portuguese populations (0.5%) and this may have occurred as a result of admixture since Portugal has significant contacts with India for about 500 years. However, this F* may really be G or H because in the Caucasus G has commonly been mislabeled as F*, and in India H has been mislabled as F* [9]

F-M427[edit]

F2 Y-chromosomes have been found to be particularly common among the Kucong or Yellow Lahu, a group of hunter-gatherers who live in the Ailao Mountains of Yunnan.[10] It is not known yet if F2 is a type of GHIJK or if it is highly divergent and does not belong to GHIJK.[11] F2 does exist but may be less divergent than G and therefore not be a main subclade of F.

H-P91[edit]

This subclade is defined by two SNPs: P91 and P104. It is most common in Sri Lanka (Karafet 2008).

http://www.phylotree.org/Y/tree/index.htm

H-P96[edit]

The H-P96 lineage is defined by seven SNPs. They are P96, M282, L279, L281, L284, L285, and L286. P96 defines the H2 subclade.

This is somewhat of a concentration of H-P96 in France, Switzerland, Germany and the Netherlands.[citation needed] http://www.phylotree.org/Y/tree/index.htm

F-L15[edit]

Because F-L15 is a subclade of F-M89, it is the most common macro-haplogroup outside of Africa with more than 80% of the world's population, therefore is predominant everywhere except for Africa, where haplogroups E, A, B predominate, as well as parts of Eastern Asia and Oceania, where C and D are most common.

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 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

Original research publications[edit]

The following research teams per their publications were represented in the creation of the YCC Tree.

Discussion[edit]

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 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 (ytree.ftdna.com)[edit]

This is Thomas Krahn at the Genomic Research Center's Draft tree Proposed Tree for haplogroup F-M89 (Krahn & FTDNA 2013)[clarification needed]. For brevity, 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

The Y-Chromosome Consortium tree[edit]

This is the official scientific tree produced by the Y-Chromosome Consortium (YCC). The last major update was in 2008 (Karafet 2008). Subsequent updates have been quarterly and biannual. The current version is a revision of the 2010 update.[12]

The ISOGG Tree[edit]

Below are the subclades of Haplogroup F-M89 with their defining mutation, according to the ISOGG tree (as of March 2010). Note that the descent-based identifiers may be subject to change, as new SNPs are discovered that augment and further refine the tree. For brevity, only the first three levels of subclades are shown.

  • CF
    • F (L132.1, M89, 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)

See also[edit]

Genetics[edit]

Backbone Tree[edit]

Evolutionary tree of human Y-chromosome DNA (Y-DNA) haplogroups
MRC Y-ancestor
A00 A0'1'2'3'4
A0 A1'2'3'4
A1 A2'3'4
A2'3 A4=BCDEF
A2 A3 B CDEF
DE CF
D E C F
GHIJKLT
G HIJKLT
H IJKLT
IJ KLT (K)
I J LT(K1) K (K2)
L T MPS (K2b) X (K2a)
MS P NO
M S QR 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. 

References[edit]

  1. ^ a b c d e Karafet, Tatiana; Mendez, Fernando L.; Meilerman, Monica B.; Underhill, Peter A.; Zegura, Stephen L.; Hammer, Michael F. (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 2336805. PMID 18385274. 
  2. ^ 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)). 
  3. ^ http://www.nature.com/nature/journal/v505/n7481/full/nature12736.html
  4. ^ Roper, L. David. "Y-Chromosome Biallelic Haplogroups". L. David Roper. Retrieved 2013-08-31. 
  5. ^ a b Sengupta, Sanghamitra; Zhivotovsky, Lev A.; King, Roy; Mehdi, S.Q.; Edmonds, Christopher A.; Chow, Cheryl-Emiliane T.; Lin, Alice A.; Mitra, Mitashree; Sil, Samir K.; Ramesh, A.; Rani, M.V. Usha; Thakur, Chitra M.; Cavalli-Sforza, L. Luca; Majumder, Partha P.; Underhill, Peter A. (1 February 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): 202–221. doi:10.1086/499411. PMC 1380230. PMID 16400607. 
  6. ^ Kivisild, T.; Rootsi, S.; Metspalu, M.; Mastana, S.; Kaldma, K.; Parik, J.; Metspalu, E.; Adojaan, M.; Tolk, H.-V.; Stepanov, V.; Gölge, M.; Usanga, E.; Papiha, S.S.; Cinnioğlu, C.; King, R.; Cavalli-Sforza, L.; Underhill, P.A.; Villems, R. (1 February 2003). "The genetic heritage of the earliest settlers persists both in Indian tribal and caste populations". The American Journal of Human Genetics 72 (2): 313–332. doi:10.1086/346068. PMC 379225. PMID 12536373. 
  7. ^ http://biorxiv.org/content/early/2013/11/22/000802.1.figures-only
  8. ^ http://www.nature.com/jhg/journal/vaop/ncurrent/extref/jhg201462x1.pdf
  9. ^ Athey, T. Whit (2005). "Pitfalls in Determinations of Y Haplogroup F*" (pdf). Journal of Genetic Genealogy 1: 35–39. 
  10. ^ 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)). 
  11. ^ biorxiv.org/content/biorxiv/early/2013/11/22/000802.1.full.pdf
  12. ^ "Y-DNA Haplotree". Family Tree DNA. Retrieved 2013-08-31.  – Family Tree DNA uses the Y-Chromosome Consortium tree and posts it on their website.
  13. ^ 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 2787129. PMID 19920170. 
  14. ^ "Melanesian and Asian Origins of Polynesians: mtDNA and Y Chromosome Gradients Across the Pacific". 
  15. ^ Regueiro, M.; Cadenas, A.M; Gayden, T.; Underhill, P.A.; Herrera, R.J. (2006). "Iran: tricontinental nexus for Y-chromosome driven migration". Human Heredity 61 (3): 132–143. doi:10.1159/000093774. PMID 16770078. 
  16. ^ "Armenian DNA Project". Family Tree DNA. 2010. 

External links[edit]