Haplogroup F-M89

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, Central 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

Haplogroup F, also known as F-M89, is a very common Y-chromosome haplogroup. This haplogroup and its subclades contain more than 90% of the world's existing non-African male population.

F-M89 contains many historically significant haplogroups, clades and subclades, branching initially into haplogroups G (M201), H (M69), and IJK (F-L15). The descendants of Haplogroup IJK incoporate haplogroups I, J, K, and, ultimately, to major haplogroups descended from haplogroup K, namely: haplogroups M, N, O, P, Q, R, S, L, and T.

The broader haplogroup F-M89 has sometimes been known as haplogroup FT, to distinguish it from the specific and much rarer paragroup F-M89*, also known as F(xGHIJK).

Origins

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] F2-M427 is found in the Dravidian, Indo-European, Sino-Tibetan and Tibeto-Burman populations in China, Nepal and India, and the minor sub-groups of F-M89 are also observed in Siberia by Balanovsk et al (2008), and in Indonesia by Hammer et al (2006).^[7] F*(xG,H,I,J,K) is also found among Turkic people in Turkmenistan and Uzbekistan, which is reported in the genetic study of Balaresque et al (2015).^[8]

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

F-M89

Individuals belonging to F-M89 (also known as FxGHIJK) and its subclades – F*, F1 (P91; P104), F2 (M427; M428) and F3 (M481) – are rare and poorly-understood. The possibility of misidentification is considered to be relatively high, due to a lack of high resolution testing and some cases may in fact belong to GHIJK.

For instance, an individual with F-M89* has been reported in Vietnam (out of a sample of 46). The Vietnamese case may be identical to subclades found in Indonesia (see below).^[9]

It is possible that an as-yet unnamed major branch of F-M89 has been identified in Indonesia. Men with F-P14* (P14/PF2704) 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. However, these Indonesian cases were not examined for other clades of haplogroup F or even the most divergent types of haplogroup H, meaning that the individuals concerned may instead belong to H or another clade of haplogroup F.^[10]

F* has been reported in two north Portuguese populations (0.5%), which may be a result of contact with India since the 16th century. As with the Vietnamese and Indonesian cases mentioned above, these instances of F* may really be G or H , i.e. in the Caucasus, haplogroup G has often been mislabeled as F*, and in India, haplogroup H has been mislabeled as F*.^[11]

F-M427

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.^[12] F2 is outside of HIJK, but it is unknown whether it falls inside of GHIJK or is basal to it.^[13]

H-P91

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

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

F-L15

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

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

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

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

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 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)

This is Thomas Krahn at the Genomic Research Center's Draft tree Proposed Tree for haplogroup F-M89 (Krahn & FTDNA 2013). 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

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.^[14]

The ISOGG Tree

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)
    • F* May be found in India,although may been confused with H.^[15] and in Polynesia F-M89 (speculated that it was because of admixture with Europeans).^[16] found in the Seminole Native American Tribe and rare in Netherlands.^[1]
    • F1 (P91, P104) - Found in Sri Lanka.^[1]
    • F2 (M427, M428) - In Lahu people (China).^[5]
    • H2 (L279, L281, L284, L285, L286, M282, P96) - In South Iran and South India.^[17] Also in Armenia^[18] and rare in Netherlands.^[1]
    • F-M481 (M481)
    • G (M201)
    • H (M69, M370)
    • IJK (L15/S137, L16/S138)
      • IJ (M429/P125, P123, P124, P126, P127, P129, P130, S2, S22)
        • I
        • J
      • K-M9 (M9, P128, P131, P132)
        • LT (L298/P326)
        • K-M526 (M526)

See also

Genetics

Backbone Tree

Evolutionary tree of human Y-chromosome DNA (Y-DNA) haplogroups
ISOGG Y-DNA Haplogroup Tree 2015(1 February 2015)PDF[n 1]
	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
Y-DNA by populations Famous Y-DNA haplotypes
↑ 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

External links

• "GENO 2.0: The Greated Journey Ever Told". National Geographic. 
• "Y-DNA Haplogroup Tree 2013, Version: 8.72". International Society of Genetic Genealogy. 25 August 2013. 
• McDonald, J. D. (2005). "World Haplogroups Maps" (PDF).