Haplogroup F-M89

Haplogroup F, also known as F-M89 and, previously, as Haplogroup FT 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.

The vast majority of individual males with F-M89 fall into its direct descendant Haplogroup GHIJK (F1329/M3658/PF2622/YSC0001299). 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 aplogroups 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.

The descendants of F are found mostly in populations speaking Dravidian, Indo-European, Sino-Tibetan and Tibeto-Burman and Turkic languages, throughout Eurasia.

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). 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

Almost all individuals carrying F-89 belong to subclades of GHIJK.

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 and the possibility of misidentification is considered to be relatively high, due to a lack of high resolution testing (especially in the past); some cases may in fact belong to subclades of GHIJK. While anecdotal and non-scholarly sources suggest that F xG,H,I,J,K may be present at low levels in many populations, ISOGG (2015) merely states: "The minor sub-groups, F*, F1, and F2 have not been well studied, but apparently occur only infrequently and primarily in the Indian subcontinent". One or more subclades of F xG,H,I,J,K have also been reported in Turkmenistan and Uzbekistan.

Men originating in Indonesia may also possess all or most subclades of F xG,H,I,J,K. In addition, an as-yet unnamed subclade of F xG,H,I,J,K may be present in Indonesia: while 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, these cases were not screened 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.

F*

Basal F-M89* has been reported among 5.2% of males in India. 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.

More controversial examples, due possibly to recent admixture include: low levels in Polynesia; some individuals among Seminole Native Americans; rare cases in the Netherlands, and; two cases in Portugal. European cases may well be a remnant of 15th and 16th century contact with India.

F1 (P91)

Main article: Haplogroup F1 (Y-DNA)

This subclade is defined by the SNP P91. It is most common in Sri Lanka.

F2 (M427)

Main article: Haplogroup F2 (Y-DNA)

F2 Y-chromosomes have been found to be particularly common among the Kucong and/or Yellow Lahu minorities in South China and adjoining countries in mainland Southeast Asia. F2 is outside of HIJK, but it is unknown whether it falls inside of GHIJK or is basal to it.

F3 (M481)

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. 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

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 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. (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

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

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

Phylogenetic history

Main article: Conversion table for Y chromosome haplogroups

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

Genetics

3

Backbone Tree

Evolutionary tree of human Y-chromosome DNA haplogroups
	"Y-chromosomal Adam"
		A00	A0-T
			A0	A1
				A1a	A1b
					A1b1		BT
						B	CT
							DE						CF
						D	E		C		F
															F1	F2		F3	GHIJK
																				G	HIJK
																						H	IJK
																							IJ	K
																						I	J		LT		K2
																										L	T		NO	K2b	K2c	K2d		K2e
																													N	O		K2b1	P
																																	M	S		Q	R
Y-DNA by populations Famous Y-DNA haplotypes

External links

• 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.
• Kivisild et al 2003, The Genetic Heritage of the Earliest Settlers Persists Both in Indian Tribal and Caste Populations
• 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
• Sanghamitra Sahoo et al 2006, A prehistory of Indian Y chromosomes: Evaluating demic diffusion scenarios
• Arunkumar et al 2012
• ISOGG, 2015, Y-DNA Haplogroup F and its Subclades - 2015 (8 September 2015).
• 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.
• Balaresque et al (2015), Y-chromosome descent clusters and male differential reproductive success: young lineage expansions dominate Asian pastoral nomadic populations, Supplementary Table 2
• http://www.phylotree.org/Y/tree/index.htm
• biorxiv.org/content/biorxiv/early/2013/11/22/000802.1.full.pdf
• 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).
• http://ytree.ftdna.com/index.php?name=Draft&parent=92331011