Haplogroup F-M89


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. in addition to GHIJK, haplogroup F has three other immediate descendant subclades: F1, F2, and F3. These three, with F*, constitute the paragroup F.
Haplogroup GHIJK branches subsequently into two direct descendants: G and HIJK. HIJK in turn splits into H and IJK. The descendants of the haplogroup IJK include the clades 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

It is estimated that the SNP M89 appeared 38,700–55,700 years ago, most likely in South Asia It has also been suggested by previous research that F-M89 first appeared in the Arabian Peninsula, Levant or North Africa, about 43,800–56,800 years ago,. 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 Southeast Asia.
Some lineages derived from Haplogroup F-M89 appear to have back-migrated into Africa from South Asia, during prehistory. Subclades of F-M89 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 the paragroup F – that is, either basal F* or the primary subclades F1, F2 and F3 – 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 has not been well studied, occurs "infrequently" in modern populations and peaks in South Asia, especially Sri Lanka. 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, which was originally named "F3", i.e – a name that has since been reassigned to F-M481.
F has been reported among 10% of males in Sri Lanka, 5.2% of males across India, 5% in Pakistan, as well as lower levels among the Tamang people, and in Iran.
Men originating in Indonesia have also been reported to carry F – 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, found that Indonesian men with the SNP 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. F1, F2 and F3 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 have been reported in individuals from Turkmenistan and Uzbekistan.
There is also evidence of westward Paleolithic back-migration of F from South Asia, to Iran, Arabia and North East Africa, as well as South-East Europe.
Neolithic migration into Europe from Southwest Asia, by first wave of farmers in Europe has been put forward as the source of F and G2a found in European Neolithic remains, dating from circa 4000 BCE. These remains, according to Herrerra et al. showed a "greater genetic similarity" to "individuals from the modern Near East" than to modern Europeans. F may have been found in Bronze Age remains from Europe, namely the individuals known as DEB 20 and DEB 38, who lived about 7,000–7,210 BP, and were found at the Derenburg Meerenstieg II site in Germany.
Three less certain cases, which have not been tested for all subclades of GHIJK, have been found among Neolithic remains in Europe. I0411, who lived 7,195–7,080 years BP, was found in the Els Trocs cave, near Bisaurri – while haplogroups G, I1 J, L1b2, Q1b1, Q1a2a, R1a1a1, R1b1a2b1a and T were ruled out, I2a1b1 and R1b1a2 were found in other remains from the same site. Similarly, three sets of remains from Hungary were not tested for all subclades of GHIJK: BAM 17, BAM 26 and TOLM 3.
Some cases reported amongst modern populations of Europeans, Native Americans and Pacific Islanders may be due to migration and admixture of F, as a result of contact with South and/or South East Asia, during the early modern era.
Such examples include:
Basal F-M89* has been reported among 5.2% of males in India. A regional breakdown was provided by Chiaroni et al : 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.
In Iran, 2.3% of Bandari males from Hormozgan Province have been found to carry basal F-M89.
Haplogorup F* has been found in only 11.67% of Yunnan Han Chinese tested. Xi'an,
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.

F1 (P91)

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

F2 (M427)

F2 Y-chromosomes have been reported among minorities from the borderlands of South China, Thailand, Burma, and Vietnam, namely the Yi and Kucong or Lahu Shi, a subgroup of the Lahu.

F3 (M481)

The newly defined and rare subclade F3 has been found in India and Nepal, among the Tharu people and in Andhra Pradesh. F-M481 should not be confused with Haplogroup H2, which was previously misclassified under F-M89, as "F3".

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 or unique event polymorphisms.

Phylogenetic trees

There are several confirmed and proposed phylogenetic trees available for haplogroup F-M89. The scientifically accepted one is the Y-Chromosome Consortium 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 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.
This is the official scientific tree produced by the Y-Chromosome Consortium. The last major update was in 2008. Subsequent updates have been quarterly and biannual. The current version is a revision of the 2010 update.
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. 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 ''''''YCC 2002 YCC 2005 YCC 2008 YCC 2010r ISOGG 2006ISOGG 2007ISOGG 2008ISOGG 2009ISOGG 2010ISOGG 2011ISOGG 2012
F-M892VI1R20Eu10H4BF*FFFFFFFFFF
F-APT/H-APT15VI1R20Eu10H4BF1H2H2H2H2H2H2H2H2H2H2

Genetics

Backbone Tree