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==Origins==
==Origins==
[[File:Haplogroup F (Y-DNA).PNG|thumb|350px|The diversion of [[Haplogroup F (Y-DNA)|Haplogroup F]] and its descendants.]]
[[File:Haplogroup F (Y-DNA).PNG|thumb|350px|The diversion of [[Haplogroup F (Y-DNA)|Haplogroup F]] and its descendants.]]
This megahaplogroup contains mainly lineages that are not typically found in sub-Saharan Africa, suggesting that its ancestral [[Haplogroup CF (Y-DNA)|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.<ref name=Karafet/>
This megahaplogroup contains mainly lineages that are not typically found in sub-Saharan Africa, suggesting that its ancestral [[Haplogroup CF (Y-DNA)|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 years ago, probably in South Asia.<ref name="Sengupta">{{cite journal |last1=Sengupta |first=Sanghamitra |first2=Lev A. |last2=Zhivotovsky |first3=Roy |last3=King |first4=S.Q. |last4=Mehdi |first5=Christopher A. |last5=Edmonds |first6=Cheryl-Emiliane T. |last6=Chow |first7=Alice A. |last7=Lin |first8=Mitashree |last8=Mitra |first9=Samir K. |last9=Sil |first10=A. |last10=Ramesh |first11=M.V. Usha |last11=Rani |first12=Chitra M. |last12=Thakur |first13=L. Luca |last13=Cavalli-Sforza |first14=Partha P. |last14=Majumder |first15=Peter A. |last15=Underhill |doi=10.1086/499411 |pmid=16400607 |pmc=1380230 |journal=[[The American Journal of Human Genetics]] |volume=78 |issue=2 |title=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 |pages=202–221 |date=1 February 2006}}</ref><ref name=Karafet/>
Please Note: The preceding estimate uses a 2008 paper as cite, while 2015 papers are rapidly improving knowledge.
More up-to-date sources (including Wikipedia!) may show (46,000 to 52,000) years ago for the TMRCA of F-M89, ''near western India''.


F is found in the [[Dravidian peoples|Dravidian]], [[Indo-European languages|Indo-European]], [[Sino-Tibetan languages|Sino-Tibetan]] and [[Tibeto-Burman languages|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).<ref>Zhong et al, (2011) [http://mbe.oxfordjournals.org/content/28/1/717.full 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, [http://mbe.oxfordjournals.org/content/early/2010/09/13/molbev.msq247/suppl/DC1 See Tables].</ref> 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).<ref>Balaresque et al (2015), [http://www.nature.com/ejhg/journal/vaop/ncurrent/full/ejhg2014285a.html Y-chromosome descent clusters and male differential reproductive success: young lineage expansions dominate Asian pastoral nomadic populations], [http://www.nature.com/ejhg/journal/vaop/ncurrent/extref/ejhg2014285x3.pdf Supplementary Table 2]</ref>
F is found in the [[Dravidian peoples|Dravidian]], [[Indo-European languages|Indo-European]], [[Sino-Tibetan languages|Sino-Tibetan]] and [[Tibeto-Burman languages|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).<ref>Zhong et al, (2011) [http://mbe.oxfordjournals.org/content/28/1/717.full 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, [http://mbe.oxfordjournals.org/content/early/2010/09/13/molbev.msq247/suppl/DC1 See Tables].</ref> 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).<ref>Balaresque et al (2015), [http://www.nature.com/ejhg/journal/vaop/ncurrent/full/ejhg2014285a.html Y-chromosome descent clusters and male differential reproductive success: young lineage expansions dominate Asian pastoral nomadic populations], [http://www.nature.com/ejhg/journal/vaop/ncurrent/extref/ejhg2014285x3.pdf Supplementary Table 2]</ref>

Revision as of 04:12, 14 October 2015

Haplogroup F-M89
Possible time of origin48,000 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 originSouth Asia[4][5][6]
AncestorCF
DescendantsF-89*, F1, F2, F3, GHIJK
Defining mutationsM89/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. This haplogroup and its subclades contain more than 90% of the world's existing non-African male population.

Structure

The vast majority of individual males with F-M89 fall into its direct descendant Haplogroup GHIJK (F1329/M3658/PF2622/YSC0001299).[7] Apart from GHIJK, Haplogroup F has four other direct descendants, all of which are rare in modern populations: the basal descendant 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 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 years ago, probably in South Asia.[8][1]

F 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).[9] 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).[10]

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

Instances of individuals belonging to FxGHIJK – basal F* (M89), or its subclades F1 (P91; P104), F2 (M427; M428) and F3 (M481) – are relatively 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.

F*

F*-M89 is found 5.2% in India[8] It is possible that an as-yet unnamed subclade of F* 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.[11]

F1 (P91)
Main article: Haplogroup F1 (Y-DNA)

This subclade is defined by the SNP P91. It is most common in Sri Lanka (Karafet 2008).[12]

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.[13] F2 is outside of HIJK, but it is unknown whether it falls inside of GHIJK or is basal to it.[14]

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 Andra Pradesh.[15] 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 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

Original research publications

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

3

Discussion

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[16] 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

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.[17]

The ISOGG Tree

See also

Genetics

3

Backbone Tree

References

  1. ^ a b c d 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. {{cite journal}}: Unknown parameter |subscription= ignored (|url-access= suggested) (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. ^ Roper, L. David. "Y-Chromosome Biallelic Haplogroups". L. David Roper. Retrieved 2013-08-31.
  6. ^ Roper. "Lineages and Results of Y-DNA Testing for Haplogroup F". L. David Roper. Retrieved 2013-08-31.
  7. ^ ISOGG, 2015, Y-DNA Haplogroup F and its Subclades - 2015 (8 September 2015).
  8. ^ a b c 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.
  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. ^ Balaresque et al (2015), Y-chromosome descent clusters and male differential reproductive success: young lineage expansions dominate Asian pastoral nomadic populations, Supplementary Table 2
  11. ^ "Nature Publishing Group: Error Page" (PDF). nature.com.
  12. ^ http://www.phylotree.org/Y/tree/index.htm
  13. ^ 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. {{cite journal}}: Unknown parameter |subscription= ignored (|url-access= suggested) (help)
  14. ^ biorxiv.org/content/biorxiv/early/2013/11/22/000802.1.full.pdf
  15. ^ 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).
  16. ^ http://ytree.ftdna.com/index.php?name=Draft&parent=92331011
  17. ^ "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.
  18. ^ http://gentis.ru/info/ydna-tutorial/hg-f/m89
  19. ^ 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.
  20. ^ "Melanesian and Asian Origins of Polynesians: mtDNA and Y Chromosome Gradients Across the Pacific".
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