Underhill (2001) proposed that haplogroup E may have arisen in
East Africa.[10] Some authors as Chandrasekar (2007), accept the earlier position of Hammer (1997) that Haplogroup E may have originated in
West Asia,[11] given that:
E is a clade of
haplogroup DE, with the other major clade,
haplogroup D, being exclusively distributed in Asia.
DE is a clade within
M168 with the other two major clades, C and F, considered to have already a
Eurasian origin.
However, several discoveries made since the Hammer articles are thought to make an Asian origin less likely:
Underhill and Kivisild (2007) demonstrated that C and F have a common ancestor meaning that DE has only one sibling which is non-African.[12]
DE* is found in both Asia and Africa, meaning that not only one, but several siblings of D are found in Asia and Africa.
Karafet (2008), in which Hammer is a co-author, significantly rearranged time estimates leading to "new interpretations on the geographical origin of ancient sub-clades".[13] Amongst other things this article proposed a much older age for haplogroup E-M96 than had been considered previously, giving it a similar age to Haplogroup D, and DE itself, meaning that there is no longer any strong reason to see it as an offshoot of DE which must have happened long after DE came into existence and had entered Asia.[13]
Kohl et al. (2009) presumed a West African origin for haplogroup E, stating: "From the 20 main haplogroups in the Y-chromosomal haplogroup tree, only 5 were detected in the analysed Amharic population in Ethiopia. Haplogroup A is near the roots of the tree and is only found among males on the African continent. The major haplogroup detected was E. Haplogroup E has its origin in
West Africa. Due to immigration
haplogroup A, which originally dominated in
Ethiopia, has been partly replaced."[7]
In 2015, Poznik & Underhill et al. claimed haplogroup E arose outside Africa, arguing that, "This model of geographical segregation within the CT clade requires just one continental haplogroup exchange (E to Africa), rather than three (D, C, and F out of Africa). The timing of this putative return to Africa, between the emergence of haplogroup E and its differentiation within Africa by 58 kya, is consistent with proposals, based on non–Y chromosome data, of abundant gene flow between Africa and Arabia 50–80 kya."[8]
In 2015, Trobetta et al. suggested an
East African origin for haplogroup E, stating: "our phylogeographic analysis, based on thousands of samples worldwide, suggests that the radiation of haplogroup E started about 58 ka, somewhere in sub-Saharan Africa, with a higher posterior probability (0.73) for an eastern African origin."[6]
Cabrera et al. (2018) hypothesizes a
Eurasian center of origin and dispersal for haplogroup E based on the similar age of the clade's parent haplogroup DE and the mtDNA haplogroup
L3. According to this hypothesis, after an initial
Out-of-Africa migration of early
anatomically modern humans around 125 kya,
haplogroup DE diversified around the Himalayas and in or westward of the
Tibet, after which E-carrying males are proposed to have back-migrated from the paternal haplogroup's place of origin in Eurasia around 70 kya along with females bearing the maternal
haplogroup L3, which the study also hypothesizes to have originated in Eurasia, into Africa. These new Eurasian lineages were then suggested to have largely replaced the old autochthonous male (such as haplogroup
B-M60) and female African lineages.[9]
Haber et al. (2019) study proposed an African origin for haplogroup E based on an analysis of the Y-chromosomal
phylogenetic structure, haplogroup divergence times, and the recently discovered haplogroup D0 found in three Nigerians, an additional branch of the DE lineage diverging early from haplogroup D. The authors support an African origin for
haplogroup DE, and the immigration of haplogroups
C, D and
FT out of Africa around 50,300–81,000 ybp. The early divergence dates found in the study for DE, E, and D0 (all dated to about 71-76 kya), which are determined to predate the migration out-of-Africa of the ancestors of Eurasians (dated to ca. 50-60 kya), are also considered by the authors to support an African origin for those haplogroups.[3]
At Nyarindi Rockshelter, in
Kenya, there were two individuals, dated to the Later
Stone Age (3500 BP); one carried
haplogroup L4b2a and another carried haplogroup E (E-M96, E-P162).[15][16]
Paragroup E-M96* refers to lineages belonging to the E clade but which cannot be classified into any known branch. E(xE1-P147, E2-M75) - that is, E which has tested negative for both P147 and M75 - has been reported in 3 males from
Lebanon,[24] 2
Amharas from
Ethiopia,[25] 2 males from
Syria,[26] 2 males from
Saudi Arabia,[27] and in a single
Bantu-speaking male from
South Africa.[13] E(xE1a-M33, E1b1-P2, E2-M75) was reported among several Southern African populations and in an Egyptian man;[28] E(xE1a-M33, E1b1a1-M2, E1b1b-M215, E2-M75) has also been observed amongst
pygmies and Bantu from
Cameroon and
Gabon;[22] and also in Burkina Faso[29] and a
Fulbe man from
Niger.[30]
Recently it was discovered that 3 East African men previously classified only as E*-M96 could be assigned to a new branch, E-V44, which is a sister branch to E1-P147; E-P147 and E-V44 share the V3725 mutation, making E2-M75 and E-V3725 the two known primary branches of E.[31] Two
Saudi private testers from
Mecca and
Jizan were also found to belong to this elusive and rare branch.[32] It is not known whether or not some (or all) other E*(xE1,E2) in previous studies would fall into V44 as well.
E-P147 (also known as E1) is by far the most numerous and widely distributed branch of E-M96. It has two primary branches:
E-M132 (E1a) and
E-P177 (E1b).
Haplogroup E1a is split into two branches: E1a1 (E-M44) which has been mostly found in
Europe,
West Asia and among
Ashkenazi Jews; and E1a2 (E-Z958) which has been exclusively identified in
Sub-Saharan Africa.[33]
Haplogroup E-P2 (E1b1) is the most frequent variant of E-M96 and the most common
Y-DNA lineage in
Africa with two main descendants:
E-V38 (E1b1a) and
E-M215 (E1b1b). Haplogroup E (xE3b,E3a) - that is, E tested negative for both M35 and M2, has been reported in 11 males from
Morocco in Zalloua et al. (2008b).[34]
Haplogroup E-M75(xM41,M54) has been found in 6% (1/18) of
Dama from Namibia,[28] 4% (1/26) of
Ganda from Uganda,[28] 3% (1/39) of
Mandinka from Gambia/Senegal,[28] and 2% (1/49) of
Sena from Mozambique .[28]
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.
This phylogenetic tree of haplogroup subclades is based on the Y-Chromosome Consortium (YCC) Tree,[38] the ISOGG Y-DNA Haplogroup Tree,[39] and subsequent published research.
^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.
PMID24166809.
S2CID23291764.
^ Haplogroup K2b (M1221/P331/PF5911) is also known as Haplogroup MPS.
^ Haplogroup K2e (K-M147) was previously known as "Haplogroup X" and "K2a" (but is a sibling subclade of the present K2a).
^K-M2313*, which as yet has no phylogenetic name, has been documented in two living individuals, who have ethnic ties to India and South East Asia. In addition, K-Y28299, which appears to be a primary branch of K-M2313, has been found in three living individuals from India. See: Poznik op. cit.;
YFull YTree v5.08, 2017, "K-M2335", and;
PhyloTree, 2017, "Details of the Y-SNP markers included in the minimal Y tree" (Access date of these pages: 9 December 2017)
^ Haplogroup K2b1 (P397/P399) is also known as Haplogroup MS, but has a broader and more complex internal structure.
^Chandrasekar; Saheb, S. Y.; Gangopadyaya, P.; Gangopadyaya, S.; Mukherjee, A.; Basu, D.; Lakshmi, G. R.; Sahani, A. K.; Das, B.; Battacharya, S.; Kumar, S.; Xaviour, D.; Sun, D.; Rao, V. R.; et al. (Sep–Oct 2007). "YAP insertion signature in South Asia". Annals of Human Biology. 34 (5): 582–6.
doi:
10.1080/03014460701556262.
PMID17786594.
S2CID11860142.
^Underhill, Peter A.; Kivisild, Toomas (2007). "Use of Y Chromosome and Mitochondrial DNA Population Structure in Tracing Human Migrations". Annual Review of Genetics. 41: 539–64.
doi:
10.1146/annurev.genet.41.110306.130407.
PMID18076332.
^Bučkova (2013). "Multiple and differentiated contributions to the male gene pool of pastoral and farmer populations of the African Sahel". Am J Phys Anthropol. 151 (1): 10–21.
doi:
10.1002/ajpa.22236.
PMID23460272.
Underhill, Peter A.; Shen, Peidong; Lin, Alice A.; Jin, Li; et al. (November 2000). "Y chromosome sequence variation and the history of human populations". Nature Genetics. 26 (3): 358–361.
doi:
10.1038/81685.
PMID11062480.
S2CID12893406.