Comprehensive Ethiopian YDNA TMRCA Estimates

Find below a comprehensive list for all central TMRCA estimates calculated from the Plaster thesis for 6 UEPs (look at this post under Interactive Chart of Figure 3.2 for the frequencies of the UEPs). P*(x R1a) & Y*(x BT,A3b2)  are not included due to their minimal frequency and very sporadic distribution. 

There were a total of 5,756 haplotypes reported with the paper for the markers DYS19, DYS388, DYS390, DYS391, DYS392 and DYS393.  30 of those haplotypes belonged to P*(x R1a) & Y*(x BT,A3b2), leaving a total of 5,726 haplotypes. These remaining haplotypes, were then categorized with the criteria of Cultural ID + Generic Language Group* + UEP, any group of haplotypes that conformed to this criteria with N >1 and with a coalescent not equal to 0 (meaning non-identical haplotypes) were processed for their TMRCA and reported, accounting for 5,668 or 98% of the total haplotypes reported for the paper.

The tables are ordered according to the frequencies of the tested UEPs in Ethiopia, i.e. E*(x E1b1a), 3985 Haplotypes  > J,  689 Haplotypes  > A3b2, 601 Haplotypes  > K*(xL,N1c,O2b,P) , 154 Haplotypes > BT*(xDE,JT), 193 Haplotypes  and E1b1a7, 46 Haplotypes .

Note that both the mean TMRCA's for Zhivotovsky (Z-TMRCA) and the pedigree rates (P-TMRCA), some times also known as germline rates, are in units of generations, the suitable length of a generation for the Z-TMRCA is 25 years, while for the P-TMRCA it may range from 28 to 33 years.

If detail of the TMRCA analysis for any of the populations listed below maybe required, go to the table here, and upload the necessary file into the Y TMRCA calculator and filter for the specific population in question.

Another Extensive thesis on East African DNA

It was brought to my attention last week, thanks to a comment on this blog made by the user 'Umi', that another thesis on East African DNA variation was publicly available online:

Complex Genetic History of East African Human Populations

This is also an extensive thesis with a wealth of information akin to Plaster's thesis, the primary differences being that this one was more focused on parts of East Africa that are found further to the South of Ethiopia, and in addition to uni-parental analysis, it also included some Autosomal model-based inference, albeit of quite low resolution in today's standards; 848 microsattelites and 479 indels (refer to Tishkoff et al. 2009 for marker details).

Due to the extensive nature of the report I haven't had a chance to cover its entire scope, instead, for starters, I have first focused on the YDNA data by creating a relative frequency chart from the results reported in Fig. 3.3.2. 

Several things to initially point out here,

• The report outlines the discovery of 4 new SNPs, TL1-4. The first two were found in Haplogroup B and downstream from B-M150 and B-M112 respectively. The last two, TL3 and TL4, were found in haplogroup E and downstream from E-U174 and E-V32 respectively. Incidentally, the fourth SNP that is under E-V32, TL4, could potentially be the same as Z808/Z809 as identified recently by the geneological community, however, as the report does not give the Y-Chromosome location of the SNP in a NCBI Build 36/37 format, this can not be verified, at least by me, at the moment.
• A couple of the frequency results in Fig. 3.3.2 do not add up, in particular, the frequency results for the Boni and the Baggara, but also to a lesser extent for the Kanuri and Teita.  I have labeled the missing frequency results with a “?” in the relative charts for those specific populations.
• The Burji and Konso are labeled as being only from Kenya throughout the report, however most Burji are from Ethiopia, and the Konso are exclusively found in Ethiopia, I have reflected this in the charts.
• STR data is not readily available to perform TMRCA estimates on, however, some TMRCA results are reported using Zhivotovsky's rates in Table 3.3.1, nevertheless, these are estimates only for different lineages found in the dataset for all the samples and not necessarily comparing TMRCAs in the different populations under study.
• J-M62, while a subclade of J-M267, is not the main subclade of J-M267 found in East Africa, that would be J-P58, therefore, the results for J-12f2.1 (x M62, M172) reported, may after all be, or largely include, J-P58 lineages, off-course those results could also include variants of J-M267 other than J-P58 and J-M62 as well since the SNP was not directly tested. 
• E-P2* lineages are abundantly found (> 30%) in the Konso, Burji and Mbugwe, however on closer examination and correlation with current data, these could be E-M329, E-V38* or even E-M215*, as none of these SNPs were directly tested. Genuine E-P2* lineages would be positive for E-P2 and negative for V38 and M215 (See Trombetta et al. 2011)
• Similarly, the E-M35* lineages reported could be members of relatively newly discovered lineages of E-Z830*( See this post for details), or some of the untested variantes of E-M35, i.e.  E-V42, V92 and maybe even E-V68 (x M78)

Sudan YDNA

This is from a relatively old study, but it seems that it is the most comprehensive YDNA breakdown we have of North and South Sudan to date.

Y-chromosome variation among Sudanese: restricted gene flow, concordance with language, geography, and history. Hassan (2008)

Here is a map of the populations tested from Fig.1 of the Study

Populations Studied

Here below is the phylogeny (as known back in 2008) of the SNPs tested, note that those in bold; E-M75, E-P2, G-M201 and T-M70 were NOT tested in the study.

SNPs tested (except those in bold)

The E-M78+ cases from above were also tested for Cruciani's V-Series SNPs as well for further resolution,

Cruciani's V-Series SNPs (2007)

Some notes:

• The high level (38%) of E-M215 (x M78) in the Borgu is quite intriguing, I wonder what variant/s of E-M215 it is?
• Almost all the J-12f2(x M172) should be J-M267.
• B-M60 is found in Southern Nilo-Saharan speakers and not the North Western ones, while A-M13 is found in both.
• The F-M89(x M52,M170,I2f2, M9) found in the north is also interesting, although it could possibly be G-M201, at least part of it.
• E-V22 has a relatively high presence in these samples, even when compared to the Egyptian samples from Cruciani '07, and most certainly higher than its presence in Ethiopia.
• The High presence of E-V12 (x V32) is also concordant with its putative area of origin, all the E-M78 found in the Nuer and the Copts is of this variety.
• The presence of E-M78* in the Masalit and the Nuba is notable.
• Off course the strangest result is the 54% R-M173 (x P25) in the Fulani, this could be some R1b*(R-M343), or some type of R1a, the latter would be very out of place for the region, while the former could be reconciled with the presence of more downstream R1b variants in Africa. 

Extensive Doctoral Thesis on Ethiopian Y and mtDNA

I was contacted earlier by Dr. Chris Plaster about a doctoral thesis on Ethiopian Y & mtDNA that was completed 2 years ago but had been embargoed to the public until only about two months ago. As this is the first time I am coming across of it, plus since it is 204 pages long I have not had a chance to go through it thoroughly, but suffice it to say that this is the most extensive work on Ethiopian NRY & mtDNA that I have seen to date, although the resolution leaves a lot to be desired, I will update this post more as I read it more thoroughly over the next few days/weeks...

Variation in Y chromosome, mitochondrial DNA and labels of identity on Ethiopia

Some numbers and figures that caught my attention at first glance:

The Discussion section also has some interesting things to say, especially with respects to haplogroups A3b2 and J, but also the remaining ones found in Ethiopia as well.

YDNA from Southern Africa

Naidoo et. al (2010) reports YDNA from 3 different groups in Southern Africa with a fair amount of resolution.

Electropherogram and phylogeny

Here below are the frequencies found:

Berber YDNA

Decent resolution composite Berber YDNA from The Berber and the Berbers, Genetic and linguistic diversities, Jean-Michel Dugoujon et. al (2009)

Phylogeny of the 29 biallelic MSY markers (in bold) tested

Update: With respect to R-P25 (x M269) found in the Siwa and Mozabite Berbers, there is an even more exact breakdown of the lineage in this table from another publication using the same samples as above. It shows for the Siwa Berbers, the 26.9% of R-P25 (x M269) being further resolved to 23.7 % R-V88* (x M18, V8, V35, V69) plus 3.2% R-V69 (a branch of R-V88), similarly for the Mozabite Berbers, the 3% of R-P25 (x M269) is all resolved to R-V88* (x M18, V8, V35, V69).

Y-DNA Variation Maps For East Africa

The supplementary information of the Chiaroni et. al 2009 paper "Y chromosome diversity, human expansion, drift, and cultural evolution", has some informative Y-DNA frequency distribution maps for the major globally distributed haplogroups. Here are the frequency distribution maps pertinent to East Africa (namely Ethiopia and periphery).

1) Estimated and calculated centroids location map (Fig. S4 -b)

Note: Centroids are not necessarily indicative of origin, diversity of the lineages in question are a better indicator of origin.

2)  Haplogroup A frequency distribution (Fig. S2 -b)

"Haplogroups A and B are the deepest branches in the phylogeny and are essentially restricted to Africa, bolstering the evidence that modern humans first arose there (14, 15). Haplogroup A is mainly found in the Rift Valley from Ethiopia to Cape Town, mostly but not exclusively in some of the oldest hunter-gatherers who still survive and speak Khoikhoi and San languages, proposed by some to be the oldest languages. The interruption of its distribution in the middle of the Rift Valley is possibly the consequence of replacement by Bantu-speaking farmers who settled the region starting in the first millennium of the Christian era."

The "Max" of 11.5% A3b2 (M13) shown above seems a bit low at first glance for East Africa, Semino et. al 2002 and Cruciani et. al 2002 together found 24 A3b2 lineages out of a total of 148 sampled in Ethiopia; Amhara (48), Oromo(78), Beta Israel (22). However, if the results of the Hassan et. al 2008 study of Sudan and the Sanchez et. al 2005 study of Somalia are added to the studies above, the frequency of A3b2 drops from ~16% in just Ethiopia to ~11.5 % (75 / 650) when Sudan and Somalia are included. Also important to note is that the Beta Israel, Dinka, Shiluk, Nuer and Nuba all carry anywhere between 33% and 62% of A3b2 lineages.

3) Haplogroup B frequency distribution (Fig. S1 -a)

 

"Haplogroup B is found mainly among African Pygmies, who live in the central African forest and are still predominantly hunters-gatherers but speak Bantu languages borrowed from farmers who arrived in the area between 2,000 and 3,000 years ago."

Haplogroup B is found at low levels in Ethiopia, with frequencies varying anywhere between 0 - 2% ( Cruciani et. al 2002, Semino et. al 2002, Moran et. al 2004). The haplogroup is however much more common in Sudan, with frequencies reaching as high as 50% in the Nuer. Generally, frequencies of Haplogroup B are found any where between 8% and 27% in the Sudan among the Nubians, Nuba, Copts, Hausa, Dinka and Shilluk. (Hassan et. al 2008)

4) Haplogroup E frequency distribution (Fig. S1 -b)

"The third predominantly African haplogroup, E, diversified some time afterward, probably descending from the East African population that generated the Out of Africa expansion. The geographic distributions of the major branches of this haplogroup, given in Fig. S1b, suggest that most of the settlement outside of Africa by haplogroup E members involves the later mutant E-M35 varieties like M78, M81, and M123 that extended to Arabia and the northern Mediterranean coast."

See the following threads for specifics on haplogroup E distribution in East Africa: E1b1b, E1b1b1a

5) Haplogroup J frequency distribution (Fig. S5 -a)

Further information on Haplogroup J in Ethiopia can be found in: Semino et. al 2002, Moran et. al 2004, Tofanelli et. al 2009, Chiaroni et. al 2009.

6) Genetic Diversity as a function of Distance from Addis Abeba (Fig. S6 -a)