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.

The Zhivotovsky Multiplier

It is reported that Zhivotovsky's effective mutation rate [1] has the effect of increasing the TMRCA of a lineage, as computed by the use of Microsattelite Genetic Distances[2], by a factor of 3-4 fold relative to TMRCAs computed via mutation rates observed in pedigree and family studies [3].

By utilizing my TMRCA calculating program, I want to explore,

1. What effect does different marker combinations have on this multiplier ?
2. What effect does marker size have on this multiplier ?
3. Is there a variation in this multiplier for different data-sets?

First, to ensure that my program correctly calculates the TMRCA when the Zhivotovsky mutation rate of 0.00069 is applied to all the markers in my database consistently (versus only the marker specific Pedigree mutation rates I have thus far been utilizing), I attempted to replicate the TMRCA computations of the following publication;

The emergence of Y-chromosome haplogroup J1e among Arabic-speaking populations Chiaroni et al. (2009)

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. 

A speculative superimposition of E-M35 variants onto Afroasiatic.

Here is a speculative superimposition of the variants of YDNA E-M215/M35 (E1b1b/1) onto an Afroasiatic internal classification, Lionel Bender's (1997) classification. 

The red question marks represent a less unsure fit.

TMRCA calculations from Plaster NRY data : Correcting an Error

Previously, I had computed TMRCAs for the YDNA STR data from the additional material that was provided along with Dr.Chris Plaster's thesis. However, after a brief communication with the author, I found out that the marker order of the STRs in the excel file was reported wrongly, the correct order for the markers are thus as follows:

DYS19 DYS388 DYS389I DYS389II DYS390 DYS391 DYS392 DYS393 DYS437 DYS438 DYS439 DYS448 DYS456 DYS635 Y GATA H4

This changes my TMRCA calculations because I am not computing the coalescent using a generic mutation rate that is equivalent for all the markers, but rather each marker has its own mutation rate attributed to it.

When I rerun my program using the newly corrected order above I get the following:

As can be seen, using the new order of markers generally reduces the number of generations to coalescent for the Plaster data-set. The previous observation of a relatively lower TMRCA for the haplozone data of E-M123 versus that of the E-M34 Plaster data-set largely disappears. 

To check if the fact that the high number of samples (129) present in the E-M123 haplozone data-set was skewing the results, I took 23 random samples (which equals the same number of samples available in the Plaster E-M34 data-set) from the larger E-M123 Haplozone dataset and re-run the TMRCA calculations on just those samples, I repeated this process 300 times, only 28% of the runs yielded a mean TMRCA less than the E-M34 Plaster data-set, if sample size was skewing the results I would expect >50% of the runs to have a mean TMRCA less than that of the E-M34 plaster dataset.

That said, the E-M34 Plaster data-set still had a relatively higher generations to coalescent than the E-M84 Haplozone dataset, E-M84 is a subclade of E-M34 and a high majority of haplotypes that belong to E-M34 also test positive for the E-M84 SNP (at least for the non-African E-M34 haplotypes that we know of).

Other than that, the new, and corrected, ordering of the markers did not have much impact in relative TMRCA terms between the Plaster and Haplozone/FTDNA data for the other lineages I had tested.

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.

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).

Finding the TMRCA of Ethiopian YDNA lineages using an ASD method.

I have been lately working on computing TMRCAs using an ASD or average square difference method on publicly available Y-STR haplotypes. The premise for finding the TMRCA using the ASD method is quite straight forward and easy to understand, a putative ancestral haplotype is calculated for a given dataset and the repeat of each sample at each marker in the dataset is subtracted from this ancestral haplotype, this result is then cumulated and divided by the number of samples and the marker specific mutation rate, the process is repeated for every single marker in the dataset and the mean is then multiplied by an assumed years per generation length, the formula below articulates this method:

TMRCA formula (ASD method)

 

Where;

N= Total number of Samples

Z= Total number of Markers

L⁰= Putative Ancestral Haplotype (Median or Modal repeats)

L= Individual sample haplotype repeats

m= Marker Specific Mutation Rate

G= Years / Generation

The biggest variable here, other than the sampling strategy of a given dataset, are the several marker specific mutation rates that are available. The process of selection of a correct mutation rate is an unsettled issue, I have therefore utilized 4 sets of mutation rates that were compiled by Paul Newlin, a collaborator at the E3b Project, these rates come from several different publications and you can read about them here for more detail:

 

1. The Chandler Mutation Rates:
   http://www.jogg.info/22/Chandler.pdf
2. Stafford Bayesian Mutation Rates:
   Essentially a compilation of other mutation rates
3. Burgarella & Navascués Mutation Rates:
   http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3039515/
4. Ballantyne Mutation Rates:
   http://www.cell.com/AJHG/retrieve/pii/S0002929710004192

In order to have an analogously accurate comparison of the TMRCAs between the different publications, I had to weed out and intersect the available markers from above with markers that are found in the public domain. This essentially left me with the following 46 markers that intersected with all 4 of the above sets of rates as well as the 66 markers that are widely used:

406s1 , 19 , 388 , 389-1 , 389-2 , 390 , 391 , 392 , 393 , 426 , 436 , 437 , 438 , 439 , 442 , 444 , 446 , 447 , 448 , 450 , 454 , 455 , 456 , 458 , 460 , 472 , 481 , 487 , 490 , 492 , 511 , 520 , 531 , 534 , 537 , 557 , 565 , 568 , 572 , 578 , 590 , 594 , 617 , 640 , 641 and gatah4.

In addition, since the Chandler mutation rates had a complete intersection with the 66 widely used markers, an additional 66 marker Chandler set was independently used that included the following markers in addition to the 46 listed above:

385a , 385b , 459a , 459b , 449 , 464a , 464b , 464c , 464d , ycaiia , ycaiib , 607 , 576 , 570 , cdya , cdyb , 395s1a , 395s1b , 413a and 413b.

  

Haplogroups A, E and J, cover well over 90% of the YDNA lineages found in Ethiopia. More specifically within these haplogroups, I was more interested in finding the TMRCA for A-M13, E-M35 and J1-M267, as these lineages cover over 70% but under 80% of said lineages, whereas the remaining 20-30% of lineages found in Ethiopia belong to E1b1*(x E1b1b,E1b1a1), other types of E lineages like E2 and E*, and some specific clades that belong to haplogroups B,T and J2.