YDNA E-M123; A closer look

YDNA E-M123; A closer look ethiohelix.blogspot.com /2014/02/ydna-e-m123-closer-look.html E-M123 (as well as E-M34) was first discovered by Underhill(2000) and is found with a low to medium frequency distribution in East Africa and the Middle East, while it has a low frequency distribution in North Africa and Europe. Phylogeny: Figure 1 shows a comparison of the basic phylogeny of E-M215/M35 as was known before 2011 (a) and after (b), with a 'who and when' key for the Discovery of the UEPs. Notice the impact the rearrangement has on the phylogenetic placement of E-M123, specifically the fact that E-M123 is shown to have a more recent common ancestor with the East and Southern African variants of E-M35, i.e. E-V42 and E-M293, before it does with any of the other variants of E-M35. Previous publications: While it is unfortunate that all of the research that has previously been published on E-M123 was done under the consideration of the older (and rather out of date) configuration of the basic structure of E-M35, it is still worth while to look at articles that have tried to untangle the origins and history of this lineage, of these, 3 come to mind:

Figure 1 - Current and previous E-M215 phylogenetic structure

(1) Semino et al., in which the following paragraph was said with respect to E-M123:

"The very low frequency of E-M123 in Ethiopia does not allow any inferences about the origin of this clade. The network of E-M78 and that of E-M123 are in agreement with the hypothesis of their ancient presence in the Near East and their subsequent expansion into the southern Balkans. The divergence time (TD) (Zhivotovsky 2001) between the Near East and European lineages has been estimated to a range of 7–14 thousand years (ky) ago. Cinnioğlu et al. ( 2004) found a high degree of variance of E-M123 in Turkey, which has been interpreted as being due to multiple founders rather than a single early dispersal event that has remained geographically circumscribed."

(2) Cruciani et al., in which this was said about the lineage:

"In our data set, all the E-M123 chromosomes also carry the M34 mutation (E-M34), with

the exception of one E-M123* subject from Bulgaria. This paragroup has been previously reported only in one individual from Central Asia (Underhill et al. 2000). Although the frequency distribution of E-M34 could suggest that eastern Africa was the place in which the haplogroup arose, two observations point to a Near Eastern origin: (1)Within eastern Africa, the haplogroup appears to be restricted to Ethiopia, since it has not been observed in either neighboring Somalia or Kenya (present study) or Sudan (Underhill et al. 2000). By contrast, E-M34 chromosomes have been found in a large majority of the populations from the Near East so far analyzed (Underhill et al. 2000; Cinniog˘ lu et al. 2004; Semino et al. 2004 [in this issue]; present study). (2) E-M34 chromosomes from Ethiopia show lower variances than those from the Near East and appear closely related in the E-M34 network (fig. 2D). If our interpretation is correct, E-M34 chromosomes could have been introduced into Ethiopia from the Near East. The high frequency of E-M34 observed for some of the Ethiopian populations could be the consequence of subsequent genetic drift, which can also explain the lower frequencies (2.3% [Underhill et al. 2000] and 4.0% [Semino et al. 2002]) reported for two large independent samples of Ethiopians."

(3) The last comes from a thesis, commonly referred to in this blog as the ' Hirbo thesis' (2011), where it said:

"The E3b3 haplotype, defined by the M123 mutation, was previously suggested to have originated in the Middle East and is found at low frequencies both in the Middle Eastern and East African populations [153, 434] (Appendix 6a). This conclusion was based on the fact that the E3b3 haplotype was observed only in Ethiopian samples from among the nine East African populations analyzed in a previous study [153], and lower STR variances in the Ethiopian E3b3 samples than in the Middle East [153]. However, extensive analysis of East African populations in the current study shows that this haplotype is found in Kenyan and Tanzanian Cushitic speakers as well, albeit, at low frequency (Figure 3.3.2, Appendix 6a). Its frequency maximum is centered in northeastern Africa (Table A9.1.1, Figure A9.1.7). Considering that the highest frequency is observed among the Ethiopian Jews [164] (Appendix 6a) a population that has been shown to be paternally [505, 565] and maternally [219] distinct from other Jewish populations, and genetically most similar to Sub-Saharan Africans [219, 505, 565], and the highest variance is observed in African populations (Table A9.1.2), the origin of E3b3 will most probably be among Cushitic/Omotic speaking populations of Southwest and Central Ethiopia."

Frequency: Below are some of the more significant (>5%) frequencies of E-M123 found in published papers. Note that almost all E-M123 haplotypes also belong to E-M34, but since some papers directly test for E-M34 and others test just for E-M123, I have noted all the UEPs as E-M123 for the sake of uniformity: 2002 Semino et al. found: 5% of E-M123 in Ethiopian Oromo

Cruciani et al. found: 14% of E-M123 in the Beta Israel of Ethiopia 2003 Cinnioglu et al. found: 5-9% of E-M123 in all regions of Turkey except regions 1,2 & 8 2004 Cruciani et al. found: 24% of E-M123 in Ethiopian_Amhara 8% of E-M123 in Ethiopian_Wolayta 8% of E-M123 in Erzurum Turkish 8% of E-M123 in Ethiopian_Oromo 8% of E-M123 in Omanite 7% of E-M123 in Bedouins 7% of E-M123 in Sicilians 5% of E-M123 in Sephardi Turks 5% of E-M123 in Northern Egyptians Semino et al. found: 13% of E-M123 in an Albanian community of the Cosenza province in Italy 12% of E-M123 in Ashkenazi Jews 10% of E-M123 in Sephardi Jews 5% of E-M123 in Tunisians 5% of E-M123 in Lebanese Arredi et al. found: 10% of E-M123 in Algerian Berbers 9% of E-M123 in Northern Egyptians 7% of E-M123 in Southern Egyptians Shen et al. found: 20% of E-M123 in Libyan Jews 12% of E-M123 in Ethiopian Jews 10% of E-M123 in Ashkenazi Jews 10% of E-M123 in Yemeni Jews Moran et al. found: 11% of E-M123 in Ethiopian Track and Field 10% of E-M123 in Ethiopian Marathon 6% of E-M123 in Ethiopian General Control 5% of E-M123 in Ethiopian Arsi Control 2005 Luis et al. found: 10% of E-M123 in Arabs from Oman 5% of E-M123 in Arabs from Egypt Flores et al. found:

31% of E-M123 in Jordainians from the Dead Sea 2006 Beleza et al. found: 12% of E-M123 in Beja, Portugal 5% of E-M123 in Coimbra, Portugal 2007 Cadenas et al. found: 8% of E-M123 in Yemenis 2008 Contu et al. found: 5% of E-M123 in Tempio, Sardinia 2009 Hammer et al. found: 10% of E-M123 in Israelite Jews 5% of E-M123 in Cohanim Jews Di Gaetano et al. found: 11% of E-M123 in Mazara del Vallo, Sicilly 11% of E-M123 in Piazza Armerina, Sicilly 10% of E-M123 in Troina, Sicilly 2011 The supplemental data of the Plaster thesis found: 25% of E-M123 in Ethiopian_Maale 13% of E-M123 in Ethiopian_Amhara 10% of E-M123 in Ethiopian_Oromo The Hirbo thesis found: 9% of E-M123 in Ethiopian_Burji 8% of E-M123 in Kenyan_Yaku 5% of E-M123 in Kenyan_Boni 2013 Bekada et al. found: 11% of E-M123 in Sahara + Mauritania 7% of E-M123 in Egypt 6% of E-M123 in Turkey

The contour map shown above is taken from Figure A9.1.7 of the Hirbo thesis and shows the general spatial frequency distribution of EM123 in Africa, Near East and Southern Europe. While the map obviously does not include data from sources published after 2011, like Bekada (2013) for instance, also note that it does not include the E-M123 data found from the Plaster thesis as well. TMRCA/Variance: Cruciani 2004 used Microsatelite networks (Figure 2D in the publication) to infer that Ethiopian E-M34 variance is lower than that found in the near east, since the Ethiopian M34 haplotypes appeared to be more closely related than the Near Eastern ones in the network. Hirbo on the other hand, inferred higher variance (Table A9.1.2) in Africa than outside of Africa. Figure 2 - E-M123 Contour Map from the Hirbo Thesis

Below, I have used the ASD approach to compute and compare TMRCAs of several E-M123/M34 datasets:

1. The Plaster E-M34, N = 34 dataset, representing haplotypes from Ethiopia, filed under Ethiopian_EM34.csv. 2. The Plaster Ethiopian Amhara Dataset, N = 9, A subset of (1) 3. The Plaster Ethiopian Maale Datastet, N = 16, A subset of (1) 4. The global E-M123 dataset from publicly available FTDNA haplotypes, N = 129, note that a very vast majority of these are not of African origin, although a few could be, filed under FTDNA_EM123.csv 5. The global E-M84 dataset from publicly available FTDNA haplotypes, N = 69, note that E-M84 is a variant of E-M34, filed under FTDNA_EM84.csv

The TMRCAs for these haplotypes were computed using the germline mutation (pedigree) rates and effective (Zhivotovsky) rates separately, see Figures 3-4 below. In addition, 2 different sets of markers

were analyzed, the first set included all markers available in the calculator, intersected with all the markers available in the Plaster thesis, yielding 14 markers. The second set comes from an intersection of the markers from the thesis with the recommended Zhivotovsky markers, yielding 9 markers.

The results of the comparative TMRCA calculations are by no means unequivocal, but nevertheless allow for several observations to be made:

The overall Ethiopian E-M34 haplotypes have comparable and greater central TMRCA estimates than the global EM123 samples with the exception of the scenario of 14 markers with the use of pedigree mutation rates (Figure 4b)

Figure 3 - Zhivotovsky Central TMRCA Estimates

The Ethiopian Maale dataset consistently shows the least central TMRCA estimate compared with the other datasets, conversely, the Ethiopian Amhara datastet consistently shows the highest central TMRCA estimate compared to all other datasets. The remaining Ethiopian haplotypes, mostly belonging to the Oromo, have an intermediate TMRCA estimate between the Amhara and Maale samples, although a lot closer to the Amhara estimates.

Figure 4a - Pedigree Central TMRCA Estimate Ranges - 9 Markers

Conclusion: The current phylogenetic positioning of EM123 (Figure 1b) reduces the probability of the lineage originating in the Near East (vs. Eastern Africa), relative to the independent positioning that the lineage used to have within E-M35 Figure 4b - Pedigree Central TMRCA Estimate Ranges - 14 Markers (Figure 1a). This is because the new position reveals that E-M123 shares a more recent common ancestor with lineages of E-M35 that are either East African (E-V42) or South/East African (E-M293) specific, rather than, either (a) showing a closer relationship to the

main variant of E-M35 that is found outside of Africa, i.e. E-M78 or (b) maintaining its old independent position within E-M35. Of the two arguments lending support to a Near Eastern origin of E-M123 brought forth by Cruciani (2004), the first, "restriction of the haplogroup within Ethiopia", has been invalidated by sampling that has been done since the report, namely (a) the finds of E-M123 in the Yaaku, Boni and Turkana of Kenya in the Hirbo Thesis, (b) one of the highest ever recorded frequencies of E-M123 found in southern most Ethiopia (Semien Omo Zone) among the Omotic speaking Maale in the Plaster thesis and (c) the E-M123 find in a Somali dataset in Sanchez (2005), albeit at quite a low frequency. The second argument, "lower variance of E-M34 chromosomes in Ethiopia", proves to be at best inconclusive and at worst wrong, after carrying out further analysis on E-M34 haplotypes from Ethiopia relative to large global samples of publicly available E-M123 haplotypes, see Figures 3 - 4, in addition to the analysis carried out in the Hirbo thesis (Table A9.1.2). The previous understanding of a decreasing frequency of E-M34 haplotypes from Northern to Southern Ethiopia has been upset by the samples that appeared with the Plaster thesis, since the highest frequency of the lineage was found in the Omotic speaking Maale, however, while the frequency appears to be higher in the South and lower in the North, the diversity of the lineage appears to have an opposite pattern, i.e. higher in the North and lower in the South. Median Joining Networks (created using the Fluxus Network Software)