P2 Clades: The Arrival of E3a and E3b Haplogroups

The MAJOR PN2 CLADES - E3a and E3b haplogroups: Investigating the backdrop against which they came about.

Recently, it has been proposed that E3b originated in sub-Saharan Africa and expanded into the Near East and northern Africa at the end of the Pleistocene (Underhill et al. 2001). - Cruciani et al. 2004, Phylogeographic analysis of haplogroup E3b...

We hear much about E3b and E3a haplogroup bearing populations in Africa, the major haplogroups on the African landscape today, but when and where did these lineages likely come about?

Here is what the present author of the blog thinks occurred, based on the information available to the author:

Between 23 and 18ky ago—Ogolian period begins, which coincides with and is likely connected to the LGM weather situation.

23,000 BP ~ 21,050 BC: "After a favourable climatic period, characterised by relatively dense and diversified Palaeolithic occupations, the arid Ogolian begins locally around 23000 years BP and is represented at Ounjougou by a significant depositional and archaeological hiatus." — Aziz Ballouche [see: Link ]

—Much of North Africa and the Sahara are characterized by adverse weather conditions, with much of the region turning arid. The Sahara at this time, extends south beyond its current boundaries to a certain point, possibly a little beyond the Niger bend.

Arid conditions extend all the way to the "horn" coast of the African Horn region, possibly encouraging populations to reside more inwards—away from that horn-shaped coastal region; rather, likely towards the region straddling southern Sudan, Ethiopia, Kenya and Uganda or even further—region straddling Uganda, Kenya, and Tanzania.

—PN2 clade (E3) bearers in the vicinity of the Sudanese-Central African Republic -Ugandan-Kenyan region give rise to E3a ~ between 21 and 18 ky ago [pending additional or new info]; E3b-M35* would have likely arose relatively earlier than E3a* [as evidenced by its near absence in some the populations that carry this], sometime prior to the Ogolian and the LGM period. At this time, it was likely the M78 derivative that came about ~ between 19 and 15 ky ago. It was also likely during this period, that some E3b-M35 variants spilled over to the "southwest Asia", which would be identified as E-M34. The E-M78* likely arose somewhere in the bidirectional-migration route between Northeast and sub-Saharan East Africa; this location was likely in the region straddling upper Egypt and Sudan of the eastern Sahara, amongst earlier E-M35 migrants from sub-Saharan East Africa. These M78 bearers were increasingly pressured to move further south due to progressive aridity, possibly as far as Uganda-Kenya and/or Tanzanian general region.

—The E3a bearing group would proceed westward, perhaps meeting groups of earlier lineages at the Shum Laka region of Cameroon, whereby quartz micro-lithic culture had already been in place by around 30 ky ago, hence preceding the rise of E3a common recent ancestor. But this group wouldn’t stay put here, at least not every section of it; they’d proceed to the savanna, grassland or vegetation holdouts in West Africa beyond the then boundaries of the Sahara. This probably occurred some time between 15ky and 13ky ago. During this period, as the Saharan aridity began to gradually slacken, some E-M78 bearing proto-Afrasan speaking nomads likely made their way into the Levant via the Sinai corridor.

Others taking refuge in the Cameroonian savanna-tropical forest general region probably followed suit, that is—after the aforementioned initial batch of migrants [bearing E3a descendants]; or else, the same group of people [from the initial migrants] shifted locations along the west African vegetation belts, once it became apparent that the far western reaches didn’t have much to offer, but the water system [as part of the Niger River]—however relatively shallow or what not—offered something additional. Finally, when the conditions in the Sahara were turning around for the better, starting between ~ 12ky and 11ky ago, these migrants would proceed northward, leaving the sort of trails that find expression at Ounjougou—Mali.

10th millennium BC ~ 12ky ago: At Ounjougou—"It is not until the Holocene and the return of humid climatic conditions, beginning in the 10th millennium BC, that it is possible to again observe evidence of human occupation." — Aziz Ballouche [see: Link ]

"Consequently, it has to be seen in the context of heavy rainfalls and a resettlement of the vegetation cover, during the 10th millennium BC, that a new population arrives on the Plateau of Bandiagara." — Human population and paleoenvironment in West Africa [see: Link ]

And...

From 30,600 to 10,000 BC: "A cultural flow, from the southeast of Subsaharan Africa and to the Sahara, could explain the diffusion of the microlithic industries all the way through West Africa. We observe them initially in Cameroon at Shum Laka (30.600-29.000 BC), then at the Ivory Coast in Bingerville (14.100-13.400 BC), in Nigeria in Iwo Eleru (11.460-11.050 BC), and finally in Ounjougou (phase 1, 10th millennium BC)." — Human population and paleoenvironment in West Africa [see: Link ]

It's very probable that this E3a bearing group(s) came into contact with the then wandering earlier-inhabitants of west Africa, who would have been pressured to move southward beyond the then Saharan desert boundaries, due to progressing aridity of the Ogolian period. These groups could have brought their central-Saharan pottery [e.g. found in Niger] traditions with them [developed perhaps sometime during the transitioning period to the wetter phase of the Sahara], just as the E3a bearing group(s) brought the microlithic traditions that they possibly picked up in the vicinity of the Shum Laka region [see above excerpt carbon dating estimations of finds] …and/or else…the new migrants produced their own versions of pottery in their new found location [as it is not noted whether these pottery had affinities with examples found in the aforementioned central Saharan region], at a time when it was trendy to carry stuff in pottery ware in the Saharan-Sahelian zone, with the filling up river systems due to the Monsoon rains.

The 10,000 and 9,000 BC (Phase 1 of the Holocene in Ounjougou): "The first sedimentary sequence of the Holocene can be observed at the Ravin de la Mouche. It's a channel dug into yellow Pleistocene silt and filled with coarse grained sand and pebbles. As a chronological reference for the upper levels of this early Holocene site, we hold ten radiocarbon dates between 9400 and 8400 BC cal. The associated lithic industry evidences predominantly a unidirectional mode of debitage. But also other technologies, such as bipolar on anvil or multidirectional, have been applied by the Early Holocene population. The raw material mainly used was quartz. The typological range consists of small retouched flakes, geometric microliths and perçoirs, but also of continuously retouched bifacial arrowheads and backed points." — Human population and paleoenvironment in West Africa [see: Link]

"By" 11,000 years BP ~ by 9050 BC:

"The age of the sediment in which they were found suggests that the six ceramic fragments discovered between 2002 and 2005 are at least 11,400 years old. Most ancient ceramics from the Middle East and the central and eastern Sahara regions are 10,000 and between 9-10,000 years old, respectively." — Human population and paleoenvironment in West Africa [see: Link]

By the 'beginning' of 8,000 BC: "Outstandingly, there has been evidence of the presence of pottery and seed grinding implements since at least the beginning of the 8th millennium BC. It is therefore the oldest site. The eighth millennium (Phase 2 of the Holocene in Ounjougou) known of this socio-economic type in sub-Saharan Africa...

The pottery and the seed grinding implements of phase 2 of Ounjougou are the oldest artefacts of this type known at present in sub-Saharan Africa. To current knowledge, the pottery of Ounjougou could either have been invented in the actual Sudano-Sahelian zone or been imported from the Central Sahara, where there has been evidence since the ninth millennium BC. Still, the oldest pottery known in the Sahara, from the site of Tagalagal in Niger, is already quite diversified at the moment of its appearance, possibly meaning that the technique has been introduced.

The lithic industry of the phases 1 and 2 on the other hand shows similarities to both more southern and Saharan industries. Quartz microliths, obtained through bipolar debitage on anvil, are a characteristic of the West African techno-complex according to Kevin MacDonald. Bifacially retouched arrowheads, in contrast, are specific for Saharan production." — Human population and paleoenvironment in West Africa [see: Link]

"The eighth millennium (Phase 2 of the Holocene in Ounjougou): The subsequent Holocene sequence is well documented by two principal sites, the Ravin du Hibou and Damatoumou. The archaeological levels can be quite clearly chronologically placed by means of a date obtained through OSL measurements (9420±410 Ka) and seven radiocarbon dates (between 8000 and 7000 BC cal). The lithic industry, exclusively quartz, is characterised by unidirectional, bidirectional and peripheral debitage, as well as by bipolar on anvil. There are essentially microlithic tools: perçoirs, backed points, notched pieces, denticulates, scrapers, retouched flakes and geometric microliths. Some small bifacially retouched arrowheads were also found on those sites. At the Ravin du Hibou, seven sherds have been found during excavation. They are heavily fragmented and thus preventing the reconstruction of the form of the vessel. Quartz has always been used as a temper. In just a single case, grog has been used in addition. Two shards show identifiable decorations. Two different techniques have been used: A rolled impression, possibly made with a peigne fileté souple or with a cordelette, and a simple comb impression. There were also seed grinding implements discovered at the Ravin du Hibou, a fragment of a seed grinding stone and a cylindrical upper grinding stone." — Human population and paleoenvironment in West Africa [see: Link]

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On the DNA side:

If we look at the samplings undertaken thus far, the west African populations on Atlantic-bordering west coasts—like the Senegalese samples, these groups undoubtedly have amongst the highest frequencies of E3a lineages, but there is something to be discerned: These groups largely carry M2, P1, and M180 lineages devoid of the M191 mutation, perhaps indicating the earlier E3a bearers, while many of the Bantu speaking groups of central, east and southern Africa carry those 191 derivatives:

Although haplotypes 22, 24, and 41 were probably all involved in the Bantu expansion, the processes that determined the current distribution of these haplotypes in the Sudanese belt (a region south of the Sahara extending from western to central Africa) seem to have been more complex and perhaps involved a separate expansion. In particular, haplotype 24 and its derivative, haplotype 22, harbor opposite clinal distributions in the region, a finding that is at odds with the hypothesis of a parallel dispersion of these two lineages in the area.

Haplotype 22 has a frequency of 23% in Cameroon (where it represents 42% of haplotypes carrying the DYS271 mutation), 13% in Burkina Faso (16% of haplotypes carrying the DYS271 mutation) and only 1% in Senegal (Semino et al. 2002), whereas haplotype 24 reaches its highest frequency (81%) in Senegal (Semino et al. 2002).

A possible explanation might be that haplotype 24 chromosomes were already present across the Sudanese belt when the M191 mutation, which defines haplotype 22, arose in central western Africa. Only then would a later demic expansion have brought haplotype 22 chromosomes from central western to western Africa, giving rise to the opposite clinal distributions of haplotypes 22 and 24. — Cruciani et al. 2002

The above suggests that the oldest E3a bearing population(s) ultimately moved to the far west corner of the continent.

From Semino et al. 2004, we have:

It is also of interest, that the Senegalese samples have higher E3* frequency, which attains its highest frequency in Ethiopian populations, than the Bantu speaking groups, where the only group tested positive, was that of the South African Bantu sample:

Bantu (South Africa) - E3* = 1.9%, Senegalese - E3* = 2.9%, Ethiopian (Amhara) - E3* = 10.4%, Ethiopian (Oromo) - E3* = 12.8% in the ascending order.

The Senegalese sample also bears the E-M.35* lineages:

In descending order…

Ethiopian (Oromo) - E-M35* = 19.2%, KhoiSan (South Africa) - E-M35* = 16.7%, Ethiopian (Amhara) - E-M35* = 10.4%, Berber (North-Central Morocco) - E-M35* = 7.9%, Berber (Southern Morocco) - E-M35* = 7.5%, Senegalese - E-M35* = 5%, Tunisian - E-M35* = 3.4%, Algerian - E-M35* = 3.1%, Arab (Morocco) - E-M35* = 2.3% , Burkina Faso -E-M35* = .9%

E-M78 in descending order….

Arab Morocco = 42.9%, Oromo = 35.9%, Amhara = 22.9%, Sudan =17.5%, Tunisian = 15.5%, Berber (Southern Morocco) = 12.5%, Arab (Morocco) = 11.4%, Berber (Morocco) = 10.9%, Algerian (32) = 6.3%, Berber (north central Morocco) = 1.6%, North Cameroon = 1.3%, Senegalese =.7%

E-M81 in descending order…

Saharawish (North Africa) = 75.9%, Berber (Morocco) = 68.7%, Berber (north central Morocco) = 65.1%, Berber (southern Morocco) = 65%, Algerian = 53.1%, Arab (Morocco) = 52.3%, Arab (Morocco) = 32.6%, Mali = 29.5%, Tunisian = 27.6%, Sudan = 5%, Senegalese = .7%

E-M33 in descending order…

Mali = 34.1%, North Cameroon = 7.9%, Senegalese = 5%, Burkina Faso = 3.8%, Saharawish (North Africa) = 3.4%, Berber (north‐central Morocco) = 3.2%, Sudan = 2.5%, Berber (Morocco) = 1.6%

E-M75 in descending order…

Bantu (South Africa) = 15.1%, Burkina Faso = 11.3%, Khoisan (South Africa) = 4.6%, Sudan = 5%, North Cameroon = 3.3%, Senegalese = 2.9%, Ethiopian (Oromo) = 1.3%

Looking at this data, among predominantly E3a-bearing Niger-Congo language speakers, Senegalese groups have the highest E3* frequency, as well as E-M35*. It follows the North Cameroon sample in this instance, in the E-M78 frequencies - though I’m not sure if those North Cameroon samples comprise of Niger-Congo speaking groups, Nilo-Saharan or some other language phylum group. In west Africa, it succeeds only Mali [and Niger, which wasn‘t included in this sample]—as one of the areas which have considerable Niger-Congo speakers—to have E-M81 bearing candidates, but then, Mali is also well known for its Saharan Tamazight speakers.

In reference to the above, some might look at a lineage as, say E-M78 and imagine it to be a trace of interaction with Saharan or coastal North African Afrasan speaking groups, but microsatellite inspection would indicate otherwise:

It is interesting that both E-P2* and E-M35* and their derivatives, E-M78 and E-M123, exhibit in Ethiopians the 12-repeat allele at the DYS392 microsatellite locus, an allele scarcely seen (Y-Chromosome STR Database), especially [b]in other haplogroups and other populations (A.S.S.-B., unpublished data). In addition, the Ethiopian DYS392-12 allele is usually associated with the unusually short DYS19-11 allele, which is typical of this area. These findings are not easily explained. One possible scenario is that an ancient differentiation of the E-P2 haplogroup occurred in loco (East Africa). However, this also implies a low mutability of the associated microsatellite motif (DYS392-12/DYS19-11). Alternatively, the microsatellite motif may be due to homoplasy.

The first scenario is more likely, since this unique microsatellite haplotype occurs in E-P2*, E-M35*, and E-M78 but is almost absent in all other haplogroups and populations. In addition, the high stability of the DYS392 locus (Brinkmann et al. 1998; Nebel et al. 2001) and of the shorter alleles of DYS19 (Carvalho-Silva et al. 1999) has been reported elsewhere. Moreover, the observation that the derivative E-M78 displays the DYS392-12/DYS19-11 haplotype suggests that it also arose in East Africa. This is illustrated by the microsatellite network (fig. 3, shaded area), which reveals that the Ethiopian branch harboring DYS392-12 is not shared with either Near Eastern or European populations.

The Ethiopian sample may not share the said allele with those populations mentioned, including the northwest African samples as far as I can tell, but it does share the said allele with the Senegalese sample, which would suggest that the Senegalese M78 derivative didn’t come from interaction with its northwest African neighbors; rather, they may well be relics of ancient migrations from east to west.

http://www.journals.uchicago.edu/na101/home/literatum/publisher/uchicago/journals/production/ajhg/2004/74/5/386295/images/medium/fg3.gif Source: Semino et al., Origin, Diffusion, and Differentiation of Y‐Chromosome Haplogroups E and J, 2004.

Some time during post 11ky ago expansions into the wet Sahara, before its return to aridity, with activity going on across the Saharan expanse, like cattle domestication for example, E3a bearers spread well into central-east Sahara. It was likely during this period that HbS mutations were localized, with the oldest E3a bearing groups nearer to the Atlantic-hugging west coasts bearing the Senegalese haplotype, while the Benin haplotype was able to have a more far-reaching expansion northward and northeast ward, due its situation in Niger River Valley vis-à-vis North Africa and the rest of the Sahara.
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Additional references to those mentioned in the body of the post:

*Semino et al., Origin, Diffusion, and Differentiation of Y‐Chromosome Haplogroups E and J, 2004.

* http://www.esd.ornl.gov/projects/qen/nercAFRICA.html

*Knight et al. 2003 : http://www.bec.ucla.edu/papers/Mountain_3-7-05.pdf

*Cruciani et al. 2004, Phylogeographic analysis of haplogroup E3b.

* Cruciani et al. 2007, Tracing Past Human Male Movements in Northern/Eastern Africa and Western Eurasia: New Clues from Y-chromosomal Haplogroups E-M78 and J-M12.

Mitochondrial DNA M1 haplogroup: A Response To Ana M. Gonzalez et al. 2007

Ana M. Gonzalez et al. published a paper on M1 expansions, 9 July 2007, and a few things about it immediately jumped at the present author. The present author lays these out shortly following the abstract below, which is there to put potential viewers of this page on "the same page" so to speak, as far as the synopsis of the paper is concerned:

Abstract:

Mitochondrial lineage M1 traces an early human backflow to Africa

Ana M Gonzalez , Jose M Larruga , Khaled K Abu-Amero , Yufei Shi , Jose Pestano and Vicente M Cabrera

BMC Genomics 2007, 8:223 doi:10.1186/1471-2164-8-223

Published 9 July 2007

Abstract (provisional)

The complete article is available as a provisional PDF. The fully formatted PDF and HTML versions are in production.

Background
The out of Africa hypothesis has gained generalized consensus. However, many specific questions remain unsettled. To know whether the two M and N macrohaplogroups that colonized Eurasia were already present in Africa before the exit is puzzling. It has been proposed that the east African clade M1 supports a single origin of haplogroup M in Africa. To test the validity of that hypothesis, the phylogeographic analysis of 13 complete mitochondrial DNA (mtDNA) sequences and 261 partial sequences belonging to haplogroup M1 was carried out.

Results
The coalescence age of the African haplogroup M1 is younger than those for other M Asiatic clades. In contradiction to the hypothesis of an eastern Africa origin for modern human expansions out of Africa, the most ancestral M1 lineages have been found in Northwest Africa and in the Near East, instead of in East Africa. The M1 geographic distribution and the relative ages of its different subclades clearly correlate with those of haplogroup U6, for which an Eurasian ancestor has been demonstrated.

Conclusions
This study provides evidence that M1, or its ancestor, had an Asiatic origin. The earliest M1 expansion into Africa occurred in northwestern instead of eastern areas; this early spread reached the Iberian Peninsula even affecting the Basques. The majority of the M1a lineages found outside and inside Africa had a more recent eastern Africa origin. Both western and eastern M1 lineages participated in the Neolithic colonization of the Sahara. The striking parallelism between subclade ages and geographic distribution of M1 and its North African U6 counterpart strongly reinforces this scenario. Finally, a relevant fraction of M1a lineages present today in the European Continent and nearby islands possibly had a Jewish instead of the commonly proposed Arab/Berber maternal ascendance.

-Abstract ends-

Present Author's Response To Ana M. Gonzalez et al.

*First, a quick synopsis of the samplings, with regards to where the n=261 M1 bearing samples come from, aside from the 588 participants mentioned in one of the tables [table 2] in the study:

From the present author's assessment of the table, it comes from the following numbers:

A total of 50 Europeans detected for M1.
A total of 154 for Africans.
A total of 28 Asians, barring 8 unknown Arabian haplotypes.
And a total of 29 Jews, who were lumped together from the various continents.
The sum of the above totals, amount to 261 "known" M1 lineages.

*With regards to the authors claim about M1 or its ancestor, having “had an Asiatic origin”, the following comes to mind:

The authors of the study at hand, themselves admit that they haven't come across M1 ancestor in either south Asia or southwest Asia. They also take note of its highest diversity in Ethiopia and east Africa. Yet through the shaky premise of their M1c expansion time frame estimations, they build a conclusion around it, by tying it to a dispersal(s) "parallel" to that of U6 - another African marker whose immediate common recent ancestor, namely proto-U6, appears to be elusive thus far.

Well, they wouldn’t be the only ones who have failed to come across any proto-M1 ancestor in southwest and south Asia [Indian Subcontinent mainly]:

Based on the high frequency and diversity of haplogroup M in India and elsewhere in Asia, some authors have suggested (versus [3]) that M may have arisen in Southwest Asia [16,17,31]. Finding M1 or a lineage ancestral to M1 in India, could help to explain the presence of M1 in Africa as a result of a back migration from India. Yet, to date this has not been achieved [15], this study). Therefore, one cannot rule out the still most parsimonious scenario that haplogroup M arose in East Africa [3]. Furthermore, the lack of L3 lineages other than M and N (indeed, L3M and L3N) in India is more consistent with the African launch of haplogroup M. On the other hand, one also observes that: i) M1 is the only variant of haplogroup M found in Africa; ii) M1 has a fairly restricted phylogeography in Africa, barely penetrating into sub-Saharan populations, being found predominantly in association with the Afro-Asiatic linguistic phylum – a finding that appears to be inconsistent with the distribution of sub-clades of haplogroups L3 and L2 that have similar time depths. — Mait Metspalu et al.

So, while they acknowledge the highest "frequencies and diversities" of M1 particularly in Ethiopia, and generally in East Africa [see below for reference], the authors base their claims about ’origins’ on their expansion estimations of M1c derivatives, presumably predominant in northwest Africa rather than east Africa, and its relative sporadic distribution in 'Europe' and 'Southwest' Asia. They attempt to buttress this, by invoking an initial parallel expansion of M1 and U6 "ancestor" lineages into north Africa via the Nile Valley [from "southwest Asia"], then an expansion from northwest Africa this time around, of U6 and M1 derivatives northward into Europe and then eastward into "southwest" Asia via the Nile Valley corridor in the Sinai peninsula, presumably with a few derivatives making their way into sub-Saharan east Africa, where they then underwent some expansion, to give rise to yet another, but later, dispersal from there into "southwest Asia" and hence, accounting for the 'majority' of M1 lineages in "southwest Asia" being east African derivatives than the north African [M1c] counterparts.

In Africa, haplogroup M1 has supra-equatorial distribution (see additional files 1 and 2). As previously reported its highest frequencies and diversities (Table 2) are found in Ethiopia in particular and in East Africa in general. Two appreciable gradients exist. Frequencies significantly diminished from East to West and also going South to sub-Saharan areas. M1 is not uncommon in the Mediterranean basin showing a peak in the Iberian Peninsula. However, it is rare in continental Europe. Although in low frequencies, its presence in the Middle East has been well established from the South of the Arabian Peninsula to Anatolia and from the Levant to Iran. - Gonzalez et al. 2007

*Furthermore,

The authors gather that their observations correlate with that of other researchers, namely Olivieri et al. (2006). To this extent, they put forth that Olivieri et al.’s M1b corresponds to their M1c, the former’s M1a2 corresponds to their M1b, and the former’s M1a1 corresponds to their M1a. They go onto to add that the coalescence ages arrived by the two research group [that of Olivieri et al. and that of the present authors] also correlate. The present authors note that their coalescence time for M1c (25.7 +/- 6.6 ky) overlaps with Olivieri et al.’s coalescence time for M1b (23.4 +/- 5.6). Similarly, they note that their coalescence age for M1a (22.6 +/- 8.1ky) falls within that of Olivieri et al.’s age for M1a1 at 20.6 +/- 3.4ky. However, this makes way for great discrepancy between the said authors and Olivieri et al., whereby their coalescence age for M1b at 13.7 +/- 4.8ky falls quite short of the latter’s age for M1a2 at 24 +/- 5.7ky. Not only are the subgroup nomenclatures distinct, but this latter discrepancy makes an unsubtle difference, so as to no longer render M1c to be older than M1b [in examining from the ongoing juxtapositioning, utilizing Olivieri et al.'s standpoint], but rather, either place M1c (Olivieri et al.'s M1b) at an age a bit younger or on par with the latter, which should be otherwise according to the present study. Though, by their own admission, the present authors favor Olivieri et al.’s methods over their own:


As our calculations are based only on three lineages and that of Olivieri et al on six, we think that their coalescence time estimation should be more accurate than ours. In fact, when time estimation is based on the eight different lineages (AFR-K143 is common to both sets) a coalescence age of 20.6 +/- ky is obtained.

*But if there is any indication about the tenuous nature of the above thesis, without going into other known details about M1, it would be this alternative viewpoint they came up with:

The alternative idea entertained by the authors, is one where M1 could actually be an autochthonous northwest African lineage, which spread northward into Europe and eastward to "Southwest Asia" and east Africa. Again, to be followed by a yet later dispersal from east Africa, likely sub-Saharan east Africa, particularly the Ethiopian populations.

*We've already seen the subjective nature of the present authors' age estimations, naturally attributable to biases underlying sampling procedures to some degree or another, as demonstrated above with the juxtapositioning of the findings of the present authors to those of Olivieri et al. (2006). Furthermore, erratic mutation rates would have undoubtedly affected the age estimation regime applied by the authors, however they may have downplayed the fact, as demonstrated by their observations surrounding the M1a2 subgroup, leading them to omit said subgroup in their lineage coalescence analysis. What makes this interesting, is that both group of authors sought to build their argument around parallel demic diffusion scenarios of U6 and M1, which has little in way of supporting material to stand on, notwithstanding the passionate efforts to push forward with argument; for instance in Olivieri et al.'s case, they say:

The hypothesis of a back-migration from Asia to Africa is also strongly supported by the current phylogeography of the Y chromosome variation, because haplogroup K2 and paragroup R1b*, both belonging to the otherwise Asiatic macrohaplogroup K, have been observed at high frequencies only in Africa (15, 16). However, because of the relatively low molecular resolution of the Y chromosome phylogeny as compared to that of the mtDNA, it was impossible to come to a firm conclusion about the precise timing of this dispersal (15, 16). - Olivieri et al. (2006)

One can almost sense Olivieri et al.'s venting their frustrations from not getting the "desired" results out on the supposed "relatively low molecular resolution of Y DNA", but indeed, as noted here earlier:

Previous genetic research work made very enthusiastic attempts to correlate the likes of U6 and possible "Eurasian"-tagged mtDNA with R1*-M173, supposedly as an attempt to buttress a possible back-migration into Africa; all but failed, with results showing considerable African mtDNA gene pool instead, for populations bearing these chromosomes.

Gonzalez et al. (2008) also fall into that trap; guess where they look towards, to make a connection between an M1 dispersal [supposedly parallel to a U6 one] and a "Middle Eastern" origin part of their argument? Interestingly, it happens to be from the same Dead Sea sample which was implicated in a clear genetic link with sub-Saharan and Eastern African groups. This is the same Dead Sea sample set that shared R1*-M173 with northern Cameroonian sample set, other African groups with these markers. This is also the same Dead Sea sample set with African G6PD-A alleles that were rare to absent in neighboring groups. And Gonzalez et al. (2008) tell us, that this is also the same sample set which is again distinguished from those of neighboring group in its higher "south of the Sahara" mtDNA markers:

Statistical analysis revealed that, whereas the sample from Amman did not significantly differ from their Levantine neighbours, the Dead Sea sample clearly behaved as a genetic outlier in the region. Its outstanding Eurasian haplogroup U3 frequency (39%) and its south-Saharan Africa lineages (19%) are the highest in the Middle East. On the contrary, the lack ((preHV)1) or comparatively low frequency (J and T) of Neolithic lineages is also striking. Although strong drift by geographic isolation could explain the anomalous mtDNA pool of the Dead Sea sample, the fact that its mtDNA lineage composition mirrors, in geographic origin and haplogroup frequencies, its Y-chromosome pool, points to founder effect as the main cause. - Gonzalez et al. (2008)

They acknowledge above that the "anamolous" character of the Dead Sea sample's Y-DNA pool "mirrors" its mtDNA gene pool, which too is replete with markers mostly found in Africa, including the aforementioned rare paraphyletic R1*-M173. However, something interesting happens, with regards to this Dead Sea sample of an "isolated" group:

Ancestral M1 lineages detected in Jordan that have affinities with those recently found in Northwest but not East Africa question the African origin of the M1 haplogroup.

Interesting, because these the same M1c chromosomes being referred to here, and whose specifics have been dealt with. Despite the apparent post-OOA emigration ties between the African groups and the Dead Sea community, reflected in not only both Y-DNA and mtDNA, but also in the X chrosome markers, Gonzalez et al. (2008) still come to the odd conclusion that its presence in the Dead Sea sample set somehow offers some sort of a challenge on the African origin of M1. The notion itself becomes quite comical, when one considers the fact that they just mentioned in the same breath, the presence of these same M1 clusters in Northwestern Africa, which happened to be their alternative hypothetical point of origin [Gonzalez et al. (2007)], as already noted. As they themselves acknowledge, that's where (northwestern Africa) said M1 clusters are widely distributed, and rather rare in the so-called "Middle East", save for this genetically "anamolous" [the authors' own words] and relatively isolated Dead Sea community, notable for its clear "past ties to sub-Saharan and eastern Africa", to put in Flores et al.'s (2005) words, a team that Gonzalez herself was a part of. "Anamolous", because to put it in the authors' own words, the considerably high post-OOA African ties of the Dead Sea sample dataset sets it appart from many other "Middle Eastern" groups, including its neighbours. So, how M1c clusters (which Gonzalez et al. (2007) dub "ancestral" based on their subjective age estimations) — that are very rare even in the "Middle East" (save for the 'anamolous' Dead Sea dataset) in contrast to their wide distribution in northwestern Africa — suddenly puts a question mark on the African origin of M1, is beyond comprehension.

Not only is there lack of apparent parallelism between R1* paragroup distribution and those aforemention markers of U6 and "Eurasian"-tagged mtDNA markers in Africa itself, as the authors (like Olivieri et al. & Gonzalez et al.) seem to be so desperately yearning for, but also the paragroup is essentially absent in all Afrasan speaking groups but those in the Northeast African corner. The marker is even rarer in so-called Southwest Asia than it is in Africa. This naturally contradicts Olivieri et al.'s acknowledgement in the following...

Indeed, M1 and U6 in Africa are mostly restricted to Afro-Asiatic–speaking areas.

Where did this "Afro-Asiatic" phylum originate? Well, look no further than to Gonzalez et al., whom as we've seen, are energetic about this idea of M1 and U6 "parallelism", not unlike Olivieri et al. (2006); they too, clearly in a way that simulteneously soothens or seeks to explain away a bit of disappoint in the course of the study, say:

The anomalous evolution of M1a2 lineages left the coalescence ages of the eastern Africa M1a expansion uncertain, but as suggested for the sister U6a1 radiation; these movements could be correlated in time with an African origin and expansion of Afroasiatic languages.

There you have it, folks, the answer to that simple question. And as if to defy the two groups of aforementioned research teams above, with regards to the proposed M1 and U6 "parallelism" in a demic expansion scenario, a newer study that came along in December 2008, points this out [a finding that appears to have been reproduced in several other studies]:

Our results highlighted a clear genetic differentiation between Berbers from the Maghreb and Egyptian Berbers. The first seems to be more related to European populations as shown by haplogroup H1 and V frequencies, whereas the latter share more affinities with East African and Nile Valley populations as indicated by the high frequency of M1 and the presence of L0a1, L3i, L4∗, and L4b2 lineages. Moreover, haplogroup U6 was not observed in Siwa. Probably, such a maternal diversity between North African Berbers would have been the result of a conjunction of several geographical, prehistoric, and historic factors which guided contacts (and thus exchanges) between local populations and migrating groups. First, in addition to the geographical distance, which certainly increases the genetic distance, the geographical location of Berber populations is very peculiar: the Berbers from the Maghreb are at the end of a long migration route, whereas Berbers from Siwa are rather in a crossroads between the Middle East, East Africa, sub-Saharan areas and the North African corridor. Therefore, meetings and exchanges between local and migrating populations were not identical in North West and North East Africa. - C. Coudray et al., The Complex and Diversified Mitochondrial Gene Pool of Berber Populations

We are told above, that M1 is substantial in the Siwa group, but no U6 was observed! Furthermore, it would make sense for the Siwa group to be a pristine representative of the aforementioned U6/M1 "parallelism" scenario, given that they are even closer to the so-called "Near East" than the northwestern African "Berbers", would it not? Perhaps it wouldn't be as funny, if Anna Olivieri herself was not a participant of this Coudray et al. study! Speaking of the so-called "Near East", the following claim is interesting, when one takes into account that this area was singled out as one of Gonzalez et al.'s proposed areas of M1 origin, because while looking at it from the alternative proposed origin, presumably the northwestern African one, we are told in a passing that...

That M1 is an autochthonous North African clade that had its earliest spread in northwestern areas marginally reaching the Near East and beyond. This would explain the shortage of basic M1 lineages in the Near East but would leave the Asiatic origin of the M1 ancestor undetermined.

...interesting.

*Another thing that hasn't been relayed through the present study, are details that follow:

The coding regions transitions are likely to change relatively slower than those of hypervariable segments, and hence, likely to remain intact within a clade. To assist in determining which clade to place a monophyletic unit, key coding region transitions have to be identified. In the case of M1, we were told:

We found 489C (Table 3) in all Indian and eastern-African haplogroup M mtDNAs analysed, but not in the non-M haplogroup controls, including 20 Africans representing all African main lineages (6 L1, 4 L2, 10 L3) and 11 Asians.


These findings, and the lack of positive evidence (given the RFLP status) that the 10400 C->T transition defining M has happened more than once, suggest that it has a single common origin, but do not resolve its geographic origin. Analysis of position 10873 (the MnlI RFLP) revealed that all the M molecules (eastern African, Asian and those sporadically found in our population surveys) were 10873C (Table 3). As for the non-M mtDNAs, the ancient L1 and the L2 African-specific lineages5, as well as most L3 African mtDNAs, also carry 10873C.

Conversely, all non-M mtDNAs of non-African origin analysed so far carry 10873T. These data indicate that the **transition 10400 C-->T, which defines haplogroup M**, arose on an African background characterized by the ancestral state 10873C, which is also present in four primate (common and pygmy chimps, gorilla and orangutan) mtDNA sequences. — Semino et al.

...which is significant, as other M lineages are devoid of M1 coding region motifs, not to mention the M1 HVS-I package. The above does demonstrate, how M lineages likely arose on an African 'background' by single-event substitutions in the designated African ancestral counterparts. The ancestral transition of 10873C is substituted by 10873T in non-African non-M haplogroups, while the 10400C transition was substituted in M lineages by 10400T; that ancestral state of 10873C remains at large in the M macrohaplogroup, unlike the so-called non-African & non-M haplogroup counterparts.

Furthermore,...

The 489C transition, as noted above and can be seen from the diagram, is peculiar to the M macrohaplogroup, again suggestive of unique event mutations characterizing the family:

The phylogenetic location of the mutations at nt 489 and 10,873 (arrow) was predicted by our analysis. The seemingly shared mutation at nt 16,129 (by G, Z and M1) is very likely an accidental parallelism. The ancestral states 10400C, 10810C and 10873C are fixed in L1 (as analysed so far) and are present in the ape sequences.


The 16129 sharing across the M1 haplogroups, seems to be one of those instances of random parallel mutation, recalling Chang Sun et al.'s observations of random parallel mutations of certain transitions across the M macrohaplogroup.

We also know that "southwest Asian" and "European" M1 lineages are derivatives of African counterparts, and the same is true for southwest Asian non-M1 affiliated M lineages from south Asia:

Compared to India, haplogroup M frequency in Iran is marginally low (5.3%) and there are no distinguished Iranian-specific sub-clades of haplogroup M. All Iranian haplogroup M lineages can be seen as derived from other regional variants of the haplogroup: eleven show affiliation to haplogroup M lineages found in India, twelve in East and Central Asia (D, G, and M8 ) and one in northeast Africa (M1)…

Indian-specific (R5 and Indian-specific M and U2 variants) and East Asian-specific (A, B and East Asian-specific M subgroups) mtDNAs, both, make up less than 4% of the Iranian mtDNA pool. We used Turkey (88.8 ± 4.0%) as the third parental population for evaluating the relative proportions of admixture from India (2.2 ± 1.7%) and China (9.1 ± 4.1%) into Iran. Therefore we can conclude that historic gene flow from India to Iran has been very limited. — Mait Metspalu et al.

With that said, Semino et al.'s older study still remains strong, the way I see it:

haplogroup M originated in eastern Africa approximately 60,000 years ago and was carried toward Asia. This agrees with the proposed date of an out-of-Africa expansion approximately 65,000 years ago10. After its arrival in Asia, the haplogroup M founder group went through a demographic and geographic expansion. The remaining M haplogroup in eastern Africa did not spread, but remained localized up to approximately 10,000-20,000 years ago, after which it started to expand. — Semino et al.

Elsewhere, I've also talked about some 'basal' M-like lineages in Africa; for instance, at least one of such was identified in the Senegalese sample.

Am. J. Hum. Genet., 66:1362-1383, 2000

mtDNA Variation in the South African Kung and Khwe and Their Genetic Relationships to Other African Populations


"The Asian mtDNA phylogeny is subdivided into two macrohaplogroups, one of which is M. M is delineated by a DdeI site at np 10394 and an AluI site of np 10397. The only African mtDNA found to have both of these sites is the Senegalese haplotype AF24. This haplotype branches off African subhaplogroup L3a (figs.2 and3), suggesting that haplogroup M mtDNAs might have been derived from this African mtDNA lineage..."

The relevant representation in this recap diagram:

Image source: Link

In the image above, the 10397 transition is shown in the L3-M linkage, while 10394, which should show up as positive (as exemplified in the above extract) in the M macrohaplogroup, shows up negative in the linkage between L3 and non-M affiliated lineages.

What does all this talk of specific transitions or nucleotide sequences tell us?

Well, to put the above compilation into perspective, and keep it simple, the point is this:

Semino et al.'s demonstration of certain characteristic basic coding transitions of the M super-haplogroup [not including the key coding region motifs unique to the M1 family], springing directly from African ancestral motifs don't require that M1 has to have a proto "non-African" M1, because all the necessary basic nucleotide sequences have been identified in the autochthonous African gene pool [findings which have been buttressed by later studies, of basic motifs in rare "M-characteristic" basic (African L3) clades], enough to explain the proposed African origin for the M lineage in general, including M1; whereas an Asian origin of M1 would necessitate an Asian "proto-M1" lineage that would explain the relatively young expansion ages of M1 and lack of descendancy from pre-existing Asian M lineages. This hasn't been achieved either by the present study or ones prior to it.

Getting to the gist:

Basal M mtDNA ~ between c. 60 - 80 ky ago

And then, M1 ~ between ~ c. 10 - 30 ky ago

The studies the present author posted, suggest that the basal motifs characteristic of the M macrohaplogroup arose in Africa, anywhere between 60 - 80 ky ago [since they would have likely been in the continent by the time of the 60 ky ago or so OOA migrations] . Sometime between 60 ky and 50 ky ago [some sources place it between 75 - 60 ky ago], these L3 offshoots were carried outside of Africa, amongst early successful a.m.h migrations, which resulted in the populations now living in the Indian-subcontinent, Melanesia and Australia who have these lineages. Not all the basal African L3M lineages, as Semino et al. convincingly put it, left the continent, as indicated by the basal L3a-M motif detected in Senegal, M1 diversity in Africa, particularly East Africa, possibly the dectection of M1 and other M lineages in tandem within a Tanzanian sample (Gonder et al. 2006), and the apparent lack of descendancy of M1 from older-coalescent Asian macrohaplogroup. Rather, it appears that the basal L3M lineages which remained in Africa, underwent a relatively limited demographic intra-African expansion until relatively recently, i.e. between 10 - 30 ky ago, compared to the Asian L3M derivatives, which underwent major expansions, naturally within the quantitatively smaller founder immigrant groups, i.e. the founder effect.

M1 is likely the culmination of relatively more recent demographic expansions of basal L3M lineages in the African continent, with M1 derivative being a successful candidate, in what could have possibly involved other derivatives which might not have expanded to the same level intra-continentally, and subsequently, extra-continentally as well.

M1 has strongly been correlated with the upper Paleolithic expansion of proto-Afrasan groups across the Sahara to coastal north Africa, and further eastward via the Sinai peninsula.