Wednesday, April 2, 2008

Correlating mtDNA Markers with The Journey of Contemporary E3a-bearers' Ancestors

mtDNA may paint a somewhat more complex picture than their Y counterparts, in no small part due to the far much deeper root [taking us back to the earliest traceable MRCA] of the maternal line of contemporary human populations, and hence much greater time depths in which complex patterns of demic processes would have taken place than those of the Y chromosome counterpart, leaving room for relatively larger margins of error in dating earlier coalescent ages, and in which case, there is the real possibility that the evidence of earlier distribution pattern of mtDNA clusters under study could well have been erased by subsequent demographic processes [to put it in a language not too different from Salas et al. 2002]. Keeping this in mind, what could be said about the possible markers that the group ancestral to contemporary west African E3a-bearing populations carried from their point of origin?

Examining several possible candidates…

Salas et al. 2002, in The Making of the African mtDNA Landscape, have noted that:

The paragroup L1 includes the MRCA of human mtDNA, which is at least 150,000–170,000 years old (Horai et al. Horai et al., 1995; Ingman et al. Ingman et al., 2000). Haplogroup L1a (Figure 4a) is common (~ 20%–25%) in East, Central, and southeastern Africa, and is almost absent in North, West, and southern Africa. The main subclade, L1a1, is ~ 33,350 (SE 16,600) years old and is quite starlike, with a predominantly East/southeastern African distribution and a root type that is common in East Africa. There has been considerable drift on several derived types in southeastern Africa. The second principal subclade, L1a2, is ~ 8,300 (SE 3,650) years old and is predominantly Central African, occurring in both Biaka and Mbuti, and, again, several types (in particular, the root type) appear at elevated frequency in southeastern Africa.

An East African origin of L1a seems likely, given that Central African types tend to be more derived in the tree

With regards to the subtype L1c, the authors say this:

Representatives in West Africa are restricted to two derived subclades, suggesting an expansion westwards relatively late in the evolution of the haplogroup. It is notable, however, that the southeastern representatives tend to be most closely related to Central African types and include types in clusters not present in West Africa. — by Salas et al.

The subtype L1b is something of an interesting case, which as put forth by the said authors,…

L1b (Figure 4b) has a completely different geographical distribution within Africa. It is concentrated in West Africa, with some overflow into Central and North Africa (particularly geographically adjacent areas, connected by the West African coastal pathway) but little in East, southeastern, or southern Africa. It is also common in African Americans (~27% of all L1b-types in the database), in agreement with the known importance of the West African coast to the Atlantic slave trade. A simple interpretation would therefore attribute a West African origin to L1b, with significant diffusion into North and Central Africa. However, because the coalescence time of L1b is estimated at only ~30,000 years—whereas its sister clade, L1c, is estimated at ~60,000 years old—a recent bottleneck and re-expansion in West Africa may have shaped the evolution of L1b. Given the likely origin of its sister clade L1c in Central Africa, a Central African origin seems plausible for L1b as well.

It is an interesting case, because it offers two possible explanations for its high concentration in west Africa, and hence in African American candidates as well, which is that:

1)it could well have originated in west Africa, and then spread to north and central Africa, that is—regions nearby west Africa, as well as the Americas via the slave trade.

2)or it could well have originated in central Africa, which seems to be the springboard point from where L1 subtypes made their way into west Africa; after all, central Africa seems to have the distinction of having considerable frequencies of all the sub-haplogroups thus far mentioned, namely L1a, L1b, and L1c.

If sway were given to the second scenario, given the said *distinctive* element of central Africa, along with the reasons given by the authors, with regards to coalescence ages of L1c and L1b with respect to one another, along with their common considerable presence in central Africa, then a case can be made that it could lend some credence put forth here earlier, about the east-to-westward migratory pathway contextualization of the origins of contemporary west African groups predominantly bearing E3a Y-chromosome markers, which was touched on in the following links:

P2 Clades: The Arrival of E3a and E3b Haplogroups

NRY Haplogroup E3a: Proposing its Origins through a Multidisciplinary lens

In making this Ychromosome-mtDNA correlation, it may well be worth taking note of the distribution patterns of the L1 subtypes:

1)L1a is common in east Africa,…

—but rarer, if not “almost absent” in west, north or south Africa.

—and scarce in African American candidates, “in comparison with other African types”, though it is also worth noting that the African American representatives of this subtype largely match southeast African examples, suggesting that region to be the source of the American candidates carrying that clade.

—and has some notable presence in central Africa and southeast Africa.

2)L1b is common in west Africa,…

—but rarer in east Africa, southeast and south Africa.

—and has notable presence in African American candidates.

—and has notable presence in central Africa and north Africa.

3)L1c is common in central Africa,…

—but rarer in west and southeast Africa, with “virtually none” in east or south Africa.

—and has considerable presence in African American candidates. Thus, it is quite likely that the elevated presence in African American candidates is due to drift, particularly when taking into account that west Africa is generally considered to be an important region where a major section of African American populations trace their ancestry, not to mention that:

A West African origin for the African American L1c types is unlikely, because American types do not match with West African ones, this region being the best represented in the database. — Salas et al.

With regards to this subtype, let’s recall that…

Representatives in West Africa are restricted to two derived subclades, suggesting an expansion westwards relatively late in the evolution of the haplogroup. It is notable, however, that the southeastern representatives tend to be most closely related to Central African types and include types in clusters not present in West Africa.
— by Salas et al.

…which would appear to lend further credence to the aforementioned “east-to-westward migratory pathway contextualization of the origins of contemporary west African groups predominantly bearing E3a Y-chromosome markers”, wherein ancestors [originating from *general* geography straddling central-Africa and Sudan] would seek refuge in the Shum Laka region, before heading westward into west Africa.

Now add to that earlier excerpt, this:

The geographic distribution of L1c is especially interesting. More than one-third of L1c haplotypes in our database belong to African Americans, and few of them show matches with continental Africans. The great majority of the remainder of L1c comes from Central Africans, with a few in the west and the southeast. There are virtually none in the east or south; of the “Pygmy” groups sampled, only the western group (the Biaka) have L1c.

Noteworthy, is that most Y marker studies tend show that “Pygmy” groups generally carry markers relatively closer to the root of the tree, but mtDNA analysis on the other hand, paint a more complex picture, perhaps indicating influences from neighboring groups or recent arrivals to the scene. As for the subtype L1c itself, we are told that:

This suggests that the origin of L1c can be placed somewhere in Central Africa towards the Atlantic west coast, in the uncharacterized areas of Angola and the Congo delta, to the south of the putative Bantu homeland, on the route of the “western stream” of the Bantu expansion.

4) Haplogroup L1d:

“Haplogroup L1d (Figure 5b) is nonstarlike and characterizes Khoisan groups (Bandelt and Forster Bandelt and Forster, 1997), where it represents about half of the total haplogroup composition for the southern African samples (!Kung and Khwe). L1d is additionally found at ~ 5% in the southeastern African samples (see also Pereira et al. Pereira et al., 2001), and there is a single East African L1d type from Lake Turkana. This distribution strongly implies an origin for L1d amongst the ancestors of the Khoisan, long before the arrival of Bantu speakers in the region.” [Salas et al.]

5) Haplogroup L1e:

“L1e is restricted almost solely to East Africa” [Salas et al.]

With regards to haplogroup L2, we are told:

1)…it appears that the founder ages for L2a are significantly older than for L1a, consistent with the phylogeographical picture, with an earlier West African origin for the L2a lineages of southeastern Africa and a more recent East African origin for the L1a lineages. Indeed, the age of the L2a founders in southeastern Africa is consistent with an origin in the earliest Bantu dispersal from the Cameroon plateau, 3,500 years ago (Phillipson Phillipson, 1993).

Something about this haplogroup that seems to also lend some credence to the “east-to-westward migratory pathway contextualization of the origins of contemporary west African groups” some time in the Ogolian period, which coincides with the LGM (Last Glacial Maximum elsewhere), is this:

It is difficult to trace the origin of L2a with any confidence. The deepest part of L2a, represented by clusters α1-α3, is most common in East Africa. However, the diversity and TMRCA are similar in East (61,250 [SE 13,500] years) and West (54,100 [SE 17,087] years) Africa. The diversity accumulated separately in East and West Africa, estimated from the main shared founder types (and disregarding the possibility of subsequent gene flow), is again similar in the two regions, at ~14,000 years (14,100 years [SE 5,100], and 13,800 years [SE 4,700], respectively), suggesting a separation shortly after the Last Glacial Maximum.

…give or take in the margin of error, the above is displaying slightly older dates for east African bound examples with respect to the west African bound ones, but otherwise, the dates respective to either geography could well be placed within the same general time frame ranges, just as noted above. But going back to the aforementioned hypothesis, let’s recall that it was stated here that…

PN2 clade (E3) bearers in the vicinity of the general expanse straddling Sudanese-Central African Republic -Ugandan-Kenyan region [get a map aid, if necessary] give rise to E3a ~ between 21 and 18 ky ago [see Semino et al. 2004 for TMRCA dates, 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…

Bearing "rare" lineages predominantly found in east Africa - i.e. the likely point of origin, along with sequential archaeological evidence for [east-to-west and thereafter, in situ west African south-to-north] repopulation events in west Africa, much of which was abandoned in the Ogolian desertification, show that the earliest E3a bearers - which finds expression in Senegalese samples - could not have arose in situ west Africa, but originated in an eastward oriented geography and migrated to west Africa, as the Ogolian aridity relaxed, bringing along with them new microlithic traditions picked up from the Shum Laka region, settled therein and thereafter underwent demic expansion, resulting in the "high diversity and frequency" of the E3a distribution in west Africa.

In one of the other link, it was stated...

—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.

Links in question:
P2 Clades: The Arrival of E3a and E3b Haplogroups

NRY Haplogroup E3a: Proposing its Origins through a Multidisciplinary lens

Keeping this in mind, the authors add that:

An easterly origin for L2a also faces the following difficulties: that the other subclades of L2 (L2b, L2c, and L2d) have a clear western distribution, and that L2d diverges earlier in the mtDNA phylogeny than L2a (Torroni et al. Torroni et al., 2001). A possible solution would be an origin for L2a somewhere **between east and west**,


followed by dispersals in both directions along the Sahel corridor.

Hence, essentially reiterating what is stated in the recitation above (in red), i.e. positioning central Africa as a likely center of refuge during the Ogolian aridity before ancestors of contemporary west African groups bearing E3a markers moved into west Africa.

2) sub-haplogroups L2b, L2c and L2d:

Haplogroups L2b, L2c, and L2d appear to be largely confined to West and western Central Africa (and African Americans), with only minor occurrences of a few derived types in the southeast. L2b also shows isolated occurrences in the east and as far north as Iberia. Therefore, an origin for all three in West and western Central Africa seems likely.

What does all this observations of L1 and L2 subtypes ultimately mean at this point? Well, one ought to come out of it with an overall image wherein central Africa had played an important role in the corridor for the "east-to-westward" migration of the ancestors of contemporary E3a-bearing groups of west Africa as a refuge center and thus, radiation point for lineages which have become important in west Africa, central Africa, southeast Africa, southern Africa, and in some cases east Africa as well. This especially becomes apparent, when one takes into account the above mentioned point about central Africa attaining the distinction of harboring these lineages in noticeable frequencies, while the case is shown to be otherwise in either west Africa and/or east Africa, or southern Africa.

With respect to haplogroup L3, we’re informed:

The lineages remaining within L3* represent ~20% of all L3A types in Africa. Although they are distributed throughout the continent, they reach the highest frequencies in East Africa, where they account for about half of all types from this region. This frequency profile suggests an origin for L3 in East Africa (Watson et al. Watson et al., 1997).

This is supported by the evidence that the out-of-Africa migration, which took place from a source in East Africa 60,000–80,000 years ago, gave rise only to L3 lineages outside Africa.

1)sub-haplogroups L3f and L3g:

Both L3f (Figure 8a) and L3g (Figure 8b) are rare and also appear to have an East African origin. L3f* and L3g are virtually restricted to East Africa (with some dispersal into Central Africa, southeastern Africa, and the Near East).

The subclade L3f1 appears to have spread at an early date into West Africa and is correspondingly also better represented in African Americans.

2)sub-haplogroup L3b:

By contrast, the commoner haplogroup L3b (Figure 8c) is predominantly West African, with a substantial representation again in African Americans. It has spilled over into North Africa and on into the Near East. There is very little dispersal into either East Africa or even Central Africa, but several derived types are present in southeastern Africa.

3)sub-haplogroup L3d:

Its sister clade, haplogroup L3d (Figure 9a), is also mainly West African and African American. A number of types are found in southeastern Africa, including one type (in L3d1), matching a Fulbe lineage, at considerably elevated frequency. A second type (in L3d3) is not seen in our southeastern African sample but occurs at high frequency in the south, in both Khwe and !Kung, and matches a type apparently found at high frequency in the Herero (Vigilant et al. Vigilant et al., 1991; not included in the network here because of sequence ambiguities).

4)sub-haplogroup L3e:

L3e (Figure 9b) is the most widespread, frequent, and ancient of the African L3 clades, comprising approximately one-third of all L3 types in sub-Saharan Africa. This haplogroup has recently been dissected in some detail by Bandelt et al. (Bandelt et al., 2001), who suggest an origin for the haplogroup in the Central Africa/Sudan region ~ 45,000 years ago.

L3e1 is distributed throughout sub-Saharan Africa, but it is especially common in southeastern Africa. This clade appears to have a west Central African origin and is rare among West Africans, although it is well represented among African AmericansThe African American types may be the result of direct transportation from Mozambique, given the lack of West African representatives.

L3e2 is more frequent in Central and West Africa. It is not possible to distinguish L3e2a without HVS-II information (a transition at np 198), and, as this information is not available in most sequences in the database, we have incorporated L3e2a into L3e2* in Figure 9b.

L3e2* appears not to have been transferred to the southeast, with one exception.

L3e2* is found mainly in Central Africa, and the derived subclade L3e2b is found primarily in West Africa, with a clear founder type within L3e2*. This indicates a range expansion from Central into West Africa (~9,000 years ago). Other instances of such expansions (for example, in haplogroup L2) may be undetectable, at present, because of poor phylogenetic resolution.

Few L3e2b types are found in southeastern Africa, but a great many are present in African Americans.

L3e3 is primarily West African, but with its root type present at elevated frequency in the southeast and with some southeastern African derivatives.

L3e4 is present in East, Central, and West Africa, with one individual in the southeast, but is too rare to draw conclusions from.

Well, what can be learned from pieces on macrohaplogroup L3? From the looks of things, L3b expanded considerably in west Africa, likely after ancestors of contemporary groups bearing E3a markers had situated therein, assuming that they were part [in very modest levels perhaps] of the dispersal involving those ancestors from their point of origin to their west African destination—which would explain lower frequencies elsewhere. Possibly the same with L3d, although in either L3b or L3d's case, the extracts above are rather vague about the timeline of the dispersals [that is certainly the case with L3f1; if there is any possible suggestion here, it may be one where one comes out thinking that L3f1 arrived in west Africa before the ancestors of E3a-bearing groups did]. Hence, inference here is made based on distribution pattern.

Of all the subtypes of L3, as presented above, L3e seems to fit in more with the earlier mentioned scenario of the radiation of mtDNA markers from central Africa as a refuge center [during the extreme periods of aridity] near and at the turn of the Ogolian aridity. Thus the likely origin of this lineage in the general region straddling central Africa and Sudan ca. 45ky ago [as proposed by Salas et al. ] would make sense, particularly as the region where ancestors of E3a groups of west Africa would have picked up carriers of that marker; this wouldn't have been far from, if not within the general area where the forebearers of E3a groups of west Africa first arose. As an afterthought, all this seems to play well with the tabulated L3e TMRCA ages given to the subtypes [numbers in brackets are standard error figures]:

L3e > 49,250 (11,750)

L3e1 > 32,150 (11,450)

L3e1a > 26,750 (12,000)

L3e2 > 37,400 (18,350)

L3e2b > 9,150 (3,100)

L3e3 > 14,150 (4,500)

L3e4 > 24,200 (10,400)

Interestingly, amongst these TMRCA figures, the common west African subtypes of L3e2b and L3e3 are also the markers with TMRCA ages that best reflect the timeframes attached to repopulation demographic processes in west Africa near and/or at the turn of the Ogolian aridity, and shortly thereafter, in accordance with archaeological evidence.

And finally, for the purpose of this topic, the following synopsis from Salas et al. may well prove to be instructive, with some special emphasis to the highlighted pieces, as they appear to buttress several the points already outlined above:

An important influence on the subsequent genetic landscape of the continent is likely to have been the LGM. Paleovegetational studies have indicated that, between 30,000 and 11,000 years ago, much of the continent was extremely arid (Adams and Faure Adams and Faure, 1997). The Sahara advanced hundreds of kilometers further south, and the equatorial rainforests were reduced to a small fraction of their present size, leaving open woodland and savanna in much of the Congo basin. This may have formed a refuge area from which modern humans later dispersed: some with haplogroup L2a east and west, with L1b west; perhaps even some with L1a east and L1d southward. The origins of these expansions may lie earlier, at the beginnings of the Later Stone Age, ~40,000 years ago. Archaeological evidence has demonstrated substantial human activity in the equatorial forest area—for example, in Cameroon and Equatorial Guinea, 35,000 years ago (Martí et al. Martí and Mercader-Florín, 2001).

It is worth noting that the mtDNA data do not support the clustering of sub-Saharan Africans into (pre-Holocene) geographical races, as assumed by many authors (Hiernaux Hiernaux, 1975; Newman Newman, 1995), if only because the so-called “Pygmies” clearly do not form a coherent group. The westerly Biaka sample includes only L1a and L1c, and the more easterly Mbuti include only L1a (shared with the Biaka), L1e and L2. Therefore, the Biaka tend to resemble other Central African populations, whereas the Mbuti more closely resemble those from East Africa, although both groups are much reduced in diversity in comparison with neighboring populations. It is also notable that the Tanzania Khoisan-speaking Hadza resemble other East Africans rather than southern African Khoisan speakers. Both results appear to be consistent with the results from classical markers (Cavalli-Sforza et al. Cavalli-Sforza et al., 1994).

The authors proceed to then make their own correlations between mtDNA distribution and Y marker distribution, although not as detailed as that in the posting here, as it particularly pertains to contemporary west African groups who are generally known for high frequencies of PN2-derived Y marker "E3a".
Salas et al. 2002, The Making of the African mtDNA Landscape