View Full Version : L3's Expansion within and out of Africa

08-07-2012, 09:15 PM
New study done this year. L3's been understudied for its importance, IMO. All the focus is on DE/YAP+.


L3 phylogeography:



The Expansion of mtDNA Haplogroup L3 within and out of Africa

Although fossil remains show that anatomically modern humans dispersed out of Africa into the Near East ∼100 to 130 ka, genetic evidence from extant populations has suggested that non-Africans descend primarily from a single successful later migration. Within the human mitochondrial DNA (mtDNA) tree, haplogroup L3 encompasses not only many sub-Saharan Africans but also all ancient non-African lineages, and its age therefore provides an upper bound for the dispersal out of Africa. An analysis of 369 complete African L3 sequences places this maximum at ∼70 ka, virtually ruling out a successful exit before 74 ka, the date of the Toba volcanic supereruption in Sumatra. The similarity of the age of L3 to its two non-African daughter haplogroups, M and N, suggests that the same process was likely responsible for both the L3 expansion in Eastern Africa and the dispersal of a small group of modern humans out of Africa to settle the rest of the world. The timing of the expansion of L3 suggests a link to improved climatic conditions after ∼70 ka in Eastern and Central Africa rather than to symbolically mediated behavior, which evidently arose considerably earlier. The L3 mtDNA pool within Africa suggests a migration from Eastern Africa to Central Africa ∼60 to 35 ka and major migrations in the immediate postglacial again linked to climate. The largest population size increase seen in the L3 data is 3–4 ka in Central Africa, corresponding to Bantu expansions, leading diverse L3 lineages to spread into Eastern and Southern Africa in the last 3–2 ka.

A couple representative excerpts:

Eastern Africa, thought to be the most genetically diverse region of the world and the likely place of origin of L3 (Torroni et al. 2006) as well as the source for non-African populations (Tishkoff et al. 2009), is clearly pivotal to most of these expansions (Scheinfeldt et al. 2010; Campbell and Tishkoff 2011). There is also evidence that at least part of this region acted as a refuge during the severest climatic episodes of the last several hundred thousand years, particularly around wooded lake margins and perhaps also in coastal regions (Barham and Mitchell 2008; Basell 2008)—although Compton (2011) has recently suggested that the Mediterranean coast and the South African coastal plain may also have acted as refugia for humans during this period. Moreover, Eastern Africa was a key secondary dispersal area for the Bantu expansion (Salas et al. 2002; Phillipson 2005). We have therefore enriched the databases of mtDNA L3 diversity in Eastern Africa by firstly characterizing at low-resolution 327 samples from Sudan, Ethiopia, and Somalia and then selecting from these 70 L3 lineages for complete mtDNA genome sequencing. The application of several methods and mutation rates for the evaluation of TMRCAs allowed us to narrow the time span for the emergence of L3 and establish an upper bound for the out-of-Africa migration. In addition, Bayesian skyline analysis of 328 complete L3 sequences and founder analysis of 2,359 L3 hypervariable segment I (HVS-I) sequences enabled us to infer both local demographic expansions and migrations within Africa.

The BSP for L3 overall points to three main episodes of population growth within Africa associated with L3 (fig. 2 and table 1). The first is steepest at ∼40 ka, although with a gradual start from before 50 ka. This signal is not observed in the BSPs of any of the individual L3 branches analyzed; it corresponds to the emergence of the various subhaplogroups between 40 and 50 ka. Although the root type of L3 probably expanded soon after its emergence 60–70 ka, given its seven basal branches, the single coalescence point was not detected in the BSP. The second episode is a steep increase in the effective population size around the beginning of the Holocene (table 1), associated particularly with the main Central African haplogroups (L3bd, L3e). It is also suggested by several other haplogroups present in Eastern Africa at the time (L3h, L3x, and L3f); no signal was detected for each of them individually (supplementary figs. S2–S5, Supplementary Material online), but it was observed when they were combined (supplementary fig. S6, Supplementary Material online). The third major expansion took place from ∼4 ka and led to the largest increase (table 1), and as the signal is only pronounced in the Central African BSP (Supplementary fig. S8, Supplementary Material online), this seems to have been a localized occurrence. Atkinson et al. (2009) performed a similar analysis on African lineages, including haplogroup L3, but the resolution of L3 was much lower in that case (80 sequences against >300 now), and they did not detect the two distinct increases in the Holocene.

08-26-2012, 10:07 PM

Contrary to Veeramah et al. reporting the absence of L3e1 haplotypes in their Ghanaian samples while being present in neighboring regions we detected at least low levels (2%) of L3e1 haplotypes in our data.

08-26-2012, 11:15 PM
What does that have to do with L3's origins and spread in and out of Africa?

08-27-2012, 12:11 AM
I was hoping that you would be able to tell me.

My first assumption when I looked at my quote was simple east to west transhumance, modern or ancient, if L3 originated in East Africa. But if you're asking me if I think L3 originated any other place than East Africa, then I wouldn't be able to say much yet for or against, since there would be no evidence for that.

L3e1 specifically seems to have a really scattered range, now that I look at sites like this: http://leherensuge.blogspot.com/2010/03/reviewing-mtdna-l-lineages-notes-l3-l4.html

I'll make some risky bets here and suggest that L3e1 originated in East Africa, L3e2 somewhere in the Central-West African Savanna, L3e3'4 around Southern Chad or the CAR and L3e5 in Egypt.

I was unable to read your paper so maybe you could clarify?