On mtDNA diversity within Africa, before the out of Africa migrations

Dienekes, Blaine, Razib, and Simon have all chimed in introducing us to a new paper from the American Journal of Human Genetics. It seems like a really interesting one, one that takes mtDNA to construct a phylogeny used to investigate what was happening to early Homo sapiens genetic diversity and populations within Africa. This study focuses on what was going on before the migrations out of Africa. The paper is titled, “The Dawn of Human Matrilineal Diversity,” and is open access. The research has already made it all the way onto some of my favorite news sources, such as Digg and Slashdot, but the big timers like CNN, BBC, the Economist, and the AFP are also carrying word.

The researchers constructed a mitochondrial phylogeny of 624 sub-Saharan individuals. They paid close attention to what’s going on with the phylogeny of the Khoisan, because previous research like Knight et al.‘s study on another loci, the Y-chromosome has shown that the Khoisan are carriers of oldest-diverging Y haplogroup, the Y-haplogroup A, indicating they may represent the deepest clade of modern humans. Recent research identified that the pygmy Khoisan populations share an ancestral and indigenous lineage of mtDNA with a neighboring population, the Bantu and this new study confirmed this.

The phylogenetic tree in this newer study is really informative. I’ve included it to the right. The researchers honed in on the mitochondrial haplogroup L, which is one of the oldest mtDNA haplogroups out there. The tree shows that early humans split into two small groups, demarcated by the L0 branch splitting from the L1’5 branch around 140,000 years ago. Based upon these two branches, the researchers were able to identify that one group was concentrated around eastern Africa (the L1’5 branch), while the other, the Khoisan’s L0 branch, in southern Africa. The sub-branches within the L1’5 clade represent all of the other L haplotypes in the entire remainder of humanity, including haplogroups of those that left Africa… further suggesting east Africa peoples were the main migrators out of Africa.

How could this happen? As populations of early humans migrated within Africa and reached southern Africa, they were cut off from the eastern African populations for a significant period of isolation to diverge into two separate clades. From ScienceDaily,

“Recent paleoclimatological data suggests that Eastern Africa went through a series of massive droughts between 135,000-90,000 years ago. It is possible that this climatological shift contributed to the population splits.”

The press is suggesting that this phenomenon indicated humans “started down the path of evolving into two separate species.” But that’s not true, they missed the part of the paper where populations came back together as a single, pan-African population about 40,000 years ago.

But, something is a little fishy, because as I already indicated, the coalescence calculations in this new paper indicate the Khoisan matrilineal ancestry diverged from the rest of the human mtDNA pool about 140,000 years ago. At that time, the five additional, currently extant maternal lineages (Haplogroups L1’5) existed in Eastern Africa, before the emergence of L0 branch. Looking at the phylogenetic tree, these haplogroups are more ancestral to the haplogroup L0 branch by at around 40,000 years, implying that the Khoisan may not be the deepest clade of living humans alive. This doesn’t match the Y-chromosome data, but we know already that mtDNA and Y-chromosome coalescent times aren’t the same… but this doesn’t match scores of other studies that indicate the Khoisan are a basal group of humans based off of their linguistic and cultural traits.

What this ultimately indicates is that eastern Africa may have truly been the cradle of humanity, at least the maternal cradle of modern humans. Which matches the fossil record, since some of the oldest remains of early human remains are also found in Eastern Africa, such as BOU-VP-16/1 and Omo 1 from Ethiopia.

    BEHAR, D., VILLEMS, R., SOODYALL, H., BLUESMITH, J., PEREIRA, L., METSPALU, E., SCOZZARI, R., MAKKAN, H., TZUR, S., COMAS, D. (2008). The Dawn of Human Matrilineal Diversity. The American Journal of Human Genetics DOI: 10.1016/j.ajhg.2008.04.002
    KNIGHT, A. (2003). African Y Chromosome and mtDNA Divergence Provides Insight into the History of Click Languages. Current Biology, 13(6), 464-473. DOI: 10.1016/S0960-9822(03)00130-1
    Quintana-Murci, L., Quach, H., Harmant, C., Luca, F., Massonnet, B., Patin, E., Sica, L., Mouguiama-Daouda, P., Comas, D., Tzur, S., Balanovsky, O., Kidd, K.K., Kidd, J.R., van der Veen, L., Hombert, J., Gessain, A., Verdu, P., Froment, A., Bahuchet, S., Heyer, E., Dausset, J., Salas, A., Behar, D.M. (2008). Maternal traces of deep common ancestry and asymmetric gene flow between Pygmy hunter-gatherers and Bantu-speaking farmers. Proceedings of the National Academy of Sciences, 105(5), 1596-1601. DOI: 10.1073/pnas.0711467105

9 thoughts on “On mtDNA diversity within Africa, before the out of Africa migrations

  1. The archaeology seems off in this paper also. For instance, “A recent study showed that ancestors of contemporary Pygmies diverged from an ancestral Central African population no more than 70 ka and that isolated was breached throughout the LSA.” The LSA doesn’t even start until maybe 40 ka, so what about the ~30k years between the MSA and LSA?

  2. Kambiz. You see a problem: “these haplogroups are more ancestral to the haplogroup L0 branch by at around 40,000 years, implying that the Khoisan may not be the deepest clade of living humans alive”.

    I think the answer lies here: “As populations of early humans migrated … and reached southern Africa, they … diverge into two separate clades”. Why do the authors assume the separation resulted from a migration south? If the migration had been the reverse, L1’5’s ancestors had arrived from southern Africa, L0 could still be the ancestral haplotype. The more recent diversity of L0 could be explained if many southern lines had become extinct since the split. Selection.

  3. Good point Terry, I see what you’re suggesting. It is certainly just as possible that the L1’5 haplogroups originated in southern Africa and moved to eastern Africa as it is the L0 haplogroups originated in eastern Africa and moved south.

    But, eastern Africa has a far more rich and thorough record of fossils and artifacts that tell us of early H. sapiens presence in the region. Southern Africa does not have as much when compared to eastern Africa. Many things coulda affected why this is so, but the most parsimonious explanation is that eastern Africa was where early H. sapiens originated and radiated outwards.

  4. Kambiz. Thanks for taking the time to reply to my earlier post. As you say, “Southern Africa does not have as much when compared to eastern Africa”. And, “Many things coulda affected why this is so”.

    One of those things is that the phylogenetic tree suggests L0 and L1’6 may have separated nearly 200,000 years ago. There’s no reason on earth why we should associate mtEve’s line with modern-looking humans this early. After all God didn’t suddenly create her, in spite of what many people seem to believe. I wouldn’t expect a sudden radical change in human physical appearance with her development. Modern human phenotype in the region could well be a result of the later movement from East Africa.

    I’ve looked at the suplimentary material and L0 is basically the only haplogroup isolated to a relatively small region. All the others are actually fairly widely distributed from Northeast Africa across the Sahel region and into Central Africa. If L0 is part of a later expansion from East Africa we would expect this line also to be widely distributed. Of course this doesn’t contradict your statement that, “eastern Africa was where early H. sapiens originated and radiated outwards”.

    I’m actually going away for a week so I won’t be able to study any response until I get back.

  5. How is ti with Chromosome Y? Currently the root is considered to be 80 k years old, or maybe younger … So to root is placed to the time of isolated groups, isn’t it interesting? Does it mean that only one isolated group had men with root while the other had even older which was later replaced? If the Chromosome Y root is younger (even 40 k years) than the conclusion is similar … the southern group’s man would be above this root and later replaced …

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