Most mtDNA lineages expanded before the Neolithic?

By Razib Khan | October 18, 2012 9:00 pm

A new short communication in Scientific Reports suggests that most demographic expansion as ascertained using mtDNA occurred before the Neolithic. MtDNA analysis of global populations support that major population expansions began before Neolithic Time:

Agriculture resulted in extensive population growths and human activities. However, whether major human expansions started after Neolithic Time still remained controversial. With the benefit of 1000 Genome Project, we were able to analyze a total of 910 samples from 11 populations in Africa, Europe and Americas. From these random samples, we identified the expansion lineages and reconstructed the historical demographic variations. In all the three continents, we found that most major lineage expansions (11 out of 15 star lineages in Africa, all autochthonous lineages in Europe and America) coalesced before the first appearance of agriculture. Furthermore, major population expansions were estimated after Last Glacial Maximum but before Neolithic Time, also corresponding to the result of major lineage expansions. Considering results in current and previous study, global mtDNA evidence showed that rising temperature after Last Glacial Maximum offered amiable environments and might be the most important factor for prehistorical human expansions.

A good aspect of this result is that they used whole mtDNA sequences. Why use short segments when we live in the age of big data? That being said I am very confused, and frankly skeptical, of the inference of coalescence before the Neolithic for Africa in particular. It’s open access so you can read the whole thing, and inspect the ‘star-like’ phylogeny patterns yourself. They’re hallmarks of rapid population expansion (or, more precisely rapid expansion of a particular genetic lineage). That I accept. But we have a great deal of circumstantial evidence of massive population expansion and replacement across South and East Africa >3,000 years ago. Not only that, but the mtDNA lineages, last I checked, don’t indicate predominant admixture with the local hunter-gatherer substrate.

What I’m hoping is that a reader might jump down to the methods and look at how they generated the dates which went into their Bayesian Skyline Plots (BSP). Perhaps there is some aspect of the parameters that they used which is ‘overshooting’ for Africa. They argue in the text that “all the African random samples also showed a 5-fold growth at ~15−11 kya, corresponding to expansion haplogroups L0a1a, L1b1a, L1b1a3, L2a1a, L3b1a, L3e1, L3e2a and L3e2b, and subsequently a 2-fold growth ~5−4kya, which might be driven by the Neolithic Revolution.” I can accept a 5-fold growth ~15−11 kya, but not a 2-fold growth more recently.

There is a problem in phylogenetics of papers coming out where the authors don’t know what they’re doing. I don’t accuse these authors of that, but I don’t have a good intuition of how they might be coming out with such high values for Africa (at least in relation to the Neolithic growth). Is my demographic model simply wrong? One of the populations in their data set are East Africa Bantu. Interestingly the Yoruba, who were not part of the Bantu Expansion, show more explosive recent population growth. This just doesn’t compute for me.

CATEGORIZED UNDER: Human Genetics, Human Genomics
  • Gail

    “There is a problem in phylogenetics of papers coming out where the authors don’t know what they’re doing.”

    I think there is a problem of blindly running a model and using the output to confirm what you expected to find, but without making any effort to determine if the model is appropriate or produces meaningful results. This report lacks any sort of critical analysis or evaluation of the model, and this makes me extremely skeptical of the results they report.

    It is also a flaw to rely only on the 1000 Genomes data – the sampling was very region specific and there are larges regions with no samples at all. Why not supplement the analysis with data from other studies to fill in the gaps on regional coverage?

    Another major flaw is how to define a star pattern in mtDNA phylogeny. There is an enormous difference in the star character of H and its subclades versus some other mtDNA haplogroups. There are huge qualitative differences in mtDNA expansion patterns, but this seems to be totally masked in their BEAST outputs. This might be a case where a simple model provides more insight than a complex statistical model.


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About Razib Khan

I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. In relation to nationality I'm a American Northwesterner, in politics I'm a reactionary, and as for religion I have none (I'm an atheist). If you want to know more, see the links at


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