Autosomal Resequence Data Reveal Late Stone Age Signals of Population Expansion in Sub-Saharan African Foraging and Farming Populations – PLoS ONE

Here’s the introduction to a paper which seeks to determine when and for what reasons modern human populations began to undergo rapid growth spurts at various times during the Late Pleistocene and on into the Neolithic:

Reconstructing the timing and magnitude of changes in human population size is important for understanding the impact of climatic fluctuation, technological innovation, natural selection, and random processes in the evolution of our species. With census population sizes estimated to be only in the millions during most of the Pleistocene [1], [2], it is obvious that human population size has increased dramatically towards the present.

A major unanswered question is whether expansion began with hunter-gatherer groups, perhaps as a result of the invention of particular technologies or behavioral innovations, or much more recently with the advent of agriculture [3]. Early mtDNA studies suggested that humans experienced a burst of population growth between 30 and 130 thousand years ago (kya)—well before the start of agriculture [4]. More recent results have extended the timeframe for sub-Saharan African growth to 213–12 kya, depending in part on mtDNA haplogroup [5], [6].

However, it is populations—not haplogroups—that are subject to growth, and many present-day hunter-gatherer groups, including those in Africa, do not exhibit any mtDNA signal of demographic expansion at all [7]. On the other hand, Y chromosome sequence data are compatible with a model of constant size for both hunter-gatherer and farming populations in Africa [8]. Autosomal microsatellites tend to indicate an early (pre-Neolithic) start to population growth, but there is disagreement among studies on the time of expansion and whether or not the expansions involved African populations [9], [10]. Zhivotovsky et al. [11] examined a large autosomal microsatellite dataset in 52 worldwide populations and concluded that African farmers, but not hunter-gatherers, exhibit the signal of population growth.

Unfortunately, inferences of demographic parameters based on the above mentioned loci may be unreliable due to the possible confounding effects of natural selection or evolutionary stochasticity (for the haploid loci), or uncertainty in our understanding of mutation rates or the underlying mutation process (for mtDNA and microsatellites) [1], [3].

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Reference: Autosomal Resequence Data Reveal Late Stone Age Signals of Population Expansion in Sub-Saharan African Foraging and Farming Populations – PLoS ONE

Cox MP,  Morales DA,  Woerner AE,  Sozanski J,  Wall JD,  et al. 2009 Autosomal Resequence Data Reveal Late Stone Age Signals of Population Expansion in Sub-Saharan African Foraging and Farming Populations. PLoS ONE 4(7): e6366. doi:10.1371/journal.pone.0006366

5 thoughts on “Autosomal Resequence Data Reveal Late Stone Age Signals of Population Expansion in Sub-Saharan African Foraging and Farming Populations – PLoS ONE

  1. It says that there are clear signals of pre-agricultural population growth in both types of populations and that the “recent” massive post-Neolithic growth is simply not detectable using genetics.

    This is, I think, the really interesting part.

      1. Not sure exactly which is the question. It is quite obvious that farming (Neolithic) lead to some solid population growth at least in the mid term. But what this paper emphasizes is that this growth is not detectable through genetics (probably because it is too recent), while the Paleolithic one can be detected as a genetic signature and is for real.

  2. Here’s an explanation for the genetic pattern observed in Africans (high levels of allele diversity, low Fst values, an excess in private polymorphisms and low linkage disequilibrium). It’s the growth of hunter-gatherer populations from 50,000 YBP on, far exceeding that found outside of Africa, an explosion comparable in scale to Holocene demographic growth that occurred in different parts of the world as a result of the invention of agriculture. Africans may not be the oldest human population, but they definitely started expanding earlier and faster than populations outside of Africa. When compared against the recent paper by Tishkoff et al., this paper by Cox et al. indicates that the opposite genetic profile observed in America and Papua New Guinea (low diversity, high divergence /Fst/, few private polymorphisms, high levels of LD) implies a rather different demographic history, with moderate population growth mixed with bottlenecks, genetic drift, lineage extinction, etc.

    Since African genetic lineages (think of mtDNA L1-L3, Y-DNA A and B) aren’t found outside of Africa, it seems unlikely that African demographic expansion resulted in any significant migration outside of Africa. It’s more likely that several small populations with an ultimate source in America (or Australasia) settled in Africa and expanded exponentially. The demographic explosion detected in Africa may have obfuscated the exact geographic sources for the original migrants into Africa. However, the peculiar phenotypic similarities between Khoisans and “Mongoloids” (lighter skin color, epicanthic fold, Mongolian spot and gracial skull morphology) may be seen as concrete signs of a historical connection.

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