This is continuation of previous work by many of the same authors. They consider two alternative models of human origins:
- A bottleneck that left only a small number of humans in Africa during the penultimate glacial age (130-190kya)
- Fragmentation of the range occupied by humans during that time, which led to a number of different groups surviving, but becoming separated by uninhabitable areas
As I've mentioned before on the blog, the authors write that:
The choice of mutation rate can impact the results and because there is a 2-3 fold di erence between the mutation rate estimated from mother-father-child trios (or quartet) ( ~10^-8=bp=generation; The 1000 Genomes Project Consortium 2010; Roach et al. 2010) and the mutation rate derived from human-chimp comparisons ( ~2.5x10^-8=bp=generation; Nachman and Crowell 2000; Fagundes et al. 2007; Gutenkunst et al. 2009; Laval et al. 2010), we considered both estimates of the mutation rate in our analyses.
There is, in fact, an interplay between three variables: time, mutation rate, and effective population size. If one fixes time and chooses a mutation rate, then they can arrive at an estimate of effective population size. This is, in fact, what the authors do, and they conclude that:
Our fi ndings are consistent with this hypothesis, but, depending on the mutation rate, we find either an eff ective population size of NA = 12,000 (95%C.I. = 9,000-15; 500 when averaging over all three demographic models) using the mutation rate calibrated with the human-chimp divergence or an e ffective population size of NA = 32,500 individuals (95%C:I: = 27,500-34,500) using the mutation rate given by whole-genome trio analysis (The 1000 Genomes Project Consortium 2010) (supplementary fi gure 4 and table 6, Supplementary Material online).I believe that in the coming years our understanding of deep human prehistory will be aided by two developments:
Relating the estimated eff ective population size to the census population size during the Pleistocene is a di cult task because there are many factors a ecting the e ective population size (Charlesworth 2009). Nevertheless, based on published estimates of the ratio between e ffective and census population size, a comprehensive value on the order of 10% has been found by Frankham (1995). This 10% rule roughly predicts that 120,000-325,000 individuals (depending on the assumed mutation rate) lived in Sub-Saharan Africa some 130 kya. Assuming that the range of humans extends over all the 24 millions km2 of Sub-Saharan Africa, the density of humans at that time would have been extremely low between 0.5 and 1.4 individual per 100 km2, which is even lower than the lowest recorded hunter gatherer density of 2 individuals per 100 km2 reported for the !Kung (Kelly 1995) and the density of 3 individuals per 100 km2 estimated for Middle Paleolithic people (Hassan 1981). However, this discrepancy disappears if humans were restricted to an area some 3-6 times smaller than the entire Sub-Saharan Africa.
- First, we will be able to estimate the autosomal mutation rate very robustly from a large number of families, so we will no longer have to calibrate it using paleontological data points such as periods of glaciation or the human-chimp divergence
- Second, we will be able to obtain ancient DNA from Pleistocene era modern humans, and hence incorporate real data points into models of human evolution
- A plethora of modern humans in a "Green Sahara" prior to the most recent Ice Age, which expanded into the Near East and gave us Skhul/Qafzeh/Jebel Faya/Nubian Complex.
- A plethora of modern humans in a "Green Arabia/Gulf Oasis" prior to 70kya that experienced a population crash due to desertification post-70kya and led to an exodus of modern humans into the rest of Eurasia, and back-to-Africa
A Green Sahara would fit the bill for a geographically limited area within Africa that would support a large population at comparable densities to modern hunter-gatherer populations of Africa. Ultimately, the puzzle of human origins can only be solved by a combination of genetics, archaeology, and palaeoanthropology.
Mol Biol Evol (2012)doi: 10.1093/molbev/mss061
Resequencing data provide no evidence for a human bottleneck in Africa during the penultimate glacial period
Per Sjödin, Agnès E Sjöstrand, Mattias Jakobsson and Michael G B Blum
Based on the accumulation of genetic, climatic and fossil evidence, a central theory in paleoanthropology stipulates that a demographic bottleneck coincides with the origin of our species Homo Sapiens. This theory proposes that anatomically modern humans – which were only present in Africa at the time – experienced a drastic bottleneck during the penultimate glacial age (130-190 kya) when a cold and dry climate prevailed. Two scenarios have been proposed to describe the bottleneck, which involve either a fragmentation of the range occupied by humans or the survival of one small group of humans. Here, we analyze DNA sequence data from 61 nuclear loci sequenced in three African populations using Approximate Bayesian Computation and numerical simulations. In contrast to the bottleneck theory, we show that a simple model without any bottleneck during the penultimate ice age has the greatest statistical support compared to bottleneck models. Although the proposed bottleneck is ancient, occurring at least 130 kya, we can discard the possibility that it did not leave detectable footprints in the DNA sequence data except if the bottleneck involves a less than a 3 fold reduction in population size. Finally, we confirm that a simple model without a bottleneck is able to reproduce the main features of the observed patterns of genetic variation. We conclude that models of Pleistocene refugium for modern human origins now require substantial revision.