The age estimate is based on microsatellites and a 6 million/25 year generation human-chimpanzee divergence. In general I carry a small basket when it comes to age estimates. Li & Durbin for example, recently estimated that divergence between African farmers and Eurasians began ~100-120ky, a date similar to the date in this paper for the San/non-San split, and even that may be older, depending on whether one uses the genealogical mutation rate from 1000Genomes or a chimp calibration.
The authors of the current paper: "Our estimate for the time of KhoeSan divergence is ~110 kya (95% CI: 52-187 kya)". I think the issue may be further complicated by the potential presence of archaic admixture in Africans, as that may make their effective population size appear larger. On the subject of archaic admixture Michael Hammer (who is a co-author in this one) has another new paper which I will cover in a separate post.
The interesting thing about this paper (aside from the age estimate) is the inference that San diverged first from other humans, rather than a hunter-gatherer first divergence out of which San and Pygmies both branched out. So, it seems that San are really basal to the rest of mankind.
We should not, however, forget that modern human evolution is looking less and less like a tree, with Neandertals, Denisovans, and now archaic African Homo emerging as relevant to our human story, and horizontal admixture in both the sapiens lineage and across Homo species (or should they be subspecies?) is becoming ever more important.
Below is the STRUCTURE analysis from the paper:
An early divergence of KhoeSan ancestors from those of other modern humans is supported by an ABC-based analysis of autosomal re-sequencing data
Krishna R Veeramah et al.
Sub-Saharan Africa has consistently been shown to be the most genetically diverse region in the world. Despite the fact that a substantial portion of this variation is partitioned between groups practicing a variety of subsistence strategies and speaking diverse languages, there is currently no consensus on the genetic relationships of sub-Saharan African populations. San (a subgroup of KhoeSan) and many Pygmy groups maintain hunter-gatherer lifestyles and cluster together in autosomal-based analysis while non-Pygmy Niger-Kordofanian speakers (non-Pygmy NKs) predominantly practice agriculture and show substantial genetic homogeneity despite their wide geographic range throughout sub-Saharan Africa. However, KhoeSan, who speak a relatively unique click-based language, have long been thought to be an early branch of anatomically modern humans based on phylogenetic analysis. To formally test models of divergence among the ancestors of modern African populations, we re-sequenced a sample of San, Eastern and Western Pygmies, and non-Pygmy NKs individuals at 40 non-genic (∼2 kb) regions and then analyzed these data within an Approximate Bayesian Computation (ABC) framework. We find substantial support for a model of an early divergence of KhoeSan ancestors from a proto-Pygmy-non-Pygmy NKs group ∼110 thousand years ago over a model incorporating a proto-KhoeSan-Pygmy hunter-gatherer divergence from the ancestors of non-Pygmy NKs. The results of our analyses are consistent with previously identified signals of a strong bottleneck in Mbuti Pygmies and a relatively recent expansion of non-Pygmy NKs. We also develop a number of methodologies that utilize ‘pseudo-observed’ data sets to optimize our ABC-based inference. This approach is likely to prove to be an invaluable tool for demographic inference using genome-wide re-sequencing data.