In particular, the early beginning of the drop would be consistent with an initial formation of distinct populations prior to 150kya, while the late end of the decline would be consistent with a final split around 50kya. This suggests a long period of partial divergence with ongoing genetic exchange between Yoruban and Non-African ancestors that began beyond 150kya, with population structure within Africa, and lasted for over 100,000 years, with a median point around 60-80kya at which time there was still substantial genetic exchange, with half the coalescences between populations and half within (see Discussion). We also observe that the rate of genetic divergence is not uniform but can be roughly divided into two phases. First, up until about 100kya, the two populations separated more slowly, while after 100kya genetic exchange dropped faster.If divergence between Yoruba and non-Africans began 150kya, then I wonder when divergence between Bushmen or the non-farmer ancestors of Pygmies and the Yoruba started. These dates are well within the time period when anatomical modernity was already in existence, but well before the time period when behavioral modernity first appears. This is important, as some people imagine that humans lived together for most of the time period since their first appearance ~200kya and only split recently at ~50kya, but this is obviously wrong. ~50kya seems to be the time for cessation of gene flow, with 100ky more of impeded gene flow.
As expected, the oldest split amongst out-of-Africa populations is between European and East Asian (CHB and MXL) populations, most of which occurs between 20-40kya (Figure 4b). Intriguingly there may be a small component (10% or less) of this separation extending much further back towards 100kya, not compatible with a single out-of-Africa event around 50kya.This is the most intriguing part of this preprint as it suggests that European/East Asian genetic differentiation may not only be due to the their post-UP divergence, but also to older strands of ancestry. Such deep differentiation may be related to the ~100kya settlement of the Near East (but not East Asia) by anatomically modern humans and the recent evidence for a deep "Basal Eurasian" lineage in Europeans but not East Asians.
bioRxiv, doi: http://dx.doi.org/10.1101/005348
Inferring human population size and separation history from multiple genome sequences
Stephan Schiffels, Richard Durbin
The availability of complete human genome sequences from populations across the world has given rise to new population genetic inference methods that explicitly model their ancestral relationship under recombination and mutation. So far, application of these methods to evolutionary history more recent than 20-30 thousand years ago and to population separations has been limited. Here we present a new method that overcomes these shortcomings. The Multiple Sequentially Markovian Coalescent (MSMC) analyses the observed pattern of mutations in multiple individuals, focusing on the first coalescence between any two individuals. Results from applying MSMC to genome sequences from nine populations across the world suggest that the genetic separation of non-African ancestors from African Yoruban ancestors started long before 50,000 years ago, and give information about human population history as recently as 2,000 years ago, including the bottleneck in the peopling of the Americas, and separations within Africa, East Asia and Europe.