May 22, 2014

MSMC preprint (Schiffels and Durbin)

From the paper:
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.

Also:
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.

Link

4 comments:

eurologist said...

"We find that all non-African populations that we analyzed show a remarkably similar history of population decline from 200kya until about 50kya, consistent with a single non-African ancestral population that underwent a bottleneck at the time of the exodus from Africa around 40-60kya."

Or, much better, consistent with an early ooA (~125 - 105 kya) of an isolated NE African population, followed by a population decline outside Africa until the UP.

Since there is no such bottleneck in Africans, otherwise one would have to propose that NE Africa had no contact with the remainder of Africa for 150,000 years - which is preposterous. However, it is of course also quite possible that the dating method is off by a factor of two or more.

"Between 30kya and 10kya we see similar expansions in population size for the CEU, TSI, GIH, and CHB populations."

Given well-known population size decreases and climatic conditions, this is hard to swallow unless a factor of ~ 2.5 in age is applied.

Generally, my sense here is that (1) the method seems to confound population size and age estimate errors, and (2) before ~ 10,000 ya, age estimates appear to be off by a factor of more than two. This is also supported by looking at figures "b" and "d" and comparing to climate and archaeological population size data.

Lank said...

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.

West Africans appear to have some divergent ancestry related to Pygmies. On the mtDNA side, they have some L1; both the L1b that's typical of West Africans, and the L1c that's found at high frequencies in Pygmies. On the Y-DNA side, A(xBT) lineages are found across West Africa.

So the pre-150 kya divergence could be picking up on the more divergent portion of Yoruba ancestry, with the more recent exchange with "non-African" ancestors actually representing Africans more closely related to proto-Eurasians.

terryt said...

"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".

I would expect that the idea 'new' species suddenly appear as a small, isolated, distinct populations confined to single regions would have
been buried long ago. Populations change through inbreeding, gene flow, and selection. Followed by more inbreeding, gene flow, and selection, etc.

"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)".

That's almost certainly too recent. Australia was settled by at least 46,000 years ago, and probably somewhat earlier. The age calculation has obviously been obscured by on-going gene flow.

"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."

Much more likely.

"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"

That is an amazing coincidence. I have just written at the U6 post:

"Yes, but obviously D and E (at least in the form DE) shared a considerable geographic range before the two became isolated in their separate regions. To me that separation must be associated with climate cooling and increased aridity. Their original geographic range must have stretched from North Africa to Central/East Asia".

Makes complete sense suddenly.

"Or, much better, consistent with an early ooA (~125 - 105 kya) of an isolated NE African population, followed by a population decline outside Africa until the UP".

Also fitting with my comments regarding the dating for the OoA.

Locrian said...

It seems to me that this is most compatible with an initial move of proto-Eurasians into NE Africa-Arabia, (as Dienekes suggests) with a two-way gene flow between Eurasians and Africans, due to proximity, followed at 80 kya by a move out of Arabia into Europe and Asia. At any rate if this stands up it is very suggestive of further directions for research. I’d like to see where all of this would put the divergence between Australians and Africans, or Southern Indians and Africans.