August 18, 2010

The mother of us all lived 200 thousand years ago

From the press release:
Cyran said human genetic models have become more complex over the past couple of decades as theorists have tried to correct for invalid assumptions. But some of the corrections -- like adding branching processes that attempt to capture the dynamics of population growth in early human migrations -- are extremely complex. Which raises the question of whether less complex models might do equally well in capturing what's occurring.

"We wanted to see how sensitive the estimates were to the assumptions of the models," Kimmel said. "We found that all of the models that accounted for random population size -- such as different branching processes -- gave similar estimates. This is reassuring, because it shows that refining the assumptions of the model, beyond a certain point, may not be that important in the big picture."
Theoretical Population Biology

Alternatives to the Wright–Fisher model: The robustness of mitochondrial Eve dating

Krzysztof A. Cyran and Marek Kimmel

Methods of calculating the distributions of the time to coalescence depend on the underlying model of population demography. In particular, the models assuming deterministic evolution of population size may not be applicable to populations evolving stochastically. Therefore the study of coalescence models involving stochastic demography is important for applications. One interesting approach which includes stochasticity is the O’Connell limit theory of genealogy in branching processes. Our paper explores how many generations are needed for the limiting distributions of O’Connell to become adequate approximations of exact distributions. We perform extensive simulations of slightly supercritical branching processes and compare the results to the O’Connell limits. Coalescent computations under the Wright–Fisher model are compared with limiting O’Connell results and with full genealogy-based predictions. These results are used to estimate the age of the so-called mitochondrial Eve, i.e., the root of the mitochondrial polymorphisms of the modern humans based on the DNA from humans and Neanderthal fossils.


1 comment:

German Dziebel said...

The authors document a shift from the chimpanzee-human divergence rate estimates to, slowly from 1997 on, to Neandertal-human divergence rate estimates. From the paper:

"Since it seems from the genetic
data (Kringset al., 1999; Greenet al., 2008; Briggset al., 2009)
that Neanderthals did not contribute mtDNA to the lineages of
presently living modern humans, the time of the mtEve should
be placed after the H. sapiens – H. neanderthalensis divergence.
Even if later studies(Serré et al., 2004;Cyran and Kimmel, 2005)
indicated that interbreeding between two human forms could not
be excluded, and moreover that there is an evidence of a small-
scale gene flow (Greenetal.,2010),it remains true that the root of currently living humans should be placed after that of humans and Neanderthals. As light admixture of atmost 25% (Serré etal., 2004) or15% (CyranandKimmel, 2005) disappeared
as a result of the genetic drift. Therefore, even if the results of
the Neanderthal Genome Project suggest possible interbreeding
between the Neanderthals and the archaic Europeans yielding
about 3% admixture of the nuclear DNA (Plagnol and Wall, 2006;
Pennisi, 2006;Green etal., 2010), treating the Neanderthals as a
mtDNA outgroup is justified."

The question arises: how do we know that what, e.g., Green et al. 2010 detected as "Neandertal admixture" in humans is in fact admixture and not common descent? Otherwise, this statement sounds like retrofitting new data into old models but still hedging against it to make room for progress in divergence estimate methods.