January 01, 2015

Bias in estimators of archaic admixture

arXiv:1412.6691 [q-bio.PE]

Bias in Estimators of Archaic Admixture

Alan R. Rogers, Ryan J. Bohlender

(Submitted on 20 Dec 2014)

This article evaluates bias in one class of methods used to estimate archaic admixture in modern humans. These methods study the pattern of allele sharing among modern and archaic genomes. They are sensitive to "ghost" admixture, which occurs when a population receives archaic DNA from sources not acknowledged by the statistical model. The effect of ghost admixture depends on two factors: branch-length bias and population-size bias. Branch-length bias occurs because a given amount of admixture has a larger effect if the two populations have been separated for a long time. Population-size bias occurs because differences in population size distort branch lengths in the gene genealogy. In the absence of ghost admixture, these effects are small. They become important, however, in the presence of ghost admixture. Estimators differ in the pattern of response. Increasing a given parameter may inflate one estimator but deflate another. For this reason, comparisons among estimators are informative. Using such comparisons, this article supports previous findings that the archaic population was small and that Europeans received little gene flow from archaic populations other than Neanderthals. It also identifies an inconsistency in estimates of archaic admixture into Melanesia.



Unknown said...

Dienekes, could this apply to the situation with Neandertal? They were known present in Europe for quite some time, but hss only migrated from Africa 70,000 ybp. If a West Eurasian population admixed with Neandertal (winning the diversity lottery), wouldn't we expect higher intragroup diversity in Europeans vice Africans, creating a contradiction? Modern Europeans individually have only 3-4% Neandertal DNA, but as a population, it's around 20%. That's a lot of "extra" diversity, yes?

Fiend of 9 worlds said...

If you run neanderthal genomes through they come out as 100% african when we should expect them to be hypereuropean. This should wake people up to the limitations of this sort of population analysis but of course it doesn't.

It's impossible to tell the true neanderthal ancestry levels from the information we have, or to even assert that any 'modern' genes actually come from anywhere but europe. It's probably over 3-4% but it could almost be much less than that due to selection.