Maximum likelihood evidence for Neandertal admixture in Eurasian populations from three genomes
Konrad Lohse, Laurent A.F. Frantz
(Submitted on 31 Jul 2013)
Although there has been much interest in estimating divergence and admixture from genomic data, it has proven difficult to distinguish gene flow after divergence from alternative histories involving structure in the ancestral population. The lack of a formal test to distinguish these scenarios has sparked recent controversy about the possibility of interbreeding between Neandertals and modern humans in Eurasia. We derive the probability of mutational configurations in non-recombining sequence blocks under alternative histories of divergence with admixture and ancestral structure. Dividing the genome into short blocks makes it possible to compute maximum likelihood estimates of parameters under both models. We apply this method to triplets of human Neandertal genomes and quantify the relative support for models of long-term population structure in the ancestral African popuation and admixture from Neandertals into Eurasian populations after their expansion out of Africa. Our analysis allows us — for the first time — to formally reject a history of ancestral population structure and instead reveals strong support for admixture from Neandertals into Eurasian populations at a higher rate (3.4%-7.9%) than suggested previously.
Haldane's Sieve 
Just look at people, we are the neanderthals. Of course, we do not look exactly like our ancestors, due to hibridization. but some of us, inherited some of our grand parents features , just look at people; some have almost no chin, other forehead sloped backwards, others nose region protruded forward, others an small occipital bun, others a Low, flat, elongated skull, others big round finger tips and large kneecaps. I have some of those features. Anybody looking at people in any bus/train statio in Europe, South America, North America, etc. will discover that most people have at two or three neanderthal features.
“Just looking” at people and finding isolated common features doesn’t mean anything for phylogeny. Just like the lookalikes of the site “totally looks like” aren’t expected to have some hidden shared ancestry causing the shared traits. If the reasoning that concluded that Asians are the ones who have more genes from neanderthals is correct, then we actually have the situation that they’re at the same time the ones that are craniofacially morphologically more different from them, despite of that. It does improve a bit with the other reasoning, that doesn’t exclude neanderthal alleles shared with Africans as “neanderthal” alleles (that makes Southern Europeans the ones with more admixture), but not much.
I’m not denying introgression/admixture or anything, just pointing that’s kind of weird to say “we are the neanderthals” based on a few traits that may well be just homoplasies, when by the same reasoning we should really say we are all Africans, if we count the bulk of the features and not only the ones in common with neanderthals. It’s more like saying “we’re all bonobos”, just looking for a few genes that we may share with them and not with chimpanzees, and also pointing to hippies in comparison.