Multiregional evolution lives!

I’m going to point to Rex Dalton’s piece today with relatively little comment:

"Neanderthals may have interbred with humans"</b></blockquote>
Genetic data points to ancient liaisons between species.
The researchers arrived at that conclusion by studying genetic data from 1,983 individuals from 99 populations in Africa, Europe, Asia, Oceania and the Americas. Sarah Joyce, a doctoral student working with Long, analyzed 614 microsatellite positions, which are sections of the genome that can be used like fingerprints. She then created an evolutionary tree to explain the observed genetic variation in microsatellites. The best way to explain that variation was if there were two periods of interbreeding between humans and an archaic species, such as Homo neanderthalensis or H. heidelbergensis.
I understand that there is more to come on this subject in the not-too-distant future, and in this case I don't have anything on paper to go on. As everybody knows, I very much expected to find a similar result. Besides that, others have published similar outcomes based on resequencing data. I titled the post, "Multiregional evolution lives," for a reason -- this study and others have been looking at genome-wide evidence of interbreeding outside of Africa. It's a multiregional model. Even I haven't been talking about levels of interaction as high as they are outlining in these models -- here they're looking at a genome-wide effect on neutral genetic loci, something you're not going to pick up significantly with today's samples unless it amounted to more than a couple percent of the human gene pool. These ongoing studies are concluding that present-day genetic variation is inconsistent with a simple model where a random-mating ancestral population gives rise to today's global population by means of a staged out-of-Africa dispersal. They next look at a model with some substantial (possibly complete) isolation between ancient human populations followed by a subsequent out-of-Africa dispersal. They show that this model fits the data significantly better. So far, so good. For a moment, I'm going to adopt a critical perspective. Previous results haven't yet been able to answer an important possible question: Can they distinguish the effects of intermixture outside Africa from an ancient population structure inside Africa? Increasingly it looks like population structure inside Africa may have been very important to the evolution of Late Pleistocene Africans. How can we distinguish these kinds of structure from each other? The short answer is that maybe we can't, yet. Human population history was not simple. If we take a simple model and add more parameters, it will fit the data better. The question is whether there may be some even better model with the same number of parameters. Population structure within Africa, selection on some loci but not others, asymmetrical migration -- all these and more might be possible. I take it as very likely that the strict out-of-Africa replacement without interbreeding is no longer credible. We've moved beyond it, and all these papers are testaments to that. They're valuable. But there's a lot of work left ahead of us, finding better models and continuing to test them with the increasing body of human (and ancient) genetic data. There's an awful lot up for grabs. Were Neandertals really a different species, a subspecies, or what? How genetically distinct were the groups within Africa that gave rise to the Middle Stone Age? Was there time for all recent humans to get Neandertal genes (as Jeff Long suggests in Dalton's story), or do some have a lot more than others? As Dalton's story notes, soon we'll have the Neandertal genome, which will give an additional perspective on this issue from a point 40,000 years in the past -- like an eyewitness at the scene. This year, we'll begin to see whole-genome data applied to these questions. There may be other ancient genomes that will surprise us. And maybe those of us on the population genetics side still have a trick or two up our sleeves. (Thanks to readers who forwarded this link!)