Did We Really Interbreed with Neanderthals?

[Jabrosky]

A new paper published in PLoS casts doubt on some of the evidence thought to have shown interbreeding between Homo sapiens and Neanderthals:

Balancing Selection on a Regulatory Region Exhibiting Ancient Variation That Predates Human—Neandertal Divergence

Ancient population structure shaping contemporary genetic variation has been recently appreciated and has important implications regarding our understanding of the structure of modern human genomes. We identified a ~36-kb DNA segment in the human genome that displays an ancient substructure. The variation at this locus exists primarily as two highly divergent haplogroups. One of these haplogroups (the NE1 haplogroup) aligns with the Neandertal haplotype and contains a 4.6-kb deletion polymorphism in perfect linkage disequilibrium with 12 single nucleotide polymorphisms (SNPs) across diverse populations. The other haplogroup, which does not contain the 4.6-kb deletion, aligns with the chimpanzee haplotype and is likely ancestral. Africans have higher overall pairwise differences with the Neandertal haplotype than Eurasians do for this NE1 locus (p<10[SUP]−15[/SUP]). Moreover, the nucleotide diversity at this locus is higher in Eurasians than in Africans. These results mimic signatures of recent Neandertal admixture contributing to this locus. However, an in-depth assessment of the variation in this region across multiple populations reveals that African NE1 haplotypes, albeit rare, harbor more sequence variation than NE1 haplotypes found in Europeans, indicating an ancient African origin of this haplogroup and refuting recent Neandertal admixture. Population genetic analyses of the SNPs within each of these haplogroups, along with genome-wide comparisons revealed significant F[SUB]ST[/SUB] (p = 0.00003) and positive Tajima's D (p = 0.00285) statistics, pointing to non-neutral evolution of this locus. The NE1 locus harbors no protein-coding genes, but contains transcribed sequences as well as sequences with putative regulatory function based on bioinformatic predictions and in vitro experiments. We postulate that the variation observed at this locus predates Human—Neandertal divergence and is evolving under balancing selection, especially among European populations.

 

[Jamber]

I've always found John Hawks' weblog informative and well balanced. He takes a rational and evidence-based approach, which I like.
Neandertal DNA | john hawks weblog

 

[Jabrosky]

I've always found John Hawks' weblog informative and well balanced. He takes a rational and evidence-based approach, which I like.
Neandertal DNA | john hawks weblog

As of today he hasn't noticed the genetics paper cited in the OP, though that may change soon.

 

[Jamber]

As of today he hasn't noticed the genetics paper cited in the OP, though that may change soon.

I get the feeling he hasn't got a heap invested in the 'yes' case, so it'll be interesting to see what he says.
cheers
Jennie

 

[Steerpike]

This will probably remain unsettled for some time.

 

[Jamber]

And there's nothing like science for overturning its own orthodoxies, so if it's ever 'settled' there'll quite possibly be a reversal down the track (did dinoaurs hold tails in the air or drag them? Warm blooded or not?).

 

[Steerpike]

And there's nothing like science for overturning its own orthodoxies, so if it's ever 'settled' there'll quite possibly be a reversal down the track (did dinoaurs hold tails in the air or drag them? Warm blooded or not?).

Yeah, science is pretty good about that (sometimes later rather than sooner (see Clovis-first), but they get there!).