What is most striking about it is the position of Vindija, an Upper Paleolithic Neandertal specimen which is clearly closer to Homo sapiens specimens than any of the Neandertal or archaic humans.
The first component is one of increasing (left-to-right) modernity, with Australopithecus on the left, and modern humans on the right. Apart from Vindija, the two West Asian samples from Kebara and Shanidar also appear quite "modern" in terms of their component 1 position.
There are two possible options: that Neandertals and modern humans were evolving in parallel towards a "modern" scapular glenoid fossa shape; or, that these Neandertals may have experienced gene flow from modern humans.
I am inclined to accept the idea of gene flow: Kebara and Shanidar are from the time when genetic evidence suggests that the major expansion of modern humans was well under way, and Vindija from a time when they had most probably already arrived in Europe. If there was AMH-to-Neandertal gene flow, these are exactly the Neandertal specimens that might be affected, and not, e.g., the >100ka European Neandertals that can be safely assumed to lack any modern human ancestry on a variety of grounds.
Dr. Hawks writes:
There is as yet no evidence that the Vindija Neandertal genomes have genetic introgression from the African populations from which present non-Africans derive most of their genetic heritage. Green and colleagues  tested explicitly for this kind of gene flow, from "modern" into Neandertal populations and found none.I am not convinced by the strength of that test, as it is based on the assumption that modern-to-Neandertal gene flow would Eurasianize the sequence we got from Vindija. That assumption is not secure, since:
- It seems increasingly likely that the major Upper Paleolithic expansion of humans originated in Asia and not in Africa, in which case the expanding moderns would be Proto-Human rather than Proto-Eurasian
- We've now had enough contrasts between Mesolithic/Neolithic and present-day DNA to cure us of the illusion that populations are largely static: we simply have no evidence (until we actually test them) as to what early modern humans in the Near East and Europe were like genetically.
I remain skeptical about the mainstream story about what this involvement is (Neandertal-to-Eurasian gene flow), and this analysis certainly seems consistent with the alternative (AMH-to-Neandertal gene flow during the expansion of modern humans out of the Near East). I can definitely co-sign the following statement by Dr. Hawks:
Frankly, I expect that the admixture estimates presented thus far will prove to be wrong. I could be wrong in this expectation, but there are many assumptions underlying genetic analyses of admixture, and it's easy for an incorrect assumption to give rise to an incorrect conclusion. I take the morphological evidence very seriously as a possible "reality-check" about the validity of genetic comparisons. After all, the morphological comparisons predicted introgression from Neandertals in the first place...UPDATE:
The scenario of gene flow from the paper can be seen below:
I want to highlight a couple of facts:
In the Levant, Tabun (120ky) is less modern than Kebara (60ky). This is exactly as we expect if there was a major human expansion c. 70ky, as I have argued for in my blog post on L3 and here. The same difference between Krapina (130ky) and Vindija (40ky), the latter just at the time when modern humans were getting there.
Notice also how "natural" Out-of-Arabia fits with the rest of the scenario: a group of expanding humans from Arabia (south-to-north) forms a natural extension that would affect Kebara, Shanidar, and ultimately Vindija. I won't even bother with the Coastal Migration Theory that seems utterly unable to explain modern-Neandertal interbreeding.
Journal of Human Evolution
The Vindija Neanderthal scapular glenoid fossa: Comparative shape analysis suggests evo-devo changes among Neanderthals
Fabio Di Vincenzo et al.
Although the shape of the scapular glenoid fossa (SGF) may be influenced by epigenetic and developmental factors, there appears to be strong genetic control over its overall form, such that variation within and between hominin taxa in SGF shape may contain information about their evolutionary histories. Here we present the results of a geometric morphometric study of the SGF of the Neanderthal Vi-209 from Vindjia Cave (Croatia), relative to samples of Plio-Pleistocene, later Pleistocene, and recent hominins. Variation in overall SGF shape follows a chronological trend from the plesiomorphic condition seen in Australopithecus to modern humans, with pre-modern species of the genus Homo exhibiting intermediate morphologies. Change in body size across this temporal series is not linearly directional, which argues against static allometry as an explanation. However, life history and developmental rates change directionally across the series, suggesting an ontogenetic effect on the observed changes in shape (ontogenetic allometry). Within this framework, the morphospace occupied by the Neanderthals exhibits a discontinuous distribution. The Vindija SGF and those of the later Near Eastern Neanderthals (Kebara and Shanidar) approach the modern condition and are somewhat segregated from both northwestern European (Neandertal and La Ferrassie) and early Mediterranean Neanderthals (Krapina and Tabun). Although more than one scenario may account for the pattern seen in the Neanderthals, the data is consistent with palaeogenetic evidence suggesting low levels of gene flow between Neanderthals and modern humans in the Near East after ca. 120–100 ka (thousands of years ago) (with subsequent introgression of modern human alleles into eastern and central Europe). Thus, in keeping with previous analyses that document some modern human features in the Vindija Neanderthals, the Vindija G3 sample should not be seen as representative of ‘classic’ – that is, unadmixed, pre-contact – Neanderthal morphology.