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Analyses of mitochondrial DNA sequences extracted from several Neanderthal remains have provided new information on their genetic relationship with modern human individuals. However, these results have been interpreted very differently among anthropologists. Here we review these results and present additional data directly addressing the question of genetic continuity among human populations during the Late Pleistocene. An analysis of additional Neanderthal and early modern human remains from Western and Central Europe do not provide any evidence of gene flow between the two groups. We also show that under reasonable assumptions of human demography, these data rule out a major genetic contribution by Neanderthals to the modern human gene pool. Finally, we present preliminary results showing that ancient DNA studies can also contribute to unraveling aspects of Neanderthal demography. Promising avenues of research, such as the investigation of Neanderthal population genetic diversity and organization, as well as analyses of mammal populations contemporary with Neanderthals, could allow us to better understand the dynamics, and perhaps causes, of the demographic changes that occurred in Eurasia during the Late Pleistocene.

At present, the direct evidence for Neanderthal genetic variation and gene phylogeny is limited to the control region of the mitochondrial DNA (mtDNA). Neanderthal mtDNA sequences are divergent from those of recent humans. This fact, when coupled with the assumptions of selective neutrality and a recently expanding human population, argues for the complete and utter extinction of Neanderthals without living issue. But an alternative hypothesis is that human mtDNA has recently undergone an episode of positive selection, or a “selective sweep.” Five converging lines of evidence suggest that mtDNA has undergone recent positive selection: (1) mtDNA variants in living humans are associated with life history and metabolic traits that changed dramatically during recent human evolution; (2) Statistical tests show that the distribution of human mtDNA variation is clearly inconsistent with neutrality; (3) Nuclear genomic variation is not consistent with a single recent population expansion as necessary to explain human mtDNA variation; (4) A neutral mtDNA necessitates a population replacement to explain its pattern of variation, but many autosomal and X chromosomal loci show strong phylogeographic or genealogical evidence for the survival of archaic human gene lineages and therefore reject population replacement; and (5) Anatomical and archaeological evidence shows some degree of anatomical and behavioral continuity between Upper Paleolithic Neanderthals and later Europeans and likewise reject population replacement. The hypothesis of positive selection on mtDNA is in accord with recent estimates of genome-wide rates of selection and is contradicted by no known evidence. Molecular and comparative evidence further suggests that the current pattern of human mtDNA variation represents only the most recent episode of positive selection among many during human evolution. Selection on mtDNA cannot prove that other Neanderthal genomic lineages survived, although such survival may be suggested by other anatomical and genetic evidence. Nevertheless, the substantial probability of such selection renders Neanderthal mtDNA variation phylogenetically uninformative.

The usefulness of cranial morphology in reconstructing the phylogeny of closely related taxa is often questioned due to the possibility of convergence or parallelism and epigenetic response to the environment. However, it has been suggested that different cranial regions preserve phylogenetic information differentially. Some parts of the face and neurocranium are thought to be relatively developmentally flexible, and therefore to be subject to the epigenetic influence of the environment. Other parts are thought to be particularly responsive to selection for adaptation to local climate. The basicranium, on the other hand, and in particular the temporal bone, is thought to be largely genetically determined and has been argued to preserve a strong phylogenetic signal with little possibility of homoplasy. Here we test the hypotheses that cranial morphology is related to population history among recent humans, and that different cranial regions reflect population history and local climate differentially. Morphological distances among ten recent human populations were calculated from the face, vault and temporal bone using three-dimensional geometric morphometrics methods. The distance matrices obtained were then compared to neutral genetic distances and to climatic differences among the same or closely matched groups. Results indicated a stronger relationship of the shape of the vault and the temporal bone with neutral genetic distances, and a stronger association of facial shape with climate. Vault and temporal bone centroid sizes were associated with climate and particularly temperature; facial centroid size was associated with genetic distances.

Using living humans as an extant referent, this paper examines the probability that the frequency differences in Neanderthal “unique” non-metric traits observed between Neanderthals and Upper Paleolithic modern humans could be sampled from two major populations of the same species. Neanderthal-like features occur in very low frequencies in living humans, if present at all. Rather, other features distinguish major human populations. The population frequency differences of these features are used as a model by which the Neanderthal — Upper Paleolithic frequency differences are assessed using a resampling simulation. This methodological approach tests the null hypothesis that the observed Neanderthal — Upper Paleolithic differences are not greater than what can be sampled from between two major human populations (Amerindians and Euroamericans). Results of the analysis fail to falsify this null hypothesis. Implications of these results for Neanderthal taxonomy are examined.

Direct AMS radiocarbon dates of around 31 ka BP (Wild et al., 2005) for several well preserved crania and other human specimens from Mladeč, Czech Republic, confirm their association with the Aurignacian. This material, which thus represents the earliest modern European remains with archaeological associations, has long featured in discussions of regional continuity or gene flow from Neanderthal into early Cro-Magnon populations. Here, the four most complete Mladeč crania are compared with Neanderthal fossils in metrical characters of the frontofacial region. Both univariate and multivariate analyses show no evidence of Neanderthal affinities, and thus of Neanderthal-derived genes.

Lotsy (1925) suggested that hybridizing plant species be grouped into larger interbreeding taxa that he named “syngameons.” Such hybridizing taxa have long been well-documented among plants, but zoologists have traditionally downplayed the role of hybridization in animal evolution. Templeton (1989), however, has recently suggested that mammalian species which freely hybridize should also be grouped into syngameons. A literature survey suggests that the ability of any two mammalian species to hybridize successfully (i.e., produce viable, fertile hybrid offspring) is negatively correlated with time since phylogenetic divergence. In this regard, the genus is a prime candidate for the presence of syngameons since the genus ( Wood and Collard, 1999) only emerged ca. 2.0 million years ago. The Late Pleistocene paleospecies is morphologically quite distinct from . The marked morphological (and genetic) distance between these two members of the genus has led many human paleontologists to infer that these two taxa are separate species. From a current systematic perspective, such a position is justified, since in almost all species concepts species are defined by characters, of which the ability to interbreed is only one. In fact, the ability to interbreed is a plesiomorphic character, and as such we should not be surprised if two sister taxa, such as and , retain this ability. There is, however, a relative dearth of paleontological evidence for such interbreeding — a somewhat surprising finding that warrants further exploration.

Neanderthals are the best-known fossil hominid group, but at the same time many aspects of their evolution are still poorly understood. The variation of numerous characters in Neanderthal populations shows a geographical gradient. From west to east, characters become less and less Neanderthal-like and more and more modern humanlike. Moreover, in Central Europe and the Near East, post-Neanderthal populations still exhibit some Neanderthal features, which is not the case in Western Europe. The spread of the first humans into Europe involved differentiation of this species by distance, whereas consecutive populations were linked by gene flow. Hence, from Western Europe to the Near East, there was a succession of human populations that developed, over time, Neanderthal characters that were more and more marked from east to west. Then, modern humans spread rapidly into Europe at about 40,000 years ago, but at least in the western part of the continent, no convincing evidence of hybridization with Neanderthals has been found. By contrast, interbreeding was still possible in the eastern part of Europe and in the Near East, but became less and less so towards the west. This hypothesis implies that the ancestors of Neanderthals arrived and evolved in Europe at a time when gene flow between Western Europe and Near Eastern populations was very limited. Hence, Near East Neanderthals cannot be interpreted as the result of a migration of a European population toward the east, but as a continuum in space and time of European inhabitants.

The general framework and the factors behind the demise of the Neanderthals are still fiercely debated, and there remain many uncertainties in the data. While accelerator dating has purged the record of spurious fossils and confirmed the ages of others, it is likely that many of our current “dates” for the last Neanderthals and the earliest moderns in Europe are minimum ages, from the perspectives of both calibration and contamination by more recent radiocarbon. While the Aurignacian probably does reflect a dispersal of modern humans, it may not represent the oldest such dispersal into Europe. And while much new morphological data support a specific distinction for , nevertheless the modern and Neanderthal lineages may be better characterized as allotaxa. Regarding the factors behind Neanderthal extinction, these are likely to have been many and varied, but almost certainly included the unstable climatic context of the period between 25–40,000 years ago. Finally, taking a wider context on the Neanderthal — relationship, we should remember that these events in western Europe were only the endpoints of hundreds of thousands of years of possible competition and interaction between these evolving lineages.