The analysis of the Neandertal genome shows that they are likely to have had a role in the genetic ancestry of present-day humans outside of Africa, although this role was relatively minor given that only a few percent of the genomes of present-day people outside Africa are derived from Neandertals.I was raised in the "regional continuity" school of modern human origins and tend to view early modern human archaic retentions as reflecting Neandertal ancestry of sorts. Historically, Neandertals have been given the taxonomic status Homo sapiens neandertalensis, as opposed to Homo sapiens sapiens, which is what modern humans are. Implicit in this is that the behavior and appearance of Neandertals was not sufficiently different from us to warrant a separate species designation.
Several studies done in the late 1980s and early 1990s seemed to cast a disparaging light on this interpretation. Branching analysis by Cann (1988) and Krings et al. in 1997 on the mitochondrial DNA of modern humans indicated strongly that modern humans had originated as a speciation event in sub-Saharan Africa between 140 and 280 thousand years ago and had replaced the modern humans they came into contact with as they migrated north. This gave rise to the removal of the "sapiens" part of the taxonomic name of Neandertals.
Having their backs against the wall, the regional continuity folks had to rely on the not-inconsequential evidence from skeletal morphology and archaeology which seem to indicate a level of continuity between Neandertals and modern humans. My Ph.D. work showed that this level of archaicness in the early modern human sample was systematically underplayed by those espousing replacement of Neandertals and that several specimens routinely considered to be modern humans were only barely so.
Then David Maddison et al. showed in the early 1990s that some of the original studies done isolating modern humans from all that had come before were not run correctly. They showed, instead, that branches that called for the origins of modern humans in other parts of the Old World were equally parsimonious with the African branch. Relethford (1991), further, suggested that, while the Krings et al analysis showed a difference between modern humans and Neandertals, there was no way to really know how much of a difference constituted a separate species.
There have been three sort of competing hypotheses regarding regional continuity. Wolpoff and others (1989, 2001, 2003) have argued that modern human arose through gene flow between different areas of the Old World. Bräuer (1990) and Smith (2005) have developed independent models involving an "assimilation" of the Neandertals into the modern populations in which limited but measurable gene flow existed between the two. It now seems that one of those models is correct.
Bräuer, G. and K. Rimbach (1990). "Late archaic and modern Homo sapiens from Europe, Africa, and southwest Asia: Craniometric comparisons and phylogenetic implications." Journal of Human Evolution 19(8): 789-807.
Cann, R. (1988). DNA and human origins. Annual Review of Anthropology, 17(1), 127-143.
Krings, M., Stone, A., Schmitz, R., Krainitzki, H., Stoneking, M., & Pääbo, S. (1997). Neandertal DNA sequences and the origin of modern humans. Cell, 90(1), 19-30.
Maddison, DR, Ruvolo, M and Swofford, DL (1992) Geographic Origins of Human Mitochondrial DNA: Phylogenetic Evidence from Control Region Sequences. Systematic Biology 1992 41(1):111-124; doi:10.1093/sysbio/41.1.111
Relethford, J. (2001). Ancient DNA and the origin of modern humans. Proceedings of the National Academy of Sciences 98(2): 390.
Smith, F., I. Jankovic, et al. (2005). "The assimilation model, modern human origins in Europe, and the extinction of Neandertals." Quaternary international 137(1): 7-19.
Wolpoff, M. and E. Trinkaus (1989). "The place of the Neandertals in human evolution." The Emergence of Modern Humans: Biocultural Adaptations in the Later Pleistocene: 97–141.
Wolpoff, M., J. Hawks, et al. (2000). "Multiregional, not multiple origins." American Journal of Physical Anthropology 112(1): 129.
Wolpoff, M., J. Hawks, et al. (2001). "Modern human ancestry at the peripheries: a test of the replacement theory." Science 291(5502): 293.
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