Genetic studies have confirmed that Neanderthals and modern humans interbred in the distant past. Scientists with the University of Montreal have uncovered shared genomic material in the human X chromosome, material which is found in both Neanderthal remains and in humans of non-African descent. ScienceDaily reports:
“Dr. Labuda and his team almost a decade ago had identified a piece of DNA (called a haplotype) in the human X chromosome that seemed different and whose origins they questioned. When the Neanderthal genome was sequenced in 2010, they quickly compared 6000 chromosomes from all parts of the world to the Neanderthal haplotype. The Neanderthal sequence was present in peoples across all continents, except for sub-Saharan Africa, and including Australia.”
This evidence strongly confirms interbreeding between human and Neanderthal populations. In a broader sense, this evidence is confirmation of the general principle that history can be found in the genome. Especially when we consider the fact that the genetic traces are found only in some modern human lineages, and not in all modern humans, we see that the modern human genome is not a strictly insulated product of spontaneous creation, but is subject to and evidence of a long biological history. (Even though humans as wholes are of course the products of Creation, as can be known both from philosophical reflection and from divine revelation.)
In a Catholic analysis, I can see two alternative takes on the notion that modern humans and Neanderthals interbred in the distant past.
First, we can assume that Neanderthals were non-humans, metaphysically considered. They would not have human souls. Although they were genetically similar enough that humans could interbreed with them, they would not be human beings, just very advanced animals. Of course in this case, we have the disturbing evidence of human-non-human interbreeding which has left genetic marks to this day, but as morally illicit as such activity would have been, it is not biologically impossible.
The second alternative is that Neanderthals were metaphysically human – certainly not genetically modern humans, but ensouled humans nonetheless. In this case, we have not evidence of human and non-human interbreeding, but simply of breeding between two genetically distinct human populations. This distinctly Neanderthal population of humans has since become extinct, but their genes remain in some modern human populations.
Judging the humanity of any given population which is known only from fossils is virtually impossible. Compared to early populations of modern humans, Neanderthals left little by way of artifacts, but there are some traces that indicate that they used complex tools, may have had complex language, and – most tellingly – may have had music, art and some religious rituals. If so, these latter signify clearly human individuals, however unique their genomes and appearances were. In this case, Neanderthals would not be an alien animal species, but fellow sons of Adam, lost in the depths of history.