Neanderthals Were Human

As everyone should know by now, all modern humans descended from populations that left Africa are also partially descended from our late cousins, the Neanderthals. A paper published a couple of weeks ago in PLoS One comes to the unsurprising conclusion that North Africans also have the same mixed ancestry. Today we have an article called Neandertal DNA Research Confirms Full Human Status. It’s by Jeff Tomkins, who when he last commented on this subject screwed up quite impressively – this time around we have a slight improvement, at least.

The question of where Neanderthals should be classified is a legitimate issue. They are traditionally considered to be their own, separate species – Homo neanderthalensis, where we are of course Homo sapiens. But an alternative method is to give Neanderthals a subspecies level status, as Homo sapiens neanderthalensis. While I’m a long way from being any kind of expert, this is a form that I’m quite fond of. However that being said that classification makes us Homo sapiens sapiens, and even one “wise” is frankly one too many.

There are a number of things going for the subspecies idea. Certain stricter definition of the very concept of a “species” have it that if two populations can at all viably interbreed, as we have evidence for here, then they must be the same species. There is also increasing evidence that Neanderthals weren’t the dumb brutes everyone imagines they were – they were arguably at least our equals in many of those things we think we are so great at, if not necessarily the same species as us. Even if we don’t want to extend our self-congratulatory species label to the Neanderthals it makes sense to call them, and likely many other Homo species, “human.” If we one-day found a “lost tribe” of Neanderthals (we wont) we would, from at least a moral and ethical standpoint, have to call them such.

Tomkins for his part seems to be on a crusade to show that Neanderthals were exactly like us, concentrating on his field of genetics. To quote yet another Todd Wood post (we’re having Todd Wood Fridays this month, it seems):

I believe this evidence of hybridization has significant consequences for the Christian debate over origins, especially for those who believe that Adam and Eve were Homo sapiens, to the exclusion of other species.  If you took that position, you now have four basic options:

1. Deny that humans and Neandertals are separate species, which strikes me as possible but quite difficult given the morphological, developmental, and genetic differences between the two.
2. Abandon your insistence that humans are only one species and allow for human speciation (either within a human “created kind” or as macroevolution from non-human ancestors).
3. Maintain your belief in a single human species separate from Neandertals by affirming the possibility of offspring from bestiality, a position that I critiqued in a recent essay.
4. Deny the evidence of interbreeding or offer a different interpretation of that evidence.

While I don’t think Tomkins ever took the position that only what we call Homo sapiens are human he is nevertheless expounding #1 here. He opens:

A new DNA study compared modern humans to Neandertals. But unlike previous ones, this study targeted Northern Africans. The new report, published in the journal PLoS ONE, further confirms the fact that Neandertals could and did interbreed with people deemed to be modern humans.

That’s fairly reasonable.

When examining research of this nature, it is important to understand some of the caveats not discussed or explained in the sensationalized press releases that surely follow such high-profile discoveries.

Even when he agrees with them, it seems, Tomkins is keen to attack genetic studies as being potentially unreliable. He first notes that not all of the Neanderthal genome was compared, merely “780,000 standardly used regions of the human genome,” and that much of that too was dropped due to poor quality. He then says:

Third, the regions they compared contain what are called single nucleotide polymorphisms (SNPs). So, comparisons are not based on actual percent DNA sequence similarity genome-wide, but instead reflect whether there was a SNP present at a particular informative location. Thus, percentages of genetic mixtures between humans and Neandertals reflect a small, limited set of DNA sequences and the reported low levels are deceptive to the un-informed general public.

This was the core of the problem with his earlier post on this subject. The researchers are not saying that Neanderthals are ~4% similar to us, but that we have a ~4% ancestor from them – in exactly the same way as you might say that you were 4% descended from Eastern Europe. Confusing these two concepts is possible, yes, but the fault in such a situation would not lie with the reporters. On the plus side, last time it was him that seemed to be confused.

The underlying fact not often discussed in Neandertal DNA papers like this is that the Neandertal genome is, for all practical purposes, identical to modern humans outside these variable regions. If the Neandertal DNA was not identical to modern humans, these types of SNP studies would not even be possible.

How “identical” is that, exactly. He cites that claim:

For example, see references 1 to 7 in: Green, R. E. et al. 2010. A Draft Sequence of the Neandertal Genome. Science. 328 (5979): 710-722.

That paper is open access, but the papers listed at those points in the references don’t seem to be relevant. You can check them out yourself, but the context in which they were cited was:

The morphological features typical of Neandertals first appear in the European fossil record about 400,000 years ago (1–3). Progressively more distinctive Neandertal forms subsequently evolved until Neandertals disappeared from the fossil record about 30,000 years ago (4). During the later part of their history, Neandertals lived in Europe and Western Asia as far east as Southern Siberia (5) and as far south as the Middle East. During that time, Neandertals presumably came into contact with anatomically modern humans in the Middle East from at least 80,000 years ago (6, 7) and subsequently in Europe and Asia.

I think there must therefore be a typo in that citation, as I doubt those seven papers/books say what Tomkins claims.

The second part of his claim, that if the genomes weren’t all but identical this kind of comparison “would not even be possible.” If there were extensive additions and deletions in the Neanderthal genome relative to ours there would still be some areas that are similar enough to ours to do this – though there would be a point, yes, when you wouldn’t be able to do it because enough time had created too many SNPs to analyse.

It’s also important to remember here that, as Wood said, there are some obvious anatomical differences between Neanderthals and ourselves that mean that trained palaeontologists can tell you with confidence which group a given skull belongs to. There are differences, that is undeniable.

Tomkins concludes with a bit of genetic entropy, claiming that “errant assumptions undergirding this type of research assume the forward progress and improvement of human DNA over the course of evolutionary history.” I’m not sure that that really is an assumption here, actually, but it is apparently “patently false.” We have yet another reference to the first paper from here, and then, finally:

And if today’s genomes are more degraded than the ancients—including Neandertals—then their DNA would actually represent a more pristine state than the genomes of modern humans. Thus, in a biblical model, modern humans would have genetic differences caused by generations of mutations and genome decay.

I’m not sure quite where he’s going with that, but there you go.