Monday, May 17, 2010

A Few Thoughts on the Neanderthal Genome

I started this blog, in part, to give some rigor to my thinking about paleontology (and the rest of the stuff that falls within the ambit of a blog with an all-encompassing title like mine has). That’s certainly the impulse behind this posting. I needed to think more closely about the recent research on the Neanderthal genome and get beyond my initial confused reaction. This then offers up a few of my thoughts on the topic (and, in the process, showing how confused my thinking remains).

The news coverage of the recent report in Science about the draft mapping of a portion of the Neanderthal genome centered on what was portrayed as a provocative hypothesis supported by the research – ancestral modern humans interbred with Neanderthals.

I was driving when I heard the first brief reports, which prompted me to engage in a quintessentially modern human behavior – shout a question at the car radio: “How the hell do they know that?” I mean, I explained to the radio broadcaster (and my wife who endured my outburst), they (the Neanderthals) are our closest hominid relatives. Shared genes are a given, so that cannot be the evidence. (More on that later.) It wasn't the claim, it was not knowing the method behind it that had me exercised.

I read some of the print news coverage of this research which did a better job of explaining it. I also read through the Science articles, which the American Association for the Advancement of Science (AAAS) is making freely available on its website. Reading the Science articles was an interesting experience as I struggled with, and then nearly always detoured around, the language and concept barriers that genetic research erects for the layperson, and sought safe haven in statements I thought I understood.

The evidence supporting the proposition of interbreeding with Neanderthals (or Neandertals as it is spelled in the Science articles) lies in what was found when the Neanderthal genome was compared to the genomes of five present-day individuals -- a Papua New Guinean, a Han from China, a French European, a San from Southern Africa, and a Yoruba from West Africa. These places of origin were chosen deliberately. Neanderthals have been found in France, but not in Papua New Guinea or China.

(I am not addressing what’s probably the most important aspect of this research – the actual mapping of a portion of the genome of an ancient hominid population. It was an amazingly complex process and opens up a whole new avenue of research in exploring the human family, including what separates and joins all of these hominid populations.)

The researchers posited that a robust signal that interbreeding had occurred was if the Neanderthal genome were more closely related to modern human genomes from some parts of the world than others. If it were equally related to the array of modern genomes under study, then, presumably, the separation of the ancestor of modern humans from the Neanderthal happened once and completely, with no subsequent dalliance.

Evidence for interbreeding was found, prompting the news buzz.

But, that wasn’t the really surprising aspect of this finding, after all many scientists had expected some local interbreeding. The unexpected result was that the Neanderthal genome was more closely related to all three of the non-African genomes than it was to the African genome. The authors assert,
A parsimonious explanation for these observations is that Neandertals exchanged genes with the ancestors of non-Africans. (p. 718, A Draft Sequence of the Neandertal Genome, Richard E. Green, et al., Science, May, 2010, Volume 328)

That means, according to Svante Pääbo, one of the authors of the reports,
The most plausible [scenario] is . . . it happens early in a population that goes out of Africa and becomes ancestral to everyone outside of Africa, not just people in Europe and Western Asia where Neandertals occurred.” (Science Magazine Podcast, transcript, 7 May 2010, emphasis added. Pääbo is director of the Max Planck Institute of Evolutionary Anthropology.)

According to this research, between one and four percent of the genome of modern non-Africans comes from Neanderthals.

I am intrigued by a number of the implications of this research. I’ll mention two, each is probably painfully obvious, but neither was to me.

First, although I’d previously understood the genomic relationship between Neanderthals and modern humans to be close, the closeness of that relationship is startling. As Green et al. write, “Neandertals are the sister group of all present-day humans.” (p. 710) Sisters, not cousins. In fact, the researchers faced a particularly difficult challenge in accounting for contamination of the Neanderthal DNA by modern human DNA because “most DNA fragments in a Neandertal are expected to be identical to present-day humans.” (p. 711, emphasis added)

Second, for the Neanderthal genes to enter the modern human genome, the offspring of modern human and Neanderthal liaisons had to be nurtured, so they could grow up and procreate. The researchers assert that the evidence supports the gene flow as being from Neanderthals to modern humans, suggesting that, very early on, a few modern humans had, what I guess could be called, a cross-species tolerance. But, don’t get your hopes up, it was apparently a very restricted phenomenon, given the limited contribution of Neanderthals genes to the non-African genome (not more than four percent of the genome).

Then there are the issues raised by the research that befuddle me. There are many, but I’ll just mention a couple. Doesn't the concept of species take a hit from this research? I shouldn't be surprised. I'm used to the difficulties in applying the concept of a species – paleontologists distinguish species largely on the basis of physical differences in the fossils found, although breeding behavior is the defining biological attribute for identifying a species (in the biological definition, separate species don’t successfully interbreed). Obviously, the behavior of ancient extinct organisms is unobservable. Or is it? In some way, this genomic research does give insight into possible behavior involving ancient hominids.

This research shows that two separate species in the Homo genus interbred successfully -- the species concept is certainly fluid. As paleontologist Ian Tattersall has noted, “Species just don’t saltate into vastly different other species.” (The Fossil Trail: How we know what we think we know about human evolution, 1995, p. 237)

Then, there’s the sequence of events that led to the non-African genome having Neanderthal traces. The scenario favored by the researchers is a group of early Homo sapiens left Africa, encountered a Neanderthal population, possibly in the Middle East, “exchanged genes,” and then spread throughout Europe and Asia. The authors acknowledge that there may be other scenarios accounting for their findings. One that seems to muddy the waters posits that there may have been a human population “substructure” in Africa, one branch, as I understand it, giving rise to Neanderthals and then that same branch generating the modern human population that left Africa.

Ultimately, I find the favored scenario of this interaction between modern humans and Neanderthals heartening, contrasting, as it does, with the violent one depicted elsewhere to explain the relatively abrupt disappearance of this, our sister group, from the face of the Earth as we moderns made our presence fully known across the broad Eurasian stage. Given who we are, both may well be true.

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