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Re: Denisova at high coverage"

Dear John

I can hardly keep up with all the archaic human stuff coming out - partly as my main occupation is health genetics - but I wanted to run something past you. Given that there is reasonable agreement that Papuans and to a lesser degree Han Chinese (and peoples in between) have Denisovan ancestry, is there still any evidence that they have Neandertal ancestry? Or is the signal of presumed Neandertal ancestry just a signal of archaic ancestry which is in fact from Denisovans?

Of course, if there is no strong evidence of Neandertal ancestry in Papuans and Chinese then it removes the need for the interbreeding to have occurred immediately out of Africa. It already seems that modern humans interbred with Neandertals and Denisovans (and perhaps with some other archaic hominin in Africa), but it seems to me that the place and time of Neandertal interbreeding could be significantly different from where first proposed?

Then the timing of the Denisovan admixture would be of interest - I haven't read today's paper yet. Did you or anyone look in Japan and Tibet (and indeed the Andamanese) where we see relict Y chromosome lineages (and to a lesser extent relict mtDNA lineages eg M12). Perhaps they could have higher proportions of Denisovan as they have been less affected by the expansions accounting for the majority of Han ancestry? Perhaps not, but there is GWAS data available for all, so methods using this could be applied.

Finally - getting out on a limb - I wonder if the Flores hominins were Denisovans? Can only be speculation, but has anyone commented on this.

Thanks for your thoughts, I hope you'll spare a second to reply.

Many thanks for your kind words. It is indeed hard to keep up, even for us!

We are very confident that these populations do have Neandertal ancestry and that it does not all come via Denisovans. The Neandertal and Denisovan genomes each have a large number of unique alleles that allow us to differentiate these signatures. In Australians and PNG, the fraction of around 6% Denisovan is in addition to around 3% Neandertal.

I agree, Tibet is a promising area. The paper by David Reich et al. last year did include a broad range of Chinese regional and ethnic minority populations, including Tibet, and did not find any evidence of Denisovan admixture there. This is very strange to me, and it remains to be satisfactorily explained.

I doubt that Flores was Denisovan although it is possible. The initial habitation of Flores more than 1 million years ago was too early to have been accomplished by the same people that gave rise to Denisovans. The Denisovans diverged from Africans and Neandertals less than 600,000 and maybe as recently as 300,000 years ago. However, the initial habitation of Flores is known only from archaeology, and the hobbit itself is much more recent, only 18,000 years old. So possibly these are not a single population, in which case it is conceivable that the hobbit is Denisovan-derived.

Re: Denisova

Dear John Hawks,
I would like really to know what decisive arguments allowed scientists to tell Denisova finger went from a female, after nuclear genome sequencing.

That is quite simple; if the specimen were a male there would be Y-chromosome sequences in the genome.

Re: "Taxonomy on tap", where I reminded readers about my lack of a principled reason to continue using "hominid" instead of "hominin".

The only principle have to stand by is communication. Anybody who teaches and talks with their students should know how stupid this change is. Reading Begun or Harrison can't be compared to Smith, or [redacted]. Reading Early Begun can't be compared with late Begun. Students (and others) have no idea which meaning of hominid is in use in any particular publication, and authors rarely address this. All this confusion to conform to current taxonomy: but does it? Probably not, as Chimps and Humans are sooner or later going to be merged under the genus Homo. Then what? A third seismic change in what it means to be human - or a terminal confusion in a profession already widely recognized to be confused.

Good reason to adopt a clade-based taxonomy. On the other hand, that would force us to split up Australopithecus.

I will add on the topic of the chimp-human "Homo" idea that this is a good reason for a big congress on the definition of Homo. The reason for recognizing us at the genus level has to be defended by the events that led to our evolution, because it can't be defended on the basis of phylogeny.

And from another reader:

Hi John
I'm the kind of person who talks about human paleontology with my
friends, although none of us are specialists. When the news came out
about the sequencing of Neanderthals and Denisovians, I started saying
hominins. My wife asked me why and I couldn't give an answer.

That's an excellent perspective, thanks for sharing!

I've been having a conversation with a long-time colleague who doesn't like the change. Many don't. I personally don't invest that much in the words, but it's clearly an interesting case of contested change in terminology.

From a reader:

I'm the TA for an Intro to Philosophy course. This week, we're discussing Paley's Design Argument, Darwin's argument(s), and the evidence that favors Darwin's arguments over Paley's.

Here's my question: I had heard that mammals during early stages of development have vestigial gill slits. But I'm having a hard time finding legitimate documentation of this. Do you know either way? If not, do you know of any other good cases of vestigial traits in humans? Unfortunately, as I'm sure you realize, there are people whose brains simply cannot process evidence for common ancestry, so I try to make the examples as anthropocentric as possible, figuring those examples have at least some shot of convincing.

The "gill slits" in a human embryo are the pharyngeal arches and clefts, which ultimately develop into many different tissues of the head and neck. They are homologous to pharyngeal arches at the same embryonic stage in other vertebrates, but they do not have any role in respiration and do not include any true gill-like tissue. P.Z. Myers has written an accessible account of the history and current understanding of the gill slits (http://www.talkorigins.org/faqs/wells/haeckel.html). They are misleading as an example of evolution because they are not vestigial gills, however, the occurrence of the same structures in embryos of all vertebrates does reflect their common descent.

The wiki page on "human vestigiality" is not bad as a summary of traits that humans have in common with other animals but are basically useless in us. (http://en.wikipedia.org/wiki/Human_vestigiality) For me, the clearest and best examples of common descent are pseudogenes (example: GULOP, which makes vitamin C in most mammals, in anthropoid primates and tarsiers the gene still exists but is nonfunctional, broken). Also, LINE insertions -- a kind of retrotransposon that makes up a large fraction of junk DNA, humans share many nonfunctional insertions with chimpanzees, gorillas, etc., even though they have no function.

Also, a better anatomical example is the recurrent laryngeal nerve -- which takes a path that doesn't make any anatomical sense, except when you consider our ancestry in animals with very different configurations of head and neck: (described well by Jerry Coyne http://geophagus.wordpress.com/2009/07/11/why-evolution-is-true/) It originates in the sixth branchial arch of the embryo, which makes this a natural example to follow up the "gill slit" argument -- a real homology that is not a superficial similarity.

Hope that helps you. The classic response to the Paleyan argument in evolutionary biology is the long list of examples of poor design. Of course, a clever person can often argue that something that works badly is nevertheless well-suited for a vestigial purpose. That makes the DNA comparisons often much more persuasive.