Thursday, 27 October 2016

Oh Creation! Interbreeding Chimps and Bonobos!

Chimpanzee genomic diversity reveals ancient admixture with bonobos | Science.

We are getting used to the relatively new science of genome analysis throwing up regular surprises and calling into question a few things we thought we understood reasonably well, but then that's science. Science wouldn't be any use if we didn't keep learning new things, revising old assumptions and so making progress.

For example, we once thought that modern humans evolved in East (or possibly South) Africa and that a small band of Homo sapiens followed an earlier migration of H. erectus and left Africa for Eurasia and thence into the Americas and the Pacific. We assumed the last band out of Africa were the ancestors of all non-African people but had emerged from Africa as a fully differentiated, distinct species, and had pretty much stayed that way. We assumed their modern genome was derived directly from that of the African forebears.

Then along came the ability to extract DNA from ancient fossils and very quickly things changed. We discovered that non-African people had not only interbred with Neanderthals and may have acquired some of their beneficial genes evolved over 250,000 years to adapt to the colder northern climate, so shortcutting our evolution, but that thy had interbred with a newly-discovered species of human, the enigmatic Denisovans. They may possibly even have interbred with the descendants of the original migration of H. erectus.

So, we now know that non-African people are derived from hybrids between several co-existing species of humans and acted very much like a ring species for a considerable period of time.

We then discovered that for a period of 2 million years, our ancestors and the ancestors of chimpanzees also interbred occasionally when they came into contact. This happened between 6.3 and 5.1 million years ago.

Now we have evidence that the common chimpanzee (Pan troglodytes) and bonobos (P. paniscus) also interbred between 200,000 and 550,000 years ago as the two species diverged from their common ancestor. This was discovered by an international team led by Marc de Manuel of Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas–Universitat Pompeu Fabra), Barcelona, Spain, who analysed the genomes of 75 chimpanzees and bonobos from 10 countries.

Our closest living relatives, chimpanzees and bonobos, have a complex demographic history. We analyzed the high-coverage whole genomes of 75 wild-born chimpanzees and bonobos from 10 countries in Africa. We found that chimpanzee population substructure makes genetic information a good predictor of geographic origin at country and regional scales. Multiple lines of evidence suggest that gene flow occurred from bonobos into the ancestors of central and eastern chimpanzees between 200,000 and 550,000 years ago, probably with subsequent spread into Nigeria-Cameroon chimpanzees. Together with another, possibly more recent contact (after 200,000 years ago), bonobos contributed less than 1% to the central chimpanzee genomes. Admixture thus appears to have been widespread during hominid evolution.

Marc de Manuel, et al.
Chimpanzee genomic diversity reveals ancient admixture with bonobos
28 Oct 2016: Vol. 354, Issue 6311, pp. 477-481. DOI: 10.1126/science.aag2602

Copyright © 2016, American Association for the Advancement of Science.
Reprinted with kind permission under licence #3977221061716

This new information is now causing us to revise not only our understanding of hominin evolution but also our understanding of how species gradually diverge especially where changes in geography and climate can bring a diverging species back into contact before evolution has progressed to the point at which successful interbreeding is no longer possible. So, especially when we try to apply concepts of 'species' to gradually diverging groups, we find that the accepted definitions become less useful as the reality is not that black and white. Divergence is a gradual progress and speciation is a process, not an event, so far as most speciations have been concerned.

Now, this is not a problem at all for evolutionary theory, as this is exactly what we would expect. In fact, it would be surprising under the circumstances if we did not find this frequent evidence of interbreeding between related and diverging species. In Darwin's Dangerous Idea, Dan Dennett puts this rather well, using the analogy of the distinction between a peninsula and an island:

Daniel Dennett
Darwin shows us that questions like "What is the difference between a variety and a species?" are like the question "What is the difference between a peninsula and an island?". Suppose you see an island half a mile offshore at high tide. If you can walk to it at low tide without getting your feet wet, is it still an island?. If you build a bridge to it, does it cease being an island?. What if you build a solid causeway? If you cut a canal across a peninsula (like the Cape Cod Canal), do you turn it into an island? What if a hurricane does the excavation work? This sort of enquiry is familiar to philosophers. It is the Socratic activity of definition-mongering or essence-hunting, looking for the "necessary and sufficient conditions" for being-an-X. Sometimes almost everyone can see the pointlessness of the quest - islands obviously don't have real essences, but only nominal essences at best. But at other times there can still seem to be a serious scientific question that needs answering.

More than a century after Darwin, there are still serious debates amongst biologists (and even more so amongst philosophers of biology) about how to define species. Shouldn't scientists define their terms? Yes, of course, but only up to a point. It turns out that there are different species concepts with different uses in biology - what works for palaeontologists is not much use to ecologists, for instance - and no clean way of uniting them or putting them in an order of importance that would crown one of them (the most important one) as the concept of species. So I am inclined to interpret the persisting debate as more a matter of vestigial Aristotelian tidiness that a useful disciplinary trait.

Dennet, D.; Darwin's Dangerous Idea; p. 95 (paperback edition)

For creationists, however, this sort of situation presents a major, if not insurmountable, problem. Creationists need to use the nebulous and undefined term 'kind' to describe something akin to species. Being nebulous and undefined makes it a useful term for when they need to switch definitions. For example, they can switch from asserting that speciation doesn't happen because of some mysterious 'impossible' process involved in 'macroevolution', to asserting that speciation not only happened but happened at a massively accelerated rate after the 'Flood' to account for all the species but the absurdity of them all being on a wooden bat for a year.

Not only does this information about interbreeding mean that it becomes almost impossible for creationists to claim that speciation is somehow a different process to normal evolution, but it also becomes impossible to attribute this alternative, warp-speed rate of evolution to an intelligent designer. It would be sheer lunacy to try to achieve complete speciation in a generation whilst allowing interbreeding. If speciation is to occur in a generation or less then the opportunities for interbreeding several times, as the data shows happened would mean that it happened most of the time! This would entirely wreck the speciation process!

So, come on creationists! How do you account for this emerging evidence of frequent interbreeding between gradually diverging species, within your co-existing alternatives of impossible speciation and warp-speed speciation? As though having two mutually contradictory 'theories' in use simultaneously wasn't bad enough, the evidence of occasional interbreeding over time destroys both of them, doesn't it?

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