Saturday, March 17, 2012

The gorilla genome

Recently the gorilla genome was published. It showed that 30% of the genome was closer to  humans or chimpanzees that chimps and humans were to each other. The creationists were delighted, for they though they thought that the 'evolutionists' had just provided them with evidence against common descent. They were wrong...

Nobody was surprised that they were wrong; it's a habit of their's. Similarly, nobody with a good understanding of evolutionary genetics was surprised that humans had some genes in common with gorillas that they didn't share with chimps. It was, indeed, expected. But, it provides an interesting lesson for some common misunderstandings of evolution.

There is a pervasive idea that humans are the pinnacle of evolution and that chimpanzees and gorillas are 'primitive'. But, in reality, chimps and gorillas have an equally long evolutionary history and have changed just as much as humans since our lineages split from one another. And one study has shown that more genes in the chimpanzee lineage have been under selection than genes in the human lineage since the split.

Another misunderstanding is that the genetic differences observed now, must have appeared at the time the lineage split. But, the divergence of two species is not instantaneous; the genetic divisions become deeper over time. Moreover, some genetic differences may have appeared long before the split and were lost, by chance, in the populations that gave rise to one lineage, but not the other. The tree diagram for individual genes may, therefore, look very different from the phylogenetic tree. This phenomenon is know as incomplete lineage sorting (ILS). 

The important thing for evolution is that on average the human genome is more similar to the chimpanzee genome than either are to the gorilla genome. And this is the case. I suspect that many of the creationists shouting about this latest paper disproving evolution know that this is the case. But, I also think they know that it is a technical and often misunderstood part of our evolutionary knowledge and are using it to spread doubt about evolution through misinformation.

To understand ILS, you have to think not just about genes, but about the populations and species that genes occur in. When there is more than one version of a gene, each version is known as an allele. In apes (and most animals) any given individual will have two copies of a gene, which may be different alleles. But, in a population there are likely to be alleles that aren't present in every individual. Similarly, in a species all possible alleles may not be present in every population.

As populations diverge to form species, some of the alleles present in the ancestor will be lost because they won't be present in both populations. Others, however, will be retained in both descendant species. Fast-forward to another division in one of the species and the same thing can happen. By chance some of the alleles present in the common ancestor to all three species will be present in only one of the recently diverged species and in the more distantly related group. If the creationists had read more than part of one sentence of the gorilla genome paper, they would have seen this process illustrated in the very first figure.

Figure 1 from Scally et al. (2012) showing the phylogenetic tree for humans (H), chimpanzees (C), gorillas (G) and orangutans (O) with an example of incomplete lineage sorting overlaid in grey. In the example, the branching of one gene (grey line) does not map with the average genetic distance between species (percentages at the bottom). If we were to look at the example gene only, we would infer a more recent common ancestor for chimps and gorillas than for humans and chips. And that's why we don't construct phylogenetic trees based on single genes. 

Further reading:
Scally, A., et al. (2012) Insights into hominid evolution from the gorilla genome sequence. Nature 483:169-175 

Bakewell, M. A., Shi, P., and Zhang, J. (2007) More genes underwent positive selection in chimpanzee evolution than in human evolution. Proceedings of the National Academy of Sciences 104 (18) 7489-7494

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