Chimps have undergone more positive selection than humans

We often assume that this common ancestor (and early members of our family for that matter) was very chimp like. However, research indicates that more genes have undergone positive selection in chimps than in humans.


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Humans and chimps share a common ancestor, which split into two species some point between 7 – 14 million years ago. We often assume that this common ancestor (and early members of our family for that matter) was very chimp like. However, there is a growing body of evidence that chimps have been evolving in a unique direction themselves, so aren’t as similar to early hominins as we might think. In fact, a study has revealed that more genes have undergone positive selection in chimps than in humans. 

If a gene codes for a trait that benefits an individual then that guy will be more likely to survive, reproduce and pass on his genes. Thus over time that gene is spread throughout the population until most people have it and that characteristic becomes part of what defines the species. This is positive selection. The study (all the way from the mystical past that is 2007) examined around 14,000 genes from both us and humans (which is about 58% of all the genes humans have) and looked for evidence that these genes had been positively selected for using some fancy genetics tricks that go completely over my head. 

All in all they found 154 genes in us which had been selected for by evolution since we split from chimps; but they found 233 genes in the chimp genome. Now, you might wonder “what if there are a bunch of positively selected genes in the 32% of the human genome they didn’t examine.” So they repeated their experiment another 2 times, taking a different sample of 14,000 genes each time. However, no matter which bits of the genome they sample they found that chimps always had more positively selected genes than humans.

The researchers then went on to examine the genes themselves. What did the positively selected genes do? Looking at the differences between chimps and humans you might think a lot of them have to do with brain development or the body plan. Yet most positively selected genes in both chimps and humans seem to have helped improve fairly unimpressive biological processes. 12 positively selected human genes, for example, influenced ion transport. 40 positively selected chimp genes were involved with protein metabolism. Not the sort of things you might expect to separate us from chimps. And in both groups most genes that were positively selected for were linked to the immune system. Still, chimps had a third more immune system related positively selected genes than humans.

Where the positively selected genes are expressed in both chimps and humans

Where the positively selected genes are expressed in both chimps and humans

However, in most other areas – brain, muscles, reproductive organs etc. – humans had more positively selected genes than chimps. Disease is an often underestimate evolutionary force. Yet genes which offer an advantage against disease can be strongly selected for. In humans, genes which offer resistant to Malaria are common amongst African populations, even though these genes can cause sickle cell anaemia in some cases. The benefits are so strong that this is an acceptable risk.

So perhaps chimps have to deal with more disease, or by chance more genes developed mutations that mean they are helpful against disease. Either way, the resulting evolutionary arms race inflated the number of genes which have undergone positive selection in chimpanzees. If we were to only look at the physical characteristics which define our two species, like brain size, locomotion and hairlessness, we may well find that humans have changed the most after all.

Still, we must not forget that chimps have been changing in their own right. They are not a frozen moment in time, identical to our common ancestor. Evolution waits for no man. Or ape.

Reference

Bakewell, M. A., Shi, P., & Zhang, J. (2007). More genes underwent positive selection in chimpanzee evolution than in human evolution. Proceedings of the National Academy of Sciences104(18), 7489-7494.

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15 thoughts on “Chimps have undergone more positive selection than humans”

  1. Marcel Williams says:

    Humans have substantially less genetic variation than chimps, bonobos, gorillas, and orangutans. They’ve also avoided at least one or two retroviruses that appear to have infected practically every primate in Africa. There are also indications that human ancestors evolved from an extremely small population. This strongly suggest, IMO, that human ancestors first evolved on small isolated islands. Human evolution on islands would explain the substantial loss in genetic variation, why human ancestors evolved from a small population, and how humans avoided exposure to retroviruses that contaminated all other primates species in Africa.

    However, such islands might be reconnected with the mainland during periods of lower sea levels.

    The first hominins appear in Africa at the beginning of the Messinian crisis when global sea levels and especially sea levels in the Mediterranean and the Red Sea were falling dramatically. Sea levels fell so low during the Messinian that eventually the Mediterranean became isolated from the Atlantic Ocean. Homo and the earliest lithic technologies first appear in Sub-Saharan Africa during another period of substantially lowering sea levels that started the Pleistocene.

    Marcel

    1. Adam Benton says:

      That is an interesting idea that I haven’t heard much about. Any recommendations for further reading would be greatly appreciated. However, there is an alternate explanation for our low genetic variation. There is evidence of a catastrophic event (a volcano I believe) almost making us extinct, lowering the human population to ~2,000 individuals or so.

      1. Chris Reynolds says:

        A lot of work has been done recently on super volcanos (such as Yellowstone National Park), and it seems likely that major eruptions which had the effect of producing extended global “winters” lasting several years happen several times in a period of about one million years. The effects of such repeated catastrophes, which can involve thousands of cubic miles of ash injected into the atmosphere, have not been considered in many older evolutionary studies.

        1. Adam Benton says:

          When did all this occur?

        2. Chris Reynolds says:

          The most recent big one was about 70,000 years ago – about the time it is often suggested modern homo sapiens entered Eurasia. S.E. Asia would be the most affected area, but short term climate change would have been world wide. Possibly a side effect was to make the then Ice Age even worse. Did this weaken the Neanderthals meaning we moved into a slot they had partially vacated? I am drafting something at the moment and will check up on details. There could be some relevant postings on my blog later in the month.

        3. Adam Benton says:

          The glacial period ~70,000 years ago was no more extreme than those which Neanderthals had already lived through. Whilst this volcano may well have contributed to it; maybe even worsening it, it probably can’t be the only explanation.

          If I recall though, isn’t this eruption meant to have severely reduced the population size of modern humans, almost wiping us out?

  2. Cynthia Echterling says:

    I wish I could find more information on Chimpanzee evolution and what their ancestors were like . Have they just not found many fossils or what?

    1. Adam Benton says:

      We have not. The grand total of all chimp fossils found is about half a dozen teeth from 500,000 years ago. There is a lot more information on Miocene apes. That’s an interesting avenue of investigation if you’re interested in ape evolution.

      1. Cynthia Echterling says:

        Thanks, I’ll check that out.

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  5. Andrew C. Holmes says:

    Hey Adam. As per usual, I have a slightly different take on reconstructing the LCA. In lieu of clogging your blog up with my own ramblings, you’ve once again inspired me to write my own blog post on this subject. Thanks again and party on! Check it out when you get a chance: http://livelikedirt.blogspot.com/2014/01/the-last-common-ancestor-of-chimps-and_28.html

    1. Adam Benton says:

      That’s a good post and is certainly a valid point. Whilst the LCA was likely different from modern chimps (particularly in terms of locomotion as I’ve said before) on balance there are still probably some key similarities. Chimps can still tell us a lot about human evolution

  6. Chris Reynolds says:

    What is really interesting is that there is no major peak relating to the brain – which suggests that there have been no significant changes to how the brain works – although I suspect that the peak for “immature” is because there have been major changes on this front to allow humans infants to have more time to “load” their brain with learning.

    I am working on a model of the brain’s neural code protocol which suggests that it is highly resistant to evolutionary change – and the work so far suggests that the difference between humans and apes is basically one of rate of learning. When cultural know-how of a group reaches a critical level it becomes advantageous to concentrate on copying ones parents and other adults. However trail and error copying is slow, and things would speed up with just a simple language where the adult can explain how to use tools, and not just imitate. And language is just a tool – so if you can talk about better tools language can also bootstrap itself to higher levels over the generations.

    To speed up the process even more, it the infant brain uncritically accepts language as the main tool, and language starts to use abstract terms, learning is greatly accelerated. (i.e. if you can tell a child what characterizes a mammal he does not have to learn about lots of different mammals.).

    My works suggesting possibly three explosive changes leading to our current levels of intelligence – none of which mean any significant change in the neural code mechanism. (1) simple language allows better tools (2) language expands to allow abstract terms – allowing more information to be packed into less learning time (3) people specialize so that it is not longer necessary for everyone to learn the complete cultural package. The first two would lead to pressure to evolve a bigger brain to hold more cultural information. The third actually frees some of the brain’s capacity to diversify into imaginative tasks such as music and the arts which may have no obvious evolutionary advantages (apart from selection of a sexual partner).

    There is a side issue relating to some of the clever Chimps in captivity – as if the big difference between humans and chimps (apart form brain size) relates to the way the adults train the children, it would seem possible that chimps which have been taught by humans will lean more effectively that chimps brought up by their chimp parents.

    SO do you agree that the results you give suggest that the main differences between human and human brains are the capacity and they why information is conveyed between generations.

    1. Adam Benton says:

      I have written about some research that indicates in many ways the human brain is a scaled up chimp brain, so I can see how not a lot of genetic change would be needed to produce our noggin. So in essence I agree with you, although I hadn’t really considered the way information is conveyed. Now you bring it up though it does seem kinda obvious

  7. km says:

    Maybe the human brain is scaled up primate brain, but it is 7 times bigger than expected, while that of chimps is only 3

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