Bonobo genome sequenced

Bonobos (Pan paniscus) are a species of chimp, closely related to their more common cousins, the “chimps” (Pan troglodytes*). The latter are the only species to be referred to as chimpanzees by the general public, despite the fact the term technically applies to the genus Pan  and thus both “chimps” and bonobos.

A bonobo. Doesn’t he look friendly? (Photo credit: tim ellis)

However, this taxonomical misnomer isn’t a bonobo’s only claim to fame. That honour lies with their sexual behaviour, which is famously promiscuous. Indeed, I’d wager most other articles you’ll read about this story start by describing them as “the chimps oversexed cousin” or something similar.

Yet their sexual behaviour is just one small part of what makes bonobos unique. They’re also a lot less aggressive, have a less hierarchical society, are more playful and less politically conniving than regular “chimps”; amongst other things. Physically they’re more gracile than chimps, with a thinner upper body and head; although they are not smaller overall (despite often being referred to as pygmy chimps).

This obviously makes them very interesting to study since if we can uncover what it is that makes P. troglodytes  and bonobos so different we may be able to work out the ultimate cause of those behaviours. If we figure out that some genetic change is responsible for their lack of aggression, for example, then perhaps chimpanzee aggression has a genetic basis. That might also have interesting implications for the source of human aggression, since we’re very closely related to both species.

However, attempts to figure out such interesting things have been hampered by the fact that only small parts of the bonobo genome have been sequenced do far. This work has provided some useful information, such as the fact that bonobos separated from the chimps because they were physically separated by the Congo River. This isolation allowed them to become more and more genetically distinct until they split into the two species we know and love between 1-2 million years ago.

The distribution of bonobos (purple) and two groups of “chimps” (green and yellow). Note how all these groups are divided by rivers.

Deciding that this lack of information needed to be rectified a team of geneticists, led by Kay Prüfer of the Max Plank Institute for Evolutionary Anthropology (quite what that blokes relationship is to EvoAnth I do not know), sequenced the bonobo genome. Whilst their data has yet to reveal anything quite as profound as the ultimate cause of aggressive behaviour it is still turning up some useful (and interesting) information.

Bonobos are a textbook example of allopatric speciation, a process described in this diagram I pinched from wikipedia

For starters they found that the bits of the bonobo genome that have a corresponding sequence in chimps are 99.6% similar, which is what you’d expect given that they are very closely related. Further, bits of the bonobo genome with a corresponding human sequence are 98.7% similar. Again, this is what you’d expect given that they’re closely related to us but more closely related to chimps.  As such the research is consistent with the typical tale of human evolution, lending it further credence (as if it needed it).

Secondly it shows that bonobos did indeed split from “chimps” ~1 million years ago and that there was no interbreeding between the two groups after this split. This is consistent with the Congo River being the driving cause of their speciation since neither species is a strong swimmer and so could not have crossed the river to interbreed after it had split them.

They also found that around 6% of the bonobo genome had been subject to incomplete lineage sorting (shortened to ILS by lazy bloggers like me). ILS is when an allele of a gene doesn’t follow the population history of a species. It might split from its genetic common ancestor before the species splits from its common ancestor. Alternatively an allele present in the common ancestor of bonobos, “chimps” and humans might only go into the human and bonobo lines by chance (perhaps dying out in the chimp lineage). If you’re still not quite sure what ILS is, P. Z. Myers gives a better explanation of ILS (with pictures!).

The possible paths an allele might take with the percentage of the bonobo genome which took that path. B, C and H refer to bonobos, chimps and humans respectively.

The net product of this ILS is that some parts of the bonobo genome look more like the human genome than they do the chimp genome. Specifically ~1.6% of the genome. Of course, this does more than give ammunition to creationists. It can also be used for something useful, such as working out the influence of natural selection. Since ILS is the product of population diversity anything which reduces this (i.e. selection against a trait) will reduce ILS.

Whilst no research into this has been done yet, the researchers do use an example to show it is possible. They point to a section of human chromosome 3 which contains the genes for various anti-tumour abilities. Since deviation from this form would likely promote tumour growth negative selection would remove such variation and with it ILS. This ILS-free zone is also present in the bonobo genome, although there is a bit more variation left. Might tumours be less of a selection pressure in bonobos?

This ILS analysis also allows them to reconstruct the population size of the common ancestor of chimps and bonobos somehow. This process escapes me, but apparently it also means they can calculate the ratio of the X chromosome to the autosomes (non-sex chromosomes) in the common ancestor. In a typical population this should be 0.75 since half the population (males) have half the number of X chromosomes. In the bonobo/chimp common ancestor it’s actually 0.83, indicating there was 2 females for every one male.

Since this is very similar to the current X chromosome/autosome ratio of bonobos (which is 0.85) the researchers suggest that it has been stable for much longer and the common ancestor with humans and chimps may also have had 2 females for every male. However, there is no actual data behind this inference (other than the bonobo data) so it remains rather speculative and more research is needed.

A venn diagram showing how much of a particular category of genetic material (segmental duplication) is shared between humans, bonobos and “chimps”

Overall this is some top quality research filling a very real gap in our knowledge. It appears to be rigorously done and has already yielded a lot of interesting information on the evolution of the bonobo, not all of which I’ve written about here. On top of that there’s the vast potential for further work to utilise this data and make some fascinating discoveries.

As if that wasn’t enough it’s also rather well written too. I make no bones about the fact genetics is not my strong suit yet I was able to understand most of what they said. Granted there were still a few bits that flew over my head I thought it was very accessible given the subject matter. If you have access to Nature I would thoroughly recommend you go have a read of it yourself.

Prüfer, K., Munch, K., Hellmann, I., Akagi, K., Miller, J., Walenz, B., Koren, S., Sutton, G., Kodira, C., Winer, R., Knight, J., Mullikin, J., Meader, S., Ponting, C., Lunter, G., Higashino, S., Hobolth, A., Dutheil, J., Karakoç, E., Alkan, C., Sajjadian, S., Catacchio, C., Ventura, M., Marques-Bonet, T., Eichler, E., André, C., Atencia, R., Mugisha, L., Junhold, J., Patterson, N., Siebauer, M., Good, J., Fischer, A., Ptak, S., Lachmann, M., Symer, D., Mailund, T., Schierup, M., Andrés, A., Kelso, J., & Pääbo, S. (2012). The bonobo genome compared with the chimpanzee and human genomes Nature DOI: 10.1038/nature11128

—–

*I’ve always wondered whether the insult “troglodyte” comes from the chimpanzee taxonomical name or vice versa.

About these ads