Bonobo Genome Sequencing and Hominid Evolution

I came across a 3 year old paper for the sequencing of the bonobo genome. I haven’t really kept up with the latest news on hominid genome sequencing, so I was a bit surprised to read that the bonobo genome appears to be the last of the ape species to get a high quality genome sequence. In this case, a long read genome sequence. I also like rooting for the underdog, so it’s nice to see the often neglected bonobo get its time in the spotlight.

https://www.nature.com/articles/s41586-021-03519-x

For those who are unfamiliar with with how genomes are sequenced (i.e. normal people), there have been 3 major generations of sequencing technologies. All of these technologies chop up many copies of the same genome into small chunks, and then sequence those small chunks. They then use the overlaps of those short sequences to reconstruct the whole genome.

Gen 1: Sanger sequencing, 700 base chunks, about 400 chunks sequenced at a time.
Gen 2: Illumina sequencing, 300 base chunks, hundreds of millions to billions of chunks sequenced at a time.
Gen 3: PacBio/Nanopore long read sequencing, 10,000 base chunks, tens or hundreds of millions of chunks sequenced at a time.

For a while, accuracy is what was holding Gen 3 sequencing back. Many of those issues have been solved and it is much more accurate than it used to be, but still slightly less accurate than Gen 1 and 2. The big advantage is the length of the reads which are orders of magnitude longer than those on older technologies. This allows for far fewer gaps in the reconstruction of the whole genome.

With the high quality bonobo genome and the other existing ape genome sequences the authors of the bonobo paper were able to align 76% of all the ape genomes, including human (if I am reading the paper correctly). This means we have a direct comparison of all those genomes over 3/4 of those genomes. To me, that’s a pretty big achievement.

These alignments mean that the authors were able to come to some very specific and interesting conclusions about the evolution of all apes (although focused mainly on bonobos). This includes patterns of incomplete lineage sorting, regions of the genome possibly under selection, examples of gene duplication and subsequent divergence, and a whole host of other details.

I’m three years late to the table, but found the paper interesting enough that I thought I would bring it to the forum’s attention. I wouldn’t be surprised to find other papers that dive deeper into this data, or perhaps more recent long read sequences for the other ape species.

Enjoy.

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A few press articles that are more accessible for the non-scientist:

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Thanks for this. Even those of us with scientific background, but not in biology may have difficulty understanding these articles. I am wondering what the implications are of a higher “proportion of incomplete lineage sorting”? Is it that the branches of the evolutionary tree with bonobos, chimpanzees and humans may be more complicated than we think now? Maybe with an undiscovered species thrown in?

I would describe it as biology is as complicated as we think. Genetic variation doesn’t necessarily go away when a speciation event occurs. You will still have many alleles for a given gene on either side of a speciation event if there is not a bottleneck, and it might take quite some time for those alleles to either move towards fixation or disappear within the lineage. Incomplete lineage sorting is something we expect to see, and I don’t think it requires invoking an undiscovered species.

This website looks to have a good explanation for how incomplete lineage sorting works (although they don’t mention bonobos, those underdogs of the ape world):

https://www.thetech.org/ask-a-geneticist/articles/2019/incomplete-lineage-sorting/

However, I think many biologists can fall into the trap of relying on a simple view of speciation and genetics. I have done it a few times myself.

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Good article, especially for those of us using gummy bears to model genetics.

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