The Bonobo genome has been sequenced!

steddyeddy

The max plank institute for evolutionary anthropology has sequenced the bonobo genome. Its just an early study with further sequencing needed but it has announced some interesting findings.

• Bonobos and chimps have 99.6% sequence similarity
• Bonobos and humanshave 98.7% sequence similarity
• The split of bonobo and chimpanzee is confirmed to have approx. 1 million years ago, with no inbreeding occurring
• 6% of the bonobo genome has evidence of incompleteLineage sorting(when an allele does not match the population history of a species)
  • This has lead to the observation that ~1.6% of the bonobo genome is more similar to humans than chimpanzees

Link here.

Birdnuts

steddyeddy wrote: »

The max plank institute for evolutionary anthropology has sequenced the bonobo genome. Its just an early study with further sequencing needed but it has announced some interesting findings.

• Bonobos and chimps have 99.6% sequence similarity
• Bonobos and humanshave 98.7% sequence similarity
• The split of bonobo and chimpanzee is confirmed to have approx. 1 million years ago, with no inbreeding occurring
• 6% of the bonobo genome has evidence of incompleteLineage sorting(when an allele does not match the population history of a species)
  • This has lead to the observation that ~1.6% of the bonobo genome is more similar to humans than chimpanzees

Link here.

The split from Chimps is alot longer in time then I had thought given the proximity of their populations in the Congo Rainforest - hasn't the Congo river changed course a number of times in that period

Mickeroo

Great news. Are Bonobo's genetically closer to humans overall then?

steddyeddy

Birdnuts wrote: »

The split from Chimps is alot longer in time then I had thought given the proximity of their populations in the Congo Rainforest - hasn't the Congo river changed course a number of times in that period

Hey birdnuts sorry for the late reply. I had to get out my old zoology text book because I forgot exactly the words to use when describing barriers to gene flow that lead to speciation. Well as you stated theres no habitat isolation between the two species to prevent breeding. Nor is there mechanical isloation due to morphological differences. If I had to guess I would have said that behavioral isolation occured between bonobos and chimps. The mating frequency and initiation of mating are quite different in both species I would have said this played a large part in keeping the genome seperate.

steddyeddy

Mickeroo wrote: »

Great news. Are Bonobo's genetically closer to humans overall then?

Well I dont think its clear from the sequencing as of yet. What is clear is that one part of their genome is more similar to ours than the same part of a chimps genome is to ours (sorry Ive confused myself there). What that part of the genome codes for will be interesting to find out. I would guess it would be something to do with the langauge centre of the brain.

darjeeling

Mickeroo wrote: »

Great news. Are Bonobo's genetically closer to humans overall then?

Bonobos are overall much closer to chimpanzees than to humans. The phenomenon of incomplete lineage sorting (ILS) means that they are more similar to humans at a small percentage of sites in the genome, but for the great majority of sites they are closer to chimpanzees.

ILS is a well modelled aspect of population genetics, and is predicted (and seen) to increase in effect when you have speciation events occurring at relatively short evolutionary time intervals, and where the population sizes between speciation events are high. Newly speciated populations can, in these circumstances, retain multiple alleles of a gene that arose prior to speciation. Subsequent speciation events and differential loss of alleles can lead to unusual patterns of allele sharing between species that do not conform to the overall relationship of the species.

For bonobos, chimps and humans, imagine the ancestral population of all three having alleles A and B at gene X. Proto-humans split off, and they and the proto-chimp/bonobos both retain both alleles. Later, the chimp/bonobo split happens, still at a time when both A and B are in the population. Later still, allele A is lost from chimps and allele B from bonobos through genetic drift. Humans happen also to lose allele B through drift. Now, if you make a phylogenetic tree for gene X you find that humans are closest to bonobos. If you do it for the genome as a whole, though, you find bonobos and chimps to be closest.

Mickeroo

^Yeah, I figured Bonobos are closer to chimps than they are to us, I meant are they closer to humans than chimps are.

steddyeddy

darjeeling wrote: »

Bonobos are overall much closer to chimpanzees than to humans. The phenomenon of incomplete lineage sorting (ILS) means that they are more similar to humans at a small percentage of sites in the genome, but for the great majority of sites they are closer to chimpanzees.

ILS is a well modelled aspect of population genetics, and is predicted (and seen) to increase in effect when you have speciation events occurring at relatively short evolutionary time intervals, and where the population sizes between speciation events are high. Newly speciated populations can, in these circumstances, retain multiple alleles of a gene that arose prior to speciation. Subsequent speciation events and differential loss of alleles can lead to unusual patterns of allele sharing between species that do not conform to the overall relationship of the species.

For bonobos, chimps and humans, imagine the ancestral population of all three having alleles A and B at gene X. Proto-humans split off, and they and the proto-chimp/bonobos both retain both alleles. Later, the chimp/bonobo split happens, still at a time when both A and B are in the population. Later still, allele A is lost from chimps and allele B from bonobos through genetic drift. Humans happen also to lose allele B through drift. Now, if you make a phylogenetic tree for gene X you find that humans are closest to bonobos. If you do it for the genome as a whole, though, you find bonobos and chimps to be closest.

According to the paper by nature

We find that more than three per cent of the human genome is more closely related to either the bonobo or the chimpanzee genome than these are to each other.

It would still be relevent to see what part of the genome was closest to ours. Im not disagreeing with what your saying but the implication could be that on some level we are more phenotypically similar to bonobos than we are to chimps.

darjeeling

Mickeroo wrote: »

^Yeah, I figured Bonobos are closer to chimps than they are to us, I meant are they closer to humans than chimps are.

Ah, right, sorry. I think both chimps and bonobos ought to be equidistant from humans, given that both evolved from a common ancestor that lived several million years after splitting from our line. ILS may mean that one or other is a small fraction of a percent closer to us, but it's unlikely to be very significant.

[edit] Oh, and if chimps or bonobos have evolved at a different rate subsequent to diverging, that would affect how relatively close they both are to humans too

steddyeddy

Mickeroo how does the sopa law work here in regards to posting whole scientific papers here if the papers free?

darjeeling

steddyeddy wrote: »

According to the paper by nature

It would still be relevent to see what part of the genome was closest to ours. Im not disagreeing with what your saying but the implication could be that on some level we are more phenotypically similar to bonobos than we are to chimps.

There may be a few phenotypic homologies between human and bonobo that aren't shared with chimps, and a few in common between chimps and humans to the exclusion of bonobos, but I wouldn't think there would be many.

From memory, when we saw the same effect happening for the gorilla / chimp / human genome comparisons, ILS declined nearer to genes. This is expected, given that genes are under stronger selection than less functionally important intergenic DNA.

steddyeddy

darjeeling wrote: »

There may be a few phenotypic homologies between human and bonobo that aren't shared with chimps, and a few in common between chimps and humans to the exclusion of bonobos, but I wouldn't think there would be many.

From memory, when we saw the same effect happening for the gorilla / chimp / human genome comparisons, ILS declined nearer to genes. This is expected, given that genes are under stronger selection than less functionally important intergenic DNA.

Since non coding dna is in part responsible for expression of other genes it wouldlnt be unreasonable to think that we have similarities even in our epigenetic controls. Im not implying relevence from a taxonomic standpoint Im just curious as to what part of the genome the 1.6% similarity belongs to. The researchers said they are looking for phenotypic expression of genes.

In addition, many of the regions that overlap genes may eventually help us understand the genetic basis of phenotypes that humans share with one of the two apes to the exclusion of the other.

steddyeddy

Great picture detailing the areas occupied by different species within the genus pan. Interesting the way the river splits certain species and sub species of but is this enough on its own to explain the divergence of the species?

Mickeroo

steddyeddy wrote: »

Mickeroo how does the sopa law work here in regards to posting whole scientific papers here if the papers free?

Not to sure to be honest, if the paper is free I wouldn't think its a problem but maybe just post a few paragraphs and link to full the paper just to be safe.

aidoh

Just to clear things up a bit further regards the 'which is closer to humans question', both chimpanzees and bonobos are our closest living relatives, since they are sister species.
Just thought I'd add that in since people often make the mistake of assuming that genetic similarity means that one or the other is 'more closely related to' ourselves.
It's worth saying because, being a zoology forum, this kind of confusion is bound to come up again.