Jeff Rogers, Baylor Human Genome Sequencing Center - “Linking the fossil record with comparative primate genomics”
Recently moved, so doesn't have a lot of results to discuss. Thus, this will be from the basis of a primatologist. What are the implcations of next gen sequencing for interpreting genomic comparison? Obviously it's huge.
First non human primate = chimpanzee (our closest species “relative”). Second was Rhesus Macaque (Single most important for biomedical research.)
Just about all of the species that are representative on the chart, (Raaum et al, 2005, J. Hum evolution 38, 237-257), are now done or slated to be sequenced soon.
Talk about baboons for a while – there are a lot of old world monkeys related to baboons, and all of them will be sequenced. There are desert baboons, plains and grassland baboons and rainforest baboons. [Ok, this is a lot of baboon information. And I've never seen so many baboon pictures in a presentation.] There are high mountain primates too, and they apparently eat grass – and are closely related to baboons. [Who knew.]
And now macaques – there are 22 species.. I think only two of them are being sequenced.
Dr. Rogers is suggesting we re-think how we decide which species to sequence, to best use the next-gen sequencing technology. Pick a few “focal species”, and then do all of the other species too. This would help with closely related genomes. It would help us get more information about genome evolution and dynamives, more information about ancestral genomes, and finally, more benefits to biomedical research. Discovery of novel animal models for studies of disease and normal functional variations.
This is, apparently, not a new proposal. They did a similar concept for Rhesus monkeys and Orangutangs. [So if they're already doing it, what is he proposing that's new?] What he's suggesting is to expand the bredth and depth of the sequencing. [ok. Fair enough.]
So, back to baboons. The olive baboon is the main reference baboon, but the others should all be done.. they're different in habitat and behaviour.
At baylor: do reference baboon to 3x sanger, 4x 454. Lots more statistics presented. Take away message: better coverage = better sequence information. You can also get good results by mixing sanger with 454.
[I lost focus here... I didn't see much worth writing down.]
Moving on to evolution and species... When you sequence another primate, you don't get a look at the ancestor. [dude... evolution 101.] Talking about some of the other species that have died out – fossil species.
Now we're on to different motion. Some monkeys walk on all four, putting weight on the palms on their hands. Others (apes) walk mainly on the feet? [I'm not so sure what this is about.] I think the point is that there are some ancestral monkeys that walk differently than any of the other living apes and monkeys. [Interesting, but highly unrelated to anything else at this conference.]
It's controversial: human ancestors were never knuckle walkers, unlike all other chips, gorillas, etc.. thus, knuckle walking evolved twice, and humans evolved bipedal motion separately without a knuckle walk intermediary.
Conclusion: there is a lot of diversity among primate, both living and extinct. We should study it to help understand our own biomedical applications.
My Comments: The wrong talk for this conference, but a nice diversion. The content was provided slowly enough that everyone could follow, which made for easy note taking. Kinda like an undergrad lecture in primatology. Still, I'm really at a loss to explain why anything presented here really is a consequence of the advent of new sequencing technology.
First non human primate = chimpanzee (our closest species “relative”). Second was Rhesus Macaque (Single most important for biomedical research.)
Just about all of the species that are representative on the chart, (Raaum et al, 2005, J. Hum evolution 38, 237-257), are now done or slated to be sequenced soon.
Talk about baboons for a while – there are a lot of old world monkeys related to baboons, and all of them will be sequenced. There are desert baboons, plains and grassland baboons and rainforest baboons. [Ok, this is a lot of baboon information. And I've never seen so many baboon pictures in a presentation.] There are high mountain primates too, and they apparently eat grass – and are closely related to baboons. [Who knew.]
And now macaques – there are 22 species.. I think only two of them are being sequenced.
Dr. Rogers is suggesting we re-think how we decide which species to sequence, to best use the next-gen sequencing technology. Pick a few “focal species”, and then do all of the other species too. This would help with closely related genomes. It would help us get more information about genome evolution and dynamives, more information about ancestral genomes, and finally, more benefits to biomedical research. Discovery of novel animal models for studies of disease and normal functional variations.
This is, apparently, not a new proposal. They did a similar concept for Rhesus monkeys and Orangutangs. [So if they're already doing it, what is he proposing that's new?] What he's suggesting is to expand the bredth and depth of the sequencing. [ok. Fair enough.]
So, back to baboons. The olive baboon is the main reference baboon, but the others should all be done.. they're different in habitat and behaviour.
At baylor: do reference baboon to 3x sanger, 4x 454. Lots more statistics presented. Take away message: better coverage = better sequence information. You can also get good results by mixing sanger with 454.
[I lost focus here... I didn't see much worth writing down.]
Moving on to evolution and species... When you sequence another primate, you don't get a look at the ancestor. [dude... evolution 101.] Talking about some of the other species that have died out – fossil species.
Now we're on to different motion. Some monkeys walk on all four, putting weight on the palms on their hands. Others (apes) walk mainly on the feet? [I'm not so sure what this is about.] I think the point is that there are some ancestral monkeys that walk differently than any of the other living apes and monkeys. [Interesting, but highly unrelated to anything else at this conference.]
It's controversial: human ancestors were never knuckle walkers, unlike all other chips, gorillas, etc.. thus, knuckle walking evolved twice, and humans evolved bipedal motion separately without a knuckle walk intermediary.
Conclusion: there is a lot of diversity among primate, both living and extinct. We should study it to help understand our own biomedical applications.
My Comments: The wrong talk for this conference, but a nice diversion. The content was provided slowly enough that everyone could follow, which made for easy note taking. Kinda like an undergrad lecture in primatology. Still, I'm really at a loss to explain why anything presented here really is a consequence of the advent of new sequencing technology.
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