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Gorilla genome sequenced

08 Mar
Kamilah the gorilla
The full genome of Kamilah, a female gorilla from San Diego zoo, has been sequenced. With this one all extant great apes, excepted the bonobo, have been fully sequenced.
The authors propose a divergence of Gorilla from the Pan-Homo branch c. 10 million years ago. But this is based on a most unlikely assumption of Pan-Homo divergence happening only 6 million years ago, when it’s surely of at least 8 million years (and maybe as many as 10 million). A corrected estimate for the Gorilla branch could then be between 13 to 18 million years in fact. 
See on this regard:
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4 Comments

Posted by on March 8, 2012 in Genetics, gorilla, human evolution

 

4 responses to “Gorilla genome sequenced

  1. Etyopis

    March 9, 2012 at 6:50 pm

    “But this is based on a most unlikely assumption of Pan-Homo divergence happening only 6 million years ago”They didn't assume human-chimp time divergence estimates to come up with these dates, you can't use that because the common ancestor of humans, gorillas and chimps appeared before pan-homo, what they did was make an assumption based on fossil evidence of the appearance of orangutans, but actually, they used units of sequence divergence and not years first. I don't think it is possible to argue about units of sequence divergence, what one can possibly argue is the mutation rate/s used to convert the units of sequence divergence into years. And for that, they are saying that a mutation rate of 1 X 10^-9 mutations per base-pair per year, which is based on fossil calibration of human-macaque sequence divergence, gives a time estimate of human-chimp separation of only 3.7 million years and human-gorilla separation of 5.95 million years, but this timetable contradicts the fossil record, so they used the mutation rates derived from “the incidence of disease-causing mutations or sequencing of familial trios” in modern human populations, which is (0.5-0.6) X 10^-9 mutations per base-pair per year, which converts the units of sequence divergence to a time estimate of human-chimp separation of 6 million years and human-gorilla separation of 10 million years. But fossil records show that the orangutan appeared only 12-16 Million years ago, so to accommodate for this, they varied the mutation rate over time, starting with 1 X 10^-9 mutations per base-pair per year for the great apes and to 0.5 X 10^-9 leading to humans, this gives a time window for the split of Humans and Gorillas of 8.5 to 12 million years, and that of Humans and Chimps of 5.5 to 7 million years, this timetable fits with the fossil evidence of the orangutans.

     
  2. Maju

    March 9, 2012 at 8:30 pm

    "But fossil records show that the orangutan appeared only 12-16 Million years ago"…They don't show that orangutan appeared only then: that's an 'ante quam' date: a minimal age (but can be twice as old, no reason to think we know all what is to know about fossil orangutans and their ancestors, right?) In fact, if we are to extrapolate from the corrected dates I propose in the entry, then the orangutan branch should be some 20 Ma old, maybe more. All the mentioned studies on chimpanzees impressed me but the one that did most was the one on New/Old Worlds monkey divergence. By the usual genetic estimates, based on confusions like this one, they "must" have diverged only 80 Ma ago, yet by common sense and the known age of separation of Africa and South America, they must have diverged (this time for real) some 130 Ma ago, when the Atlantic Ocean began to be formed. Otherwise they would need to swim to America across the ocean, what is a total nonsense.

     
  3. Etyopis

    March 10, 2012 at 2:15 am

    "They don't show that orangutan appeared only then: that's an 'ante quam' date: a minimal age (but can be twice as old, no reason to think we know all what is to know about fossil orangutans and their ancestors, right?)"Well, they are saying fossils found before 16 Million Years ago look very different than what is expected from a great ape common ancestor, and for this they are citing a certain anthropologist Walter Hartwig, and this book, Do you have any other sources from Anthropologists that found pre-16 million year primate fossils resembling what is to be a great ape common ancestor? Because, admittedly my knowledge on this is very limited, but I have never seen any?"In fact, if we are to extrapolate from the corrected dates I propose in the entry"I noticed that your low end human-chimp estimate is 1 million years older than their high-end human-chimp estimate, what exactly are you basing this on Maju?

     
  4. Maju

    March 10, 2012 at 3:01 am

    "Do you have any other sources from Anthropologists that found pre-16 million year primate fossils resembling what is to be a great ape common ancestor?"No. I have never before confronted before the issue of orangutan ancestry: only chimpanzee, bonobo, humans and the mentioned issue of new/old world monkey schism. I think that these are enough triangulation references to be skeptic of these conclusions (i.e. diverse data vs. one single data point) but I guess there can be different opinions. "I noticed that your low end human-chimp estimate is 1 million years older than their high-end human-chimp estimate, what exactly are you basing this on Maju?"Have you read my references (links at bottom of article)? On all that:1. Caswell 2008 pondered that, if the Pan-Homo divergence date is of 8 Ma (instead of his reference of 7 Ma) then the bonobo-chimp divergence would be coincident with the formation of the Congo river as such c. 1.5-2 Ma (the later date actually seems to demand a Pan-Homo divergence date of 10 Ma).2. Zsurka 2010 offered some data on Bonobo mtDNA, which extrapolated to the Pan internal and external divergence (by me – read please), appear to confirm Caswell's claims. 3. Wilkinson 2010 found that:We use the posterior distribution from the fossil analysis as a prior distribution on node ages in a molecular analysis. Sequence data from two genomic regions (CFTR on human chromosome 7 and the CYP7A1 region on chromosome 8) from 15 primate species are used with the birth–death model implemented in mcmctree in PAML to infer the posterior distribution of the ages of 14 nodes in the primate tree. We find that these age estimates are older than previously reported dates for all but one of these nodes.These estimates also allow Toumaï (S. Tchadiensis, c. 7 Ma.) to be a human ancestor or otherwise in the branch leading to Homo and not to Pan. And then you also have the problem with the age of Simiiformes (monkeys and great apes) overall being too recent to allow for new world/old world divergence without impossible migrations through the ocean. This is again an artifact of taking the fossil record at face value and using systematically too recent molecular clock estimates.It's a systematic problem: a vicious circle of positive academic acritical feedback (scholasticism in other words).

     

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