December 21, 2012

Hominid speciation: sudden or gradual?

It depends apparently: bonobos may have diverged quite suddenly while in other cases, including the Pan-Homo split, the process of speciation appears to have been more gradual.

Thomas Mailund et al., A New Isolation with Migration Model along Complete Genomes Infers Very Different Divergence Processes among Closely Related Great Ape Species. PLoS ONE 2012. Open access LINK [doi:10.1371/journal.pgen.1003125]

Abstract

We present a hidden Markov model (HMM) for inferring gradual isolation between two populations during speciation, modelled as a time interval with restricted gene flow. The HMM describes the history of adjacent nucleotides in two genomic sequences, such that the nucleotides can be separated by recombination, can migrate between populations, or can coalesce at variable time points, all dependent on the parameters of the model, which are the effective population sizes, splitting times, recombination rate, and migration rate. We show by extensive simulations that the HMM can accurately infer all parameters except the recombination rate, which is biased downwards. Inference is robust to variation in the mutation rate and the recombination rate over the sequence and also robust to unknown phase of genomes unless they are very closely related. We provide a test for whether divergence is gradual or instantaneous, and we apply the model to three key divergence processes in great apes: (a) the bonobo and common chimpanzee, (b) the eastern and western gorilla, and (c) the Sumatran and Bornean orang-utan. We find that the bonobo and chimpanzee appear to have undergone a clear split, whereas the divergence processes of the gorilla and orang-utan species occurred over several hundred thousands years with gene flow stopping quite recently. We also apply the model to the Homo/Pan speciation event and find that the most likely scenario involves an extended period of gene flow during speciation.

8 comments:

  1. "while in other cases, including the Pan-Homo split, the process of speciation appears to have been more gradual".

    I'm sure you will recall the several occasions when I have tried to point that out to you.

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    Replies
    1. No, I don't. And anyhow I'm sure that you said without supporting evidence, so it was worthless chatter and not interesting stuff. Sadly you're too much into that: "I think, I believe, I told you"...

      Your truth not, Truth.
      And come with me in search of it.
      Keep yours for yourself
      .
      (Antonio Machado).

      Delete
  2. "And anyhow I'm sure that you said without supporting evidence, so it was worthless chatter"

    Rubbish. I provided supporting evidence but, as usual when the evidence doesn't fit your belief, you insisted the evidence was wrong. I've got to head off for a wedding now so I'll return with the paper tomorrow. And besides which, the idea that species instantly separate is so obvioulsy unlikely that I'm surprised a person as intelligent as you seem to be can consider the possibility for a moment.

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    1. "And besides which, the idea that species instantly separate is so obvioulsy unlikely"...

      First: I never said that.

      Second: there is at least one example: the Pan genus. Bonobos appear to have separated almost "instantly" according to this very paper, what is consistent to the notion hat they diverged because they became isolated at the formation of the Congo River some 1.3 million years ago.

      Also notice that besides the Pan-Homo case, only imperfect quasi-speciation cases are reported: two types of gorillas and two types of orangutans. So the Pan-Homo case is at the very least not the common case (because gorillas and orangutans may still re-merge with patience and the appropriate ecological conditions - if they don't go extinct first).

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  3. "Bonobos appear to have separated almost 'instantly' according to this very paper, what is consistent to the notion hat they diverged because they became isolated at the formation of the Congo River some 1.3 million years ago".

    I thought that the reason for that rapid speciation was obvious, as you've pointed out. So I didn't bother mentioning it.

    " I provided supporting evidence but, as usual when the evidence doesn't fit your belief, you insisted the evidence was wrong".

    So here is the abstract to the paper that I'm sure I have brought to your attention more than once:

    http://www.ncbi.nlm.nih.gov/pubmed/16710306

    Hopefully you can access the whole paper somewhere. Here is a criticism and reply:

    http://genepath.med.harvard.edu/~reich/2008_Nature_Wakeley_Correspondence.pdf

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    Replies
    1. Why do you quote yourself and reply to your own quote?

      In any case thanks for the links. I'm sure that they are very interesting once I find that "somewhere" where I can access the paper.

      Delete
    2. In the accessible review paper there are things I do not understand, notably why if the age estimate of HC sites is found to be c. 85% of the raw autosomal estiamate the authors appear to claim an "speciation time" of c. 75% only. Shouldn't be the speciation time at the most the time of the most recent genetic exchange? That or earlier because, as they toy with, different but closely related species can still exchange genetic material via hybrids (introgression and such). What is an species after all?!

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  4. "Why do you quote yourself and reply to your own quote?"

    I wanted to provide a context for the paper.

    "Shouldn't be the speciation time at the most the time of the most recent genetic exchange?"

    As I understand things the fact that the speciation time appears to be spread out is the main point of the paper. Mind you I read it years ago when it first came out.

    "What is an species after all?!"

    Quite. And that problem holds for Neanderthals, Denisovans and modern humans.

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