Reassessing the time at which human-chimp lineages diverged

A new statistical calculation called the hidden Markov model has been applied to four regions of the human, chimpanzee and gorilla genomes as reported in the PLoS Genetics journal.

But, before I jump into a discussion of the implications of this paper, let me explain to those unfamiliar with the hidden Markov model that it was,

“developed in the 1960s and originally applied to speech recognition.”

The calculation takes observable sequences, such as DNA from several genomes in this case, and seeks to fish out hidden parameters. It does this by isolating common genetic patterns from outliers throughout the genomes being compared. Of which the amount of difference and similarities can help calibrate a molecular clock. If you are curious about this statistical test, please check out Wikipedia’s entry on hidden Markov models.

In the paper, “Genomic Relationships and Speciation Times of Human, Chimpanzee, and Gorilla Inferred from a Coalescent Hidden Markov Model,” the authors analyze the results from these hidden Markov model calculations and claim their findings shifts the gap between human-chimpanzee divergence from 5-7 million years ago to around about 4 million years ago. Furthermore, they claim they have evidence that,

“it took only 400,000 years for humans to become a separate species from the common chimp-human ancestor.”

The abstract, if you care,

“The genealogical relationship of human, chimpanzee, and gorilla varies along the genome. We develop a hidden Markov model (HMM) that incorporates this variation and relate the model parameters to population genetics quantities such as speciation times and ancestral population sizes. Our HMM is an analytically tractable approximation to the coalescent process with recombination, and in simulations we see no apparent bias in the HMM estimates. We apply the HMM to four autosomal contiguous human–chimp–gorilla–orangutan alignments comprising a total of 1.9 million base pairs. We find a very recent speciation time of human–chimp (4.1 ± 0.4 million years), and fairly large ancestral effective population sizes (65,000 ± 30,000 for the human–chimp ancestor and 45,000 ± 10,000 for the human–chimp–gorilla ancestor). Furthermore, around 50% of the human genome coalesces with chimpanzee after speciation with gorilla. We also consider 250,000 base pairs of X-chromosome alignments and find an effective population size much smaller than 75% of the autosomal effective population sizes. Finally, we find that the rate of transitions between different genealogies correlates well with the region-wide present-day human recombination rate, but does not correlate with the fine-scale recombination rates and recombination hot spots, suggesting that the latter are evolutionarily transient.”

You maybe asking, how did they do this? Molecular clocks, friends, which I briefly mentioned above. Molecular clocks are effectively patterns in mutations in genomes that we expect to stay fairly consistent throughout evolutionary time. Previous molecular clocks, as reported on Time Tree, average for the time of nuclear divergence between human and chimpanzee lineages to be around 5.56 million years ago. The new hidden Markov model recalibrates, narrowing several parameters such as the time at which humans diverged from other ape lineages.

The following figures from the paper best portrary the results. You will see errors above the points plotted, and those are associated with the estimatation calculated via hiden Markov model. On the x-axis targets 1 refers to Chromosome 7, targets 106 to Chromosome 20, targets 121 to Chromosome 2, and 122 to Chromosome 20. The first is a population genetics parameter for time of divergence and the second time of speciation.

Divergence times for human-chimp lineages

Note how a, or human chromosomes, sampled, consistently stays around 4mya.

Speciation times for human-chimp divergence

Note how t1, or human chromosomes, compared, stays around 4mya, too. While the error bars are large, the study is pretty convincing. This study is also interesting.

It shows us that up until 4 million years ago, there was a lot of genetic introgression but a complete cessation of gene flow occurred abruptly. As John Lynch, from Stranger Fruit, points out,

“The age of 4.1 million years would apparently put the split during the time of such taxa as Australopithecus anamensis, A. afarensis and Kenyanthropus platyops. It will be interesting to see how this affects our current understanding of hominid evolution.”

Some news reports about this paper:

4 thoughts on “Reassessing the time at which human-chimp lineages diverged

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  2. This is an amazing study. Thinking about the implications, especially with all the hominids we’ve come to note in the fossil record, is going to take some cunning skills.

    However, without devling too deeply, we can assume that the Last Common Ancestor (LCA) of Humans and Chimps diverged during a time when Africa was seething with hominids. With Sahelanthropus, among others, dating as far back as 7 million years, this means that our LCA did not split into independent species until well after the appearance of certain hominid species. What was it about the African environment, between 1-7 million years ago, that enabled so many bipedal primates to emerge? Was it an overall trend towards a dryer climate? Was it increased competition between Hominid Species?

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