Patterns of autosomal divergence between the human and chimpanzee genomes support an allopatric model of speciation

A few days ago I wrote about the hypothesis of complex speciation between humans and chimps, and today I’ll briefly discuss another paper on the human / chimp speciation:

Patterns of autosomal divergence between the human and chimpanzee genomes support an allopatric model of speciation

Matthew T. Webster, Gene 443 70-75, 2009


There is a large variation in divergence times across genomic regions between human and chimpanzee. It has been suggested that this could partly result from selection against ancestral gene flow between incipient species in regions of the genome containing genetic incompatibilities. It is possible that such barriers to gene flow could arise in specific genes or in chromosomal inversions. I analysed patterns of lineage sorting that occur between human, chimpanzee and gorilla genomic sequences by examining divergent site patterns in > 18 Mb genomic alignments. I develop a method to normalise site patterns by the mutational spectrum to minimise errors caused by misinference caused by recurrent mutation. Here I show that divergence times appear to be uniform between coding and noncoding sequences and between inverted and non-rearranged portions of chromosomes. I therefore find no evidence to support the large-scale accumulation of genetic incompatibilities at speciation genes or chromosomal inversions in the ancestral population of humans and chimpanzees. In addition, site patterns that are discordant with the species tree occur more frequently in regions with high human recombination rates. This could indicate the action of selective sweeps in the ancestral population, but could also be indicative of increased rates of homoplasy in these regions. I argue that these observations are compatible with a neutral allopatric model of speciation.

Models of speciation

Speciation happens when gene flow stops between one group of a species and another (and doesn’t start again later or we get something like the hybridization scenario I wrote about in my earlier post).

There are different ways this can happen.  For instance, one group might somehow find itself geographically isolated from the other – e.g. find themselves on the other side of a large river – effectively isolating the group from the rest of the species.  This is know as allopatric speciation (or depending on exactly how this plays out, peripatric speciation).

In this scenario, the speciation happens at the time where the groups are isolated.  From that point and onwards the groups are essentially different species, since gene flow has stopped.  It will take some time before the groups are incapable if inter-breeding, but unless they actually merge again at some time before then, the time of the speciation event is the time the groups get separated.

That doesn’t mean that the genomic divergence time between the two species matches the time back to the speciation event.  Some individuals in one of the groups might be closer related to individuals in the second group than the other individuals in the first group for a few generations.  So the genetic distance between the two species is a bit larger than the “species distance”.  Add in recombination and the picture gets a bit more complex.

Still, we can talk about a specific point in time where the speciation time occurred and we have a mathematical model – the coalescent model – of the genome distance between the two species that depends on this time and the population genetics in the ancestral species before then.

The speciation can also be caused by “genetic isolation”.

If a new mutation enters the group, where homozygotes for either the wildtype or the mutants are fitter than the heterozygotes, then the group will tend to split into two.  The mutants and the wildtypes.

Without recombination, there wouldn’t be much difference in the genomic distance between the two resulting species.  The heterozygotes would be selected against and the two homozygotes would diverge.

With recombination, again the situation gets a bit more complicated.  The heterozygotes would still be selected against, but assuming heterozygoes still manage to mate from time to time, you would get homozygote offsprings of heterozygoes who are just as fit as other homozygotes.

Because there is selection against heterozygoes you will tend to split the species into two – the two homozygoes – but the divergence will be deeper at the locus of the mutation than it will in the rest of the genome.

We call such a locus a “speciation gene” and candidates for such genes are functional genes (where we expect some selection) or structural variations such as inversions.

Back to the paper…

What Webster looks at in this paper is the patterns of divergence – especially deep coalescence events with incomplete lineage sorting where we observe sites grouping human and gorilla or chimp and gorilla – in the genome.

He then looks at these patterns in genes, introns, inversions … the candiates for speciation genes, to see if these looks like they are more divergent than the rest of the genome.  If so, then the speciation between humans and chimps could be caused by speciation genes.  If not, then the speciation could be allopatric (the same “species divergence” throughout the genome, but of course not the exact same sequence divergence since the coalescence times will still vary along the genome).

Long story short, he doesn’t find any evidence for deeper divergence these places so we cannot rule out an allopatric speciation here.

He does find a correlation between recombination rate and deep divergence, which can be explained by either increased mutability in regions of high recombination or selective sweeps in the ancestral species.  The latter is much more interesting, really, but we cannot rule out the first explanation so I won’t comment much on this here…


I do have a slight problem with the analysis in the paper, though.

It seems to me that by just looking at differences in divergence time between genes and the rest of the genome – or between inversions and the rest of the genome or whatnot – is not particularly powerful for detecting speciation genes.

When comparing general groups like this, it seems to me that a few speciation genes would simply be drowned out by the larger number of “plain old genes”.  So all the analysis is really saying is that there isn’t a large number of speciation genes between humans and chimps, not that there are none.

The paper doesn’t claim any more than this either, but it would be interesting to work out just how large a fraction of the genes would have to be speciation genes – and how large a difference between the divergence of speciation genes and the rest of the genome there has to be – to be able to distinguish between the two scenaria with this analysis.

I haven’t done the math yet, but I plan to when I get the time…

Webster, M. (2009). Patterns of autosomal divergence between the human and chimpanzee genomes support an allopatric model of speciation Gene, 443 (1-2), 70-75 DOI: 10.1016/j.gene.2009.05.006

Author: Thomas Mailund

My name is Thomas Mailund and I am a research associate professor at the Bioinformatics Research Center, Uni Aarhus. Before this I did a postdoc at the Dept of Statistics, Uni Oxford, and got my PhD from the Dept of Computer Science, Uni Aarhus.

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