Gene Expression

Evolution (human) happens….

One of the things that really pisses me off about the Evolution-Creation “debate” is that it uses up oxygen that could be profitably allotted to documenting the tsunami of data emerging out of the “post-genomic” era. The actual examination of evolution is not just an academic exercise, as much of the recent work coming out of laboratories deals with humans.1 For example, Dienekes points me to this preprint in The American Journal of Human Genetics, Spread of an inactive form of caspase-12 in humans due to recent positive selection:

…There is strong evidence for positive selection from low diversity, skewed allele frequency spectra and the predominance of a single haplotype. We suggest that the inactive form of the gene arose in Africa ~100-500 thousand years ago (KYA) and was initially neutral or almost neutral, but that positive selection beginning ~60-100 KYA drove it to near-fixation. We further propose that its selective advantage was sepsis resistance in populations that experienced more infectious diseases as population sizes and densities increased.

Dienekes provides a map that shows the distribution of the alleles:

In other news, Dienekes again points me to something I’ve been keeping track of, the argument by Alan Templeton that Out-of-Africa is rejected by multiple loci analysis. That is, Out-of-Africa is predicated in large part (though not exclusively) on uniparentally inherited neutral markers, mtDNA and nonrecombinant Y. Leaving aside whether these are neutral (some lineages of mtDNA might actually be more fit than others for a variety of reasons), other loci can give different results, which is what Templeton uses as the linchpin for his hypothesis. This post by Carl Zimmer has an image which graphically illustrates Templeton’s model. Basically it shows a trellis, where alleles shift between populations and ancestry is reticulated between different homonid lineages.

This breaks out of the old Multiregionalism vs. Out-of-Africa dichotomy, it is not simple and evades a general solution to questions of modern human origins (I suspect that the balance of evidence will point to mostly African ancestry, with a residue of advantageous alleles from other lineages, some worldwide in distribution and some localized).2 Templeton’s model is not the only one out there that attempts to draw on the wealth of information that genomics offers in reconstructing gene phylogenies and inferring from that to population phylogeny (he probably uses too few loci according to an acquaintance of mine). It is often stated that the homonid family tree is a bush, if these models pan out the origin of modern humans may resemble brambles and knots far more than the current consensus.

Related: Out-of-Africa again & again…again, Dawkins reconsiders Out of Africa? and The Middle Model and Endless Forms Most Continuous.

1 – Humans are a very important “model organism,” as studying human genetics allows you to make a good argument to the NIH as well as the NSF when it comes to getting grant money.

2 – What’s your s?. Remember, selection happens.


  1. #1 budak
    February 3, 2006

    The culturewars also sadly distract some of the best minds in science and biology (not too mention politicians) from vital work in taxonomy, systematics, ecological studies as well as conservation advocacy…. meanwhile, the crusading troops continue to lap up Welles’ 10 icons even as a mountain of new research is generated each day that corroborates evolutionary theory from both field and molecular observations.

  2. #2 Peter Frost
    February 5, 2006

    Templeton’s model is based on the following assumptions:

    1. New mutations arise at a fairly constant rate.

    2. Strongly polymorphic gene loci are thus very old. Weaky polymorphic loci are conversely very young.

    3. Once the mutation rate is established, these polymorphisms can provide a yardstick for measuring the age of our species.

    There are two serious problems with this model:

    1. Many, perhaps most of the polymorphisms he uses are influenced by natural selection. “Purifying” (or normalizing) selection makes polymorphisms look younger than they really are. Conversely, heterozygote advantage makes polymorphisms look older than they really are.

    2. The mutation rate at autosomal loci is much slower than at mtDNA loci. The margin of error in calculating the age of an autosomal polymorphism is thus correspondingly larger. Polymorphisms that, for random stochastic reasons, look younger than their real age, don’t attract the attention of researchers — because there is too little diversity to make any study worthwhile; however, polymorphisms that look older than their real age receive much more attention — because there’s a lot more diversity to study.

    There is thus an observational bias in the literature that provides much more data on gene loci that look older than they really are.

    Templeton could have corrected this bias by doing original research on loci with very little diversity. Instead, he has simply harvested the findings of other researchers — while not informing the reader about any biases that might result.