More on adapting to climate
In a previous post I mentioned this review of a recent PLoS Genetics paper. I still haven’t read the actual paper, I am ashamed to admit, but we will read it for a journal club at BiRC next week. Anyway, this morning I read another interesting review, again at Genetic Future: Climate genes: positive or balancing selection?
I should probably bring it to our journal club.
The points in this review is that a linear relationship between climate and gene frequency would only be linear if we ignored the history of the human diaspora out of Africa. The time where selection has affected the genes varies a lot from South East Asia, where humans got to early, to South America, where humans got to late.
Would this type of selection actually result in a neat linear trend, like that seen for the RAPTOR gene? Well, it might, if the timing was just right, but it’s by no means a necessary outcome. There are at least three variables in play here, each of which will have some effect on the current frequency of a positively selected allele: the strength of selection, the starting frequency of the allele in that population, and the amount of time the population has existed in its current environment. For positive selection to result in a clean linear correlation between allele frequency and a climate variable, the latter two factors would have to have had a negligible impact, so that most of the variation is determined by selection intensity.
I think that’s pretty unlikely given what we know about human population history: native Americans, for instance, are the descendants of a cold-adapted population living in Siberia that only relatively recently moved down into the warmer climates of central America; selection has not yet had much time to act in these populations. In contrast, humans in Southern Asia have been in their current climate much longer, giving selection more time to do its work. Thus for variants under positive selection, current frequency will be substantially affected by historical contingencies, and the correlation between allele frequency and selective strength will be rough at best.
There’s also a reference to Voight et al. 2007, a paper I reviewed a few weeks back, on signals of selection in humans, based on extended haplotypes around genes under positive selection. Apparently, these signals are missing for the climate genes.
There is an alternative to positive selection, that could also explain the association between climate and gene frequency:
You’ve probably already guessed my hypothesis: at least some of the genes pulled out from this study (and probably the ones with the tightest correlations) have been the targets of balancing selection. Balancing selection could be acting on climate genes in different ways, but in my mind the most likely mechanism is via heterozygote advantage.
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This model would result in each population reaching a stable allele frequency that is correlated with the local temperature, regardless of its starting frequency and how long the population had been subjected to that particular environment – so long as there has been enough time for the population to reach equilibrium. This scenario is much more likely to result in a linear correlation between allele frequency and climate variables than a simple positive selection model.
Now, what I am wondering is, how strong does the selection have to be for the allele frequency to reach equilibrium in the late arrival populations (say South Americans), and what kind of signals would we look for in the genome to test if balancing, rather than positive, selection is going on?
I really don’t know — I am too new to genetics to even have a clue — but I bet that this is old stuff in the genetics literature. I’ll have to ask around…