Mailbag: Holding on to ancient DNA

Hi, It is often claimed that ancient genes that were once very adaptable are discarded over time by drift, bottle necks etc. What if an ancient trait were again valuable as climate swings or other environmental opportunites and are now again favorable. My point is that if an organism, especially in a variable climate, that carried this gene would be at a selelctive advantantage if that trait were inherited. The inheritable trait being the ability to retain ancient DNA. Also, this trait could be inherited in pieces spread over more than one organism, which are recombined through hybridization with the same results.

The most basic version of this is frequency-dependent polymorphism. Suppose that an allele is useful when rare, and harmful when common. Over the long term, it will never approach fixation, but nor will it become extinct unless the advantages are weak relative to the size of the population.

Now, suppose that the allele is advantageous only some of the time, and otherwise neutral. Now it can drift to fixation. If the times when it is useful are far enough apart, it can drift to loss. But anytime the environment is favorable for the allele, it will get a little boost. The tendency will be toward fixation, biased just to the extent of the strength of selection and duration of the favorable time intervals.

OK, add another element of complexity. The allele is favored during some intervals, and disfavored during others. Motoo Kimura described the dynamics of this scenario; the ultimate fate of the allele depends on the duration of the time intervals, of course, and may lead to an unstable polymorphism, fixation or loss.

You propose a “reserve” mechanism, where the genome holds on to old variants to resurrect them at some later time when they become useful.

Of course, we potentially have such a mechanism now, as we can dig up ancient DNA and experiment with it in vivo. But you suggest that a reserve of ancient genetic material might be adaptive.

I believe the dynamics of such a mechanism would be the same as if the population were merely larger. In that case, drift (and selection against recessives) would be much slower to eliminate alleles that had lost their advantage. So when the environment changed, the population could respond more quickly without waiting for the old variants to reappear by de novo mutations.

Also, a larger population makes it much more likely for mutations to happen.

There’s no evidence that a store of ancient genetic variants lie silent in our genomes, but I think you might look at actual gene silencing mechanisms as a parallel to your suggestion. We do retain functional genes within our genomes that we turn off by methylation early in development. The genes either act early in development, are imprinted by maternal or paternal origin, or are turned off in tissues that don’t need them. That’s a way of maintaining variations for use in some circumstances but not all.