I have mentioned before that at one point in my life I wanted to study conservation genetics. This field can be thought of a subdiscipline of molecular ecology — wherein researchers use molecular markers to test hypotheses regarding demography in their population of interest. Jacob at Salamander Candy has a post on the usefulness of neutral markers in conservation. Here’s a taste:
The problem is, a growing body of evidence suggests that patterns of variation and divergence in adaptive traits are not well reflected by neutral markers (refs 1-8). In the hypothetical species mentioned above, a small amount of gene flow between east and west would be enough to swap small numbers of alleles. This would hardly affect the divergent neutral genotypes at all, but newly introduced advantageous alleles would increase in frequency even if they were originally rare. For example, maybe all the northern ones have adaptations for cold temperatures and the southern ones are adapted to warmth. This pattern would not be reflected in the neutral markers.
Neutral markers are only useful for inferring recent demographic history. I don’t think anyone has ever argued that they can be used to identify selection history. It has been pointed out, however, that many molecular ecologists don’t understand the assumptions that go along with using certain molecular markers or don’t perform the appropriate statistical tests when analyzing their data. Even if we understand the limits of molecular markers for studying populations, how useful are they? Jacob makes a good point regarding what we are ultimately interested in conserving:
It’s much easier to just take some tissue samples, extract DNA, and look at neutral molecular patterns. This convenience, combined with the “coolness factor” of new technology, and the large amount of information obtainable from molecular analysis, has made neutral markers popular in conservation biology. Remember, though, we’re not really interested in conserving neutral biodiversity per se, so its only useful to the extent that it’s a proxy for adaptive biodiversity.
There are definitely people who spend a fair bit of time characterizing adaptations in natural populations. These researchers also identify non-neutral characteristics that differentiate populations. The problem is that these projects are much more time consuming than ones which sample a random collection of neutral loci. Sometimes we only have the time and resources to infer demographic history rather than unique adaptations within populations.
These issues are related to stuff Razib has been writing about at Gene Expression. Razib’s posts deal with human population history and the introduction of advantageous alleles from archaic humans. In the case of the conservation examples, selection prevents the introgression of alleles between populations if there are different selection pressures in the two populations. Introgression between populations will differ depending on the selective regimes around a particular locus. That means that the majority of loci will reveal the general history of a population, whereas individual loci may tell a unique story if they were under selection.