Implicit in the title The Origin Of Species is the question: why the plural? In other words, why isn’t there a singular apex species which dominates this planet? One can imagine an abstract system where natural selection slowly but gradually sifts through variation and designs a best-of-all-replicators. And yet on the contrary it seems that our planet has exhibited an overall tendency of going from lower to higher diversity. The age of stromatolites may be the last epoch when we had the best-of-all-replicators.
These sorts of deep questions about variation drive many of the research projects in evolutionary biology. Often one focuses on a narrow zone of interest. An organism for example which might serve as an illustrative model for more general processes. Or, a particular dynamic which interlocks with other processes to form a whole phenomenon. But on occasion you have to sit and ponder the whole shebang. Why genetic diversity? More specifically, why not more diversity of genetic diversity? The issue here is what is sometimes termed Lewontin’s paradox.
Consider two populations. One population goes through an extreme bottleneck, while the other maintains a large population over the generations. What would you presume in regards to genetic variation? Naturally, the former would have far less genetic variation than the latter, because drift would have powerfully expunged many alleles during the bottleneck period. In contrast, in large populations many alleles are present floating in transient between emergence and extinction. The magnitude of genetic drift as a frequency is inversely proportional to population size. A smaller breeding population results in more volatility, and therefore more extinction of alleles, and fixation of others.
Taken to the broader canvas of the tree of life the prediction naturally is that species which have large effective populations will have much more genetic diversity than those with small effective populations. There is some relationship, but it is actually rather weak. And the range of genetic variation is not proportionate to the range of variation of population sizes.
A new paper in PLoS Biology reviews this literature, as well as suggesting possibilities for the future. Revisiting an Old Riddle: What Determines Genetic Diversity Levels within Species? One aspect highlighted is that not only is there a relatively narrow range in genetic diversity, but there is also a great deal of intra-phyla variation. This figure illustrates the pattern well:
Not to get too far into the weeds (because you should read the paper), but a major issue is likely to be the exact nature of natural selection, and whether it maintains or diminishes variation. I suspect the latter, as I think balancing selection is a secondary phenomenon among evolutionary genetic dynamics. Also, the paper is an excellent starting point for a literature dive. For example, I did not know that the effective population ratio on the sex chromosomes is likely more influenced by their being more exposed to selection than differences between male and female reproductive variation.