I've started making an outline:
- Genetic diversity in eukaryote species: Not a lot. The members of a species typically have very similar chromosomes, with the same genes arranged in the same order. Different versions of the genes differ by no more than a few %, and there are very few differences in gene content or arrangement.
- We take this for granted, but it's probably one of the many consequences of sexual reproduction. Individuals with chromosomes whose genes have been rearranged (by, for example, an inversion) are at a big disadvantage in sexually reproducing species, because such chromosomes don't pair properly with normal chromosomes at meiosis and the resulting gametes often have two versions of some genes and none of others.
- What about in bacterial species? I should probably start by considering what we want 'species' to mean in Bacteria.
- For most eukaryotes, the 'biological species concept' is the most useful way to group individuals into species. In its simplest form, it says that all individuals that can reproduce sexually with each other should be considered members of the same species.
- But bacteria don't have eukaryote-type (meiotic) sexual reproduction. They don't have any process that regularly combines the sets of genes from two individuals and then shuffles them into two 'recombined' sets. Maybe I'll talk here about what bacteria do have that puts genes into new combinations, or maybe I'll leave this till later.
- But we can define bacterial species as groups of individuals for which at least 50% (75%? 90%?) of their genes are recently descended from a common ancestor (recent enough that sequence divergence is no more than a few %), and for which most of these genes are syntenic (arranged in the same order). This definition works for most of the groupings that microbiologists consider for other reasons to deserve being called species.
- For this 50% or 75% or 90% of the genome, the members of a bacterial species are a lot like a eukaryotic species.
- But these species are far more genetically diverse than are eukaryote species, because of the other 10% or 25% or 50%. Many of these sequences are stupendously diverse...