Fst

Okay, back to evolution. I know, my other blogs are probably more interesting for most of you, if there are indeed any of you!

But, I have a problem I am trying to think through, and it helps if I write it down. Or in this case, type it out.

There are regions on cocci chromosomes that have low Fst. Fst is a measure of gene flow. Values close to 0 indicate that there is a lot of gene flow- in this case between species. Values close to 1 would indicate no gene flow. Now, what you would expect with 2 different species is values closer to 1 for most of the comparisons- 2 different speices should not be having sex and producing progeny, in sensu stricto.

However, there is good evidence that the 2 species of cocci do indeed have sex, and do produce viable offspring, which can then mate with either parental species (or maybe not, maybe only one, but for this argument let's say it is promiscuous).

Is looking at Fst values a good way to measure this for whole genome analysis? What if the genes are highly variable? What is the effect of repetitive elements in the region? Pseudogenes? I am concerned only because the pattern emerging is highly correlated with genome position, and makes me think something else is going on.