Population Genetics Questions

[mika]

Hi Everyone,

First of all, i just wanna say its great that theres this forum here so everyone can help each other with relevant topics.

Anyway, some background:

Im looking at population genetics of a fungus Rhynchosporium secalis. So far, i have done microsatellite analysis of several hundred samples of this pathogen from various locations/populations. I intend to statistically analyse this data but i do not know where to start. So far, i do not know what questions i should be looking at answering except the following two:

1) id like to compare the genotypic diversity of fungal isolates across geographical range

2) because the pathogen infects two separate species, id like to compare diversity across isolates from both host species.

Having said this, i do not know what other hypotheses or pertinent issues i should be looking at. Any advice/suggestions with regards to this would be greatly appreciated.

Secondly, i have decided on the following work flow:

1) check that the 14 microsat loci i have used are indeed neutral (according to previous studies, they should be but i was told i should double check)

2) check individual populations to see if any 'populations' have similar allele frequencies/genotypes and as such can be lumped together as one metapopulation. I intend to do this by testing Gst, allele frequencies, presence and frequencies of local alleles.

I do not know how i should proceed from there. I am very new to population genetics and would like to know if anyone has a general work-flow/procedure generally adopted when studying population genetics of any organism.

Any help/advice/suggestions would be more than greatly appreciated.

Thanks guys

Cheers
Mika