I am doing population genetics structure analyses with cereal crop plants (Fonio millet). I have 157 samples/accessions that are coming from different locations in West Africa.
I've run the Principal component analysis.
Results showed that there're 8 individuals from Togo separated and clusters apart from the rest of individuals (check the image in the link):
I want to investigate more this separation, what causes this clear clusters of these 8 samples? and how to test the hypotheses?
In a genetic perspective; many processes could involve in shaping the genetic of species:
-Genetic drift can affect the structure ???
-Natural selection ??
-Deleterious mutations ??
I did PCA analysis on the two subgenomes, and one of the subgenomes separated 8 accessions coming from south Togo from the rest of Togo's samples and the other accession
I've also conducted chromosomes-wise PCA, and the separation was only with chromosomes 3A and 9A
I didn't find any particular pattern for chromosomes 3A and 9A when conducting FST, or allele frequencies.
There must be something, but how to reveal it?