Phylogeography with R

Question

[Nuria_bl]

Hi,

I am starting with R and I have done a haplotype network with the package pegas. Now, I would like to do some tests to determine if there is segregation between different groups. I have a matrix of mtDNA sequences (in DNAbin format) and I have seen that the best tests for this case are AMOVA and Фst coefficient. I would like to receive confirmation that I am right and how I could do these tests. I have tried diff_stats(alignment_genind) but when I write phi_st = TRUE I get this error:

(alignment_genind <- as.genind.DNAbin(x=alignmentSpain, pop=pops))

diff_stats(alignment_genind, phi_st = TRUE)

Warning messages: 1: In within_dists/(as.numeric(pop.freqs) * 2) : longer object length is not a multiple of shorter object length 2: In within_dists/(as.numeric(pop.freqs) * 2) : longer object length is not a multiple of shorter object length

Thanks in advance,

Nuria.

[reza.jabal]

Have you done any MDS analysis?

[Nuria_bl]

No...should I do it?

[reza.jabal]

Yes if you wuld want to investigate your population stratification.

[Nuria_bl]

Thanks! I have done a MDS and I can see very well the two separated groups that I believed I had. The problem is that I get only few haplotypes representing several individuals each one, so It looks as If I had few samples. In addition, in those cases in which one haplotype represents individuals from more than one population my point take the colour of one population only. I'll try to solve this.