Phylogeography with R
0
1
Entering edit mode
7.6 years ago
Nuria_bl ▴ 10

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 –§st 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.

R • 2.7k views
ADD COMMENT
1
Entering edit mode

Have you done any MDS analysis?

ADD REPLY
0
Entering edit mode

No...should I do it?

ADD REPLY
1
Entering edit mode

Yes if you wuld want to investigate your population stratification.

ADD REPLY
0
Entering edit mode

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.

ADD REPLY

Login before adding your answer.

Traffic: 1196 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6