[adegenet-forum] problem with DAPC/find clusters analyses with rad seq data

[Lu Maffey]

Hi Thibaut and everyone!

I need some help with a DAPC analyses I'm trying to perform on my radseq
data (whole genome for different mosquitoe samples, total of 65
individuals). (I'm new with Adegenet so I apologize in advance if this
question is quite basic!). The samples are from different locations and I'm
trying to stablish if there is population structure within the data. I have
previously performed analyses using Structure which showed that there are
different clusters (of course using fewer SNPs than the total number
available because of the panmixia assumption). So I've created the genlight
object with all the SNPs(after filtering low frequencies in plink) but when
I use find.clusters, the BIC against number of clusters graph only shows
increasing values of BIC. It never decreases. So I know that it's not the
only way to determine the number of clusters to perform the analysis but
I'm not sure wether this means that the program doesn't recognize any
clusters within the data or some other issue. I've tried using the same
value I've obtained for this data in Structure and it shows a similar
asignation but I'm not sure if thisis correct.
If I perform a DAPC analyses, when I use the scatter function to show the
results, the graph only shows the groups numbers, but no individual dots.
Could you please give me some insight about what's going on here?

Thank you very much in advance!

cheers

Lu
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.r-forge.r-project.org/pipermail/adegenet-forum/attachments/20180416/07a63550/attachment.html>