Detection of loci under selection using Arlequin 3.5.2.2
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2.1 years ago
okozhar • 0

I am working with RADseq data and want to identify loci under selection using hierarchical island model method implemented in ARLEQUIN. The input file for Alrequin was converted from VCF format to .arp with PGDSpider. the VCF file itself was obtained from "populations" program of Stacks v.2. Using this input file, I have run hierarchical AMOVA and pairwise Fst on a population level in Arlequin successfully. However, when I try to use the detection of loci under selection in Arlequin, I get an error: "Observed F-statistics lead to invalid migration rates. Coalescent simulations cannot be performed. Perform a simple AMOVA to check that all F-statistics are within the interval ]0..1["

Based on the error message, I understand that my distance matrix is probably incorrect. But I don't fully understand why that would happen and how to fix this in order to make the program work. It says "perform simple AMOVA". Does simple mean locus by locus AMOVA?

Also, can missing data cause such error?

I am posting this here with the hope that someone may be able to explain to me what are the probable causes of this error and what are the steps I should try next. I am new to this analysis and realize that I may be missing something obvious, but I will be very grateful for insight.

Many thanks, Olga

arlequin radseq naturalselection SNP loci • 791 views
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4 months ago
lpittet • 0

Hi Olga,

I am having the exact same problem and was wondering whether you have found the problem and a solution to detect loci under selection ?

Have a nice day,

Loïc

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