Computational protocol: Lower selfing rates in metallicolous populations than in non-metallicolous populations of the pseudometallophyte Noccaea caerulescens (Brassicaceae) in Southern France

Similar protocols

Protocol publication

[…] We used GENETIX (version 4.05, ) to compute allelic frequencies, number of alleles, inbreeding coefficient FIS [using the method with 1000 bootstrap 95 % confidence intervals (CIs)] and the amount of linkage disequilibrium between loci, and Genepop () to test for linkage equilibrium among loci. Combining the information of these two software programs, no pair of loci had a statistically significant correlation coefficient higher than 50 % in more than two populations; therefore, we kept all loci in the following analyses. We used the permutation test in FSTAT () to compare the observed and expected heterozygosity, FIS and FST, of the metallicolous and non-metallicolous ecotypes (5000 permutations of populations between ecotypes). [...] We tested for the presence of isolation by distance among populations using the R package ‘fields’ () to calculate the geographic distance matrix among populations based on their GPS coordinates. We then tested for the presence of isolation by distance each year with Mantel tests in the ‘adegenet’ R package (), within each ecotype and on the whole data set. Additionally, following the guidelines provided by , we regressed FST/(1 – FST) on the geographic distance. […]

Pipeline specifications

Software tools Genepop, adegenet
Application Population genetic analysis