Computational protocol: Gene Flow among Populations of Two Rare Co-Occurring Fern Species Differing in Ploidy Level

Similar protocols

Protocol publication

[…] Binary (presence/absence) data were prepared in the program FAMD and then imported into the program Arlequin , where most of the analyses were performed. A mantel test was performed using PopTools .The mean gene diversity was calculated for each population and averaged over all populations within a species. In addition, the number of haplotypes (band patterns) for each species and population was calculated. Distribution of genetic variability among and within populations was investigated using an AMOVA and tested with a permutation test (1000 permutations). A Mantel test was used to test for the relationship between pairwise Fst values between populations and pairwise geographic distance (in meters) between centroids of localities hosting the populations (obtained in study ). The relationship between the total size of the population and its genetic diversity was examined using a simple linear regression in the program R . [...] We calculated the mean expected and observed heterozygosity and inbreeding coefficient over all populations for both species using PopGene . […]

Pipeline specifications

Software tools Arlequin, POPGENE
Application Population genetic analysis