Computational protocol: Genetic diversity of Avena ventricosa populations along an ecogeographical transect in Cyprus is correlated to environmental variables

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Protocol publication

[…] All fragment sizes were transformed into binary data (presence/absence) and organized in a single matrix table. FreeTree [] was employed to compute the genetic similarities between taxa and for the construction of the dendrogram, illustrated with the TreeView application ( Popgene [] was used to estimate Shannon diversity index and the percentage of polymorphic loci, as well as, for the construction of the population level dendrogram. Genotypic variations were calculated across various populations via the analysis of molecular variance (AMOVA) using GenAlEx 6.5 []. The significance of the resulting variance components and the inter-population genetic distances were tested using 999 random permutations.Bayesian model-based clustering approach was used in order to identify the genetic structure of the Avena ventricosa populations, with the Structure 2.3.4 software []. The Structure algorithm was run using the admixture model, with 10 independent replicate runs per K value (number of clusters) ranging from 1 to 10. Each run involved a burning period of 100,000 iterations, and a post burning simulation length of 500,000. Validation of the most likely number of clusters K and graphical representations of cluster assignments was performed with pophelper ( […]

Pipeline specifications

Software tools TreeViewX, POPGENE, GenAlEx, pophelper
Applications Phylogenetics, Population genetic analysis
Organisms Homo sapiens, Avena sativa