Computational protocol: Population structure and genetic diversity in the nannandrous moss Homalothecium lutescens: does the dwarf male system facilitate gene flow?

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Protocol publication

[…] Principal coordinate analysis (PCoA) of female shoots and dwarf males in all four populations was performed using the Excel plugin GenAlEx (version 6.5) [, ]. The analysis were based on the pairwise genetic distance (i.e. number of loci with differing alleles) matrix, with data standardization (i.e. division by the square root of n-1). Resulting graphs were edited in Adobe Illustrator CS6.The software STRUCTURE (version 2.3.4) was used to detect within and between population structure []. Data was entered in haploid form. We used an admixture, correlated allele frequencies model and a priori information about population (AP, KP, LQ and CK) to determine the most likely number of population clusters K. We set K from 1 to 24 using a burn-in of 20 000 and 50 000 replications. Analyses were repeated 15 times for each run of a certain K. The average and standard deviation (SD) of the likelihood of the model of each K was used to calculate ∆K [] in Structure Harvester []. The models with the highest and second highest ∆K were selected as the models with the most support. CLUMPP (version 1.1.2) was used to align the 15 repetitions for each selected K, using G’, Greedy algorithm for K = 4 and LargeKGreedy algorithm for K = 15 (other options as default) []. Results from CLUMPP were visualized by the Distruct software (version 1.1) [] and edited in Adobe Illustrator CS6. […]

Pipeline specifications