Average heterozygosity Ht (i.e. gene diversity) for each SNP was calculated with the genetic distance and phylogenetic analysis package DISPAN [ 55].
Thereafter, optimal thermodynamic performance conditions for HRSGs are calculated with the help of the genetic algorithm.
The quality of the phylogenetic information was determined by plotting transition and transversion rates as a function of the genetic distance calculated with a K80 model using DAMBE software [32], [33].
Those QTLs explained 33% of the genetic variance, calculated with the whole data set, but this value was reduced to 7.5% when the cross validation method was used.
The plot of a principal coordinate analysis (PCoA), based on individual genetic distances calculated with 208 AFLP markers, is presented in Additional file 2. The first two axes explained 71.8% and 3.0% of the variation, respectively (explaining 74.8% of total variability).
DAMBE was also used to check for saturation of nucleotide substitutions using a plot of the number of transitions and transversions for each pairwise comparison against the genetic distance calculated with the F84 model of nucleotide substitution [ 40], which allows different equilibrium nucleotide frequencies and a transition rate-transversion rate bias.
Genetic distances were calculated with both the complete and synonymous clock models and converted into years using the published calculator91.
FIS was calculated with SPAGeDI (Spatial Pattern Analysis of Genetic Diversity) that offers a way to estimate the allele frequencies in polyploids by assuming that each of the alleles in a partial heterozygote has an equal likelihood of being present more than once66.
Principal components of genetic variation were calculated with EIGENSTRAT software [106] as described in Hunter et al, 2007 [102].
Pairwise genetic distances were calculated with Kimura's two parameter method [35] SimPlot Version 3.5.1 was used for the analysis of recombinant subtypes[36].
