Non-parametric statistical tests, Wilcoxon's rank sum test and Spearman's rank correlation, were carried out using STATA 9 (StatCorp LP, Texas, USA) as the indices of divergence were not assumed to be normally distributed.
Furthermore, genomic regions that are associated with behaviour, immune response and feed efficiency were detected based on FST (fixation index) estimates of divergence in cattle using high-density SNP assays [ 4].
Using this approach, two studies have related an index of phenological divergence to an estimate of pollen flow between populations, one in hybrid zones of Eucalyptus aggregata and Eucalyptus rubida (Field et al. 2011) and the other between two varieties of maize in an experimental field (Della Porta et al. 2008).
The proposed method uses the Kullback-Leibler divergence (KLD) as the index of difference in distribution between two groups.
The resulting set of accuracy scores was compared against a number of indices of genomic divergence.
The nearly 300,000 accuracy scores obtained from these trials were used to construct general models of distinguishability versus taxonomic and compositional indices of genomic divergence.
Previous work showed an association between genetic differentiation in allozymes and RI, but did not consider whether other co-occurring indices of genetic divergence (such as mtDNA) and major ecological factors known to be important for Ensatina might explain the observed levels of RI.
Genetic evidence using microsatellite markers in multiple studies also suggests that these stocks are genetically distinct from each other using different metrics such as Bayesian structure analysis, amova, and indices of pairwise divergence (e.g. FST, RST, and θST; see Miller 2003; Parker et al. 2009; Sepulveda-Villet et al. 2011 for details).
FST is a sensitive index of allele-frequency divergence that is scaled from zero to one (see [ 36] for a review); because of this normalization, species with low overall polymorphism can nonetheless have high FST among populations (indicating low gene flow or diversifying selection), or vice versa.
