A test of deviation from HWE across all loci and populations was also significant.
c P value for χ2 test of deviation from the assumption of Hardy Weinberg equilibrium, among controls only.
Mean IPNV prevalence was determined by region, and a χ test of deviation from the overall Scottish mean was conducted (Table 1).
For trichome phenotype data in BC1 and F2 plants, χ-tests for goodness-of-fit were used to test for deviations of the observed data from the theoretically expected segregation (1 1 for BC1P1 and 3 1 for F2 populations).
Two important properties have been widely used in comparative biology to formulate tests of deviations from the patterns expected under BM.
Results from the tests of deviations from Hardy-Weinberg proportions for these variants are listed in Web Appendix 2. Overall, 90 variants in 50 genes were available for estimation of allele frequency and genotype prevalence.
For each polymorphic locus, we calculated the number of alleles (A), observed heterozygosity (Ho), and expected heterozygosity (He); tests of deviations from Hardy Weinberg equilibrium (HWE) and linkage disequilibrium (LD) were performed using the software Arlequin version 3.5.1.3 (Excoffier and Lischer, 2010).
Chi-square Hardy Weinberg equilibrium (HWE) test calculator for biallelic markers available at http://www.oege.org/software/hwe-mr-calc.shtml [7] was used to test for deviations of genotype frequencies from HWE.
Resampling is typically used to test for deviations of observed network topology from the expected one but occupancy, abundance and richness data have also been analysed with these methods.
Differences in the control of type I errors between models were also assessed by calculating for each trait and model, the test statistics of the Kolmogorov Smirnov test for deviation of the P-values from a uniform distribution.
Thirdly, the test results of deviations from mutation-drift equilibrium (Tajima's D, Fu's Fs) support the hypothesis of a recent worldwide population expansion following a bottleneck or a selective sweep.
