In the multiple population comparisons, pathogen populations from different sampling points or hosts were considered simultaneously in a single analysis.
Finally, in order to allow for multiple population comparisons of EHH, we computed XP-Rsb for every SNP site and population versus all other HGDP-CEPH populations as described in Moreno-Estrada et al. [ 28].
Pair-wise and multiple population comparisons in genotype frequencies were performed using contingency χ2 tests to detect differences in pathogen populations sampled from different hosts or sampling times [ 71].
Pairwise FST values were consistently significant between populations located in different lakes for all three SNP sets, even though multiple population comparisons within Iliamna Lake suggested no differentiation (see additional file 1).
We used both pair-wise and multiple population comparisons to evaluate the effects of evolutionary time (different sampling points) and host genotypes on the population dynamics of P. nodorum.
Multiple population comparisons were conducted by using all populations sampled from the same host across different sampling points simultaneously, generating a c x l contingency table, where c is the number of sampling points and l is the number of genotypes detected.
Of these, only one locus (0.2%) (ID 431) was a replicated outlier in three multiple pairwise population comparisons of which two were statistically independent, that is, comparisons that did not share a population.
Of these, only one (0.22%) was a replicated outlier in multiple independent dune-fen population comparisons and thus possibly reflecting truly parallel divergence.
The binomial test (which estimates the probability of obtaining the observed number of significant tests at the 0.05 level given the total number of tests) was used to detect significant departures from null hypothesis across multiple tests, such between pairwise population comparisons across genes.
Our analysis is based on comparison of multiple populations, rather than changes through time in a single population.
For comparisons between multiple populations in the experiment with Ly49 receptor levels on NK cell subsets, one-way ANOVA was used with Bonferroni's post test if p<0.05.
