This is so because in our analyses we test all four algorithms on exactly the same data, and we have no reason to think that annotation quality differences would differentially affect the performance of ortholog prediction algorithms in our study.
Because in our analyses, the MetS independently of its components was not associated with a significantly increased risk of CV mortality (HR 1.19 [95% CI 0.93 1.53]), this suggests that if the increased risk of all-cause mortality associated with the MetS is true, the increase must be due to non-CV causes.
The two loci that were previously determined to be associated with differentiating resident from anadromous life-history forms (Omy_ndk-152 and Omy_LDHB-2_i6; Narum et al. 2011) could not be directly tested for association with life-history forms because most populations in our analyses were field identified as anadromous (e.g., juvenile smolt or adult steelhead phenotypes).
There were slightly more females than males included in our analyses, possibly because, in general, females are more likely than males to consult their GP regularly.
We purposely selected the countries that we included in our analyses because we wanted them to be fairly heterogeneous in terms of level of science performance, culture, language of instruction, and the mix of OECD and non-OECD countries.
We included five additional survey questions in our analyses because each question could potentially correlate with the three ID questions, though we did not have any specific expectations regarding these potential correlations.
Pielou's classical Shannon evenness definition as ln(q = 1D /ln(S) was included in our analyses because of its traditionally widespread use in ecology.
We did not include inheritance rank as a predictor of behaviour in our analyses, because the rank of wasps on the same nest cannot be considered independent, since no position can be occupied by more than one wasp.
The institution of the S. aureus PNA FISH assay was statistically adjusted for in our analyses because a shorter time to identification of S. aureus could reduce the time to appropriate definitive therapy.
We considered indexes of sibling competition (i.e. level of brood reduction, clutch size, duration of nestling period) as the independent variables in our analyses because the hypothesis tested is that sibling competition influences the evolution of nestling conspicuousness.
Second, even though the MACS followed large numbers of seroconverters until clinical AIDS or death, we were unable to use those disease outcomes in our analyses because calendar year is linked to progress in HIV/AIDS disease management (e.g., prophylaxis and treatment of opportunistic infections, and development of more potent antiretroviral therapies).
