Investigating differences in multivariate phenotypes between groups and hybrid populations
We used a Bayesian mixed-effects model to investigate if trait means varied between Caribbean, SSI generalist-only, and SSI radiating groups while accounting for the effects of species and population. We used the brms function from the BRMS package to fit a model with a student’s T distribution, and uninformative priors (Bürkner 2017). The model included the 18 trait measurements as the multivariate response variable, group type and species designation as fixed effects, and population ID as a random effect.
We fit a Bayesian fixed-effects model with a student’s T distribution, and uninformative priors to investigate differences in trait values between Crescent Pond and Little Lake F2 hybrids. This model included the 18 trait measurements as the multivariate response variable and population as a fixed effect. While testing for differences in trait values between hybrid groups is not a primary goal of this study, detected differences could indicate population level differences in the genetic architecture of these traits. Furthermore, the output of this model provides estimates of uncertainty around average trait values which were used to investigate departures from null expectations. Specifically, we used these estimates to determine which phenotypes deviated from additive trait value expectations (Appendix Table E4)
For both models we extracted posterior samples and estimated the median values and 95% highest density intervals (HDI) to make inferences about differences in trait values between the levels of our fixed effects using functions from the brms and emmeans packages (Lenth 2023; Figures 3 & 7).