Supplementary Materials and Methods
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Table S5. Settings and priors used in the correlation analysis performed in SIMMAP 1.5 [74]. 
Table S6. Correlation results for diapause and habitat. 
Table S7. Linear mixed models implemented in the R [71] package nlme [82] were used to examine the effect of developmental trajectory on morphological and physiological divergence during embryology for each of the studied species. Developmental stage (number of somite pairs), developmental trajectory (diapause versus direct-developing) and their interaction were entered as fixed effects. Repeated measurements were taken on eggs as they progressed through development (i.e. longitudinal data set). To account for this non-independence [83] random effects for egg identity (individual intercept and slope allowed to vary) were included. Here we report the fixed effect parameter estimates produced by restricted maximum likelihood estimation. In cases where the full-model failed to converge due to overparameterization, the random slope effect (~Somites|Subject) was excluded, and the model rerun with only random intercepts (~1|Subject). 
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