Supplementary Materials and Methods
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Fig. S6. Graphs depicting the relationship between somite number and head width at optic cups (upper left panel), head width at otic vesicles (upper right panel), head length (lower left panel), and heart rate (lower right panel) for Fundulopanchax deltaensis. Definitively determining whether embryos entered into diapause II or were direct-developing was challenging for this species (see text). The interpretation we favor (lower panel) is that all embryos entered diapause II, albeit in some cases for a very brief period of time before resuming development. 
Supplementary Tables Table S1. Models of molecular evolution chosen by jModeltest [11] on the basis of Akaike Information Criterion. 
Table S2. Minimum and maximum constraints used in molecular dating (timetree) analyses. 
Table S3. Summary of BiSSE models in diversitree that are relevant to testing the hypothesis of multiple (full model) versus single (trait of interest evolved once) origins of diapause. λ = speciation rate, μ = extinction rate, q = transition between states; state 0 = no diapause II, state 1 = diapause II present. 
Table S4. AIC and lnLik comparison of full model and model where diapause was constrained to have evolved once (single origin) for each of the four trees. Analyses were performed in diversitree. Auto / IR and Hard / Soft refers to autocorrelated and independent rates with either hard or soft bounded constraints. 
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