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Fig. 3 Choice model parameter estimates and effect likelihood.

The effect likelihood ratio tests show the importance of each attribute as measured by -log p-value of the LR test) and each bar represents this value relative to the value of the most important attribute.

Cox proportional hazards analysis was also performed to determine hazard ratios and test for statistical significance of their differences using the Effect Likelihood Chi Square test.

Statistical significance for heritability of the traits or of their flexibility were assessed by comparing the full model to a model with no clone or period*clone random effect (likelihood ratio test, library lme [84]).

A codon-based site-by-site fixed effect likelihood (FEL) analysis comparing selective pressures between the two species along internal branches and leaves of the phylogenetic tree was also performed (ComparesSelectivePressure.bf in HYPHY) [75].

We verified the homogeneity of this experimental design and did not detect a 'patch effect' (Likelihood ratio tests; P = 0.9 for the flowers and P = 0.74 for the leaves).

Four different approaches were used to identify codons under selection: single-likelihood ancestor counting (SLAC), fixed-effects likelihood (FEL), internal fixed effects likelihood (IFEL) and relaxed-effects likelihood (REL) methods [68], [93].

We performed the tests using three methods [SLAC (single likelihood ancestor counting), REL (random-effects likelihood) and FEL (fixed-effects likelihood)] [ 57].

We did not detect positively selected sites for 3FTxs with single-likelihood ancestor counting (SLAC), but did with fixed-effects likelihood (FEL) and random-effects likelihood (REL, Table 7).

These models were single likelihood ancestor counting (SLAC) and fixed effects likelihood (FEL) [18].

For the HyPhy analysis, the random effects likelihood (REL) model of molecular evolution was used.