Functional chloroplasts in metazoan cells - a unique evolutionary strategy in animal life

Table 4 Reconstructed ancestral character states for chloroplast retention in the most recent common ancestor of (A) the Plakobranchoidea, and (B) the clade comprising E. chlorotica, E. crispata, E. serca and E. viridis.

Clade	Character state	Posterior probability	log(harmonic mean of likelihoods)	BF test statistic 2 [logA-logB]
A	non-retention	0.005 ± 0.016	-31.9672	7.31
	short-term retention	0.891 ± 0.180	-28.3106	-
	long-term retention	0.103 ± 0.179	-30.2700	3.92
B	non-retention	0.002 ± 0.011	-35.4964	14.43
	short-term retention	0.526 ± 0.261	-28.2813	-
	long-term retention	0.472 ± 0.261	-30.4022	4.24

Taxa were coded as having non-retention, short-term retention, or long-term retention of functional chloroplasts based on PAM data. The evolution of kleptoplasty was then modeled using Bayesian Inference via Markov-Chain Monte Carlo methods to estimate the posterior probability of alternative character states. Posterior probabilities (means ± one standard deviation) were calculated from an MCMC chain run for 20 million generations. Bayes factor (BF) tests were used to compare log-likelihood scores of models in which the ancestor was assigned one of the possible character states; values >2 represent positive evidence and values >5 represent strong evidence for models fixing the ancestral state as short-term retention.

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