Table 1.

Results from the six analyses (A1–A6) carried out to infer chromosome number changes in Araceae under Bayesian and maximum likelihood optimization

		Coding scheme						Rate parameters				Events inferred with PP >0·5				Chromosome no. at Araceae root node			Chromosome no. ranges at Araceae root node
Analysis	Tree: outgroups	All poly.	Red. poly.	Inf.	Best model	LogLik	AIC	δ	λ	ρ	μ	Losses	Gains	Dupl.	Demi.	Bayes: Best n; PP	Bayes: 2nd best n; PP	ML	n	Sum PP	n	Sum PP
A1	+	+			Mc2	–219·5	445	45·9	3·9	6·9	–	98·1	8·4	14·3	14·3	18; 0·18	16; 0·16	16	16–18	0·5	8–18	0·9
A2	+		+		Mc2	–236·4	478·9	56·4	0	6·3	–	112·2	0	11·5	13	18; 0·26	17; 0·13	16	17–19	0·51	10–20	0·85
A3	+			+	Mc2	–245·7	497·3	58·2	0	5·7	–	120·1	0	11·9	13·9	18; 0·26	19; 0·12	17	17–19	0·52	10–20	0·9
A4	–	+			Mc2	–196·6	399·1	50·4	1·8	6·6	–	86·6	3·2	10·5	9·3	18; 0·38	17; 0·3	17	17–19	0·86
A5	–		+		Mc2	–213·2	432·4	53·6	0	5·6	–	87·2	0	9·8	9·4	18; 0·42	17; 0·23	17	17–19	0·9
A6	–			+	Mc2	–222·4	450·7	58·1	0	5·4	–	94·4	0	9·7	10·5	18; 0·37	19; 0·34	18	17–19	0·85

Only the best-fitting models are shown. Tree (column 2) refers to whether outgroups were included or not; coding scheme refers to how genera with polymorphic haploid chromosome numbers were coded. All poly., all chromosome number polymorphism coded (scheme 1); Red. poly., reduced polymorphism coding (scheme 2); Inf., phylogenetically informed coding (scheme 3). Best model, Mc2 (constant rate model with duplication rate ρ and demi-duplication rate μ; compare Table 2); Logarithmic likelihood (LogLik) and AIC scores; rate parameters (δ = chromosome loss rate, λ = chromosome gain rate, ρ = duplication rate, μ = demi-duplication rate); frequency of the four possible event types with a posterior probability (PP) > 0·5; haploid chromosome number inferred at the root node under Bayesian optimization with the respective PP, and under maximum likelihood (ML). The last column shows the chromosome number range inferred for the root node, each with its PP.