Table 1. POInT estimates for different datasets and ancestral orders.

Description	Ancestral locia	# breaksb	#double breaksc	WGD-bf lnLd	Fixation rate (γ)e	Bias strength (ε)f
At-α, Full: C. violacea order	7243	6614	3021	-25357.46	0.160	0.538
At-α, Full: Optimized order	7243	5468	1129	-24497.04	0.169	0.645
At-α, High-synteny: C. violacea order	4556	3544	1039	-12837.67	0.205	0.718
At-α, High-synteny: Optimized order	4556	2266	252	-12442.51	0.220	0.786
Grass ρ, Pineapple order	3091	4387	2299	-8822.89	0.049	0.400
Grass ρ, Optimized order	3091	2457	434	-8199.10	0.061	0.730
Yeast WGD	4065	4346	796	-19374.10	0.137	0.955g

^a: Number of ancestral loci studied.

^b: Number of synteny breaks across the polyploid genomes.

^c: Number of cases where both parental subgenomes showed a synteny break after an ancestral locus (see Methods).

^d: ln-likelihood from fitting WGD-bf to this ancestral order.

^e: Maximum likelihood estimate of the relative duplicate fixation rate for this ancestral order (see Fig 2).

^f: Maximum likelihood estimate of the relative rate of retention from the more fractionated subgenome for this ancestral order (see Fig 2).

^g: ε not significantly different from 1.0; see Fig 2.