Birth-death prior on phylogeny and speed dating

Table 1 Parameter inference simulations. Results from pairwise MAP runs on 100 generated tree topologies using the combined method, the r × t-method, and the l-method.

Tree size	Method¹	MAP value	MAP diff²		Rates diff³		Times diff⁴		Comp time⁵
		average	average	worst	average	worst	average	worst	relative
10 leaves	combined	-8046.54	0.48	3.39	0.58	1.46	0.26	0.72	1
	r × t	-8046.72	0.32	13.03	0.36	4.61	0.17	1.73	2
	l	-8049.34	0.012	0.20	0.00068	0.0084	0.0015	0.05	1
100 leaves	combined	-65249.12	1.61	8.60	4.72	10.64	1.24	3.39	2
	r × t	-65257.40	4.66	23.10	14.08	21.66	5.11	9.19	10
	l	-65258.41	0.16	1.54	0.034	0.071	0.060	0.41	1

¹The combined method and the r × t-method infer optimal substitution rates and divergence times. The l-method infer optimal branch lengths which are subsequently partitioned into rates and times. The latter problem is much easier and the inferred rates and times less optimal.
²Difference in log-likelihood between two MAP runs on the same tree.
³Difference in substitution rate norm between two MAP runs on the same tree.
⁴Difference in divergence time norm between two MAP runs on the same tree.
⁵Approximate computation time relative to the l-method.

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