Table 2.

Regressions through the origin relating contrasts in log substitution rates to contrasts in transformed clade sizes across sister pairs

Phylogeny	Mono. Filter	Rank	Sequence set	Subst. Rate	No. pairs	Coeff	Std. Err	t	P value ( >|t|)
Rabosky et al. (2018)	Full	Families	Mito.All	Total	50	0.82	0.68	1.20	0.24
			Mito.Coding	dS	77	− 0.68	1.11	− 0.61	0.54
				dN	78	− 0.07	0.35	− 0.21	0.83
			Nuc.RAG1	Total	113	0.92	0.25	3.63	< 0.01
				dS	65	0.72	0.28	2.60	0.01
				dN	62	0.47	0.33	1.43	0.16
		Genera	Mito.All	Total	64	0.07	0.55	0.12	0.90
			Mito.Coding	dS	235	0.08	0.14	0.62	0.54
				dN	138	− 0.05	0.10	− 0.53	0.60
			Nuc.RAG1	Total	256	0.22	0.10	2.14	0.03
				dS	355	0.02	0.08	0.29	0.77
				dN	247	0.18	0.10	1.90	0.06
	Filtered	Families	Mito.All	Total	41	0.97	0.79	1.24	0.22
			Mito.Coding	dS	58	0.24	0.57	0.42	0.68
				dN	63	0.03	0.37	0.07	0.94
			Nuc.RAG1	Total	82	0.74	0.31	2.38	0.02
				dS	44	0.43	0.37	1.17	0.25
				dN	43	0.50	0.42	1.20	0.24
		Genera	Mito.All	Total	48	− 0.19	0.55	− 0.35	0.73
			Mito.Coding	dS	144	− 0.05	0.13	− 0.40	0.69
				dN	83	0.21	0.10	2.13	0.04
			Nuc.RAG1	Total	121	0.32	0.19	1.71	0.09
				dS	199	− 0.02	0.11	− 0.19	0.85
				dN	131	0.07	0.14	0.49	0.63
Betancur-R et al. (2013)	Yes	Families	Nuc.ETOL	Total	78	0.64	0.30	2.13	0.04
				dS	75	0.81	0.36	2.26	0.03
				dN	78	0.08	0.21	0.36	0.72

Regressions were conducted on the phylogenies of Rabosky et al. (2018) and Betancur-R et al. (2013), and with or without filtering pairs for mutual monophyly of formal taxa (Mono. Filter). Data is shown for mitochondrial sequences with rRNA (Mito.All) and without (Mito.Coding). Nuclear data consists of RAG1 only for the Rabosky tree and of 19 nuclear marker from the Euteleost tree of life (ETOL) for the Betancur tree. Total, synonymous (dS) and nonsynonymous (dN) substitution rates are tested as predictors of clade size. t statistics and P values are for Wald tests. Results with P < 0.05 are in italics