The prevalence of terraced treescapes in analyses of phylogenetic data sets

Table 1 Data set profiles and results of terrace and decisiveness analyses

Taxon	Number of taxa	Number of loci	Number of sites^	Taxon coverage density	Terrace size	ρ (resolution) of strict consensus of trees on terrace	Min. loci needed for decisiveness (kmin), p = .05	Gene (locus) sampling sufficiency (ζ)	Ref.
Birds	7000	32	39,611	0.12	1.30E + 388	**	129,035	−8.3	[39]
Lichenized fungi	1317	9	7433	0.44	11,655	**	574	−4.16	[40]
Saxifragales	946	51	48,242	0.06	**	NA	2,107,107	−10.63	[33]
Bats	815	29	20,364	0.15	1.43E + 41	0.78	44,209	−7.33	[41]
Rosaceae*	529	7	11,728	0.3	1.72E + 23	0.77	2627	− 5.93	[42]
Primates	372	79	61,198	0.37	70.8 million	0.92	982	− 2.52	[43]
Caryophyllaceae*	225	7	11,753	0.29	718.3 billion	0.77	2349	− 5.82	[42]
Scincid lizards	213	6	5283	0.78	3	~ 1.00	37	−1.83	[44]
Chameleons	202	6	5054	0.92	1	1	14	−0.83	[45]
Solanum*	187	7	11,875	0.31	211.9 million	0.68	1730	− 5.51	[42]
Primula*	185	6	9408	0.43	2835	0.92	466	−4.35	[42]
Ranunculus*	170	7	9504	0.31	3	0.99	1889	− 5.6	[42]
Mammals	169	26	35,600	0.94	1	1	11	0.86	[46]
Insects	144	479	413,459	0.95	1	1	10	3.88	[34]
Iris*	137	6	8098	0.33	1	1	1384	−5.44	[42]
Eucalyptus*	136	6	7512	0.23	27	0.9	5416	− 6.81	[42]
Asplenium*	133	6	9797	0.21	95	0.64	8269	−7.23	[42]
Euphorbia*	131	7	11,648	0.28	759	0.87	2681	−5.95	[42]
Rhododendron*	117	7	9536	0.35	81	0.95	1034	−5	[42]
Ficus*	112	5	5645	0.36	851,445	0.8	12,357	−7.81	[42]
Syzygium*	106	5	5775	0.35	45	0.96	994	−5.29	[42]
1000 Plants.1	102	8	290,719	0.97	1	1	7	0.15	[47]
1000 Plants.2	102	620	290,719	0.91	1	1	13	3.88	[47]
Caryophyllales.1	95	209	87,082	0.98	1	0.99	8	3.23	[48]
Caryophyllales.2	95	1122	504,850	0.92	1	0.99	12	4.56	[48]
Allium*	57	6	6938	0.24	973,215	0.32	4231	− 6.56	[42]

^: Site counts do not include alignment columns containing no data, and may differ from counts reported in the original literature. k_min: theoretical minimum number of loci that would need to be sampled to guarantee that a data set of a given sampling density and taxon count would be decisive for a random, unrooted tree, assuming random distribution of taxon samples. ζ: gene (locus) sampling depth “sufficiency”: k_min normalized to the number of genes (loci) sampled and transformed for scale. ζ < 0 indicates insufficient sampling depth, ζ > = 0 sufficient sampling depth. * denotes a subsample of the Zanne et al. [42] vascular plant “megamatrix”. **: tree enumeration or consensus tree construction terminated prior to program completion

ISSN: 2730-7182