Table 1.

Gene tree discordance relative to the Pachycereeae species tree (Fig. 2B)

Gene confidence set	90% set	80% set	70% set	60% set	50% set
N genes	458	786	1,065	1,668	2,291
Gene tree concordance, %*
Edge A†	76	75	74	68	65
Edge B	77	75	75	73	70
Whole tree	63	61	58	52	47
MP-EST edge length‡
Edge A	1.01	0.96	0.94	0.78	0.69
Edge B	1.22	1.21	1.15	1.04	0.93
BPP edge length§
All partition
Edge A	1.23	1.14	1.09	0.95	0.88
Edge B	1.22	1.22	1.18	1.14	1.10
Neutral partition
Edge A	1.24	1.16	1.09	0.97	0.89
Edge B	1.28	1.29	1.24	1.21	1.18
Third partition
Edge A	1.22	1.11	1.08	0.95	0.87
Edge B	1.32	1.34	1.24	1.18	1.12

^*Agreement of gene tree edge bipartitions or entire gene tree with species tree.

^†See Fig. 2B for location of edges.

^‡In coalescent time units. 1 CTU = 2N_e generations.

^§In CTUs estimated from 2D/θ, where D and θ are sequence divergence-scaled edge length and scaled effective population size, respectively, taken from BPP output.