Table 1.

Bootstrap support for deuterostome phylogenetic trees

Tree algorithm	Uro	Chor	Hemi	Echin	Hemi + Echin	Chor + Uro	Basal Deut?
Full dataset (29 deuterostomes)
NJ, Kimura	100	60	94	100	67	—	Chor
NJ, Kimura with γ	100	65	89	99	—	—	Echin
MP	96	83	93	89	80	59	2 + 2
ME, Kimura	100	68	92	99	56	—	Chor
ME, Kimura with γ	99	66	93	97	—	—	Chor
ME, Paralinear	99	56	95	97	—	—	Chor
≤0.1400 subs/site (19 deuterostomes)
NJ, Kimura	100	70	100	100	—	—	Chor
NJ, Kimura with γ	100	72	100	100	—	—	Echin
MP	100	79	93	88	66	54	2 + 2
ME, Kimura	100	71	99	98	—	—	poly
ME, Kimura with γ	100	68	100	98	—	—	poly
ME, Paralinear	100	58	99	100	—	—	poly
≤0.1200 subs/site (16 deuterostomes)
NJ, Kimura	100	71	100	100	80	—	Chor
NJ, Kimura with γ	100	67	100	99	64	—	Chor
MP	100	67	100	96	86	65	2 + 2
ME, Kimura	100	63	100	100	83	—	Chor
ME, Kimura with γ	100	74	100	100	70	—	poly
ME, Paralinear	100	63	100	100	89	—	Chor
ML	100	53	100	100	100	—	Chor
gambit and paralinear outgroup
Nephtys (0.1518)	100	71	98	90	86	83	2 + 2
Glycera (0.1432)	100	74	98	94	78	85	2 + 2
Artemia (0.2478)	100	68	86	99	86	—	poly
Tenebrio (0.2327)	100	—	100	87	89	—	poly
Anemonia (0.3373)	99	59	93	98	73	—	Chor

Summary of analyses of the full dataset (28 deuterostomes), a subset including those taxa with a branch length ≤0.1400 substitution per site, and a deuterostome subset with branch lengths of ≤0.1200 substitution per site. Bootstrap values are shown for the monophyly of urochordates (Uro), chordates (including cephalochordates, Chor), hemichordates (Hemi), and echinoderms (Echin). Bootstrap values for a monophyletic hemichordates + echinoderms and a monophyletic chordates + urochordates are shown when greater than 50%. The basal deuterostome in each analysis is shown unless there was a polytomy (poly). Instances where hemichordates + echinoderms was a sister group to chordates + urochordates are shown labeled “2 + 2.” Methods include NJ and ME trees with Kimura two-parameter, Kimura two-parameter with γ correction, or paralinear distances, and MP. ML and gambit analysis were carried out only for the smallest dataset (≤0.1200 subs per site). gambit was used with paralinear distances and a correction for site-to-site variation by using a variety of outgroups. The Kimura two-parameter γ corrected distances between each outgroup and Antedon are shown in parentheses. The most reliable analyses are shown in bold.