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Fig. 1. The cladogram of the most frequent tree obtained from the Maximum Likelihood analysis of 2301 nuclear genes without evidence of positive selection. Branch support is quantified as the frequency that the node is supported by a gene alignment where the most frequent tree was not rejected or the gene’s ML tree was significantly different from the most frequent tree (see text). The tree is rooted between the two major clades identified in this group
Fig. 2. The 50% majority rule consensus phylogram of the stationary trees obtained from the Bayesian inference analysis of concatenated neutral nuclear genes at four-fold degenerate sites mid-point rooted between the two major clades previously identified. Branch support values are the BI posterior probabilities (PP), MP bootstrap (BSMP) and ML bootstrap (BSML) for genes rejecting evidence of positive selection. Branches leading to deep water species are colored in purple. The branch leading to S. droebachiensis is colored blue, as this species occurs primarily in shallow water but can range to a depth of 300 m. Adult depth range: s, shallow (0-50 m); m, medium (0-200 m); d, deep (0-1600 m). Distributions: West Pacific (WP), East Pacific (EP), holarctic (HA). The cross-section of the ultrastructure of primary spines [59]: rectangular (r), trapezoid (z), triangular (t) or ansiform (a)
Fig. 3. The 50% majority rule consensus phylogram of the stationary trees obtained from the Bayesian inference analysis of concatenated mitochondrial genes at all sites. Branch support are the Bayesian Inference posterior probabilities (BI PP), Maximum Parsimony bootstrap (MP BS) and Maximum Likelihood bootstrap (ML BS) for concatenated mitochondrial genes above and four-fold degenerate sites below the branch. Asterisks on the branch labels denote strong support for the method or all methods (BI PP > =99, MP BS > =95, ML BS > =95). Unsupported nodes are indicated with ‘-‘. Single quotation marks next to a taxon name denote the de novo assembled individual from this study of the species. Scale bar, substitutions per site
Fig. 4. The molecular clock enforced dated phylogram from Bayesian Inference (BI) among fourfold degenerate sites from partial alignments of 2,562 nuclear genes without evidence of positive selection calibrated on fossil data. The Bayes Factor test shows no difference with the clock-enforced tree and clock-non-enforced tree. Blue 95% HPD node bars are filled according to posterior probability. Vertical arrows mark the approximate timing of the opening of the Bering Strait [69]. The scale bars denote time based on two dates of calibration based on the fossil record: 13–19 Ma at node A with 12S mitochondrial sequence (Lee, 2003 rate estimate’) [35] and 5–12 Ma at node C (‘Fossil’) [67]
References :
Kober,
Phylogenomics of strongylocentrotid sea urchins.
2013, Pubmed,
Echinobase
Kober,
Phylogenomics of strongylocentrotid sea urchins.
2013,
Pubmed
,
Echinobase
