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Link to original content: http://www.ncbi.nlm.nih.gov/pubmed/24399481
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. 2014 Mar;63(2):272-9.
doi: 10.1093/sysbio/syt109. Epub 2014 Jan 6.

Conflicting phylogenies for early land plants are caused by composition biases among synonymous substitutions

Cymon J Cox  1 , Blaise Li, Peter G Foster, T Martin Embley, Peter Civán
Affiliations

Conflicting phylogenies for early land plants are caused by composition biases among synonymous substitutions

Cymon J Cox et al. Syst Biol. 2014 Mar.
No abstract available

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Figures

F<sc>igure</sc> 1.
Figure 1.
Summary trees of conflict between chloroplast protein-coding gene data (a) and their translated proteins (b) of the data set Karol10-nuc. Trees are depicted without the outgroup taxa (Chlorokybus and Mesosigma) and the seed plant clade is collapsed—full trees are presented in the Supplementary Material. Taxa are indicated as follows: algal charophytes (blue), bryophytes (Marchantia—liverwort, Physcomitrella and Tortula—mosses, Anthoceros—hornwort; green), lycopods (mauve), and ferns (orange). a) Bayesian MCMC (p4) with model 3*(GTR + I + Γ4 + CV2) + Rm + PP, marginal likelihood -Lh = 452713.8554 (Supplementary Fig. S1); b) Bayesian MCMC (p4) with model gcpREV + I + Γ4 + PP, marginal likelihood -Lh = 178265.1502 (Supplementary Fig. S9). The branch leading to Selaginalla species has been arbitrarily shortened (original length = 0.261519). All protein analyses maximally supported a monophyletic bryophytes (hornworts, mosses, liverworts) but only weak (<0.95 PP) support for relationships among tracheophyte groups (lycopods, ferns, seed plants) was observed.
F<sc>igure</sc> 2.
Figure 2.
Correspondence analysis of the first and second principal components of the variation of RSCU among the taxa in the Karol10-nuc chloroplast gene data set. Algae: blue; bryophytes: green; ferns: orange; lycopods: mauve; seed plants: red.
F<sc>igure</sc> 3.
Figure 3.
Comparison of mean model parameter values compared between data of all substitutions (all) and the codon-degenerated data consisting of only nonsynonymous substitutions (non-syn) of the Karol10-nuc data: a) composition frequencies, both empirical values and marginal estimates, and b) marginal estimates of substitution exchange rates. Marginal estimates are mean posterior values from the homogeneous MCMC analyses shown in Supplementary Figures S6 and S15 for “all” and “non-syn” data respectively. The error bars represent the 95% confidence interval (1.96 standard deviations of the mean of the posterior sample).
F<sc>igure</sc> 4.
Figure 4.
Summary tree of the maximum-likelihood bootstrap analysis of the codon-degenerated Karol10-nuc data. Tree structure summation and taxon colors follow those detailed in the legend of Figure 1.
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