Cnidaria host genome phylogeny reconstructed using Bayesian methods from 18S, 5.8S and ITS data, and is a 50% majority rule consensus taken from the MCMC analyses after plateau (i.e. ‘burn-in’ trees discarded).

<div><p>The Bayesian posterior probabilities are given for each node.</p> <p>Taxa containing a HEG are highlighted; the non-functional HEG is boxed.</p> <p>Taxonomic classification is also distinguished; O(A)  =  Octocorallia (Alcyonaria); C  =  Corrimorpharia; S  =  Scleratinia; Z  =  Zoanthiniaria.</p></div

Comparison of Actinarian and HEG phylogenies.

<div><p> <b>A.</b> The numbers above each branch are the Bayesian posterior probabilities (again after burn-in trees discarded), and those below the branch are the support generated from a likelihood bootstrap analysis (n = 1000).</p> <p>The HEG tree is unrooted (it is unknown) and displayed in such a way as to minimise the differences with the host tree.</p> <p> <b>B.</b> The null distribution for the likelihood ratio test generated by evaluating δ for 1000 non-parametric bootstrap resampled data sets, 50% of which are drawn entirely from the host data and 50% from the HEG data.</p> <p>The likelihood ratio for the observed partition is shown.</p></div

3′ RNA processing motifs in zygomycetes, basidiomycetes and fission yeasts

<p><b>Copyright information:</b></p><p>Taken from "Comparative mitochondrial genomics in zygomycetes: bacteria-like RNase P RNAs, mobile elements and a close source of the group I intron invasion in angiosperms"</p><p>Nucleic Acids Research 2005;33(2):734-744.</p><p>Published online 02 Feb 2005</p><p>PMCID:PMC548346.</p><p>© The Author 2005. Published by Oxford University Press. All rights reserved</p> The 3′ termini of the mitochondrial SSU rRNA and of mRNA were determined by nuclease S1 assays and run on a sequencing gel against a commercial 10 bp ladder (Invitrogen 10821-015) that was 3′ labeled with ddATP (P). For experimental details see Materials and Methods. The positions of 3′ termini for both molecules are indicated in the derived consensus sequences by arrows. A small fraction of the undigested form of the SSU rRNA probe is apparent on the gel. In the lower part of the figure, additional, similar motifs in fissions yeasts and basidiomycetes are presented. Uppercase letters indicate 100% conservation and lowercase letters correspond to at least 60% nucleotide conservation. Lowercase Cs between brackets indicate the C-clusters of variable length

Maximum likelihood tree of the Hexamitinae-enteromonad clade based on SSU rRNA genes (GTR Γ I), rooted as per Figure 1

Statistical support – ML bootstraps/RELL bootstraps/ML distance bootstraps/Bayesian posterior probability. Isolate PYX was identical in sequence with isolate PSEUD. Isolate PYX was therefore not included in the analysis but added to the tree by hand. Bootstrap support values <p><b>Copyright information:</b></p><p>Taken from "Molecular phylogeny of diplomonads and enteromonads based on SSU rRNA, alpha-tubulin and HSP90 genes: Implications for the evolutionary history of the double karyomastigont of diplomonads"</p><p>http://www.biomedcentral.com/1471-2148/8/205</p><p>BMC Evolutionary Biology 2008;8():205-205.</p><p>Published online 15 Jul 2008</p><p>PMCID:PMC2496913.</p><p></p

Maximum likelihood tree of Fornicata based on SSU rRNA genes (GTR Γ I model)

Statistical support – ML bootstraps/RELL bootstraps/ML distance bootstraps/Bayesian posterior probability. Isolate PYX was identical in sequence with isolate PSEUD. Isolate PYX was therefore not included in the analysis but added to the tree by hand. Bootstrap support values <p><b>Copyright information:</b></p><p>Taken from "Molecular phylogeny of diplomonads and enteromonads based on SSU rRNA, alpha-tubulin and HSP90 genes: Implications for the evolutionary history of the double karyomastigont of diplomonads"</p><p>http://www.biomedcentral.com/1471-2148/8/205</p><p>BMC Evolutionary Biology 2008;8():205-205.</p><p>Published online 15 Jul 2008</p><p>PMCID:PMC2496913.</p><p></p

Molecular phylogeny of diplomonads and enteromonads based on SSU rRNA, alpha-tubulin and HSP90 genes: Implications for the evolutionary history of the double karyomastigont of diplomonads-0

arrest of cytokinesis. The cell does not divide after the first karyokinesis and secondary karyokinesis results in a cell with four karyomastigonts. This cell then divides into two cells, each with a double karyomastigont. C. Model of evolutionary change from double karyomastigont morphology to single karyomastigont morphology, either by cytokinesis without karyokinesis, or by fusion of nuclei. (modified from Siddall, Hong and Desser 1992).<p><b>Copyright information:</b></p><p>Taken from "Molecular phylogeny of diplomonads and enteromonads based on SSU rRNA, alpha-tubulin and HSP90 genes: Implications for the evolutionary history of the double karyomastigont of diplomonads"</p><p>http://www.biomedcentral.com/1471-2148/8/205</p><p>BMC Evolutionary Biology 2008;8():205-205.</p><p>Published online 15 Jul 2008</p><p>PMCID:PMC2496913.</p><p></p