Yuji Inagaki

..We advise that homogeneity in codon usage across taxa in a data set be confirmed before codon model-based phylogenetic estimation is attempted...

..We concluded that larger scale multi-gene phylogenies are necessary to elucidate the origin and evolution of Centrohelida...

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..We also address the validity of fast-evolving gene exclusion in multi-gene phylogenetic analyses, in light of this gene sampling bias...

..Finally, the relative timing of the first emergence of EFL gene in eukaryotes was contemplated based on the current EF-1alpha/EFL distribution...

..globosa possessed a novel set of morphological features, and could not be classified into any taxa in the Discoba clade. Instead we classified T. globosa into Tsukubamonadidae n. fam. under Tsukubamonadida n. ord...

..All the analyses of the 11-protein data set robustly grouped L. chlorophorumwith members of the "core chlorophytes." Thus, we here propose that Lepidodiniumplastids are of core chlorophyte origin...

..Based on the results, we postulate that cercozoan EF-1α genes have been vertically inherited, and the current EFL-containing species may have secondarily lost their EF-1α genes...

..Various scenarios of MAT and MATX gene family evolution in diatoms are re-evaluated in light of the new data...

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..chlorophorum plastid and the green algal plastids considered in this study. Finally, the possible evolutionary events required for the reassignment of AUA from Ile to Met in Lepitodinium plastids were discussed...

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..sorex, and Rhopalodia gibba. Phylogenetic analyses considering these new sequences clearly indicate that the SBs were acquired by a common ancestor of rhopalodiacean diatoms and have been retained during host speciation...

..These split introns have properties that distinguish them from other trans-splicing systems known within eukaryotes, suggesting that Giardia independently evolved a unique system to splice split introns...

..The performance of a non-homogeneous analysis was also validated by analyzing a real-world sequence data set with significant base heterogeneity...

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..Combining both morphological and molecular phylogenetic analyses, D. brevis is classified as a new free-living excavate in the Fornicata incertae sedis...

..On the basis of the results of both morphological and molecular studies, we discuss the possibility that P. bilix might provide key information on the early evolution of major groups of photosynthetic eukaryotes...

..The present analyses place P. fragile in a position that is incongruent with the early branching status of P. fragile amongst P-vivax-related primate Plasmodium species propose by Escalante et al. (Proc Natl Acad Sci USA 2005 102: 1980)...

..Although difficult to detect by standard whole-gene phylogenetic analyses, interspecific HR in highly conserved genes may occur at an appreciable frequency, potentially confounding deep phylogenetic inference and hypothesis testing...

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..The focus is on distance methods, but previous simulation results suggest that the zones of inconsistency for distance methods contain the zones of inconsistency for maximum likelihood methods as well...

..Supporting evidence for the theory is presented in this review. A possible evolutionary process from the ancient to the present-day genetic code is also discussed...

..To our knowledge, this is the first unequivocal case of LGT followed by functional modification to be described; this mechanism could be a potentially important force in establishing genes with novel functions in genomes...

..Such methods will be helpful in studying the phylogenetic, structural, and functional bases of changes in evolutionary rates at sites, a phenomenon that has important consequences for deep phylogenetic inference...

..We re-assess the available genetic data for HBS1 in light of our analyses, and propose that this protein may function in stop codon-independent peptide release...

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..We suggest that codon usage heterogeneity could be a more general problem for DNA level analyses of protein-coding genes, even when third codon positions are excluded...

..Altogether, it appears that EFL has replaced eEF-1alpha several times independently. This finding could be an indication of an ancient paralogy or, more likely, eukaryote-to-eukaryote lateral gene transfer...

..The Foraminifera+Cercozoa affinity recovered in the latter multi-gene analyses is most likely genuine, and thus our data presented here provide further support for the close relationship between these two protist lineages...

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..Since these phylotypes were not identified in the raw sediment samples, the approach incorporating a cultivation step successfully found at least a fraction of the "hidden" microeukaryotic diversity in the environment examined...

..This relationship demonstrates that loss of nucleomorphs must have taken place in haptophytes independently of any other red alga-containing lineages and that the ancestor of both already contained a red algal endosymbiont...

..Thus, future data analyses of larger multi-gene data sets, preferentially under the unlinked model, are required to conclusively understand Chl-c plastid evolution...

..However, in the light of Lepidodinium GAPDH data, we need to closely examine whether the monophyly of the plastids in the above lineages inferred from plastid-targeted GapC genes truly reflects that of the host lineages...

..Finally, based on a reverse transcriptase quantitative PCR assay and the genome information of Thalassiosira and Phaeodactylum, we propose the loss of elongation factor function in Thalassiosira EF-1alpha...

..We assess the feasibility of this alternative binding orientation with a triplet stop codon and the eRF1 domain 1 structures using molecular modeling techniques...