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Diversity of microbial eukaryotes in sediment at a deep-sea methane cold seep: surveys of ribosomal DNA libraries from raw sediment samples and two enrichment cultures
TLDR
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.
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Large-Scale Phylogenomic Analyses Reveal That Two Enigmatic Protist Lineages, Telonemia and Centroheliozoa, Are Related to Photosynthetic Chromalveolates
TLDR
It is indicated that telonemids and centrohelids are members of an emerging major group of eukaryotes also comprising cryptomonads and haptophytes, and this group is possibly closely related to the SAR clade comprising stramenopiles (heterokonts), alveolates, and Rhizaria.
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Comprehensive multigene phylogenies of excavate protists reveal the evolutionary positions of "primitive" eukaryotes.
TLDR
The first multigene phylogenetic analyses to include a comprehensive sampling of excavate groups are reported, calling into question the concept of Discicristata as a supergroup of eukaryotes united by discoidal mitochondrial cristae and makes it implausible that jakobids represent an independent early-diverging eukARYotic lineage.
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Multiple Gene Phylogenies Support the Monophyly of Cryptomonad and Haptophyte Host Lineages
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Covarion shifts cause a long-branch attraction artifact that unites microsporidia and archaebacteria in EF-1alpha phylogenies.
TLDR
It is shown that the M + A affinity can be attributed to those alignment sites associated with large differences in evolutionary site rates between the eukaryotic and archaebacterial subtrees, and failure to model the significant evolutionary rate distribution differences between the ingroup and outgroup sequences is apparently responsible for the artifactual basal position of microsporidia in phylogenetic analyses of EF-1alpha sequences.
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A phylogenetic mosaic plastid proteome and unusual plastid-targeting signals in the green-colored dinoflagellate Lepidodinium chlorophorum
TLDR
This study analyzes the phylogenetic origin and N-terminal extensions of plastid-targeted proteins from Lepidodinium chlorophorum, a member of the only dinoflagellate genus that harbors a green secondary plastsid rather than the red algal-derived, peridinin-containing plastids usually found in photosynthetic dinof lagellates.
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Phylogenetic artifacts can be caused by leucine, serine, and arginine codon usage heterogeneity: dinoflagellate plastid origins as a case study.
TLDR
The results cast doubt on the single origin of peridinin-type and 19' HNOF-type plastids in dinoflagellates previously suggested on the basis of psaA and psbA concatenated gene phylogenetic analyses and 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.
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A class of eukaryotic GTPase with a punctate distribution suggesting multiple functional replacements of translation elongation factor 1alpha.
TLDR
A GTPase called EF-like (EFL), which is very similar to, but also distinct from, canonical eEF-1alpha, which is found in a wide variety of eukaryotes but its distribution is punctate: organisms that possess EFL are not closely related to one another, and EFL appears to be absent from the closest relatives of organisms that do possess it.
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Evolution of the eukaryotic translation termination system: origins of release factors.
TLDR
It is suggested that the current translation termination system in eukaryotes evolved from the archaea-like version of eRF1, eRF3 was introduced into the system prior to the divergence of extant eukARYotes, including G. lamblia, which might be the first eUKaryotic branch among the organisms considered.
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Testing for differences in rates-across-sites distributions in phylogenetic subtrees.
TLDR
This article presents methods that can be useful in detecting whether different rates occur in two different subtrees of the larger tree and where these differences occur and Parametric bootstrapping and orthogonal regression methodologies are used to test for rate differences and make statements about the general differences in the rates at sites.
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