| 1. |
- Adl, Sina M., et al.
(författare)
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Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes
- 2019
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Ingår i: Journal of Eukaryotic Microbiology. - : WILEY. - 1066-5234 .- 1550-7408. ; 66:1, s. 4-119
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Tidskriftsartikel (refereegranskat)abstract
- This revision of the classification of eukaryotes follows that of Adl et al., 2012 [J. Euk. Microbiol. 59(5)] and retains an emphasis on protists. Changes since have improved the resolution of many nodes in phylogenetic analyses. For some clades even families are being clearly resolved. As we had predicted, environmental sampling in the intervening years has massively increased the genetic information at hand. Consequently, we have discovered novel clades, exciting new genera and uncovered a massive species level diversity beyond the morphological species descriptions. Several clades known from environmental samples only have now found their home. Sampling soils, deeper marine waters and the deep sea will continue to fill us with surprises. The main changes in this revision are the confirmation that eukaryotes form at least two domains, the loss of monophyly in the Excavata, robust support for the Haptista and Cryptista. We provide suggested primer sets for DNA sequences from environmental samples that are effective for each clade. We have provided a guide to trophic functional guilds in an appendix, to facilitate the interpretation of environmental samples, and a standardized taxonomic guide for East Asian users.
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| 2. |
- He, Ding, et al.
(författare)
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Reducing long-branch effects in multi-protein data uncovers a close relationship between Alveolata and Rhizaria
- 2016
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Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier. - 1055-7903 .- 1095-9513. ; 101, s. 1-7
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Tidskriftsartikel (refereegranskat)abstract
- Rhizaria is a major eukaryotic group of tremendous diversity, including amoebae with spectacular skele- tons or tests (Radiolaria and Foraminifera), plasmodial parasites (Plasmodiophorida) and secondary endosymbionts (Chlorarachniophyta). Current phylogeny places Rhizaria in an unresolved trichotomy with Stramenopila and Alveolata (supergroup ‘‘SAR”). We assembled a 147-protein data set with exten- sive rhizarian coverage (M147), including the first transcriptomic data for a euglyphid amoeba. Phylogenetic pre-screening of individual proteins indicated potential problems with radically misplaced sequences due either to contamination of rhizarian sequences amplified from wild collected material and/or extremely long branches (xLBs). Therefore, two data subsets were extracted containing either all proteins consistently recovering rhizarian monophyly (M34) or excluding all proteins with P3 xLBs (defined as P2? the average terminal branch length for the tree). Phylogenetic analyses of M147 give conflicting results depending on the outgroup and method of analysis but strongly support an exclusive Rhizaria + Alveolata (R + A) clade with both data subsets (M34 and M37) regardless of phylogenetic method used. Support for an R + A clade is most consistent when a close outgroup is used and decreases with more distant outgroups, suggesting that support for alternative SAR topologies may reflect a long-branch attraction artifact. A survey of xLB distribution among taxa and protein functional category indicates that small ‘‘informational” proteins in particular have highly variable evolutionary rates with no consistent pattern among taxa.
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| 3. |
- Meibohm, Jan, et al.
(författare)
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Chiral fermions in asymptotically safe quantum gravity
- 2016
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Ingår i: European Physical Journal C. - : Springer Science and Business Media LLC. - 1434-6044 .- 1434-6052. ; 76:5
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Tidskriftsartikel (refereegranskat)abstract
- We study the consistency of dynamical fermionic matter with the asymptotic safety scenario of quantum gravity using the functional renormalisation group. Since this scenario suggests strongly coupled quantum gravity in the UV, one expects gravity-induced fermion self-interactions at energies of the Planck scale. These could lead to chiral symmetry breaking at very high energies and thus to large fermion masses in the IR. The present analysis which is based on the previous works (Christiansen et al., Phys Rev D 92:121501, 2015; Meibohm et al., Phys Rev D 93: 084035, 2016), concludes that gravity-induced chiral symmetry breaking at the Planck scale is avoided for a general class of NJL-type models. We find strong evidence that this feature is independent of the number of fermion fields. This finding suggests that the phase diagram for these models is topologically stable under the influence of gravitational interactions.
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| 4. |
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| 5. |
- Poznański, Jarosław, et al.
(författare)
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Global pentapeptide statistics are far away from expected distributions
- 2018
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 8:1
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Tidskriftsartikel (refereegranskat)abstract
- The relationships between polypeptide composition, sequence, structure and function have been puzzling biologists ever since first protein sequences were determined. Here, we study the statistics of occurrence of all possible pentapeptide sequences in known proteins. To compensate for the non-uniform distribution of individual amino acid residues in protein sequences, we investigate separately all possible permutations of every given amino acid composition. For the majority of permutation groups we find that pentapeptide occurrences deviate strongly from the expected binomial distributions, and that the observed distributions are also characterized by high numbers of outlier sequences. An analysis of identified outliers shows they often contain known motifs and rare amino acids, suggesting that they represent important functional elements. We further compare the pentapeptide composition of regions known to correspond to protein domains with that of non-domain regions. We find that a substantial number of pentapeptides is clearly strongly favored in protein domains. Finally, we show that over-represented pentapeptides are significantly related to known functional motifs and to predicted ancient structural peptides.
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