Category: Papers by CGEB labs

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Supertrees Based on the Subtree Prune-and-Regraft Distance.
Syst Biol. 2014 Jul;63(4):566-81
Authors: Whidden C, Zeh N, Beiko RG
Abstract
Supertree methods reconcile a set of phylo…

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Compositional complexity of the mitochondrial proteome of a unicellular eukaryote (Acanthamoeba castellanii, supergroup Amoebozoa) rivals that of animals, fungi, and plants.
J Proteomics. 2014 Jul 12;109C:4…

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Alignment Errors Strongly Impact Likelihood-Based Tests for Comparing Topologies.
Mol Biol Evol. 2014 Aug 1;
Authors: Levy Karin E, Susko E, Pupko T
Abstract
Estimating phylogenetic …

Characterisation of Tulamoeba bucina n. sp., an Extremely Halotolerant Amoeboflagellate Heterolobosean Belonging to the Tulamoeba-Pleurostomum Clade (Tulamoebidae n. fam.).

J Eukaryot Microbiol. 2014 Sep 17;

Authors: Kirby WA, Tikhonenkov DV, Mylnikov AP, Janouškovec J, Lax G, Simpson AG

Abstract
Most protozoans that have been cultivated recently from high salinity waters appear to be obligate halophiles. Phylogenetic analyses indicate that these species mostly represent independent lineages. Here we report the cultivation, morphological characterisation, and phylogenetic analysis of two strains (XLG1 and HLM-8) of a new extremely halotolerant heterolobosean amoeboflagellate. This species is closely related to the obligate halophiles Tulamoeba peronaphora and Pleurostomum flabellatum, and more specifically to the former. Like Tulamoeba, the new species has a monopodial limax amoeba stage, however, its cyst stage lacks an intrusive pore plug. The flagellate stage bears a combination of a planar spiral feeding apparatus and unequal heterodynamic flagella, which discriminate it from described Pleurostomum species. Strain XLG1 grows at salinities from 35‰ to 225‰. This degree of halotolerance is uncommon in protozoa, as most species showing growth in seawater are unable to grow at 200‰ salinity. The unrelatedness of most halophilic protozoa suggested that independent colonization of the hypersaline environment is more common than speciation within it. However, this study supports the idea that the Tulamoeba-Pleurostomum clade underwent an adaptive radiation within the hypersaline environment. A new species Tulamoeba bucina n. sp. is described, with Tulamoebidae n. fam. proposed for the Tulamoeba-Pleurostomum clade. This article is protected by copyright. All rights reserved.

PMID: 25227416 [PubMed – as supplied by publisher]

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Seasonal assemblages and short-lived blooms in coastal northwest Atlantic Ocean bacterioplankton.
Environ Microbiol. 2014 Sep 22;
Authors: El-Swais H, Dunn KA, Bielawski JP, Li WK, Walsh DA
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The trouble with (group II) introns.
Proc Natl Acad Sci U S A. 2014 May 6;111(18):6536-7
Authors: Doolittle WF
PMID: 24757059 [PubMed – indexed for MEDLINE]

The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing.
PLoS Biol. 2014 Jun;12(6):e1001889
A…

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Interactions in the microbiome: communities of organisms and communities of genes.
FEMS Microbiol Rev. 2014 Jan;38(1):90-118
Authors: Boon E, Meehan CJ, Whidden C, Wong DH, Langille MG, Beiko RG
…

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A SUF Fe-S Cluster Biogenesis System in the Mitochondrion-Related Organelles of the Anaerobic Protist Pygsuia.
Curr Biol. 2014 May 21;
Authors: Stairs CW, Eme L, Brown MW, Mutsaers C, Susko E, Della…

Distinguishing between “function” and “effect” in genome biology.
Genome Biol Evol. 2014 May 9;
Authors: Doolittle WF, Brunet TD, Linquist S, Gregory TR
Abstract
There is renewed debate among biolog…