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Tests for two trees using likelihood methods.
Mol Biol Evol. 2014 Apr;31(4):1029-39
Authors: Susko E
Abstract
This article considers two similar likelihood-based test statistics for…

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An amino acid substitution-selection model adjusts residue fitness to improve phylogenetic estimation.

Mol Biol Evol. 2014 Apr;31(4):779-92

Authors: Wang HC, Susko E, Roger AJ

Abstract
Standard protein phylogenetic models use fixed rate matrices of amino acid interchange derived from analyses of large databases. Differences between the stationary amino acid frequencies of these rate matrices from those of a data set of interest are typically adjusted for by matrix multiplication that converts the empirical rate matrix to an exchangeability matrix which is then postmultiplied by the amino acid frequencies in the alignment. The result is a time-reversible rate matrix with stationary amino acid frequencies equal to the data set frequencies. On the basis of population genetics principles, we develop an amino acid substitution-selection model that parameterizes the fitness of an amino acid as the logarithm of the ratio of the frequency of the amino acid to the frequency of the same amino acid under no selection. The model gives rise to a different sequence of matrix multiplications to convert an empirical rate matrix to one that has stationary amino acid frequencies equal to the data set frequencies. We incorporated the substitution-selection model with an improved amino acid class frequency mixture (cF) model to partially take into account site-specific amino acid frequencies in the phylogenetic models. We show that 1) the selection models fit data significantly better than corresponding models without selection for most of the 21 test data sets; 2) both cF and cF selection models favored the phylogenetic trees that were inferred under current sophisticated models and methods for three difficult phylogenetic problems (the positions of microsporidia and breviates in eukaryote phylogeny and the position of the root of the angiosperm tree); and 3) for data simulated under site-specific residue frequencies, the cF selection models estimated trees closer to the generating trees than a standard Г model or cF without selection. We also explored several ways of estimating amino acid frequencies under neutral evolution that are required for these selection models. By better modeling the amino acid substitution process, the cF selection models will be valuable for phylogenetic inference and evolutionary studies.

PMID: 24441033 [PubMed – indexed for MEDLINE]

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The pre-endosymbiont hypothesis: a new perspective on the origin and evolution of mitochondria.

Cold Spring Harb Perspect Biol. 2014 Mar;6(3)

Authors: Gray MW

Abstract
Mitochondrial DNA (mtDNA) is unquestionably the remnant of an α-proteobacterial genome, yet only ~10%-20% of mitochondrial proteins are demonstrably α-proteobacterial in origin (the “α-proteobacterial component,” or APC). The evolutionary ancestry of the non-α-proteobacterial component (NPC) is obscure and not adequately accounted for in current models of mitochondrial origin. I propose that in the host cell that accommodated an α-proteobacterial endosymbiont, much of the NPC was already present, in the form of a membrane-bound metabolic organelle (the premitochondrion) that compartmentalized many of the non-energy-generating functions of the contemporary mitochondrion. I suggest that this organelle also possessed a protein import system and various ion and small-molecule transporters. In such a scenario, an α-proteobacterial endosymbiont could have been converted relatively directly and rapidly into an energy-generating organelle that incorporated the extant metabolic functions of the premitochondrion. This model (the “pre-endosymbiont hypothesis”) effectively represents a synthesis of previous, contending mitochondrial origin hypotheses, with the bulk of the mitochondrial proteome (much of the NPC) having an endogenous origin and the minority component (the APC) having a xenogenous origin.

PMID: 24591518 [PubMed – indexed for MEDLINE]

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Getting “function” right.
Proc Natl Acad Sci U S A. 2014 Aug 19;111(33):E3365
Authors: Brunet TD, Doolittle WF
PMID: 25107292 [PubMed – indexed for MEDLINE]

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Rhodoluna lacicola gen. nov., sp. nov., a planktonic freshwater bacterium with stream-lined genome.

Int J Syst Evol Microbiol. 2014 Sep;64(Pt 9):3254-63

Authors: Hahn MW, Schmidt J, Taipale SJ, Doolittle WF, Koll U

Abstract
A pure culture of an actinobacterium previously described as ‘Candidatus Rhodoluna lacicola’ strain MWH-Ta8 was established and deposited in two public culture collections. Strain MWH-Ta8(T) represents a free-living planktonic freshwater bacterium obtained from hypertrophic Meiliang Bay, Lake Taihu, PR China. The strain was characterized by phylogenetic and taxonomic investigations, as well as by determination of its complete genome sequence. Strain MWH-Ta8(T) is noticeable due to its unusually low values of cell size (0.05 µm(3)), genome size (1.43 Mbp), and DNA G+C content (51.5 mol%). Phylogenetic analyses based on 16S rRNA gene and RpoB sequences suggested that strain MWH-Ta8(T) is affiliated with the family Microbacteriaceae with Pontimonas salivibrio being its closest relative among the currently described species within this family. Strain MWH-Ta8(T) and the type strain of Pontimonas salivibrio shared a 16S rRNA gene sequence similarity of 94.3 %. The cell-wall peptidoglycan of strain MWH-Ta8(T) was of type B2β (B10), containing 2,4-diaminobutyric acid as the diamino acid. The predominant cellular fatty acids were anteiso-C15 : 0 (36.5 %), iso-C16 : 0 (16.5 %), iso-C15 : 0 (15.6 %) and iso-C14 : 0 (8.9 %), and the major (>10 %) menaquinones were MK-11 and MK-12. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and two unknown glycolipids. The combined phylogenetic, phenotypic and chemotaxonomic data clearly suggest that strain MWH-Ta8(T) represents a novel species of a new genus in the family Microbacteriaceae, for which the name Rhodoluna lacicola gen. nov., sp. nov. is proposed. The type strain of the type species is MWH-Ta8(T) ( = DSM 23834(T) = LMG 26932(T)).

PMID: 24984700 [PubMed – indexed for MEDLINE]

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A phylogenomic view of ecological specialization in the Lachnospiraceae, a family of digestive tract-associated bacteria.
Genome Biol Evol. 2014 Mar;6(3):703-13
Authors: Meehan CJ, Beiko RG
…