ProtTest: selection of best-fit models of protein evolution

Abascal, Federico; Zardoya, Rafael; Posada, David

doi:10.1093/bioinformatics/bti263

Cited by 2,785 publications

(1,983 citation statements)

References 14 publications

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“…Using 81 curated sequences, multiple sequence alignments were inferred using MSAProbs (Liu, Schmidt, & Maskell, 2010) and MUSCLE (Edgar, 2004) with the default settings. Both of these alignments were best‐fit by the PROTCATWAG model (Lartillot & Philippe, 2004; Le & Gascuel, 2008), with model fitness assessed using the Akaike information criterion (Abascal, Zardoya, & Posada, 2005). The 81 protein sequences used in this study are available to download from the following URL: http://www.phylobot.com/582058404/RuBisCO.noalign.fasta …”

Section: Methodsmentioning

confidence: 99%

Constraining the timing of the Great Oxidation Event within the Rubisco phylogenetic tree

et al. 2017

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Ribulose 1,5‐bisphosphate (RuBP) carboxylase/oxygenase (RuBisCO, or Rubisco) catalyzes a key reaction by which inorganic carbon is converted into organic carbon in the metabolism of many aerobic and anaerobic organisms. Across the broader Rubisco protein family, homologs exhibit diverse biochemical characteristics and metabolic functions, but the evolutionary origins of this diversity are unclear. Evidence of the timing of Rubisco family emergence and diversification of its different forms has been obscured by a meager paleontological record of early Earth biota, their subcellular physiology and metabolic components. Here, we use computational models to reconstruct a Rubisco family phylogenetic tree, ancestral amino acid sequences at branching points on the tree, and protein structures for several key ancestors. Analysis of historic substitutions with respect to their structural locations shows that there were distinct periods of amino acid substitution enrichment above background levels near and within its oxygen‐sensitive active site and subunit interfaces over the divergence between Form III (associated with anoxia) and Form I (associated with oxia) groups in its evolutionary history. One possible interpretation is that these periods of substitutional enrichment are coincident with oxidative stress exerted by the rise of oxygenic photosynthesis in the Precambrian era. Our interpretation implies that the periods of Rubisco substitutional enrichment inferred near the transition from anaerobic Form III to aerobic Form I ancestral sequences predate the acquisition of Rubisco by fully derived cyanobacterial (i.e., dual photosystem‐bearing, oxygen‐evolving) clades. The partitioning of extant lineages at high clade levels within our Rubisco phylogeny indicates that horizontal transfer of Rubisco is a relatively infrequent event. Therefore, it is possible that the mutational enrichment periods between the Form III and Form I common ancestral sequences correspond to the adaptation of key oxygen‐sensitive components of Rubisco prior to, or coincident with, the Great Oxidation Event.

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Section: Methodsmentioning

confidence: 99%

Constraining the timing of the Great Oxidation Event within the Rubisco phylogenetic tree

et al. 2017

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“…We used ProtTest [43] to select the best-fitting substitution matrix for our alignments of each of the four genes. In each case, the LG matrix [44] was chosen over the JTT [36] and WAG [37] matrices used in the original analysis by both the AIC and BIC criteria (see Table S1).…”

Section: Methodsmentioning

confidence: 99%

Informational Gene Phylogenies Do Not Support a Fourth Domain of Life for Nucleocytoplasmic Large DNA Viruses

2011

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Mimivirus is a nucleocytoplasmic large DNA virus (NCLDV) with a genome size (1.2 Mb) and coding capacity ( 1000 genes) comparable to that of some cellular organisms. Unlike other viruses, Mimivirus and its NCLDV relatives encode homologs of broadly conserved informational genes found in Bacteria, Archaea, and Eukaryotes, raising the possibility that they could be placed on the tree of life. A recent phylogenetic analysis of these genes showed the NCLDVs emerging as a monophyletic group branching between Eukaryotes and Archaea. These trees were interpreted as evidence for an independent “fourth domain” of life that may have contributed DNA processing genes to the ancestral eukaryote. However, the analysis of ancient evolutionary events is challenging, and tree reconstruction is susceptible to bias resulting from non-phylogenetic signals in the data. These include compositional heterogeneity and homoplasy, which can lead to the spurious grouping of compositionally-similar or fast-evolving sequences. Here, we show that these informational gene alignments contain both significant compositional heterogeneity and homoplasy, which were not adequately modelled in the original analysis. When we use more realistic evolutionary models that better fit the data, the resulting trees are unable to reject a simple null hypothesis in which these informational genes, like many other NCLDV genes, were acquired by horizontal transfer from eukaryotic hosts. Our results suggest that a fourth domain is not required to explain the available sequence data.

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“…The ingroup was considered monophyletic with respect to the outgroup (O. vulgaris). We employed the partitions selected by Partition Finder Protein (see above), and the mtREV model for all partitions as selected by PROTTEST (Abascal et al, 2005) among the ones available in BEAST. The final Markov chain was run twice for 50 million generations, sampling every 1,000 generations and the first 5 million was discarded as part of the burn-in process, according to the convergence of chains checked with Tracer v.1.5.…”

Section: Estimation Of Divergence Timesmentioning

confidence: 99%

The mitochondrial genome of Ifremeria nautilei and the phylogenetic position of the enigmatic deep-sea Abyssochrysoidea (Mollusca: Gastropoda)

Osca

Templado

Zardoya

2014

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The complete nucleotide sequence of the mitochondrial (mt) genome of the deep-sea vent snail Ifremeria nautilei (Gastropoda: Abyssochrysoidea) was determined. The double stranded circular molecule is 15,664 pb in length and encodes for the typical 37 metazoan mitochondrial genes. The gene arrangement of the Ifremeria mt genome is most similar to genome organization of caenogastropods and differs only on the relative position of the trnW gene.The deduced amino acid sequences of the mt protein coding genes of Ifremeria mt genome were aligned with orthologous sequences from representatives of the main lineages of gastropods and phylogenetic relationships were inferred. The reconstructed phylogeny supports that Ifremeria belongs toCaenogastropoda and that is closely related to hypsogastropod superfamilies.Results were compared with a reconstructed nuclear-based phylogeny.Moreover, a relaxed molecular-clock timetree calibrated with fossils dated the divergence of Abyssochrysoidea in the Late Jurassic-Early Cretaceous indicating a relatively modern colonization of deep-sea environments by these snails.

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ProtTest: selection of best-fit models of protein evolution

Abstract: ProtTest is available under the GNU license from http://darwin.uvigo.es

Cited by 2,785 publications

References 14 publications

Constraining the timing of the Great Oxidation Event within the Rubisco phylogenetic tree

Constraining the timing of the Great Oxidation Event within the Rubisco phylogenetic tree

Informational Gene Phylogenies Do Not Support a Fourth Domain of Life for Nucleocytoplasmic Large DNA Viruses

The mitochondrial genome of Ifremeria nautilei and the phylogenetic position of the enigmatic deep-sea Abyssochrysoidea (Mollusca: Gastropoda)

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