MODELTEST: testing the model of DNA substitution.

Posada, David; Crandall, Keith A.

doi:10.1093/bioinformatics/14.9.817

Cited by 18,439 publications

(11,809 citation statements)

References 12 publications

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“…The optimal model of evolution for each gene data set using the supertree as a reference tree was determined using ModelTEST [123] in combination with PAUP* under an Akaike information criterion (AIC) as implemented in the Perl script autoMT.pl v1.0. The applicability of a molecular clock was tested using a likelihood ratio test with a nominal P of 0.05 corrected for multiple comparisons using a sequential Holm-Bonferroni correction [124].…”

Section: Methodsmentioning

confidence: 99%

Updating the evolutionary history of Carnivora (Mammalia): a new species-level supertree complete with divergence time estimates

2012

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BackgroundAlthough it has proven to be an important foundation for investigations of carnivoran ecology, biology and evolution, the complete species-level supertree for Carnivora of Bininda-Emonds et al. is showing its age. Additional, largely molecular sequence data are now available for many species and the advancement of computer technology means that many of the limitations of the original analysis can now be avoided. We therefore sought to provide an updated estimate of the phylogenetic relationships within all extant Carnivora, again using supertree analysis to be able to analyze as much of the global phylogenetic database for the group as possible.ResultsIn total, 188 source trees were combined, representing 114 trees from the literature together with 74 newly constructed gene trees derived from nearly 45,000 bp of sequence data from GenBank. The greater availability of sequence data means that the new supertree is almost completely resolved and also better reflects current phylogenetic opinion (for example, supporting a monophyletic Mephitidae, Eupleridae and Prionodontidae; placing Nandinia binotata as sister to the remaining Feliformia). Following an initial rapid radiation, diversification rate analyses indicate a downturn in the net speciation rate within the past three million years as well as a possible increase some 18.0 million years ago; numerous diversification rate shifts within the order were also identified.ConclusionsTogether, the two carnivore supertrees remain the only complete phylogenetic estimates for all extant species and the new supertree, like the old one, will form a key tool in helping us to further understand the biology of this charismatic group of carnivores.

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Section: Methodsmentioning

confidence: 99%

Updating the evolutionary history of Carnivora (Mammalia): a new species-level supertree complete with divergence time estimates

2012

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“…Maximum likelihood (ML) tree construction was based on the MLST sequences and the best‐fitting ML model under the Akaike information criterion was GTR (general time reversible) + Γ (gamma distribution) for nucleotides as identified by ModelTest (Posada & Crandall, 1998). The most likely DNA tree and corresponding bootstrap support values were obtained by PhyML using Mega 5.0 software (Tamura et al., 2011) with nearest‐neighbor interchange branch swapping and 100 bootstrap replicates.…”

Section: Methodsmentioning

confidence: 99%

VIM‐1 carbapenemase‐producing Escherichia coli in gulls from southern France

Vittecoq

Laurens

Brazier

et al. 2017

Ecology and Evolution

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Acquired carbapenemases currently pose one of the most worrying public health threats related to antimicrobial resistance. A NDM‐1‐producing Salmonella Corvallis was reported in 2013 in a wild raptor. Further research was needed to understand the role of wild birds in the transmission of bacteria resistant to carbapenems. Our aim was to investigate the presence of carbapenem‐resistant Escherichia coli in gulls from southern France. In 2012, we collected 158 cloacal swabs samples from two gull species: yellow‐legged gulls (Larus michahellis) that live in close contact with humans and slender‐billed gulls (Chroicocephalus genei) that feed at sea. We molecularly compared the carbapenem‐resistant bacteria we isolated through culture on selective media with the carbapenem‐susceptible strains sampled from both gull species and from stool samples of humans hospitalized in the study area. The genes coding for carbapenemases were tested by multiplex PCR. We isolated 22 carbapenem‐resistant E. coli strains from yellow‐legged gulls while none were isolated from slender‐billed gulls. All carbapenem‐resistant isolates were positive for bla VIM ‐1 gene. VIM‐1‐producing E. coli were closely related to carbapenem‐susceptible strains isolated from the two gull species but also to human strains. Our results are alarming enough to make it urgently necessary to determine the contamination source of the bacteria we identified. More generally, our work highlights the need to develop more bridges between studies focusing on wildlife and humans in order to improve our knowledge of resistant bacteria transmission routes.

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“…As only a single model of molecular evolution can be used across the partitions, the ML analysis was performed with the GTRMIX model and 1000 bootstrap replicates were run. The model of molecular evolution applied to each gene partition in the Bayesian analysis, GTR+I+G, was estimated in jModeltest 2.1.4 (Darriba et al 2012) using the Akaike information criterion (Posada and Crandall 1998). The Bayesian Markov chain Monte Carlo (B/MCMC) analyses were run in MrBayes 3.1.2 (Huelsenbeck and Ronquist 2003; Ronquist et al 2005) with six chains simultaneously, each initiated with a random tree, for 10 million generations; trees were sampled every 100th generation for a total sample of 100 000 trees.…”

Section: Methodsmentioning

confidence: 99%

Molecular analyses uncover the phylogenetic placement of the lichenized hyphomycetous genusCheiromycina

et al. 2017

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The genus Cheiromycina is one of the few genera of lichenized hyphomycetes for which no sexual reproductive stages have been observed. The genus includes species from boreal to temperate regions of the Northern Hemisphere where it is found growing on bark or wood. Congeners in Cheiromycina are characterized by a noncorticate thallus, nearly immersed in the substrate and presenting powdery unpigmented sporodochia, and containing chlorococcoid photobionts. The relationships of members of Cheiromycina with other fungi are not known. Here we inferred the phylogenetic placement of Cheiromycina using three loci (nuSSU, nuLSU, and mtSSU) representing C. flabelliformis, the type species for the genus, C. petri, and C. reimeri. Our results revealed that the genus Cheiromycina is found within the family Malmideaceae (Lecanorales) where members formed a monophyletic clade sister to the genera Savoronala and Malmidea. This phylogenetic placement and the relationships of Cheiromycina with other lichenized hyphomycetous taxa are here discussed.

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MODELTEST: testing the model of DNA substitution.

Abstract: The MODELTEST package, including the source code and some documentation is available at http://bioag.byu. edu/zoology/crandall_lab/modeltest.html.

Cited by 18,439 publications

References 12 publications

Updating the evolutionary history of Carnivora (Mammalia): a new species-level supertree complete with divergence time estimates

Updating the evolutionary history of Carnivora (Mammalia): a new species-level supertree complete with divergence time estimates

VIM‐1 carbapenemase‐producing Escherichia coli in gulls from southern France

Molecular analyses uncover the phylogenetic placement of the lichenized hyphomycetous genusCheiromycina

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