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Model checking software for phylogenetic trees using distribution and database methods

José Ignacio Requeno, José Manuel Colom
2013 Journal of Integrative Bioinformatics  
However, the performance of traditional model checking is penalized when scaling the system for large phylogenies. To this end, two strategies are presented here.  ...  Model checking, a generic and formal paradigm stemming from computer science based on temporal logics, has been proposed for the study of biological properties that emerge from the labeling of the states  ...  Slicing the State Phylogenetic model checking usually associates a complete DNA sequence per node of the tree.  ... 
doi:10.2390/biecoll-jib-2013-229 pmid:24231143 fatcat:xslrev5pbvebjd3clfyugb6joq

Phylogenetics, likelihood, evolution and complexity

A.P. Jason de Koning, Wanjun Gu, Todd A. Castoe, David D. Pollock
2012 Computer applications in the biosciences : CABIOS  
evolutionary models in a phylogenetic framework.  ...  Phylogenetics, likelihood, evolution and complexity (PLEX) is a flexible and fast Bayesian Markov chain Monte Carlo software program for large-scale analysis of nucleotide and amino acid data using complex  ...  For example, it is not uncommon for phylogenetic analysis of large datasets to now incur compute times on the order of months, even with models that are fairly simple from a mechanistic, biochemical perspective  ... 
doi:10.1093/bioinformatics/bts555 pmid:22976081 pmcid:PMC3496332 fatcat:lnwctjnrvnab5krkzou5j2o5bu

iPhy: an integrated phylogenetic workbench for supermatrix analyses

Martin O Jones, Georgios D Koutsovoulos, Mark L Blaxter
2011 BMC Bioinformatics  
We thank Ben Elsworth (IEB, Edinburgh) for access to the NEMBASE4 resource, Silvia Bulgheresi (Vienna) for access to Laxus oneistus sequences and colleagues in the Institute of Evolutionary Biology for  ...  Peter Hollingsworth (RBGE, Edinburgh) and Joseph Hughes (Glasgow) provided beta test analysis of early versions of iPhy. Authors' contributions The project was conceived by MJ and MB.  ...  For each subset, phylogenetic analysis was carried out using MrBayes 3.1 [29] using a GTR+G+I model with separate model parameters for each gene partition and two independent runs of 4 chains for 500000  ... 
doi:10.1186/1471-2105-12-30 pmid:21261969 pmcid:PMC3037854 fatcat:xubw73dyazaelk4yquwbkk6it4

Modeling body size evolution in Felidae under alternative phylogenetic hypotheses

José Alexandre Felizola Diniz-Filho, João Carlos Nabout
2009 Genetics and Molecular Biology  
The PVR explained 65% to 67% of body size variation and all Moran's I values for the PVR residuals were non-significant, indicating that both these models explained phylogenetic structures in trait variation  ...  We used phylogenetic correlograms and phylogenetic eigenvector regression (PVR) to model body size evolution in 35 worldwide Felidae (Mammalia, Carnivora) species using two alternative phylogenies and  ...  Correlograms may also Feline phylogenies and phylogenetic analysis be not very sensitive when using large distance classes between time slices, as used here, because of the small number of species.  ... 
doi:10.1590/s1415-47572009005000004 pmid:21637664 pmcid:PMC3032953 fatcat:2spkbez7qfb73l3unuiz5vqlcy

Mitochondrial COI Gene Sequence Analyses of Puntius ticto and Compared with Seven Species of Genus Puntius of Family Cyprinidae: A Finding for Phylogenetic Positioning and DNA Barcoding as Model Study for Cryptic Species

RK Garg, Nidhi Dubey, N Batav, Pooja Pandey, RK Singh
2017 Journal of Proteomics & Bioinformatics  
Present investigation may be treated model study for wildlife scientists for banding smuggling protected species under false pretenses and the importance of DNA barcoding in stopping such illegal trade  ...  The present study examined partial mitochondrial cytochrome c oxidase subunit I gene sequence of mitochondrial DNA for phylogenetic positioning of Puntius ticto among eight species of genus Puntius and  ...  The authors also wish to thank to laboratory mates for his help during this work and Department of Fisheries, Government of M.P. for providing fish specimens for research study.  ... 
doi:10.4172/jpb.1000445 fatcat:hh3uf53nvvhebe3j7vmpbkk3ci


Miguel Verdú, Juli G. Pausas
2013 Evolution  
For understanding in situ diversification triggered by novel conditions it is necessary to focus on the time slice where such conditions occur.  ...  Phylogenetic methods to detect lineage diversification have been traditionally used within a particular taxonomic clade, but rarely applied to detect local diversification.  ...  of the phylogenetic trees than the constant-rate model in which time was not split.  ... 
doi:10.1111/evo.12049 pmid:23730767 fatcat:xfhhgjstp5axfm22jy2igjdqte

Bayesian models for comparative analysis integrating phylogenetic uncertainty

Pierre de Villemereuil, Jessie A Wells, Robert D Edwards, Simon P Blomberg
2012 BMC Evolutionary Biology  
We show that BUGS is a useful, flexible general purpose tool for phylogenetic comparative analyses, particularly for modelling in the face of phylogenetic uncertainty and accounting for measurement error  ...  Although there is some application-specific software for fitting Bayesian models accounting for phylogenetic error, more general and flexible software is desirable.  ...  phylogenetic bootstrap analysis.  ... 
doi:10.1186/1471-2148-12-102 pmid:22741602 pmcid:PMC3582467 fatcat:zplzphnq5rhn7lpvbebjezifta

Ecological causes of uneven diversification and richness in the mammal tree of life [article]

Nathan S. Upham, Jacob A. Esselstyn, Walter Jetz
2019 bioRxiv   pre-print
Yet the causes of differential diversification are little known despite their relevance for sustaining biodiversity into the future.  ...  Why differential bursts of species diversification occur, and how long they persist, has implications for sustaining biodiversity.  ...  (b) Phylogenetic path analysis [60] of 705 putative causal relationships between traits and rates leading to clade species richness for time-706 sliced clades.  ... 
doi:10.1101/504803 fatcat:mayoq7thqzejdk3szjyhixina4

Estimating dispersal and evolutionary dynamics in diploporan blastozoans (Echinodermata) across the great Ordovician biodiversification event

Adriane R. Lam, Sarah L. Sheffield, Nicholas J. Matzke
2020 Paleobiology  
The BSM analysis was divided into three time slices to analyze how dispersal paths changed before and during the great Ordovician biodiversification event (GOBE) and within the Late Ordovician mass extinction  ...  The best-fit biogeographic model incorporated jump dispersal, indicating this was an important speciation strategy.  ...  Limbeck for reading earlier versions of this article. We thank B. Deline and an anonymous reviewer for critical comments and suggestions that greatly strengthened this contribution.  ... 
doi:10.1017/pab.2020.24 fatcat:zg7i35semjexhazf3bj3t42ee4

Spatial Changes in the Bacterial Community Structure along a Vertical Oxygen Gradient in Flooded Paddy Soil Cores

H. Ludemann, I. Arth, W. Liesack
2000 Applied and Environmental Microbiology  
The extraction of total RNA followed by reverse transcription-PCR of the bacterial 16S rRNA and T-RFLP analysis resulted for both oxic and anoxic zones of flooded soil cores in community fingerprint patterns  ...  similar to those obtained by the rDNA-based analysis.  ...  ACKNOWLEDGMENTS We thank Sonja Fleissner for excellent technical assistance.  ... 
doi:10.1128/aem.66.2.754-762.2000 pmid:10653747 pmcid:PMC91892 fatcat:kmzmw6fdsjbqfprff7eipfmm3a

Concerted Evolution of Duplicate Control Regions in the Mitochondria of Species of the Flatfish Family Bothidae (Teleostei: Pleuronectiformes)

Dong-He Li, Wei Shi, Thomas A. Munroe, Li Gong, Xiao-Yu Kong, Bi-Song Yue
2015 PLoS ONE  
Additionally, phylogenetic and ancestral state reconstruction analysis also provided evidence to support the hypothesis that duplicate CRs evolved concertedly.  ...  Contributed reagents/materials/analysis tools: WS. Wrote the paper: WS. Revised the manuscript critically for important intellectual content: TAM.  ...  -X Shen for their helpful comments on the manuscript. We thank A. D. Connell, B. Yau and H.-D Lin for sample collections. Author Contributions Conceived and designed the experiments: XYK WS.  ... 
doi:10.1371/journal.pone.0134580 pmid:26237419 pmcid:PMC4523187 fatcat:5kbyqw2n5jh7fmv6bfk6rkplm4

A western representative of an eastern clade: phylogeographic history of the gypsophilous plant Nepeta hispanica [article]

Ignacio Ramos-Gutierrez, Juan Carlos Moreno Saiz, Mario Fernandez-Mazuecos
2022 bioRxiv   pre-print
Three approaches were used: (a) interspecific phylogenetic analyses based on nuclear DNA sequences of the ITS region to unveil the relationships and times of divergence between N. hispanica and its closest  ...  plastid DNA regions trnS-trnG and psbJ-petA to evaluate the degree of genetic isolation between populations of N. hispanica, their relationships and their genetic diversity; and (c) ecological niche modelling  ...  Ecological niche modelling Figure 5 shows the result of the maximum entropy distribution modelling, both for the present and for past time slices.  ... 
doi:10.1101/2022.01.05.475097 fatcat:7jaswziamjh7bd7d6ca4dr3cp4

Supplementary methods from The evolution of traits and functions in herbivorous coral reef fishes through space and time

Alexandre C. Siqueira, David R. Bellwood, Peter F. Cowman
2019 Figshare  
For the phylogenetic inferences, we benefited from the CIPRES Science Gateway [9] computing environment.  ...  Gene datasets were aligned using the Muscle algorithm [7] in Geneious Pro version 11.1 [1] and checked by eye.  ... 
doi:10.6084/m9.figshare.7706543 fatcat:rbgdq4l3vjg4vljha3zeth2cg4

Processing-Dependent and Clonal Contamination Patterns of Listeria monocytogenes in the Cured Ham Food Chain Revealed by Genetic Analysis

Marina Morganti, Erika Scaltriti, Paolo Cozzolino, Luca Bolzoni, Gabriele Casadei, Marco Pierantoni, Emanuela Foni, Stefano Pongolini, C. A. Elkins
2015 Applied and Environmental Microbiology  
The spread ofL. monocytogeneswithin and between plants, as indicated by its clonal behavior, is a matter of concern for the hygienic management of establishments.  ...  ., ham production (19 plants) and postproduction, which was divided into deboning (43 plants) and slicing (25 plants) steps.  ...  ACKNOWLEDGMENT This study was supported by Italian Health Ministry grant PRC2010_013 for a postdoctoral fellowship to Erika Scaltriti.  ... 
doi:10.1128/aem.03103-15 pmid:26590278 pmcid:PMC4725272 fatcat:ngkxes4mifh5hogc64gziwadbu

Identifiability of Large Phylogenetic Mixture Models

John A. Rhodes, Seth Sullivant
2011 Bulletin of Mathematical Biology  
Phylogenetic mixture models are statistical models of character evolution allowing for heterogeneity.  ...  Such models are of increasing interest for data analysis, as they can capture the variety of evolutionary processes that may be occurring across long sequences of DNA or proteins.  ...  Acknowledgements Thanks to John Huelsenbeck for stimulating this work through describing his own investigations with mixture models with many components.  ... 
doi:10.1007/s11538-011-9672-2 pmid:21717285 fatcat:rbxasjj4lbhi5fhmpbbxzr74em
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