2014
The impact of incorporating molecular evolutionary model into predictions of phylogenetic signal and noise
Su Z, Wang Z, López-Giráldez F, Townsend J. The impact of incorporating molecular evolutionary model into predictions of phylogenetic signal and noise. Frontiers In Ecology And Evolution 2014, 2: 11. DOI: 10.3389/fevo.2014.00011.Peer-Reviewed Original ResearchPhylogenetic inferencePhylogenetic signalRate of evolutionMolecular evolutionary modelsAccurate phylogenetic inferenceFour-taxon treesYeast genus CandidaMolecular evolutionConsensus treeNucleotide substitutionsPrediction of signalsDistribution of signalsEvolutionary modelsModel choiceGenus CandidaUnrealistic modelsCorrect modelInferenceTreesRPB1PhylogenyCladePhylogeneticsRPB2Markov model
2013
Evaluating Phylogenetic Informativeness as a Predictor of Phylogenetic Signal for Metazoan, Fungal, and Mammalian Phylogenomic Data Sets
López-Giráldez F, Moeller AH, Townsend JP. Evaluating Phylogenetic Informativeness as a Predictor of Phylogenetic Signal for Metazoan, Fungal, and Mammalian Phylogenomic Data Sets. BioMed Research International 2013, 2013: 621604. PMID: 23878813, PMCID: PMC3708382, DOI: 10.1155/2013/621604.Peer-Reviewed Original ResearchConceptsPhylogenomic data setsPhylogenetic informativenessPhylogenetic signalEffects of homoplasyPoor phylogenetic resolutionPhylogenetic resolutionSister cladeOutgroup taxaPhylogenetic researchTaxonomic groupsPhylogenetic inferenceAdvantageous genesGenesMetazoansCladeTaxaDiverse groupDiverse time scalesHomoplasyHaphazard samplingMammalsFungiOrganismsFungalMarkers
2005
Phylogenetic inference and comparative evolution of a complex microsatellite and its flanking regions in carnivores
DOMINGO-ROURA X, LÓPEZ-GIRÁLDEZ F, SAEKI M, MARMI J. Phylogenetic inference and comparative evolution of a complex microsatellite and its flanking regions in carnivores. Genetics Research 2005, 85: 223-233. PMID: 16174341, DOI: 10.1017/s0016672305007512.Peer-Reviewed Original ResearchConceptsPhylogenetic inferenceRepetitive motifsFlanking regionsBasal positionNon-coding lociAncestral DNA sequencesShort repetitive motifsHigh mutation rateRepeat additionDNA sequencesCarnivore phylogenyComplex microsatelliteMutational changesCarnivore speciesMutation rateMonotypic familyAilurus fulgensRed pandaMutational hotspotsTree topologyLociRepeat expansionComparative evolutionMeles melesDeletion