2017
Birth/birth-death processes and their computable transition probabilities with biological applications
Ho LST, Xu J, Crawford FW, Minin VN, Suchard MA. Birth/birth-death processes and their computable transition probabilities with biological applications. Journal Of Mathematical Biology 2017, 76: 911-944. PMID: 28741177, PMCID: PMC5783825, DOI: 10.1007/s00285-017-1160-3.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsAnimalsBayes TheoremCommunicable DiseasesComputational BiologyComputer SimulationEnglandEpidemicsHistory, 17th CenturyHost-Parasite InteractionsHumansLikelihood FunctionsMarkov ChainsMathematical ConceptsModels, BiologicalMonte Carlo MethodPlagueProbabilityStochastic ProcessesConceptsBirth-death processTransition probabilitiesFinite-time transition probabilitiesSIR modelMonte Carlo approximationJoint posterior distributionLikelihood-based inferenceApproximate Bayesian computationStatistical inferenceMatrix exponentiationPosterior distributionProcess approximationBivariate extensionBayesian computationFraction representationLaplace transformCorrelation structureUnivariate populationsRemoved (SIR) modelSmall systemsBivariate processEfficient algorithmApproximationDirect inferenceFast method
2015
Historical Biogeography Using Species Geographical Ranges
Quintero I, Keil P, Jetz W, Crawford FW. Historical Biogeography Using Species Geographical Ranges. Systematic Biology 2015, 64: 1059-1073. PMID: 26254671, PMCID: PMC4838013, DOI: 10.1093/sysbio/syv057.Peer-Reviewed Original ResearchConceptsSpecies' geographical rangeGeographic rangeGeographical rangeHistorical biogeographyEvolutionary historySpecies' geographic rangeDistribution of speciesComplex geographic patternHistorical biogeographic analysisSpecies locationsSpecies rangeGeographic locationBird generaEcological factorsExplicit frameworkGeographic patternsPhylogeographic analysisBiogeographic inferenceSpatial variationBiogeographic analysisPhylogenetic informationDiversification processTerminal lineagesPhylogenetic treePhylogeographic reconstruction
2013
Diversity, Disparity, and Evolutionary Rate Estimation for Unresolved Yule Trees
Crawford FW, Suchard MA. Diversity, Disparity, and Evolutionary Rate Estimation for Unresolved Yule Trees. Systematic Biology 2013, 62: 439-455. PMID: 23417679, PMCID: PMC3622899, DOI: 10.1093/sysbio/syt010.Peer-Reviewed Original ResearchConceptsPhylogenetic treePhylogenetic diversityTrait disparityEvolutionary relationshipsYule treeMammalian order CarnivoraPhenotypic trait valuesComparative evolutionary studiesEvolutionary rate estimationSet of taxaOrganism of interestTrait evolutionPhenotypic evolutionEvolutionary biologistsInferred phylogenyEvolutionary studiesUnresolved cladeTrait valuesMacroevolutionary studiesTrait dataRelated organismsOrder CarnivoraCladeBrownian motionBranch lengths