Factors influencing phylogenetic inference: a case study using the mammalian carnivores. 2000

O R Bininda-Emonds
Department of Zoology, University of Oxford, Oxford, OX1 3PS, United Kingdom. orbininda@ucdavis.edu

Phylogenetic reconstruction has undergone numerous developments in tree selection criteria (e.g., phenetics, cladistics, maximum-likelihood), available data sources (morphology versus molecules, and subsets of the latter), and practical limits on study size. Together with study age, I examined the effects of these variables on inferences of phylogeny for the mammalian order Carnivora. The raw data comprised 274 source trees spread among 13 carnivore taxa (generally families), which I divided into categories for each variable and combined using the supertree technique matrix representation with parsimony analysis. Incongruence between the resultant tree topologies or the underlying data was assessed using four comparison measures, each with slightly different properties: the triplet measures "do not conflict" and "explicitly agree," the partition metric, and the incongruence length difference metric. Except for a few cases reflecting historical problem areas in carnivore systematics, no significant differences in incongruence levels were found among the different categories within each variable, between the variables themselves, or between the taxa. Thus, most estimates of carnivore phylogeny cannot be distinguished from one another (and may even point toward the same solution) regardless of the methodology or data source employed. This conclusion held regardless of the comparison measure used.

UI MeSH Term Description Entries
D010802 Phylogeny The relationships of groups of organisms as reflected by their genetic makeup. Community Phylogenetics,Molecular Phylogenetics,Phylogenetic Analyses,Phylogenetic Analysis,Phylogenetic Clustering,Phylogenetic Comparative Analysis,Phylogenetic Comparative Methods,Phylogenetic Distance,Phylogenetic Generalized Least Squares,Phylogenetic Groups,Phylogenetic Incongruence,Phylogenetic Inference,Phylogenetic Networks,Phylogenetic Reconstruction,Phylogenetic Relatedness,Phylogenetic Relationships,Phylogenetic Signal,Phylogenetic Structure,Phylogenetic Tree,Phylogenetic Trees,Phylogenomics,Analyse, Phylogenetic,Analysis, Phylogenetic,Analysis, Phylogenetic Comparative,Clustering, Phylogenetic,Community Phylogenetic,Comparative Analysis, Phylogenetic,Comparative Method, Phylogenetic,Distance, Phylogenetic,Group, Phylogenetic,Incongruence, Phylogenetic,Inference, Phylogenetic,Method, Phylogenetic Comparative,Molecular Phylogenetic,Network, Phylogenetic,Phylogenetic Analyse,Phylogenetic Clusterings,Phylogenetic Comparative Analyses,Phylogenetic Comparative Method,Phylogenetic Distances,Phylogenetic Group,Phylogenetic Incongruences,Phylogenetic Inferences,Phylogenetic Network,Phylogenetic Reconstructions,Phylogenetic Relatednesses,Phylogenetic Relationship,Phylogenetic Signals,Phylogenetic Structures,Phylogenetic, Community,Phylogenetic, Molecular,Phylogenies,Phylogenomic,Reconstruction, Phylogenetic,Relatedness, Phylogenetic,Relationship, Phylogenetic,Signal, Phylogenetic,Structure, Phylogenetic,Tree, Phylogenetic
D002335 Carnivora An order of MAMMALS, usually flesh eaters with appropriate dentition. Suborders include the terrestrial carnivores Fissipedia, and the aquatic carnivores CANIFORMIA.
D000818 Animals Unicellular or multicellular, heterotrophic organisms, that have sensation and the power of voluntary movement. Under the older five kingdom paradigm, Animalia was one of the kingdoms. Under the modern three domain model, Animalia represents one of the many groups in the domain EUKARYOTA. Animal,Metazoa,Animalia
D001699 Biometry The use of statistical and mathematical methods to analyze biological observations and phenomena. Biometric Analysis,Biometrics,Analyses, Biometric,Analysis, Biometric,Biometric Analyses

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