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Model selection and model averaging in phylogenetics: advantages of akaike information criterion and bayesian approaches over likelihood ratio tests.
Model selection is a topic of special relevance in molecular phylogenetics that affects many, if not all, stages of phylogenetic inference. Here we discuss some fundamental concepts and techniques of… Expand
Phylogenomics resolves the timing and pattern of insect evolution
Toward an insect evolution resolution Insects are the most diverse group of animals, with the largest number of species. However, many of the evolutionary relationships between insect species have… Expand
Incorporating molecular evolution into phylogenetic analysis, and a new compilation of conserved polymerase chain reaction primers for animal mitochondrial DNA
DNA data has been widely used in animal phylogenetic studies over the past 15 years. Here we review how these studies have used advances in knowledge of molecular evolutionary processes to create… Expand
Model misspecification and probabilistic tests of topology: evidence from empirical data sets.
- T. R. Buckley
- Mathematics, Medicine
- Systematic biology
- 1 May 2002
Probabilistic tests of topology offer a powerful means of evaluating competing phylogenetic hypotheses. The performance of the nonparametric Shimodaira-Hasegawa (SH) test, the parametric… Expand
Combined data, Bayesian phylogenetics, and the origin of the New Zealand cicada genera.
We have applied Bayesian and maximum likelihood methods of phylogenetic estimation to data from four mitochondrial genes (COI, COII, 12S, and 16S) and a single nuclear gene (EF1alpha) from several… Expand
Accurate branch length estimation in partitioned Bayesian analyses requires accommodation of among-partition rate variation and attention to branch length priors.
Molecular phylogenetic studies are making increasing use of partitioned Bayesian analyses via software tools like MrBayes, version 3 (Ronquist and Huelsenbeck, 2003). Data partitioning is important… Expand
PHYLOGEOGRAPHY OF THE NEW ZEALAND CICADA MAORICICADA CAMPBELLI BASED ON MITOCHONDRIAL DNA SEQUENCES: ANCIENT CLADES ASSOCIATED WITH CENOZOIC ENVIRONMENTAL CHANGE
- T. R. Buckley, C. Simon, G. Chambers
- Biology, Medicine
- Evolution; international journal of organic…
- 1 July 2001
Abstract.— New Zealand's isolation, its well‐studied rapidly changing landscape, and its many examples of rampant speciation make it an excellent location for studying the process of genetic… Expand
Differentiating between hypotheses of lineage sorting and introgression in New Zealand alpine cicadas (Maoricicada Dugdale).
- T. R. Buckley, Michael Cordeiro, D. C. Marshall, C. Simon
- Medicine, Biology
- Systematic biology
- 1 June 2006
Lineage sorting and introgression can lead to incongruence among gene phylogenies, complicating the inference of species trees for large groups of taxa that have recently and rapidly radiated. In… Expand
Biogeography and phylogeny of the New Zealand cicada genera (Hemiptera: Cicadidae) based on nuclear and mitochondrial DNA data
Aim Determine the geographical and temporal origins of New Zealand cicadas. Location New Zealand, eastern Australia and New Caledonia. Methods DNA sequences from 14 species of cicadas from New… Expand
Improved resolution on the phylogenetic relationships among Pseudomonas by the combined analysis of atpD, carA, recA and 16S rDNA
A study of representatives of the bacterial genus Pseudomonas, analysing a combined data set of four molecular sequences with completely different properties and evolutionary constraints, is… Expand