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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 ofExpand
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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 haveExpand
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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 createExpand
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Model misspecification and probabilistic tests of topology: evidence from empirical data sets.
Probabilistic tests of topology offer a powerful means of evaluating competing phylogenetic hypotheses. The performance of the nonparametric Shimodaira-Hasegawa (SH) test, the parametricExpand
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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 severalExpand
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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 importantExpand
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PHYLOGEOGRAPHY OF THE NEW ZEALAND CICADA MAORICICADA CAMPBELLI BASED ON MITOCHONDRIAL DNA SEQUENCES: ANCIENT CLADES ASSOCIATED WITH CENOZOIC ENVIRONMENTAL CHANGE
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 geneticExpand
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Differentiating between hypotheses of lineage sorting and introgression in New Zealand alpine cicadas (Maoricicada Dugdale).
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. InExpand
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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 NewExpand
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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, isExpand
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