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Signal, noise, and reliability in molecular phylogenetic analyses.
This work analyzed 8,000 random data matrices consisting of 10-500 binary or four-state characters and 5-25 taxa to study several options for detecting signal in systematic data bases, finding the skewness of tree-length distributions is closely related to the success of parsimony in finding the true phylogeny.
An Empirical Test of Bootstrapping as a Method for Assessing Confidence in Phylogenetic Analysis
Bootstrapping is a common method for assessing confidence in phylogenetic anal? yses. Although bootstrapping was first applied in phylogenetics to assess the repeatability of a given result,…
Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support.
- T. Wilcox, Derrick J. Zwickl, T. Heath, D. Hillis
- Biology, MedicineMolecular phylogenetics and evolution
- 1 October 2002
The phylogenetic analysis suggests that New World dwarf boas are not monophyletic, and is finds Exiliboa and Ungaliophis to be most closely related to sand boas, boas and advanced snakes, whereas Tropidophis and Trachyboa form an independent clade that separated relatively early in snake radiation.
Ribosomal DNA: Molecular Evolution and Phylogenetic Inference
An analysis of aligned sequences of the four nuclear and two mitochondrial rRNA genes identified regions of these genes that are likely to be useful to address phylogenetic problems over a wide range of levels of divergence.
Evidence from 18S ribosomal DNA that the lophophorates are protostome animals
- K. Halanych, J. Bacheller, A. Aguinaldo, S. Liva, D. Hillis, J. Lake
- Biology, MedicineScience
- 17 March 1995
Sequence analyses show that lophophorates are protostomes closely related to mollusks and annelids, which deviates from the commonly held view of deuterostome affinity.
SUCCESS OF PHYLOGENETIC METHODS IN THE FOUR-TAXON CASE
The success of 16 methods of phylogenetic inference was examined using consis? tency and simulation analysis. Success?the frequency with which a tree-making method cor? rectly identified the true…
Phylogeny and biogeography of a cosmopolitan frog radiation: Late cretaceous diversification resulted in continent-scale endemism in the family ranidae.
- F. Bossuyt, Rafe M. Brown, D. Hillis, D. Cannatella, M. Milinkovitch
- Biology, MedicineSystematic biology
- 1 August 2006
A scenario in which the ancestors of several clades reached Eurasia via the Indian subcontinent, and the ancestor of Ceratobatrachinae entered via the Australia-New Guinea plate, best fits the paleogeographic models and requires the fewest number of dispersal/vicariance events.
Discriminating between phylogenetic signal and random noise in DNA sequences
Increased taxon sampling greatly reduces phylogenetic error.
The measurement of phylogenetic error across a wide range of taxon sample sizes is considered, and it is concluded that the expected error based on randomly selecting trees must be considered in evaluating error in studies of the effects ofTaxon sampling.
The Ascomycota tree of life: a phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits.
A 6-gene, 420-species maximum-likelihood phylogeny of Ascomycota, the largest phylum of Fungi, and a phylogenetic informativeness analysis of all 6 genes and a series of ancestral character state reconstructions support a terrestrial, saprobic ecology as ancestral are presented.