Testability and the Refutation and Corroboration of Cladistic Hypotheses

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Branch Support and Tree Stability

K Bremer (1994)

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The excess of transitions among nucleotide substitutions: new methods of estimating transition bias underscore its significance.

John Wakeley (1996)

Estimates of transition bias provide insight into the process of nucleotide substitution, and are required in some commonly used phylogenetic methods. Transitions are favored over transversions among spontaneous mutations, and the direction and strength of selection on proteins and RNA appears to depend on mutation type. As the complexity of the nucleotide-substitution process has become apparent, problems with classical methods of estimating transition bias have been recognized. These problems arise because there Is a fundamental difference between ratios of numbers of differences among sequences and ratios of rates, and because classical methods are not easily generalized. Several new methods are now available.

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Alignment-ambiguous nucleotide sites and the exclusion of systematic data.

J Gatesy, R. DeSalle, Benedict W Wheeler (1993)

Molecular systematists generally rely on computer algorithms to establish the alignment of DNA sequences. However, when alignment regions are characterized by multiple insertions and deletions, these gap-filled stretches of DNA are often excised before phylogenetic reconstruction. This exclusion of systematic data is generally determined by subjective criteria. We explore a replicable methodology in which the comparison of several multiple sequence alignments can be used to eliminate regions of unstable sequence alignment. Using crocodilian and insect mitochondrial (mt) ribosomal (r) DNA as examples, we caution against the removal of sequence data prior to phylogenetic reconstruction.