Multiple Sequence Alignment in Phylogenetic Analysis

Phylogeny of genes for secretion NTPases: Identification of the widespread tadA subfamily and development of a diagnostic key for gene classification

“…We performed an aggressive heuristic search with 5,000 replicates of random addition of taxa followed by the subtree pruning and regrafting function of PAUP, saving only one tree at each replicate. All characters and state transformations were given equal weight, and columns with gaps were retained as phylogenetically informative characters (35). The resulting 5,000 trees were tested with the more rigorous tree-branch reconnection (TBR) technique.…”

Molecular phylogeny of the brachyuran crab superfamily Majoidea indicates close congruence with trees based on larval morphology

“…For 28S, both leading/trailing ends and some hyper-variable regions within the alignment (flanked by conserved sequences) of the alignment were excluded (36% of the total sequence). Although removal of ambiguously aligned regions has been shown to significantly improve tree topology in simulations (Talavera and Castresana, 2007), the choice of whether to include these areas (and other portions of the data, such as COI third positions) heavily influences tree topology and should ideally be made in a way that optimizes topological stability (Phillips et al, 2000). We thus examined the stability of the combined sequence alignments under a range of alignment inclusion (untrimmed vs. GBlocks-trimmed sequences) and COI third-position weighting (0, 0.5, 1) scenarios using character congruence as a criterion for optimality using the Incongruence Length metric (ILD) (Farris et al, 1995;Mikevich and Farris, 1981), where ILD = (Length combined À P Length individual loci )/Length combined (see also Ahyong and O'Meally, 2004).…”

“…We sampled the chain every 100 generations, and discarded the first 25% of the samples (which generally corresponded to when likelihood values became stationary) as the burn-in. Although utilization of gaps as character data can be phylogenetically informative in parsimony-based analyses, there are few well-tested methods for implementing gap information into model-based approaches to phylogenetic inference (Simmons et al, 2007, Phillips et al, 2000, and we thus treated all gaps as missing data. Although the majority of species were sequenced for all three loci (Table 1), because of logistical constraints (multiple failed sequencing attempts for some species-locus combinations), not all loci were sequenced for each species, and thus portions of our dataset were missing.…”

Are Iberian endemics Iberian? A case-study using water beetles of family Dytiscidae (Coleoptera)

“…The analyses of the new sequences was performed in a two step procedure (Phillips et al, 2000), aligning sequences in ClustalW (Higgins et al, 1992, default values) followed by hand correction of obvious mistakes, and tree searches on the aligned matrix using parsimony analysis in PAUP4.0b6 (Swofford, 2000), with gaps coded as a fifth character (Giribet & Wheeler, 1999). PAUP searches consisted of TBR heuristic explorations of 10,000 replicates.…”