Edward Susko

TL;DR: PMSF provided more accurate estimates of phylogenies than the mixture models from which they derive and allows full nonparametric bootstrap analyses to be conducted under complex site‐heterogeneous models on large concatenated data matrices.

TL;DR: Concaterpillar, a hierarchical clustering method based on likelihood-ratio testing that identifies congruent loci for phylogenomic analysis, is developed, which produces a phylogeny with stronger support for five eukaryote supergroups including the Opisthokonts, the Plantae, the stramenopiles + Apicomplexa, the Amoebozoa, and the Excavata.

TL;DR: It is concluded that phylogenetic analyses do not support tree-thinking, and it is argued that representations other than a tree should be investigated in this case because a non-critical concatenation of markers could be highly misleading.

TL;DR: This work investigates the use of Markov models of evolution for reduced amino acid alphabets or bins of amino acids, and finds that binning can improve topological estimation in practice.

TL;DR: It is shown that the M + A affinity can be attributed to those alignment sites associated with large differences in evolutionary site rates between the eukaryotic and archaebacterial subtrees, and failure to model the significant evolutionary rate distribution differences between the ingroup and outgroup sequences is apparently responsible for the artifactual basal position of microsporidia in phylogenetic analyses of EF-1alpha sequences.