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Recovering evolutionary trees under a more realistic model of sequence evolution.
TLDR
The overall conclusions from this study are that irregular A,C,G,T compositions are an important and possible general cause of patterns that can mislead tree-reconstruction methods, even when high bootstrap values are obtained.
Spectral analysis of phylogenetic data
TLDR
Spectral analysis using the Fast Hadamard transform allows optimal trees to be found for at least 20 taxa and perhaps for up to 30 taxa, and a corresponding spectral analysis for distance data is introduced.
A Framework for the Quantitative Study of Evolutionary Trees
TLDR
A direct method for calculating expected data from an evolutionary model for two state characters is described, and it is shown that for n = 4 taxa, parsimony will always converge to the correct tree, but there are examples with n = 5 where Parsimony will converge on an incorrect tree, even for equal rates of evolution.
Outgroup misplacement and phylogenetic inaccuracy under a molecular clock--a simulation study.
TLDR
A simulation study of the phylogenetic methods UPGMA, neighbor joining, maximum parsimony, and maximum likelihood for a five-taxon tree under a molecular clock identified another region of the parameter space where, although consistent for a given method, some incorrect trees were each selected with up to twice the frequency of the correct tree for sequences of bounded length.
Mutation and Evolutionary Rates in Adélie Penguins from the Antarctic
TLDR
Results are in contrast to the view that molecular rates are time dependent, and the rate of evolution of the same HVR I region, determined using DNA sequences from 162 known age sub-fossil bones spanning a 37,000-year period, was 0.7%.
Toward resolving deep neoaves phylogeny: data, signal enhancement, and priors.
TLDR
Improved conditional down-weighting techniques to reduce noise relative to signal for deeper divergences and find increased agreement between data sets are described and form a basis for further testing with both nuclear-coding sequences and rare genomic changes.
Mammalian evolution: timing and implications from using the LogDeterminant transform for proteins of differing amino acid composition.
TLDR
Most major divergences amongst lineages leading to modern orders, appear to occur well before the Cretaceous/Tertiary (K/T) boundary, particularly the possibility of competition between the small dinosaurs and the new mammal clades.
Four new mitochondrial genomes and the increased stability of evolutionary trees of mammals from improved taxon sampling.
TLDR
The evolutionary tree for mammals is expected to be resolved quickly, and the stability of trees from independent data sets, as detected from a triplet Markov analysis.
A discrete Fourier analysis for evolutionary trees.
TLDR
The extension ofrete Fourier transformations to provide invertible relationships between a phylogenetic tree T (with three probability parameters of nucleotide substitution on each edge corresponding to Kimura's 3ST model) and the expected frequencies of the nucleotide patterns in the sequences is reported.
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