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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. Expand
Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus
TLDR
A phylogeny of chloroplast genomes inferred from 41 proteins and 8,303 amino acids sites indicates that at least two independent secondary endosymbiotic events have occurred involving red algae and that amino acid composition bias in chloropleft proteins strongly affects plastid genome phylogeny. Expand
Early penguin fossils, plus mitochondrial genomes, calibrate avian evolution.
TLDR
A test for events around the Late Cretaceous is reported by describing the earliest penguin fossils, analyzing complete mitochondrial genomes from an albatross, a petrel, and a loon, and describing the gradual decline of pterosaurs at the same time modern birds radiate. Expand
Distributions of Tree Comparison Metrics—Some New Results
Measures of dissimilarity (metrics) for comparing trees are important tools in the quantitative analysis of evolutionary trees, but many of their properties are incompletely known. The present paperExpand
Mitochondrial genomes and avian phylogeny: complex characters and resolvability without explosive radiations.
TLDR
By showing the avian tree is, in principle, resolvable, it is demonstrated that the radiation of birds is amenable to standard evolutionary analysis. Expand
Genome-scale phylogeny and the detection of systematic biases.
TLDR
A compositional bias is identified as responsible for this inconsistency and it is reduced effectively by coding the nucleotides as purines and pyrimidines (RY-coding), reinforcing the original tree. Expand
The root of the mammalian tree inferred from whole mitochondrial genomes.
TLDR
It is reported that recoding nucleotides to RY-characters, and partitioning maximum-likelihood analyses among subsets of data reduces such biases, and improves the fit of models to the data, respectively. Expand
Tinamous and moa flock together: mitochondrial genome sequence analysis reveals independent losses of flight among ratites.
TLDR
It is inferred that flight to have been lost among ratites multiple times in temporally close association with the Cretaceous-Tertiary extinction event, circumvents requirements for transient microcontinents and island chains to explain discordance between ratite phylogeny and patterns of continental breakup. Expand
Mass Survival of Birds Across the Cretaceous- Tertiary Boundary: Molecular Evidence
TLDR
Data for several other terrestrial vertebrate groups indicate a similar pattern of survival and, taken together, favor incremental changes during a Cretaceous diversification of birds and mammals rather than an explosive radiation in the Early Tertiary. Expand
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