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Relaxed Phylogenetics and Dating with Confidence
This work describes how it can be used to estimate phylogenies and divergence times in the face of uncertainty in evolutionary rates and calibration times and provides a means for measuring the clocklikeness of datasets and comparing this measure between different genes and phylogenies.
Time dependency of molecular rate estimates and systematic overestimation of recent divergence times.
It is invalid to extrapolate molecular rates of change across different evolutionary timescales, which has important consequences for studies of populations, domestication, conservation genetics, and human evolution.
Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times.
The estimation of phylogenetic divergence times from sequence data is an important component of many molecular evolutionary studies, and a variety of local- and relaxed-clock methods have been proposed and implemented.
Time‐dependent rates of molecular evolution
An overview of the current understanding of time-dependent rates in animals, bacteria and viruses is presented and the challenges in calibrating estimates of molecular rates are described, particularly on the intermediate timescales that are critical for an accurate characterization of time‐dependent rates.
Genome-scale phylogeny and the detection of systematic biases.
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.
The root of the mammalian tree inferred from whole mitochondrial genomes.
Tinamous and moa flock together: mitochondrial genome sequence analysis reveals independent losses of flight among ratites.
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.
Dating of divergences within the Rattus genus phylogeny using whole mitochondrial genomes.
The evolutionary history of the extinct ratite moa and New Zealand Neogene paleogeography
- M. Bunce, T. Worthy, A. Cooper
- GeologyProceedings of the National Academy of Sciences
- 18 November 2009
This work synthesizes mitochondrial phylogenetic information from 263 subfossil moa specimens from across NZ with morphological, ecological, and new geological data to create the first comprehensive phylogeny, taxonomy, and evolutionary timeframe for all of the species of an extinct order.
Evidence for time dependency of molecular rate estimates.
There has been mounting evidence that instantaneous mutation rates substantially exceed substitution rates, in a range of organisms (e.g., Denver et al., 2000; Howell et al. 2003; Howell and Holmes, 2001; Lambert and Lambert, 2002; Mao and Mao, 2006; Mumm and Parsons, 1997; Parsons et al.'s 1997; Santos et al, 2005).