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Partitionfinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses.
Two new objective methods for the combined selection of best-fit partitioning schemes and nucleotide substitution models are described and implemented in an open-source program, PartitionFinder, which it is hoped will encourage the objective selection of partitions and thus lead to improvements in phylogenetic analyses.
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.
Whole-genome analyses resolve early branches in the tree of life of modern birds
A genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves recovered a highly resolved tree that confirms previously controversial sister or close relationships and identifies the first divergence in Neoaves, two groups the authors named Passerea and Columbea.
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.
Calibrating molecular estimates of substitution rates and divergence times in birds
- S. Ho
- 1 July 2007
A number of more sophisticated calibration methods have recently been introduced, culminating in the development of probability distribution-based calibrations, and guidelines for choosing a calibration technique are offered.
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.
Estimating the phylogeny and divergence times of primates using a supermatrix approach
This work presents an up-to-date, comprehensive estimate of the structure and tempo of primate evolutionary history, using Bayesian phylogenetic methods to analyze data supermatrices from 219 species across 67 genera and 3 nuclear genes from 26 genera.
Radiation of Extant Cetaceans Driven by Restructuring of the Oceans
- M. Steeman, M. Hebsgaard, E. Willerslev
- Environmental Science, GeographySystematic biology
- 5 October 2009
It is found that the toothed whales are monophyletic, suggesting that echolocation evolved only once early in that lineage some 36–34 Ma, and support is found for increased diversification rates during periods of pronounced physical restructuring of the oceans.
Skyline‐plot methods for estimating demographic history from nucleotide sequences
A technical review of skyline‐plot methods that are able to reconstruct changes in population sizes through time, based on coalescent theory, and some general principles relating to sampling design and data collection are described.