Measurably evolving populations

By Alexei J. Drummond, Oliver George Pybus, Andrew Rambaut, R. Forsberg, Allen G. Rodrigo. 2003

402 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/2c2cdb4b6427aa5fed998c5e85b2b59f2e852a20

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Citations in the corpus

Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen) (2016, neutral): “Drummond et al. (2003a) sketched, in the context of two sequences, a simple likelihood ratio test of the null hypothesis that there is zero measurable molecular evolution between sampling times.”
Bayesian Phylogeography Finds Its Roots (2009, background): “Demographic inference is a wellknown example of genealogy-based population genetics that benefited from these advances [24,25].”
Rates of evolutionary change in viruses: patterns and determinants (2008, background): “Not only do some viruses represent 'measurably evolving populations”
Bayesian Inference of Sampled Ancestor Trees for Epidemiology and Fossil Calibration (2014, background): “However, serially sampled data generated by different evolutionary processes can be analysed using phylogenetic methods [12] and, in some cases, the assumption that all sampled taxa are leaf nodes is not appropriate.”
The fossilized birth–death process for coherent calibration of divergence-time estimates (2013, methodology): “Under this model, absolute node age estimates are calibrated by a single diversification model and arbitrary calibration densities are not necessary.”
Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics. (2008, background): “First, such data allow one to estimate branch lengths of genealogies in units of time and simultaneously estimate the mutation rate (Drummond et al. 2002, 2003).”
The Evolution and Emergence of RNA Viruses (2009, background): “Such rapid evolution has meant that RNA viruses have also been classifi ed as ‘measurably evolving populations’ (Drummond et al. 2003b) (although this does not mean that evolution is only measurable in RNA viruses; Elena and Lenski 2003).”
Calibrating molecular estimates of substitution rates and divergence times in birds (2007, background): “Provided that the ages of the specimens are adequately distinct relative to the total depth of the phylogenetic tree, they can provide sufficient information for calibration (Drummond et al. 2002, Drummond et al. 2003 ).”
Bayesian coalescent inference of past population dynamics from molecular sequences. (2005, background): “Although this error may be small for highly variable sequences, such as those from rapidly evolving viruses (Drummond, Pybus, and Rambaut 2003;Drummond et al. 2003), it is impractical to ignore phylogenetic error in the majority of less variable data sets.”
Relaxed Phylogenetics and Dating with Confidence (2006, background): “(2) Known ages of the sequences: Recently it has also been demonstrated that calibrations can be associated with the sequences at the tips of the tree if they are sampled at significantly different times [29,30,66] with respect to their rate of evolution.”
Global emergence of Batrachochytrium dendrobatidis and amphibian chytridiomycosis in space, time, and host. (2009, background): “Using population genetic theory, researchers have recovered epidemiological parameters from genetic data using a suite of analytical phylogenetic techniques that have found extensive use in understanding many important fungal, viral, and bacterial pathogens (32, 37, 50) (Figure 2).”
Survey of Branch Support Methods Demonstrates Accuracy, Power, and Robustness of Fast Likelihood-based Approximation Schemes (2011, background): “For example, trees reconstructed from measurably evolving populations tend to lack resolution at most nodes supporting a star-like model of evolution (Drummond et al. 2003).”
Fast Dating Using Least-Squares Criteria and Algorithms (2015, methodology): “[Active-set method; algorithms; computer simulations; dating; influenza (H1N1); least-squares; linear algebra; molecular clock; serial data; substitution rate estimation; temporal precedence constraints; viruses.]”
As Time Goes by: A Simple Fool's Guide to Molecular Clock Approaches in Invertebrates* (2009, methodology): “3) within our data set in the absence of suffi cient population genetics data, we here use an approach based on a suggestion of Edwards and Beerli (2000). We assume that the effective population sizes in extant species refl ect the population sizes of the ancestral species.”