Bayesian coalescent inference of past population dynamics from molecular sequences.

By Alexei J. Drummond, Andrew Rambaut, Beth Shapiro, Oliver George Pybus. Molecular biology and evolution, 2005

3,142 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/4e98dde420b63f896fc7e1ca79a5c5e3b15351b8

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Citations in the corpus

The diversification of eastern South American open vegetation biomes: Historical biogeography and perspectives (2011, methodology): “…based on ancient DNA (Ramakrishnan and Hadly, 2009), migration rate estimations (Hey and Nielsen, 2004), past population demography dynamics (Drummond et al., 2005), and phylogeography coupled with GIS-based predictive models, such as distribution modeling (Carstens and Richards, 2007;…”
Sky islands of southwest China. I: an overview of phylogeographic patterns (2014, background): “, Fu’s test [14]), mismatched distribution [15] and Bayesian skylines [16].”
Isolation and introgression in the Intermountain West: contrasting gene genealogies reveal the complex biogeographic history of the American pika (Ochotona princeps) (2010, methodology): “, 1984), applied the Bayesian skyline plot tree prior (Drummond et al., 2005), fixed the mean mutation rate and assumed a strict molecular clock.”
Bayesian Phylogeography Finds Its Roots (2009, methodology): “To allow for variation in the underlying coalescent process giving rise to the phylogeny, we assume a piece-wise constant multiple change-point model on the effective populationsize with 20 coalecent-interval groups [25].”
Quaternary range dynamics of ecologically divergent species (Edraianthus serpyllifolius and E. tenuifolius, Campanulaceae) within the Balkan refugium (2011, methodology): “Initial analysis using the Bayesian skyline plot (Drummond et al., 2005), the most general demographic model, with different group intervals did not indicate any detectable fluctuations in population size (data not shown).”
When bigger is not better: The economics of hunting megafauna and its implications for Plio-Pleistocene hunter-gatherers (2016, background): “Even without paleontological sources, independent measures of prey abundances are possible through biomolecular analyses to evaluate the relative size of different animal populations (e.g., Drummond et al., 2005; Stiller et al., 2010).”
Phylogeography and ecological niche modelling of the New Zealand stick insect Clitarchus hookeri (White) support survival in multiple coastal refugia (2010, methodology): “We reconstructed the timing and magnitude of changes in effective population size using the Bayesian skyline method (Drummond et al., 2005) as implemented in beast v.1.4.8 (Drummond & Rambaut, 2007) and mismatch statistics (Slatkin & Hudson, 1991) implemented in DnaSP v.4.0.”
Population Demography and Genetic Diversity in the Pleistocene Cave Lion (2015, background): “In steppe bison, a severe demographic reduction started some 44–34,000 cal a BP (Drummond et al., 2005; Shapiro et al., 2004).”
Phylogeography takes a relaxed random walk in continuous space and time. (2010, background): “…(1985) (HKY85) continuous-time Markov chain model of nucleotide substitution; we include discrete gamma-distributed rate variation (Yang 1995 ) and assume an flexible Bayesian skyline or skyride effective population size prior over the unknown phylogeny (Drummond et al. 2005; Minin et al. 2008).”
Seven Shortfalls that Beset Large-Scale Knowledge of Biodiversity (2015, background): “However, this uncertainty can hamper accurate predictions of variability in population size (e.g., McCarthy et al. 1994) or introduce errors in coalescence analyses through the use of invalid estimates of demographic history (Pybus et al. 2000, Drummond et al. 2005).”