Coalescent Theory: An Introduction

By John Wakeley. 2008

874 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/093d2ade2b024d3df0c5f3c2af360db76a3b03aa

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Citations in the corpus

A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies (2009, background): “…that, as k gets larger, jumps between different copied haplotypes should become less likely and those haplotypes should be copied with higher fidelity; this is because a chromosome will coalesce faster into a larger genealogy, leaving less time for recombination and mutation events to occur [18].”
Ecologically differentiated stress-tolerant endosymbionts in the dinoflagellate genus Symbiodinium (Dinophyceae) Clade D are different species (2014, background): “In strictly clonal populations, multilocus haplotypes should produce genealogies with allele combinations that are linked across many loci (Hudson and Kaplan 1985, Wakeley 2008).”
The Ubiquitous Ewens Sampling Formula (2016, background): “Perhaps the most major advance in evolutionary population genetics in the last three decades, Kingman’s coalescent has resulted in the widely adopted coalescent theory within population genetics [87] as well as the mathematical study of partition-valued and more general combinatorial stochastic proc”
DNA Barcoding is not enough: mismatch of taxonomy and genealogy in New Zealand grasshoppers (Orthoptera: Acrididae). (2008, background): “The disparity between gene trees and species trees is well recognized (e.g., Doyle, 1997) and has fueled a rapid development in coalescent theory and analysis (Wakeley, 2004).”
Distribution modelling and statistical phylogeography: an integrative framework for generating and testing alternative biogeographical hypotheses (2007, methodology): “interpretations concerning the biogeographical and demographic past are based on a visual inspection of a gene tree), the analysis of genetic data can proceed by means of statistical phylogeographic approaches (Knowles & Maddison, 2002), whereby the stochasticity of genetic processes is explicitly c”
Species taxonomy of birds: Which null hypothesis? (2014, background): “Coalescence models allow inference regarding recent histories of divergence with variable levels of gene flow (Wakeley 2008, 2010, Hey 2010) and thus deeper insight into the speciation process than was possible with classical constructs based simply on spatial distribution (Harrison 2012).”
Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data (2009, methodology): “Many of the statistics commonly used for population genetic inference, such as FST and Tajima’s D, are summaries of the AFS (see [18, 22]).”
A maximum pseudo-likelihood approach for estimating species trees under the coalescent model (2010, background): “Although the likelihood function of the species tree under the multispecies coalescent model has already been derived by Rannala and Yang [25], research on the maximum likelihood (ML) estimation of species trees under the coalescent remains limited [7,33,34].”
ASAP: assemble species by automatic partitioning (2020, background): “This relates to the average time to the MRCA that is 2 × (1 − 1/m), expressed in coalescent time (Wakeley, 2009).”
Evolutionary dynamics on any population structure (2016, methodology): “Our method uses coalescent theory [14, 15] and relies on calculating the meeting times of random walks [16, 17].”
Efficient ancestry and mutation simulation with msprime 1.0 (2021, background): “It has proved to be a powerful model, and is now central to population 66 genetics (Hudson, 1990; Hein et al., 2004; Wakeley, 2008).”
Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes (2015, background): “The model has proved to be highly extensible, and these and many other complexities required to model real populations have successfully been incorporated [3].”
Delimiting species without monophyletic gene trees. (2007, background): “Analytical expectations derived from population genetic theory (Hudson, 1992; Rosenberg, 2002; Wakeley, 2006) indicate that a substantial amount of time is required after the initial divergence of species before there will be a high probability of observing reciprocal monophyly at a sample of multip”