Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics

By J. Hey, Rasmus Nielsen. Proceedings of the National Academy of Sciences of the United States of America, 2007

1,017 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/f28fa237d247dd3ce8b8e1f16d1ce57ea47880df

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In Genetics

Citations in the corpus

Mitochondrial introgression and replacement between yellowhammers (Emberiza citrinella) and pine buntings (Emberiza leucocephalos) (Aves: Passeriformes) (2009, methodology): “…yellowhammers and allopatric pine buntings based on mitochondrial ND2 data and an assumption of neutrality, we used the software IMa (Hey, 2007; Hey & Nielsen, 2007), which used a Bayesian Markov chain Monte Carlo approach to fit the ND2 sequence data to an ‘Isolation with Migration’ model…”
How to fail at species delimitation (2013, methodology): “…that model population-level processes such as genetic drift in combination with migration (Beerli & Felsenstein 2001), expansion (Kuhner et al. 1998), population divergence (Hey & Nielsen 2007) or combinations of these processes (Gutenkunst et al. 2009) are widely applied to phylogeographical data.”
Isolation with migration models for more than two populations. (2010, methodology): “This MCMC simulation generates samples from the posterior density PðG; tjXÞ, and these are then used to build an estimate of the joint posterior probability of the model parameters, pðHjXÞ(Hey and Nielsen 2007).”
The phylogeographic architecture of the fucoid seaweed Ascophyllum nodosum: an intertidal ‘marine tree’ and survivor of more than one glacial–interglacial cycle (2010, methodology): “…effective population size (Q = Nel), asymmetrical migration rates (m/l = Nem/Q) and population divergence time were estimated using the software im (Hey & Nielsen, 2007). im uses Markov chain Monte Carlo (MCMC) sampling and applies the isolation-with-migration model to genetic data taken from…”
Phylogeography's past, present, and future: 10 years after Avise, 2000. (2010, methodology): “Another common statistical approach is to assume a single model and estimate parameters under the model using full likelihood/Bayesian approaches that make use of all of the data (Beerli and Felsenstein, 2001; Hey and Nielsen, 2004, 2007; Kuhner, 2006; Kuhner et al., 1998).”
The role of molecular genetics in sculpting the future of integrative biogeography (2008, methodology): “Although continuing development of methods based on coalescent theory (Beaumont, 2004; Anderson et al., 2005; Beerli, 2006; Carstens and Richards, 2007; Edwards et al., 2007; Hey and Nielsen, 2007; Hickerson et al., 2007; Knowles and Carstens, 2007) and niche-modelling (above citations) are reinvigo”
Non-linear regression models for Approximate Bayesian Computation (2008, methodology): “Although many likelihood-based methods have been proposed in this framework, these meth-ods are restricted to particular demographic and genetic processes (Stephens and Donnelly 2000; Wilson et al. 2003; Kuhner 2006; Hey and Nielsen 2007).”
Species Tree Inference with BPP Using Genomic Sequences and the Multispecies Coalescent (2018, methodology): “0 implement an option of integrating out analytically the h parameters, using conjugate inversegamma priors (Hey and Nielsen 2007).”
Phylogeographic studies of plants in China: Advances in the past and directions in the future (2012, methodology): “For example, the isolation and migration (IM) model and the corresponding calculations can be extended to the multiple-loci data (Hey & Nielsen, 2004) and multiple populations (Hey & Nielsen, 2007; Hey, 2010; Choi & Hey, 2011).”
Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow (2014, background): “One popular way to infer whether gene flow is occurring is to apply a coalescent-based model for gene flow, referred to as the isolation-with-migration (IM) model (Nielsen & Wakeley 2001; Hey & Nielsen 2004, 2007; Hey 2010).”
Robust Demographic Inference from Genomic and SNP Data (2013, methodology): “including full-likelihood methods [6–9], summary-statistics likelihood based methods [10,11], or different flavours of Approximate”
Divergence with Gene Flow: Models and Data (2010, methodology): “…changes that permit the use of data sets with multiple loci (Hey & Nielsen 2004), relax the assumption of constant population sizes (Hey 2005), reduce the state space of MCMC simulation to just genealogies (Hey & Nielsen 2007), and allow the study of more than two related populations (Hey 2010).”
After continents divide: comparative phylogeography of reef fishes from the Red Sea and Indian Ocean (2013, methodology): “We calculated the effects of time and gene flow on genetic divergence between populations using Bayesian coalescentbased estimation with IMa2 8.26.11 (Hey & Nielsen, 2007; Hey, 2010).”