Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach

By Peter Beerli, Joseph Felsenstein. Proceedings of the National Academy of Sciences of the United States of America, 2001

1,775 citations recorded by the source corpus.

Subfields: Ecology, Statistics and Probability

View Paper: https://www.semanticscholar.org/paper/37bbd5d56e6b3d64e5e595e775bcc38e1066f36b

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Citations in the corpus

Optimizing dispersal and corridor models using landscape genetics (2007, positive): “As a second measure of gene flow, we estimated migration rates ( M ) using migrate (Beerli & Felsenstein 2001).”
Ancient Admixture in Human History (2012, neutral): “Later studies by Thompson (1975); Lathrop (1982); Waddell and Penny (1996); and Beerli and Felsenstein (2001) are more similar in spirit to our methods, in that they describe frameworks for fitting population mixture events (not just simple phylogenetic trees) to the allele frequencies observed in…”
Paradigm shifts in marine fisheries genetics: ugly hypotheses slain by beautiful facts (2008, neutral): “Coalescence (Beerli and Felsenstein 2001).”
Evolving coral reef conservation with genetic information (2014, background): “Historical of Historical rates of gene flow can be estimated using coalescent approaches [Migrate: Beerli and Felsenstein (2001), IMa: Hey and Nielsen (2007)]. flow among sites Traditionally many investigators have used the inverse of F ST as an estimate of gene flow, this expectation, however,…”
Low connectivity and declining genetic variability along a depth gradient in Corallium rubrum populations (2011, methodology): “Effective population size was estimated for each site using the Brownian microsatellite mutation model in program MIGRATE 2.4.1 (Beerli and Felsenstein 2001).”
Putting the ‘landscape’ in landscape genetics (2007, methodology): “…for populations by identifying asymmetric gene flow using private alleles (Kennington et al., 2003), and estimating the number of migrants into a population using either a coalescent approach (Beerli and Felsenstein, 2001) or assignment tests (Paetkau et al., 1995; Wilson and Rannala, 2003).”
Visualizing spatial population structure with estimated effective migration surfaces (2014, methodology): “Our model-based approach is conceptually related to early work on inferring migration rates from genetic data [27], although the details – and particularly the use of “resistance distance”, a concept introduced in population genetics by [28] – are much closer to recent work on landscape…”
Population genetic analysis of Arapaima gigas, one of the largest freshwater fishes of the Amazon basin: implications for its conservation (2005, methodology): “…in the gene flow analysis (Table 4) using a coalescent algorithm implemented in the program MIGRATE (Beerli & Felsenstein, 2001), although the model implemented in MIGRATE (Beerli & Felsenstein, 2001) is largely free of the assumptions underlying the FST-based methods for deriving Nm values.”
Is FST obsolete? (2002, methodology): “Beerli and Felsenstein (1999, 2001) have developed a method that simultaneously estimates the effective sizes of multiple populations as well as rates of migration between every pair of populations.”
Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. (2003, methodology): “Beerli and Felsenstein (1999, 2001) and population size parameters H for humans; C for chimpanzees; and HC, HCG, and HCGO for the threeimplemented MCMC algorithms for likelihood analysis of subdivided populations under the finite-sites model. ancestral species.”
ASYMMETRIC HYBRIDIZATION AND SEX-BIASED GENE FLOW BETWEEN EASTERN SPOT-BILLED DUCKS (ANAS ZONORHYNCHA) AND MALLARDS (A. PLATYRHYNCHOS) IN THE RUSSIAN FAR EAST (2004, background): “It is unfortunate that N e m could not be calculated for mtDNA gene fl ow arising from female spotbills that mated with male Mallards because of limits of the ML estimation procedure (Beerli and Felsenstein 2001).”
The evolution of molecular markers — just a matter of fashion? (2004, background): “However, it should be noted that several methods for estimating population parameters, such as migration and recombination, that take multiple hits into accoun”
Correlating viral phenotypes with phylogeny: accounting for phylogenetic uncertainty. (2008, methodology): “Such approaches have recently been implemented in a Bayesian framework and applied to virus genetic data (Beerli and Felsenstein, 2001; Wilson and Rannala, 2003; Ewing et al., 2004).”