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CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP
  • J. Felsenstein
  • Biology, Medicine
  • Evolution; international journal of organic…
  • 1 July 1985
TLDR
The recently‐developed statistical method known as the “bootstrap” can be used to place confidence intervals on phylogenies and shows significant evidence for a group if it is defined by three or more characters. Expand
Evolutionary trees from DNA sequences: A maximum likelihood approach
TLDR
A computationally feasible method for finding such maximum likelihood estimates is developed, and a computer program is available that allows the testing of hypotheses about the constancy of evolutionary rates by likelihood ratio tests. Expand
Phylogenies and the Comparative Method
TLDR
A method of correcting for the phylogeny has been proposed, which specifies a set of contrasts among species, contrasts that are statistically independent and can be used in regression or correlation studies. Expand
Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach
TLDR
A maximum likelihood estimator based on the coalescent for unequal migration rates and different subpopulation sizes is developed and used to estimate gene flow in the Nile valley by using mtDNA data from three human populations. Expand
Maximum-likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach.
TLDR
A new method for the estimation of migration rates and effective population sizes is described, which uses a maximum-likelihood framework based on coalescence theory and is as good as or better than those from an optimized FST-based measure. Expand
Cases in which Parsimony or Compatibility Methods will be Positively Misleading
Felsenstein, J. (Department of Genetics, University of Washington, Seattle, WA 98195) 1978. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool.Expand
Maximum likelihood estimation of population growth rates based on the coalescent.
TLDR
This paper describes a method for co-estimating 4Nemu (four times the product of effective population size and neutral mutation rate) and population growth rate from sequence samples using Metropolis-Hastings sampling and suggests that sampling additional unlinked loci is much more effective in reducing the bias than increasing the number or length of sequences from the same locus. Expand
Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis.
TLDR
A polynomial-time algorithm that computes the likelihood of a species tree directly from the markers under a finite-sites model of mutation effectively integrating over all possible gene trees is described. Expand
Phylogenies from molecular sequences: inference and reliability.
Article de synthese sur les methodes d'obtention de phylogenese a partir de sequences moleculaires, tests statistiques des phylogeneses et simulations sur ordinateur
The evolutionary advantage of recombination.
TLDR
Computer simulations of substitution of favorable mutants and of the long-term increase of deleterious mutants verified the essential correctness of the original Fisher-Muller argument and the reality of the Muller ratchet mechanism. Expand
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