@article{fdi:010053197,
  title = {{T}ime-dependent speciation and extinction from phylogenies : a least squares approach},
  author = {{P}aradis, {E}mmanuel},
  editor = {},
  language = {{ENG}},
  abstract = {{M}olecular phylogenies contribute to the study of the patterns and processes of macroevolution even though past events (fossils) are not recorded in these data. {I}n this article, {I} consider the general time-dependent birth-death model to fit any model of temporal variation in speciation and extinction to phylogenies. {I} establish formulae to compute the expected cumulative distribution function of branching times for any model, and, building on previous published works, {I} derive maximum likelihood estimators. {S}ome limitations of the likelihood approach are described, and a fitting procedure based on least squares is developed that alleviates the shortcomings of maximum likelihood in the present context. {P}arametric and nonparametric bootstrap procedures are developed to assess uncertainty in the parameter estimates, the latter version giving narrower confidence intervals and being faster to compute. {I} also present several general algorithms of tree simulation in continuous time. {I} illustrate the application of this approach with the analysis of simulated datasets, and two published phylogenies of primates ({C}atarrhinae) and lizards ({A}gamidae).},
  keywords = {{B}irth-death ; diversification ; extinction ; phylogeny ; speciation},
  booktitle = {},
  journal = {{E}volution},
  volume = {65},
  numero = {3},
  pages = {661--672},
  ISSN = {0014-3820},
  year = {2011},
  DOI = {10.1111/j.1558-5646.2010.01179.x},
  URL = {https://www.documentation.ird.fr/hor/fdi:010053197},
}