Accommodating phylogenetic uncertainty in evolutionary studies.

By John P. Huelsenbeck, Bruce Rannala, John P. Masly. Science, 2000

327 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/23f955d3e9c06490a9f7403318a8e35b166ec8bc

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Citations in the corpus

Biological and biomedical implications of the co-evolution of pathogens and their hosts (2002, methodology): “Improved statistical methods for distinguishing genetic divergence from adaptive causes of correlated genetic change across population”
Sexual Conflict, Ecology, and Breeding Systems in Shorebirds (2006, methodology): “cross-species studies are now regarded as the “gold-standard” (Huelsenbeck et al. 2000).”
The seven deadly sins of comparative analysis (2009, methodology): “Finally, increasingly it is possible to quantify the uncertainty in phylogenetic reconstructions and to directly incorporate this into comparative tests using Bayesian methods (e.g. Huelsenbeck, 2000).”
The phylogeny and evolution of Figitidae (Hymenoptera: Cynipoidea) (2007, background): “…straightforward (theoretical) interpretation of probabilities (Huelsenbeck and Rannala, 2004) and the way uncertainties in trees and parameter values can be accommodated: instead of basing conclusions on point estimates, uncertainty in tree topology can be integrated out (Huelsenbeck et al., 2000).”
Phylogenetic relationships and species concepts in Parmelia s. str. (Parmeliaceae) inferred from nuclear ITS rDNA and β-tubulin sequences (2004, methodology): “Several Parmelia s. str. nuITS and partial -tubulin sequences from GenBank (http://www.ncbi.nlm.nih. gov) were included in the analyses, and pertinent collections are indicated in Table 1.”
Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation (2019, background): “only trees rather than the consensus tree alone [33,34].”
SIMMAP: Stochastic character mapping of discrete traits on phylogenies (2006, methodology): “The Bayesian approach accommodates phylogenetic uncertainty by evaluating character maps on trees sampled from the posterior distribution [11,12].”
Innovative Approaches to the Relationship Between Diet and Mandibular Morphology in Primates (2012, background): “2001), results should not be conditioned on a single phylogenetic hypothesis (Huelsenbeck et al. 2000; Pagel and Lutzoni 2002).”
A likelihood approach to estimating phylogeny from discrete morphological character data. (2001, methodology): “Furthermore, the Bayesian approach makes it possible to test hypotheses involving phylogenies without depending on any particular hypothesized tree (e.g., Huelsenbeck, 2000b), so likelihood models are expected to play an ever-increasing role in systematics and related disciplines.”
Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence. (2003, background): “These measures allow workers to identify trees or parts of a tree that are well supported by the data and thus adequate to serve as the basis for evolutionary inference of biological systems (Huelsenbeck, Rannala, and Masly 2000; Lutzoni et al. 2001; Pagel and Lutzoni 2002).”
Stochastic mapping of morphological characters. (2003, methodology): “…under a stochastic process, such as the birth–death process (Losos, 1994; Martins, 1996) or examining the evolution of a character on all trees with the results from each tree weighted by the probability of the tree being correct (Losos and Miles, 1994; Pagel, 1994; Huelsenbeck et al., 2000).”