Overcredibililty of molecular phylogenies obtained by Bayesian phylogenetics. Proc Natl Acad Sci USA

Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, 328 Mueller Laboratory, University Park, PA 16802, USA.
Proceedings of the National Academy of Sciences (Impact Factor: 9.67). 01/2003; 99(25):16138-43. DOI: 10.1073/pnas.212646199
Source: PubMed


Bayesian phylogenetics has recently been proposed as a powerful method for inferring molecular phylogenies, and it has been reported that the mammalian and some plant phylogenies were resolved by using this method. The statistical confidence of interior branches as judged by posterior probabilities in Bayesian analysis is generally higher than that as judged by bootstrap probabilities in maximum likelihood analysis, and this difference has been interpreted as an indication that bootstrap support may be too conservative. However, it is possible that the posterior probabilities are too high or too liberal instead. Here, we show by computer simulation that posterior probabilities in Bayesian analysis can be excessively liberal when concatenated gene sequences are used, whereas bootstrap probabilities in neighbor-joining and maximum likelihood analyses are generally slightly conservative. These results indicate that bootstrap probabilities are more suitable for assessing the reliability of phylogenetic trees than posterior probabilities and that the mammalian and plant phylogenies may not have been fully resolved.

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    • "However, ML support for the core lamiid relationships presented here is not strong, despite the large number of characters included in the analyses, indicating that there is still uncertainty surrounding some core lamiid relationships . Although the Bayesian support for these relationships is generally strong ( Fig. 1 ), posterior probability values are oft en infl ated compared to ML bootstrap values (e.g., Suzuki et al., 2002 ; Cummings et al., 2003 ; Erixon et al., 2003 ), as noted already. Diffi culty in resolving core lamiid relationships might be due to an ancient rapid radiation ( Bremer et al., 2004 ), refl ecting the short internal branch lengths connecting the core lamiid lineages in Fig. 2 . "
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    American Journal of Botany 10/2015; DOI:10.3732/ajb.1500298 · 2.60 Impact Factor
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    • "The combinability of DNA markers was assessed by comparing clade support between individual data partitions (Wiens, 1998). Because Bayesian posterior probability values are often biased high (Alfaro et al., 2003; Erixon et al., 2003; Suzuki et al., 2002), we used the more conservative parsimony bootstrap supports to identify clade conflict between the DNA partitions. Incongruent clades with bootstrap supports >80% were taken as evidence for not combining data sets. "
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