id	author	title	date	pages	extension	mime	words	sentences	flesch	summary	cache	txt
cord-355927-nzoiv9pj	Lemmon, Alan R.	The Effect of Ambiguous Data on Phylogenetic Estimates Obtained by Maximum Likelihood and Bayesian Inference	2009-05-21		.txt	text/plain	9468	455	50	Furthermore, within a Bayesian framework, priors on branch lengths and rate heterogeneity parameters can exacerbate the effects of ambiguous data, resulting in strongly misleading bipartition posterior probabilities. The results of this study have major implications for all analyses that rely on accurate estimates of topology or branch lengths, including divergence time estimation, ancestral state reconstruction, tree-dependent comparative methods, rate variation analysis, phylogenetic hypothesis testing, and phylogeographic analysis. We show that at least 5 factors determine the direction and magnitude of bias resulting from ambiguous characters: the number and taxonomic distribution of ambiguous characters, the strength of topological support from unambiguous characters, the degree of among-site rate variation, and the method and assumptions of the analysis (including the priors assumed in a Bayesian analysis). These rates were chosen, based on preliminary simulations, to produce data sets containing a range of phylogenetic information, resulting in posterior probabilities (given 500 unambiguous sites) for the true topology of 1/3, 2/3, 1, 1, 2/3, and 1/3, respectively.	./cache/cord-355927-nzoiv9pj.txt	./txt/cord-355927-nzoiv9pj.txt