Increased Taxon Sampling Greatly Reduces Phylogenetic Error

Abstract

Several authors have argued recently that extensive taxon sampling has a positive and important effect on the accuracy of phylogenetic estimates. However, other authors have argued that there is little benefit of extensive taxon sampling, and so phylogenetic problems can or should be reduced to a few exemplar taxa as a means of reducing the computational complexity of the phylogenetic analysis. In this paper we examined five aspects of study design that may have led to these different perspectives. First, we considered the measurement of phylogenetic error across a wide range of taxon sample sizes, and conclude that the expected error based on randomly selecting trees (which varies by taxon sample size) must be considered in evaluating error in studies of the effects of taxon sampling. Second, we addressed the scope of the phylogenetic problems defined by different samples of taxa, and argue that phylogenetic scope needs to be considered in evaluating the importance of taxon-sampling strategies. Third, we examined the claim that fast and simple tree searches are as effective as more thorough searches at finding near-optimal trees that minimize error. We show that a more complete search of tree space reduces phylogenetic error, especially as the taxon sample size increases. Fourth, we examined the effects of simple versus complex simulation models on taxonomic sampling studies. Although benefits of taxon sampling are apparent for all models, data generated under more complex models of evolution produce higher overall levels of error and show greater positive effects of increased taxon sampling. Fifth, we asked if different phylogenetic optimality criteria show different effects of taxon sampling. Although we found strong differences in effectiveness of different optimality criteria as a function of taxon sample size, increased taxon sampling improved the results from all the common optimality criteria. Nonetheless, the method that showed the lowest overall performance (minimum evolution) also showed the least improvement from increased taxon sampling. Taking each of these results into account re-enforces the conclusion that increased sampling of taxa is one of the most important ways to increase overall phylogenetic accuracy.

New insights into the phylogeny of glass sponges (Porifera, Hexactinellida): Monophyly of Lyssacinosida and Euplectellinae, and the phylogenetic position of Euretidae

“…In contrast to our previous study , the most species-rich hexactinellid order, Lyssacinosida, is now recovered as monophyletic, independent of model choice, re-emphasizing the importance of taxon sampling for phylogenetic inference (e.g., Zwickl and Hillis, 2002). Another factor that might have contributed to this result is the replacement of the erroneous or pseudogenic 18S sequence of Farrea occa (see Voigt et al, 2008) with new sequences from Farrea sp.…”

Phylogeny for the faint of heart: a tutorial

“…Methods such as maximum likelihood tend to be less affected than others, but rarely strikingly so [22]. Generally, it is best to break up the long branches, by adding intermediate sequences to a tree [23]. To return to the flower analogy, with highly derived forms, if you can find some of the intermediate relatives it becomes much easier to see how they fit in with the rest of your taxa.…”

Combining phylogenomic and supermatrix approaches, and a time-calibrated phylogeny for squamate reptiles (lizards and snakes) based on 52 genes and 4162 species

“…Whether it is better to sample more taxa or more genes to resolve higher-level phylogenies was once a major debate in systematics (e.g. Graybeal, 1998;Rannala et al, 1998;Poe and Swofford, 1999;Rosenberg and Kumar, 2001;Zwickl and Hillis, 2002;Poe, 2003;Heath et al, 2008). Although the topic is less hotly debated now, the question is still highly relevant and very much unresolved.…”