Highly Incomplete Taxa Can Rescue Phylogenetic Analyses from the Negative Impacts of Limited Taxon Sampling

Abstract

BackgroundPhylogenies are essential to many areas of biology, but phylogenetic methods may give incorrect estimates under some conditions. A potentially common scenario of this type is when few taxa are sampled and terminal branches for the sampled taxa are relatively long. However, the best solution in such cases (i.e., sampling more taxa versus more characters) has been highly controversial. A widespread assumption in this debate is that added taxa must be complete (no missing data) in order to save analyses from the negative impacts of limited taxon sampling. Here, we evaluate whether incomplete taxa can also rescue analyses under these conditions (empirically testing predictions from an earlier simulation study).Methodology/Principal FindingsWe utilize DNA sequence data from 16 vertebrate species with well-established phylogenetic relationships. In each replicate, we randomly sample 4 species, estimate their phylogeny (using Bayesian, likelihood, and parsimony methods), and then evaluate whether adding in the remaining 12 species (which have 50, 75, or 90% of their data replaced with missing data cells) can improve phylogenetic accuracy relative to analyzing the 4 complete taxa alone. We find that in those cases where sampling few taxa yields an incorrect estimate, adding taxa with 50% or 75% missing data can frequently (>75% of relevant replicates) rescue Bayesian and likelihood analyses, recovering accurate phylogenies for the original 4 taxa. Even taxa with 90% missing data can sometimes be beneficial.ConclusionsWe show that adding taxa that are highly incomplete can improve phylogenetic accuracy in cases where analyses are misled by limited taxon sampling. These surprising empirical results confirm those from simulations, and show that the benefits of adding taxa may be obtained with unexpectedly small amounts of data. These findings have important implications for the debate on sampling taxa versus characters, and for studies attempting to resolve difficult phylogenetic problems.

Do missing data influence the accuracy of divergence-time estimation with BEAST?

“…For example, other empirical analyses suggest that extensive missing data can have relatively little impact on estimated branch lengths (e.g. Wiens and Tiu, 2012;Jiang et al, 2014). Therefore, it seems that dating methods that rely on branch-length estimates from previous likelihood or Bayesian analyses should also be robust to missing data (e.g.…”

“…These include studies that addressed the impact of including incomplete taxa, the impact of incomplete characters, and the impacts of missing data on branch-length estimation and support values (e.g. Wiens, 2003Wiens, , 2005Driskell et al, 2004;Philippe et al, 2004;Wiens and Moen, 2008;Burleigh et al, 2009;Lemmon et al, 2009;Sanderson et al, 2010Sanderson et al, , 2011Cho et al, 2011;Pyron et al, 2011;Wiens and Morrill, 2011;Crawley and Hilu, 2012;Simmons, 2012Simmons, , 2014Wiens and Tiu, 2012;Hovmöller et al, 2013;Roure et al, 2013;Jiang et al, 2014). However, an important and largely unresolved question is how missing data impact divergence-time estimation.…”

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

“…Simulations and empirical analyses show that even highly incomplete taxa can potentially subdivide long branches and lead to more accurate phylogenetic estimates when there is long-branch attraction due to limited taxon sampling (e.g. Wiens, 2005;Wiens and Tiu, 2012;Roure et al, 2013). Second, will adding the set of many incomplete genes improve branch support (e.g.…”

Selecting Molecular Markers for a Specific Phylogenetic Problem

“…The issue of missing data versus (taxon and gene) sampling has been a focus of heated debate for over a decade [7,[53][54][55]. A gene may be eliminated that has not been sampled for many species, such as genes only sampled in species with full genome sequences available.…”

“…Molecular data from more than 260 thousand nominal species is now widely accepted as a paramount source of biological information in all life sciences [7]. This is an exciting time.…”