Pruning Rogue Taxa Improves Phylogenetic Accuracy: An Efficient Algorithm and Webservice

Abstract

The presence of rogue taxa (rogues) in a set of trees can frequently have a negative impact on the results of a bootstrap analysis (e.g., the overall support in consensus trees). We introduce an efficient graph-based algorithm for rogue taxon identification as well as an interactive webservice implementing this algorithm. Compared with our previous method, the new algorithm is up to 4 orders of magnitude faster, while returning qualitatively identical results. Because of this significant improvement in scalability, the new algorithm can now identify substantially more complex and compute-intensive rogue taxon constellations. On a large and diverse collection of real-world data sets, we show that our method yields better supported reduced/pruned consensus trees than any competing rogue taxon identification method. Using the parallel version of our open-source code, we successfully identified rogue taxa in a set of 100 trees with 116 334 taxa each. For simulated data sets, we show that when removing/pruning rogue taxa with our method from a tree set, we consistently obtain bootstrap consensus trees as well as maximum-likelihood trees that are topologically closer to the respective true trees.

The methanogenic redox cofactor F420 is widely synthesized by aerobic soil bacteria

“…This was first done for CofH and the same taxa as in the resulting sequence set were used for the phylogenetic analysis of the other proteins for consistency. RogueNaRok (Aberer et al, 2013) was used to remove fast-evolving sequences (all belonging to Firmicutes, Tectomicrobia, Thermoleophilia and Rubrobacteria) that otherwise caused long-branch attractions and hence unreliable evolutionary inferences (Anderson and Swofford, 2004). Sequences were aligned using MAFFT (Katoh and Standley, 2013) or MUSCLE (Edgar, 2004), with gaps and poorly aligned variable regions in the alignment removed using Gblocks (Castresana, 2000).…”

Embracing discordance: Phylogenomic analyses provide evidence for allopolyploidy leading to cryptic diversity in a MediterraneanCampanula(Campanulaceae) clade

“…We used Rogue NaRok (Aberer et al. 2013) to identify such OTUs. This analysis, optimized for support using a majority rule consensus threshold, identified four individuals of C. erinus as rogue samples.…”

Intertwining phylogenetic trees and networks

“…When the levels of conflict are great, however, researchers may resort to networks -often as a last option after all other tree-based methods have failed -to have some way of making sense of the patterns within a dataset. The only alternative is filtering the 'rogue' taxa that are causing topological conflict or a decrease in branch support (Aberer et al 2013). The wide range of available network methods (Huson & Bryant 2006) have remained underutilised, likely because of the difficulties that arise when comparing trees and networks (such as matching tree branches to network edges).…”