An Empirical Assessment of Long-Branch Attraction Artefacts in Deep Eukaryotic Phylogenomics

Abstract

In the context of exponential growing molecular databases, it becomes increasingly easy to assemble large multigene data sets for phylogenomic studies. The expected increase of resolution due to the reduction of the sampling (stochastic) error is becoming a reality. However, the impact of systematic biases will also become more apparent or even dominant. We have chosen to study the case of the long-branch attraction artefact (LBA) using real instead of simulated sequences. Two fast-evolving eukaryotic lineages, whose evolutionary positions are well established, microsporidia and the nucleomorph of cryptophytes, were chosen as model species. A large data set was assembled (44 species, 133 genes, and 24,294 amino acid positions) and the resulting rooted eukaryotic phylogeny (using a distant archaeal outgroup) is positively misled by an LBA artefact despite the use of a maximum likelihood-based tree reconstruction method with a complex model of sequence evolution. When the fastest evolving proteins from the fast lineages are progressively removed (up to 90%), the bootstrap support for the apparently artefactual basal placement decreases to virtually 0%, and conversely only the expected placement, among all the possible locations of the fast-evolving species, receives increasing support that eventually converges to 100%. The percentage of removal of the fastest evolving proteins constitutes a reliable estimate of the sensitivity of phylogenetic inference to LBA. This protocol confirms that both a rich species sampling (especially the presence of a species that is closely related to the fast-evolving lineage) and a probabilistic method with a complex model are important to overcome the LBA artefact. Finally, we observed that phylogenetic inference methods perform strikingly better with simulated as opposed to real data, and suggest that testing the reliability of phylogenetic inference methods with simulated data leads to overconfidence in their performance. Although phylogenomic studies can be affected by systematic biases, the possibility of discarding a large amount of data containing most of the nonphylogenetic signal allows recovering a phylogeny that is less affected by systematic biases, while maintaining a high statistical support.

Phylogenomics: the beginning of incongruence?

“…First, because using several taxa enables a better detection of multiple substitutions, increasing the taxon sampling is particularly important. All recent empirical phylogenomic studies [23,25,[28][29][30][31] except one [1] support this conclusion. This latter study [1] should be treated with caution because the tree used as reference (the MP nt tree of Figure 1a) is almost certainly incorrect.…”

“…Extensive data removal is often impractical in single-gene analyses because too few positions remain available, producing a poorly resolved tree [33]. This limitation becomes negligible in phylogenomics, and highly supported trees cleared of tree reconstruction artifacts can be recovered when more than half of the data have been discarded [23,28,30]. We therefore suggest putting the emphasis on the development and refinement of objective methods aimed at detecting and removing the part of the data containing a high level of nonphylogenetic signal [6].…”

Origin and Distribution of Calvin Cycle Fructose and Sedoheptulose Bisphosphatases in Plantae and Complex Algae: A Single Secondary Origin of Complex Red Plastids and Subsequent Propagation via Tertiary Endosymbioses

“…Long branches often lead to a reduced statistical support (compare supplementary Fig. S1b and c), but in the presence of a distant outgroup or a fastevolving ingroup, they may furthermore yield an artifactual topology (long-branch attraction artifact [LBA; Brinkmann et al 2005;Felsenstein 1978]). Accordingly, the statistical support for the plastid subtree containing all lineages of complex algae increases after the removal of divergent ascomycete and distantly related bacterial outgroup sequences (compare supplementary Fig.…”

Genomic data do not support comb jellies as the sister group to all other animals

“…In particular, the inclusion of outgroups very distant from the ingroup can cause reconstruction artifacts by attracting fast-evolving (long-branched) ingroup species toward the root (25,(27)(28)(29)(30)(31). A typical solution is to introduce more closely related outgroups to "break up" the long branch leading to the ingroup, but long-branch attraction artifacts can be further minimized by also removing the distant outgroups.…”