Heterotachy and long-branch attraction in phylogenetics

Abstract

Background: Probabilistic methods have progressively supplanted the Maximum Parsimony (MP) method for inferring phylogenetic trees. One of the major reasons for this shift was that MP is much more sensitive to the Long Branch Attraction (LBA) artefact than is Maximum Likelihood (ML). However, recent work by Kolaczkowski and Thornton suggested, on the basis of simulations, that MP is less sensitive than ML to tree reconstruction artefacts generated by heterotachy, a phenomenon that corresponds to shifts in site-specific evolutionary rates over time. These results led these authors to recommend that the results of ML and MP analyses should be both reported and interpreted with the same caution. This specific conclusion revived the debate on the choice of the most accurate phylogenetic method for analysing real data in which various types of heterogeneities occur. However, variation of evolutionary rates across species was not explicitly incorporated in the original study of Kolaczkowski and Thornton, and in most of the subsequent heterotachous simulations published to date, where all terminal branch lengths were kept equal, an assumption that is biologically unrealistic.

Accurate gene-tree reconstruction by learning gene- and species-specific substitution rates across multiple complete genomes

“…The methodology introduced here, although general, allowed us to address the problem of long-branch attraction at the species level (Bergsten 2005;Philippe et al 2005). It is known that when fast-evolving lineages are intermixed with slowly evolving lineages, the longer branches tend to cluster together and join further back in evolutionary time, due to increased rates of homoplasy in rapidly evolving lineages.…”

“…Numerous studies have addressed the accuracy of phylogeny reconstruction methods using mainly simulated alignments (Saitou and Imanishi 1989;Kuhner and Felsenstein 1994;Tateno et al 1994;Philippe et al 2005) and, in some cases, microevolution observed experimentally (Hillis et al 1994;Bull et al 1997;Woods et al 2006). With multiple complete genomes, regions of conserved gene order (synteny) provide a natural test for phylogenetic methods (Rokas et al 2003;Ciccarelli et al 2006), since all genes within these regions are typically coinherited from a single gene in the common ancestor of the species ( Fig.…”

“…We used SPIDIR to infer gene trees in both flies and fungi, and show that it leads to significantly higher reconstruction accuracies. In particular, we find that our strategy can address the long-branch attraction problem for species-level heterotachy (Bergsten 2005;Philippe et al 2005), by learning to expect longer branches for faster-evolving lineages.…”

Evolution of viruses and cells: do we need a fourth domain of life to explain the origin of eukaryotes?

“…Therefore, because viral sequences evolve fast, they are very prone to be affected by a very well-known phylogenetic reconstruction artefact, the long branch attraction (LBA) described by Felsenstein in the late 1970s [58]. It is also well known that the use of poor taxonomic sampling, simplistic phylogenetic reconstruction methods (such as the non-probabilistic distance-or parsimony-based ones) and/or inadequate substitution models can exacerbate LBA problems [59][60][61][62][63][64]. Given their high evolutionary rates, viruses are ideal candidates to get trapped in what has been called the 'Felsenstein zone', namely the conditions where long branches are misplaced in phylogenetic trees [65].…”

Phylogenetic analyses place the monotypic Dryopolystichum within Lomariopsidaceae

“…Since Dracoglossum and Lomariopsis were resolved on long branches in preliminary analyses (not shown), we conducted two additional analyses in which each one of the two long-branched genera, Dracoglossum and Lomariopsis , was excluded to examine whether phylogenetic placement and branch support for Dryopolystichum ’s placement changed. Since maximum parsimony (MP) phylogeny is considered to be more susceptible to long-branch attraction (Philippe et al 2005), we analyzed the concatenated dataset under MP in order to compare those results with our ML phylogeny. The MP analyses were conducted using TNT (Goloboff et al 2008) following the search strategy detailed in Sundue et al (2014).…”