Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

By Hervé Philippe, H. Brinkmann, D. Lavrov, D. Timothy, J. Littlewood, M. Manuel, Gert Wö Rheide, Denis Baurain. PLoS Biology, 2011

1,060 citations recorded by the source corpus.

In the quest to reconstruct the Tree of Life, researchers have increasingly turned to phylogenomics, the inference of phylogenetic relationships using genome-scale data (Box 1). Mesmerized by the sustained increase in sequencing throughput, many phylogeneticists entertained the hope that the incongruence frequently observed in studies using single or a few genes [1] would come to an end with the generation of large multigene datasets. Yet, as so often happens, reality has turned out to be far more complex, as three recent large-scale analyses, one published in PLoS Biology [2]–[4], make clear. The studies, which deal with the early diversification of animals, produced highly incongruent (Box 2) findings despite the use of considerable sequence data (see Figure 1). Clearly, merely adding more sequences is not enough to resolve the inconsistencies.

Subfields: Genetics, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/c032b81df71c5b5745454ef5b2afa4f715cc3f92

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Citations in the corpus

The New Tree of Eukaryotes. (2019, background): “Therefore, merely adding genes can amplify artefacts rather than overriding them [25].”
A basin redox transect at the dawn of animal life (2012, background): “Moving up the metazoan phylogenetic tree, the exact relationships of cnidarians, ctenophores and placozoans to bilaterians are unclear, but all are likely more closely related to bilaterians than they are to sponges (Philippe et al., 2011).”
PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes (2013, background): “We currently favor conserved proteins by drawing proportionally more residues from them, tending to identify residues that are “slightly saturated” 54 .”
Error in Phylogenetic Estimation for Bushes in the Tree of Life (2013, background): “In the extreme this homoplasy could lead to substitutional saturation [32,33].”
Pitfalls in supermatrix phylogenomics (2017, positive): “Moreover, we used less permissive Gblocks parameters, reducing positions from 21 152 to 18 463 (Philippe et al. 2011b).”
Inferring Phylogenies from RAD Sequence Data (2012, background): “RAD data are not resistant to the problems typically encountered in genome level molecular phylogenetics [33].”
Origin and early diversification of the phylum Cnidaria Verrill: major developments in the analysis of the taxon's Proterozoic–Cambrian history (2014, background): “However, we believe that the results of the mitogenomic analyses are not conclusive, as they are based on limited taxon sampling and are further handicapped by the inappropriateness of part of the mitogenome for addressing the phylogenetic questions involved (cf. Philippe et al. 2011).”
The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes (2014, background): “Multiple genome alignment is a fundamental tool in genomics essential for tracking genome evolution [6-8], accurate inference of recombination [9-14], identification of genomic islands [15,16], analysis of mobile genetic elements [17,18], comprehensive classification of homology [19,20], ancestral g”
High-Throughput Genomic Data in Systematics and Phylogenetics (2013, background): “Although systematic error may have the greatest effect when phylogenetic information is weak (e.g., Lemmon et al. 2009), some types of systematic error can overwhelm substantial phylogenetic information (Rodriguez-Ezpeleta et al. 2007, Philippe et al. 2011).”
Applications of next-generation sequencing to phylogeography and phylogenetics. (2013, background): “Second, they appear to have little overlap with known paralogous genes (Derti et al., 2006), whose occurrence is difficult to detect and can confound phylogenetic inference (Philippe et al., 2011).”
OMA standalone: orthology inference among public and custom genomes and transcriptomes (2018, background): “gard to phylogenetic analysis have previously been highlighted (Philippe et al. 2011b); simplistic orthology inference methods may miss orthologs (Dalquen and Dessimoz 2013) or erroneously identify paralogous pairs of genes as orthologs as a result of differential gene losses (Dessimoz et al.”