Decisive Data Sets in Phylogenomics: Lessons from Studies on the Phylogenetic Relationships of Primarily Wingless Insects

Abstract

Phylogenetic relationships of the primarily wingless insects are still considered unresolved. Even the most comprehensive phylogenomic studies that addressed this question did not yield congruent results. To get a grip on these problems, we here analyzed the sources of incongruence in these phylogenomic studies by using an extended transcriptome data set. Our analyses showed that unevenly distributed missing data can be severely misleading by inflating node support despite the absence of phylogenetic signal. In consequence, only decisive data sets should be used which exclusively comprise data blocks containing all taxa whose relationships are addressed. Additionally, we used Four-cluster Likelihood Mapping (FcLM) to measure the degree of congruence among genes of a data set, as a measure of support alternative to bootstrap. FcLM showed incongruent signal among genes, which in our case is correlated neither with functional class assignment of these genes nor with model misspecification due to unpartitioned analyses. The herein analyzed data set is the currently largest data set covering primarily wingless insects, but failed to elucidate their interordinal phylogenetic relationships. Although this is unsatisfying from a phylogenetic perspective, we try to show that the analyses of structure and signal within phylogenomic data can protect us from biased phylogenetic inferences due to analytical artifacts.

Coping with living in the soil: the genome of the parthenogenetic springtail Folsomia candida

“…The evolutionary split between F. candida and O. cincta is substantial. They belong to different families and have evolved very different adaptive traits [37, 38]. The observation that roughly 30% of HGT has persisted in both species after divergence suggests that these genes are important in the ecology of Collembola.

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Re-evaluating the phylogeny of Sipuncula through transcriptomics

“…Missing data can have negative effects on phylogenetic reconstructions, such as inflating node support despite the absence of phylogenetic signal or producing misleading estimates of topology and branch lengths (e.g., Lemmon et al, 2009;Dell'Ampio et al, 2014) and it is thus recommended to graphically display the amount of missing data on phylogenetic trees or gene matrices (e.g., Roure et al 2013), as we have done here (Figs. 1 and 2).…”

“…Long outstanding issues have been resolved for within-phylum relationships among arthropods, molluscs, and annelids, to mention just some of the largest animal phyla (e.g., Meusemann et al, 2010;Kocot et al, 2011;Smith et al, 2011;Struck et al, 2011;von Reumont et al, 2012;Andrade et al, 2014;Weigert et al, 2014). A third wave now focuses on resolving lower-level phylogenetic questions, relying almost entirely on Illumina-based technology (e.g., Johnson et al, 2013; Kocot et al, 2013;Wheat and Wahlberg, 2013;Dell'Ampio et al, 2014;Fernández et al, 2014aFernández et al, , 2014b. The time is prime to address the phylogeny of Sipuncula through phylogenomic techniques.…”

Cause of gene tree discord? Distinguishing incomplete lineage sorting and lateral gene transfer in phylogenetics

“…Do these neL resolutions represent "Lhole-genome evidence"? Or reflect biases in data processing steps and tree reconstruction methods (e.g., Dell'Ampio et al, 2014;Fernández-Mazuecos et al, 2017)? Or are driven by strong signals in small number of genes or sites (Lhich could be outliers; e.g., Shen et al, 2017;Xi et al, 2014)?…”