Systematic bias and the phylogeny of Coleoptera—A response to Cai et al. (2022) following the responses to Cai et al. (2020)

Abstract

Systematic bias is one of the major phylogenetic issues arising over the last two decades.Using methods designed to reduce compositional and rate heterogeneity, hence systematic bias, Cai and co-workers (2022) (= CEA22) reanalyzed the DNA sequence dataset for Coleoptera of Zhang et al. ( 2018) (= ZEA). CEA22 suggest that their phylogenetic results and major evolutionary hypotheses about the Coleoptera should be favoured over other recently published studies. Here, we discuss the methodology of CEA22 with particular attention to how their perfunctory reanalysis of ZEA obfuscates rather than illuminates beetle phylogeny. Similar to published rebuttals of an earlier study of theirs, we specifically find that many of their claims are misleading, unsupported, or false. Critically, CEA22 fail to establish the stated premise for their reanalysis. They fail to demonstrate how composition or rate heterogeneity supposedly impacted the phylogeny estimate of ZEA, let alone the results of other recent studies. Moreover, despite their claim of comprehensive sampling of Coleoptera, their dataset is neither the most diverse with respect to species and higher taxa included, nor anywhere near the largest in terms of sequence data and sampled loci. Although CEA22 does contribute additional fossils for calibration, those seeking the best available estimate for Coleoptera phylogeny and evolution based on molecular data are advised to look elsewhere.

Untangling the evolution of soldier beetles (Coleoptera: Cantharidae) and the evaluation of the morphological phylogenetic signal in a soft‐bodied elateroid lineage

“…The molecular topologies reflect the dataset composition, completeness, applied models, analysis parameters and in the case of large and complex datasets also stochastic processes such as a starting seed (Bocak et al., 2014; Young and Gillung, 2020). The hypotheses based on a single analysis are problematic, and we must consider all evidence (Vasilikopoulos et al., 2021; Boudinot et al., 2022). Further, we must evaluate independent information sources (Eernisse and Kluge, 1993; Kusy et al., 2022).…”

When a key innovation becomes redundant: Patterns, drivers and consequences of elytral reduction in Coleoptera

“…We follow the latest higher level classification of extant Coleoptera by Cai et al (2022), which was partly compiled based on prior phylogenomic analyses (McKenna et al, 2019;Zhang et al, 2018), but refer to the criticism of the analytical approach and treatment of stem-group taxa by Boudinot et al (2023b). We keep the sequence of For a reliable estimation of the prevalence of elytral loss within every extant family of beetles, we have presented the most updated and revised figures for the current number of described extant species in each family, resulting in the highest yet total number of species for Coleoptera (see Supplementary File S1 for methodological details).…”

“…We follow the latest higher level classification of extant Coleoptera by Cai et al (2022), which was partly compiled based on prior phylogenomic analyses (McKenna et al, 2019; Zhang et al, 2018), but refer to the criticism of the analytical approach and treatment of stem‐group taxa by Boudinot et al (2023b). We keep the sequence of higher taxa in our Systematic Review section as in Cai et al (2022), with the exception of the sequence of suborders, where we keep the traditional sequence (i.e., Archostemata, Myxophaga, Adephaga and Polyphaga; McKenna et al, 2019) because this part of the beetle tree‐of‐life has not yet been fully resolved.…”