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Issue: Vol. 7 No. 2: April 2024
Type: Comments and perspectives
Published: 2024-04-19
DOI: 10.11646/palaeoentomology.7.2.2
Page range: 176-183
Abstract views: 204
PDF downloaded: 165

Resolving incongruences in insect phylogenomics: A reply to Boudinot et al. (2023)

State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Centre for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing 210008, China
School of Earth Sciences University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol, BS8 1TQ, UK; Department of Earth Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EQ UK
School of Earth Sciences University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol, BS8 1TQ, UK; School of Life Sciences University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol, BS8 1TQ, UK
School of Earth Sciences University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol, BS8 1TQ, UK
Coleoptera phylogenetics compositional heterogeneity model testing systematic bias

Abstract

Over the last two decades, advances in molecular phylogenetics have established a new understanding of beetle phylogeny. However, some historically contentious relationships, particularly among early-diverging beetle clades, remain to be resolved. In a recent paper (Cai et al., 2022), we identified model-dependent signals in beetle phylogeny and showed how the removal of the most compositionally heterogeneous sites, in combination with the use of across-site compositionally heterogeneous models leads to results that are more congruent with the distribution of morphological characters and the beetle fossil record. In their reply, Boudinot et al. (2023) suggested that our analyses are affected by a range of shortcomings, encompassing almost every aspect of our study. Unfortunately, the arguments presented by Boudinot et al. (2023) are based on misinterpretation of the results of statistical tests, as well as misconceptions concerning substitution models, model testing and its role in phylogenomics. Here we clarify these misconceptions and show that the critiques raised by Boudinot et al. (2023) have no merit.

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