Phylogenomics of weevils revisited: data curation and modelling compositional heterogeneity

Abstract

Weevils represent one of the most prolific radiations of beetles and the most diverse group of herbivores on land. The phylogeny of weevils (Curculionoidea) has received extensive attention, and a largely satisfactory framework for their interfamilial relationships has been established. However, a recent phylogenomic study of Curculionoidea based on anchored hybrid enrichment (AHE) data yielded an abnormal placement for the family Belidae (strongly supported as sister to Nemonychidae + Anthribidae). Here we reanalyse the genome-scale AHE data for Curculionoidea using various models of molecular evolution and data filtering methods to mitigate anticipated systematic errors and reduce compositional heterogeneity. When analysed with the infinite mixture model CAT-GTR or using appropriately filtered datasets, Belidae are always recovered as sister to the clade (Attelabidae, (Caridae, (Brentidae, Curculionidae))), which is congruent with studies based on morphology and other sources of molecular data. Although the relationships of the ‘higher Curculionidae’ remain challenging to resolve, we provide a consistent and robust backbone phylogeny of weevils. Our extensive analyses emphasize the significance of data curation and modelling across-site compositional heterogeneity in phylogenomic studies.

Ant backbone phylogeny resolved by modelling compositional heterogeneity among sites in genomic data

“…PPAs indicated that CAT-GTR + G4 ( Z -score = 3.974), the model that was favoured based on my model comparison test, describes site-specific amino acid preferences substantially better than other tested models. This result was not surprising, since CAT-GTR + G4 is known to be by far the best-fitting model that can explicitly accommodate among-site compositional heterogeneity 21 – 24 .…”

Foveapeltis gen. nov., an unusual cleroid genus with large hypomeral cavities from mid‐Cretaceous amber (Coleoptera: Cleroidea)

“…'s ( 2019 ) data with the site‐heterogeneous model CAT‐GTR + G4. Site‐heterogeneous models could generally improve the accuracy of phylogenetic analyses (e.g., Li, Engel, et al., 2023 ), and specifically, compared with Gimmel et al. ( 2019 ), the result by Li et al.…”

Phylogenomic analysis and molecular identification of true fruit flies

“…AHE gene sets mainly target coding regions, whereas UCE gene sets target coding and noncoding genomic regions (Zhang and Lai, 2020c). AHE has been used to uncover phylogenomic relationships of flower flies (Young et al, 2016), lacewings (Winterton et al, 2018;Cai et al, 2023), beetles (Li et al, 2023) and moths (Homziak et al, 2019). UCE has been used for phylogenetic analysis to recover the relationships of many groups, such as fish (Faircloth et al, 2013), arachnids (Starrett et al, 2017), birds (Stiller et al, 2024), wasps (Cooper et al, 2020), and scale insects (Liu et al, 2022).…”