Data from: Phylogenomic analyses of the Cucujiformia

The Cucujiformia, with remarkable morphological, ecological, and
behavioral diversity, is the most evolutionarily successful group within
Coleoptera. However, the phylogenetic relationships among superfamilies
within Cucujiformia remain elusive. To address the issues, we conducted a
transcriptome-based macro-evolutionary study of this lineage. We sequenced
the genomes and transcriptomes of three species from the superfamily
Curculionoidea (two from Curculionidae and one from Brentidae), and
obtained a dataset of more than 569,990 amino acid alignments from 143
species of Cucujiformia. With the most complete collection of
whole-genomes and transcriptomes so far, we compared the performance of
different data matrices with universal-single-copy orthologs (USCO). The
resultant trees based on different datasets were consistent for the
majority of deep nodes. Two USCO amino acid matrices (i.e., USCO75 and
USCO750-abs80) provided well-resolved topology. The analyses confirm that
old Cucujoidea sensu is a non-monophyletic group, consisting of
Erotyloidea, Nitiduloidea and Cucujoidea sensu. Moreover, Erotyloidea is
the early-diverging group in Cucujoidea sensu, followed by the clade
Nitiduloidea. The preferred topologies supported a “basal” split of
Coccinelloidea from the remaining superfamilies, and Cleroidea formed the
second splitting group. The following phylogeny was supported at the
superfamily level in Cucujiformia: (Coccinelloidea, (Cleroidea,
((Lymexyloidea, Tenebrionoidea), (Erotyloidea, (Nitiduloidea, (Cucujoidea,
(Chrysomeloidea, Curculionoidea))))))). Our comprehensive analyses
recovered well-resolved higher-level phylogenetic relationships within the
Cucujiformia, providing a stable framework for comprehending its
evolutionary history.