Bioinformatics of combined nuclear and mitochondrial phylogenomics to define key nodes for the classification of Coleoptera
File(s)
Published version
Author(s)
Type
Journal Article
Abstract
Nuclear genome sequencing for phylogenetics is resource-intensive while mitochondrial genomes can be sequenced and analyzed with relative ease for building densely sampled phylogenetic trees of the most species-rich lineages of animals. Here, we develop a conceptual approach and bioinformatics workflow for combining nuclear single-copy orthologs with less informative but densely sampled mitochondrial genomes, for a detailed tree of Coleoptera (beetles). Basal relationships of Coleoptera were first inferred from > 2,000 BUSCO loci mined from GenBank’s Short Read Archive for 119 exemplars of all major lineages under various substitution models and levels of matrix completion, to reveal universally supported nodes. Second, the corresponding mitogenomes were extracted and combined with an additional 373 species selected for broad taxonomic and biogeographic coverage, roughly in proportion to the known global species diversity of Coleoptera. Bioinformatic processing of mitogenomes was conducted with a novel pipeline for rapid, accurate annotation of protein-coding genes. Finally, phylogenetic trees from all 491 mitogenomes were generated under a backbone constraint from the universal basal nodes, which produced a well-supported tree of the major lineages at the family and superfamily level. Being genetically unlinked and showing unique character variation, mitogenomes provide a unique perspective of the phylogeny. Comparison with 3 recent nuclear phylogenomic studies resulted in the recognition of > 80 nodes universally present across all analyses. These may now support the higher classification of Coleoptera and serve as backbone of further studies, as numerous full mitogenomes and mitochondrial DNA barcodes are added to an increasingly complete phylogenetic tree of this super-diverse insect order.
Editor(s)
Matschiner, Michael
Date Issued
2026-05-01
Date Acceptance
2025-07-04
Citation
Systematic Biology, 2026, 75 (3), pp.445-467
ISSN
1063-5157
Publisher
Oxford University Press
Start Page
445
End Page
467
Journal / Book Title
Systematic Biology
Volume
75
Issue
3
Copyright Statement
© The Author(s) 2025. Published by Oxford University Press on behalf of the Society of Systematic Biologists. This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.
License URL
Identifier
https://www.ncbi.nlm.nih.gov/pubmed/41288263
PII: 8342120
Subjects
BEETLES
BRANCH SUPPORT
BUSCO
Coleoptera
EVOLUTION
Evolutionary Biology
Life Sciences & Biomedicine
matrix completeness
mitogenome annotation
mitonuclear phylogenomics
MODEL
model selection
PERFORMANCE
PHYLOGENETIC ANALYSIS
phylogenomics
Phylogeny
RIBOSOMAL-RNA
Science & Technology
SELECTION
SEQUENCE ALIGNMENT
Publication Status
Published
Coverage Spatial
England
Article Number
syaf031
Date Publish Online
2025-11-25