Global integration of phylogenomic data and fine-scale partitioning strategies refine the evolutionary tree of Adephaga beetles (Insecta: Coleoptera)

Over the past decade, genomic-scale data have revolutionized insect phylogenomics by allowing the generation of increasingly comprehensive genomic and taxonomic datasets. However, because different approaches have been used, it is often difficult to understand to what extent these data can be integrated to reconstruct evolutionary trees. In this study, we focus on the beetle suborder Adephaga to explore whether genomic data produced in the past decade can be combined to reconstruct the largest phylogenomic tree of this clade to date. To that end, we collected publicly available transcriptomes, genomes, and target sequence capture data of Adephaga beetles to generate a global dataset. Taking advantage of a newly developed bioinformatic pipeline, we demonstrate the overall compatibility of data types, especially of ultraconserved elements and exon-capture data. We also examined the impact of factors such as the treatment of off-target flanking genomic regions, data trimming regimes and pa..., We combined several Adephaga genomic-level datasets available from the National Center for Biotechnology Information (NCBI) database https://www.ncbi.nlm.nih.gov/, DNA Read Archive of the DNA Database of Japan (DDBJ) https://www.ddbj.nig.ac.jp/, and the Dryad Digital Repository: https://datadryad.org. Sequence data is composed of anchored hybrid enrichment data (ExC), genomic assemblies (GEN), transcriptomes (TRA), and ultraconserved elements (UCE). In an early draft of this manuscript, ExC data was referred to as AHE; in the majority of these files, AHE was changed from AHE to ExC. However, in some cases, it was not reasonable to convert AHE to ExC; e.g., the “BOLD_characterization” and “Matrices” folders.
Here we provide the output and scripts used to generate the characterization of loci, locus partitioning, and the resulting joined probeset from these analyses. We also provide the Gaedephaga UCE fasta file. Additional data analysis ouptut of IQTree2 for phylogenetic inferences, PDF'..., , # Global integration of phylogenomic data and fine-scale partitioning strategies refine the evolutionary tree of Adephaga beetles (Insecta: Coleoptera)

Dryad DOI: https://doi.org/10.5061/dryad.w9ghx3fzf

## Supplemental_Tables_dryadcorrections.xlsx

Each tab in the xlsx sheet is described here:

#### SuppFile1_Taxa

Taxa accessions, Locus Recovery, and BOLD IDs

Table of all taxa used for analyses within this manuscript. Associated ID (Other Code), Accession codes (Code), references, species identity, locality, data source (type of data), locus recovery by probe source, assembly statistics (length, min, max, average length), and BOLD identification are available for each taxon results: queryID, best genus guess, best species guess, database search, percentage match, and lowest percentage match for bold ID. NA's in this sheet are data that are unavailable or not applicable.

#### SuppFile1_MLTreeStats

Four tables of maximum likelihood and information criterion values of trees generated...,