%0 Journal Article
%T Sampling Design, Genomic Data Types, and Reproducibility Practices in the Expansion of Large-Scale Insect Phylogenomics
%A Ana Rodrigues
%A Tiago Martins
%A Bruno Lopes
%J Entomological Research Letters
%@ 3108-639X
%D 2025
%V 5
%N 2
%R 10.51847/50BwZ5cu1x
%P 84-95
%X Large-scale phylogenomics has transformed insect systematics by expanding both taxonomic coverage and the number of loci available for inference. Expansion, however, has not produced a uniform methodological landscape. Sampling depth varies among lineages and taxonomic levels; genomes, transcriptomes, and targeted-enrichment datasets differ in locus recovery and reuse potential; missing data arise through several non-equivalent processes; and large matrices can retain gene-tree conflict or analytical sensitivity. This scoping review maps these dimensions while treating reproducibility as distinct from data volume or nominal node support. The reviewed evidence shows that museum collections can expand otherwise difficult sampling, whole-genome and transcriptomic resources support complementary phylogenomic strategies, and target capture can operate from deep to shallow phylogenetic scales. Yet probe divergence, specimen history, matrix filtering, laboratory conditions, and analytical choice can alter the recoverable evidence. We therefore propose that insect phylogenomic studies be interpreted through separate sampling, data-generation, matrix-composition, conflict, and reproducibility dimensions rather than a single notion of genomic completeness. This separation clarifies where increasing scale strengthens inference and where additional validation remains necessary.
%U https://esvpub.com/article/sampling-design-genomic-data-types-and-reproducibility-practices-in-the-expansion-of-large-scale-i-onlg6pw2xcplvv6