Low-Coverage Genome Sequencing Outperforms Target Enrichment Phylogenomics

Genome-scale data have transformed phylogenetic inference, yet most studies continue to rely on reduced-representation approaches that target a subset of loci to reduce cost and increase taxon sampling. Although effective, these methods require specialized laboratory workflows, constrain long-term data reuse, and may perform poorly with degraded DNA. Low-coverage whole genome sequencing (lcWGS) offers a streamlined alternative: shallow to moderate sequencing of complete genomes followed by bioinformatic extraction of loci of interest. Despite its promise, lcWGS has not been rigorously benchmarked against targeted enrichment using historical museum specimens. Here, we directly compared lcWGS and ultraconserved element (UCE) target enrichment across taxonomically diverse bee specimens collected between 1934 and 2021. Both data types were generated from the same Illumina libraries, enabling a controlled, head-to-head evaluation. Using standard UCE analytical pipelines, we quantified locus recovery, gene-tree support, and phylogenetic performance across sequencing methods and specimen age classes. We further assessed recovery of additional marker classes, including mitogenomes, BUSCO loci, and UCEs from a newly-designed, expanded probe set. Across all age categories, lcWGS consistently outperformed target enrichment, recovering more UCE loci and substantially longer alignments, with the largest gains observed in highly degraded specimens. Gene trees derived from lcWGS exhibited higher mean bootstrap support and greater topological concordance, translating into improved species-tree inference. In addition, lcWGS enabled recovery of markedly more non-target loci, expanding analytical flexibility beyond the original marker set. These results demonstrate that lcWGS not only matches but frequently exceeds the performance of targeted enrichment in museum-based phylogenomics, while providing broader genomic utility. As sequencing costs continue to decline, lcWGS represents a robust and forward-looking strategy for phylogenetic research, particularly in taxa with modest genome sizes and challenging DNA quality.