The best of both worlds: Assessing the utility of the CO1 locus in the phylogenomic age

The advent of next-generation sequencing (NGS) and phylogenomics has produced a rapid rise in the amount of molecular data available for understanding evolutionary relationships. Generally, this has led to increased resolution and statistical support in phylogenetic reconstructions. However, NGS data is more expensive to produce on a per-sample basis compared to approaches targeting a small number of markers, limiting the number of taxa which can be sampled. To address this, we develop a ‘taxon stitching’ method which leverages a recently developed anchored hybrid enrichment (AHE) probe kit and DNA barcode sequences (CO1) to get the best of both worlds – strongly supported relationships at deep and shallow taxonomic levels for large numbers of taxa. Using AHE, we produced a nearly complete genus-level phylogeny of the Phaegopterina, a speciose subtribe within the hyperdiverse tiger moth lineage (Lepidoptera: Noctuoidea: Erebidae), which currently contains >3,000 species organized into nearly 160 genera. By combining this AHE backbone phylogeny with publicly available COI sequences we were able to greatly increase our species-level sampling, including the addition of rarely collected species, and identify many paraphyletic genera. This approach significantly reduces per-sample costs compared to a similarly sampled AHE-only dataset. This has the potential to further accelerate our understanding of evolutionary relationships and trait evolution across the tree of life, particularly in species-rich lineages for which NGS-only approaches may be cost prohibitive.