New analytical approaches for improved alignment quality in genome-targeted capture methods: Insights from the phylogenetic reconstruction of blowflies (Diptera: Calliphoridae)

Targeted genome capture methods, like anchored hybrid enrichment (AHE), are widely used for reconstructing insect phylogenies. These approaches are particularly effective for hyper-diverse taxa because AHE can recover genomic-level data cost-effectively for hundreds of individuals. Targeted capture data can be integrated with other genomic resources like transcriptomes or genomes. Here, we present the use of AHE to reconstruct the phylogeny of Calliphoridae (Diptera: Oestroidea); the dataset comprises approximately 1000 loci and nearly 200 species of blowflies. We employed new analytical approaches to enhance the use of bycatch data and improve the accuracy of our tree estimation. We utilized specialized ortholog databases and data pruning to improve our alignment quality and remove alignments with potential paralogs. The new phylogeny provided valuable insights into the systematics of currently proposed subfamilies, their internal relationships, and the evolution of feeding habits within this group of important flies.