Integrating Sanger and next‐generation sequencing data sheds light on phylogenetic relationships among gelechioid moths (Lepidoptera: Gelechioidea)

Abstract Accounting for the estimated number of undescribed species, Gelechioidea are thought to be among the most species‐rich superfamilies of Lepidoptera, with 18,500 described species, including numerous pests of economically significant crops such as cotton, tomato and wheat. Family‐level topology of the superfamily and the extent and the number of accepted families have received important revisions throughout the previous phylogenetic work on the group. Here we extracted 1767 nuclear protein‐coding genes from genomic and transcriptomic data from 57 ingroup taxa, including Haplochrois buvati Baldizzone and Urodeta hibernella Staudinger, for which the whole‐genome sequences were generated in this study. We first analyse this phylogenomic dataset within a maximum likelihood framework to revisit the interfamilial relationships within Gelechioidea and then integrate it with the existing taxon‐rich, Sanger‐sequenced data from up to 24 genes to re‐evaluate the extent of the 20 currently accepted families by analysing this integrated dataset encompassing 381 ingroup taxa. Although we also recover some of the previously suggested multifamilial clades, the backbone topology we infer presents novel arrangements of families compared to previously published work: overall, we observe that Gelechioidea have diversified in four main lineages and find Stenomatinae (Depressariidae) to be sister to the rest of Gelechioidea. We therefore elevate it to family, Stenomatidae stat. nov . Moreover, we find the current circumscription of Elachistidae to be non‐monophyletic and propose a new delimitation to include the subfamilies Elachistinae, Parametriotinae, Cacochroinae (Depressariidae) and Ethmiinae stat. nov .