Phylogenomics of prominent moths (Lepidoptera: Notodontidae): A subfamily-level reclassification

We present the first taxonomically comprehensive phylogenomic dataset for Notodontidae to stabilize subfamily classification. Conflicting classifications of Notodontidae have confounded the understanding of this diverse group (over 4,700 described species), partly because there has been limited taxonomic and geographic sampling, and morphological homoplasy is widespread. We note less rampant homoplasy in larvae and highlight larval characters wherever possible in addressing subfamily diagnostics. This study incorporates as many as 854 anchored hybrid enrichment loci from 150 species. Our dataset is the first to include taxa from all continents where Notodontidae occur, as well as type genera and (when possible) type species of all previously recognized subfamilies. Our genomic dataset is analyzed using maximum likelihood, multispecies coalescent, and parsimony phylogenetic methods. We recognize 21 subfamilies, four of which are given new names based on phylogenomic analyses corroborated..., Sequence data is derived from published full genomes and previously published anchored hybrid enrichment (AHE) as well as recently sequenced specimens for AHE.
All downstream data processing follows the modified AHE pipeline originally developed by Breinholt et al. (2018) https://academic.oup.com/sysbio/article/67/1/78/3796843 
Raw reads are found at NCBI SRA PRJNA1153979, , # Phylogenomics of prominent moths (Lepidoptera: Notodontidae): A subfamily-level reclassification

freely available from: [https://smithsonian.figshare.com/articles/book/Phylogenomics_of_Prominent_Moths_Lepidoptera_Notodontidae_A_Subfamily-Level_Reclassification/28912337?file=54125117](https://smithsonian.figshare.com/articles/book/Phylogenomics_of_Prominent_Moths_Lepidoptera_Notodontidae_A_Subfamily-Level_Reclassification/28912337?file=54125117)

## Description of the data and file structure

This repository is associated with St Laurent et al. 2025, Smithsonian Contributions to Zoology, Phylogenomics of Prominent Moths (Lepidoptera: Notodontidae): a subfamily-level reclassification.

In the study, we gathered genomic data from published sources and samples newly sequenced for target capture, anchored hybrid enrichment, using the LEP1 probe set. All raw reads from this and associated studies are available on NCBI SRA: [https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1153979.](https://www...,