Supplementary files for the manuscript: A grafted phylogenomics framework clarifies problematic species boundaries in alpine Sciadia moths (Geometridae: Ennominae)

This publication contains the supplementary files for the manuscript: A grafted phylogenomics framework clarifies problematic species boundaries in alpine Sciadia moths (Geometridae: Ennominae) Abstract High mountain ecosystems are unique and among the most vulnerable to climate change, yet many endemic taxa remain taxonomically unresolved, hindering effective conservation planning. The alpine moth genus Sciadia (Ennominae, Geometridae) exemplifies this challenge. The genus currently includes 13 European species restricted to the Alps, Pyrenees, and Dinaric Alps. Our focus is on the Sciadia tenebraria species complex, which comprises eight closely related species showing incongruence among external and genitalia morphology, DNA barcodes, and life-history assignments under the current taxonomy, together with both sympatric and allopatric population structure. To resolve species boundaries, we implemented a grafted phylogenomic framework integrating full-length mitochondrial COI, six nuclear genes, and whole-genome sequencing (WGS) data across hierarchical sampling depths. Our dataset included DNA barcodes from five type specimens (two holotypes, two paratypes, and one paralectotype) with specimens collected between 1908 and 2021. Museomics WGS generated 570 orthologous genes, yielding a concatenated alignment of ~727 k bp. Across mitochondrial, nuclear multilocus, grafted phylogenomic, and species tree analyses, we consistently recovered six well-supported evolutionary lineages. Lineage membership remained stable despite minor topological differences among datasets. Current morphology-based species assignments were extensively intermixed across lineages, revealing substantial taxonomic discordance. Our results demonstrated that integrating genome-scale data with historical name-bearing type material provides a robust framework for clarifying species boundaries in Sciadia and reliably links life history information to evolutionary lineages. Our genomically anchored species hypotheses establish an essential foundation for accurate biodiversity assessment and conservation of alpine ecosystems under ongoing climate change.