Full Alignment The sequences obtained for individual loci were aligned via Mafft v. 7.407 (Katoh and Standley 2013) using the default automatic alignment option. For Maximum Likelihood (ML) analyses, the alignments of the individual loci included flanking regions (head, tail, or both) of each locus and were concatenated before analysis and resulted in an alignment length of 1,833,533 base pairs. Lampyridae_align.fasta Cleaned Alignment file Breinholt et al. (2017) showed that trimming data from the probe or flanking region has little effect on the final topology, consequently, we elected not to trim these regions (Lemmon et. al. 2012). However, it is possible that missing data may bias phylogenetic reconstruction (Lemmon et al. 2009; however, see also Wiens and Morrill 2011), therefore, we generated a second dataset utilizing a portion of the pipeline of Breinholt et al. (2017) (alignment_DE_trim.py) to remove sites from the alignment with <75% density, (i.e. completeness), and with entropy >1.5 (to account for sites estimated to be nearly random). This resulted in a trimmed alignment of 401,423 base pairs. Lampyridae_align_clean.fasta Partition file for full alignment Partition file for full alignment of 436 loci 2_Partition_File_for_Supp_fig_2.txt Partition file for clean alignment Partition file for alignment file after cleaning. 3_Partition_clean_For_Supp_fig_3.txt Lampyridae_AHE AHE phylogeny, IQ-Tree reconstruction based on full dataset; Newick format.

Fireflies (Lampyridae) are a diverse family of beetles which exhibit an array of morphologies including varying antennal and photic organ morphologies. Due in part to their morphological diversity, the classification within the Lampyridae has long been in flux. Here we use an anchored hybrid enrichment approach to reconstruct the most extensive molecular phylogeny of Lampyridae to date (436 loci and 98 taxa) and to evaluate firefly higher-level classification. We propose several classification changes supported by morphological evidence: (1) Lamprigera, Vestini (incl. Vesta, Dodacles, Dryptelytra, and Ledocas), Photoctus, and Araucariocladus are transferred to Lampyridae incertae sedis, (2) Phausinae subfamilia nova is erected for Phausis and Lamprohiza, (3) Psilocladinae status nova is reestablished for the genus Psilocladus, (4) Pollaclasis is transferred to the Cyphonocerinae, (5) Memoan is transferred to Amydetinae, and (6) Scissicauda is transferred to Lampyrinae.