Clarifying the phylogeny and systematics of the recalitrant tribe Leptocircini (Lepidoptera: Papilionidae) with whole genome data.

Leptocircini is a dazzling tribe of Papilionidae, including dragontails, kite swallowtails, and swordtails. This tribe is widely distributed, notably throughout the tropics of Africa, Southeast Asia, and the Americas, making it a fascinating model in evolutionary biology. However, despite accounting for 25% of the global swallowtail butterfly diversity, Leptocircini have been surprisingly neglected in phylogenetic analyses. This has left unanswered questions about their taxonomy and systematics. Here, we present a new taxonomic working list for Leptocircini, featuring 162 valid species. Using a combination of long and short reads data, we produced five new reference genomes, and we generated highly covered and scaffolded whole genomes for 148 individuals to infer densely sampled phylogenetic hypotheses. Based on mitochondrial or thousands of nuclear genes and multiple phylogenetic approaches, a robust phylogenomic tree is recovered, representing ~90% of the known species, which allowed examination of several key phylogenetic hypotheses. We found the monotypic genus Protographium Munroe to be sister of genus Graphium Scopoli. Additionally, we found that subgenus Paranticopsis Wood-Mason and de Nicéville is nested within subgenus Pathysa Reakirt, which we found is likely attributed to an ancient gene flow. We therefore synonymize Paranticopsis, syn.rest. To keep a consistent approach to subgeneric classification across the tribe and family, we devided genus Eurytides Hübner into three subgenera: Mimoides Brown, Eurytides sensu stricto, and Protesilaus Swainson. This led to several taxonomic implications: Asiographium Möhn, syn.rest., Boreographium Grishin, syn.n., Hyalaus Grishin, syn.n., and Neographium Möhn, syn.n. are synonymized with Eurytides (Mimoides); and Eurygraphium Möhn, syn.rest. is synonymized with Eurytides (Eurytides). Our analyses finally raised concerns about potential taxonomic inflation in two species-groups within Graphium and Eurytides (Protesilaus). This study illuminates the clade’s evolutionary history and paves the way for further research on this diverse group of charismatic butterflies.This repository contains:IQTREE_1402_NT: A folder containing a subfolder with the 1402 nucleotide alignments used for phylogeny, along with the concatenated matrix, partition file, and all log and result files from the IQ-TREE analysis (-m MFP+MERGE).IQTREE_1402_NT_GTR_G:A folder containing the concatenated matrix, partition file, and all log and result files from the IQ-TREE analysis with the -m GTR+I+G option.S1_ASTRAL_1402_NT: A folder containing a file with the 1402 gene trees and the resulting tree file from the ASTRAL analysis.S2_IQTREE_4525_AA: A folder containing a subfolder with the 4525 amino acid alignments used for phylogeny, the concatenated matrix, and the resulting tree from the IQ-TREE analysis.S3_IQTREE_1402_AA: A folder containing a subfolder with the 1402 amino acid alignments used for phylogeny, the concatenated matrix, and the resulting tree from the IQ-TREE analysis.S4_Mitogenome_analysis: A folder containing a subfolder with the 15 mitochondrial gene alignments used for phylogeny, along with the concatenated matrix, partition file, and all log and result files from the IQ-TREE analysis.S8-9_IQTREE_1402_NT_gCF_sCF: A folder containing a file with the 1402 gene trees, along with all log and result files from the gCF/sCF IQ-TREE analysis, and the resulting tree file.Commands_Leptocircini_reference_assemblies: A file containing the main command lines, software version information, and options used to produce the reference genomes.Commands_Leptocircini_Illumina_assemblies: A file containing the main command lines, software version information, and options used to produce the shotgun genomes.