DOI: 10.5061/dryad.bk3j9kdkz
title: Rapid evolution of host repertoire and geographic range in a young and diverse genus of montane butterflies

description: Evolutionary changes in geographic distribution and larval host plants may
 promote the rapid diversification of montane insects, but this scenario
 has been rarely investigated. We studied the rapid radiation of the
 butterfly genus Colias, which has diversified in mountain
 ecosystems in Eurasia, Africa, and the Americas. Based on a dataset of 150
 nuclear protein-coding genetic loci and mitochondrial genomes, we
 constructed a time-calibrated phylogenetic tree of Colias species with
 broad taxon sampling. We then inferred their ancestral geographic ranges,
 historical diversification rates, and the evolution of host use. We found
 that the most recent common ancestor of Colias was likely
 geographically widespread and originated ~3.5 Ma. The group
 subsequently diversified in different regions across the world, often in
 tandem with geographic expansion events. No aspect of elevation was found
 to have a direct effect on diversification. The genus underwent a burst of
 diversification soon after the divergence of the Neotropical lineage,
 followed by an exponential decline in diversification rate toward
 the present. The ancestral host repertoire included the legume genera
 Astragalus and Trifolium but later expanded to include a wide
 range of Fabaceae genera and plants in more distantly related families,
 punctuated with periods of host range expansion and contraction. We
 suggest that the widespread distribution of the ancestor of all extant
 Colias lineages set the stage for diversification by isolation of
 populations that locally adapted to the various different environments
 they encountered, including different host plants. In this scenario,
 elevation is not the main driver but might have accelerated
 diversification by isolating populations.
description: # Rapid evolution of host repertoire and geographic range in a young and
 diverse genus of montane butterflies  These supplementary materials
 contain all necessary data and code for analyses from the paper entitled
 "Rapid evolution of host repertoire and geographic range in a young
 and diverse genus of montane butterflies". ## Description of files,
 figures, and tables **Appendix1.fasta** is a matrix of mtDNA combined
 sequences of *Colias*. **Appendix2.fasta** is a matrix of nuDNA combined
 sequences of *Colias*. #### Files hosted by Zenodo (link in Related Works
 section) **Code.Zip** is the code used in this study. **Data.Zip**
 contains four folders: Files in Folder 1 are gene and species tree files.
 Files in Folder 2 are time-calibrated tree files generated by PAML
 analysis. Files in Folder 3 are phylogenetic network reconstructions using
 SNaQ analysis. Files in Folder 4 are data for analyses of biogeography,
 diversification, and host repertoire. **Supplementary Figures** include
 Figures S1-S11: Figure S1. The altitudinal range for *Colias* species
 included in the study, colored by biogeographical distribution. Figure S2.
 Species Tree inferred by ASTRAL from gene trees of 32 nuclear gene loci
 containing all samples. Figure S3. nuDNA ML tree inferred with IQ-TREE
 from 150 nuclear gene loci. Figure S4. mtDNA ML tree inferred with IQ-TREE
 from mitochondrial genomes. Figure S5. Species tree constructed with
 ASTRAL based on 15 mitochondrial gene loci data. Figure S6.
 Time-calibrated tree obtained from the MCMCTREE analysis. Figure S7. The
 joint posterior probability for each pair of categorical (y-axis) and
 quantitative (x-axis) regional features. Figure S8. Posterior distribution
 of speciation rates for geographical ranges of different sizes. Figure S9.
 Posterior distribution of extinction rates for ranges of different sizes.
 Figure S10. Results of diversification analyses for the second-best model
 of shifts in diversification within *Colias*. Figure S11. Extant network
 of interactions between *Colias* species and their host plant genera.
 **Thirteen tables** are included in the supplementary materials: Table S1.
 List of *Colias* taxa used in this study. Table S2. Summary of the
 Phylogenetic location of missing species. Table S3. The nested PCR primers
 for the 150 NPC genes were amplified in this study. Table S4. The
 geographic distribution and altitude information of *Colias*. Table S5. A
 matrix between 55 *Colias* species and 62 host plant genera. Table S6.
 Summary information for the 150 nuDNA loci used in this study. Table S7.
 Summary of the nuDNA sequencing results from 74 *Colias* individuals.
 Table S8. Summary of nuDNA sequencing coverage per locus per sample. Table
 S9. Summary of the mtDNA sequencing results from 74 individuals of
 *Colias*. Table S10. GenBank accession numbers of the newly sequenced NPC
 and mitochondrial markers. Table S11. Posterior probabilities of
 biogeographical ranges at the root node of the *Colias* tree. Table
 S12. Posterior probabilities of biogeographical ranges at the MRCA of
 Clade B in the *Colias* tree. Table S13. Module robustness.