Rapid evolution of host repertoire and geographic range in a young and diverse genus of montane butterflies
Data files
Nov 05, 2024 version files 14.37 MB
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Appendix1.fasta
934.55 KB
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Appendix2.fasta
13.43 MB
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README.md
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Abstract
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.
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.
- Wang, Houshuai; Mo, Shifang; Zhu, Yaowei et al. (2024). Rapid evolution of host repertoire and geographic range in a young and diverse genus of montane butterflies. Zenodo. https://doi.org/10.5281/zenodo.13932428
- Wang, Houshuai; Mo, Shifang; Zhu, Yaowei et al. (2024). Rapid evolution of host repertoire and geographic range in a young and diverse genus of montane butterflies. Zenodo. https://doi.org/10.5281/zenodo.13932427
- Mo, Shifang; Zhu, Yaowei; Braga, Mariana P et al. (2024). Rapid Evolution of Host Repertoire and Geographic Range in a Young and Diverse Genus of Montane Butterflies. Systematic Biology. https://doi.org/10.1093/sysbio/syae061