Genome-wide macroevolutionary signatures of key innovations in butterflies colonizing new host plants

The mega-diversity of herbivorous insects is attributed to their co-evolutionary associations with plants. Despite abundant studies on insect-plant interactions, we do not know whether host-plant shifts have impacted both genomic adaptation and species diversification over geological times. We show that the antagonistic insect-plant interaction between swallowtail butterflies and the highly toxic birthworts began 55 million years ago in Beringia, followed by several major ancient host-plant shifts. This evolutionary framework provides a valuable opportunity for repeated tests of genomic signatures of macroevolutionary changes and estimation of diversification rates across their phylogeny. We find that host-plant shifts in butterflies are associated with both genome-wide adaptive molecular evolution (more genes under positive selection) and repeated bursts of speciation rates, contributing to an increase in global diversification through time. Our study links ecological changes, genome-wide adaptations and macroevolutionary consequences, lending support to the importance of ecological interactions as evolutionary drivers over long time periods.


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This study aims at testing whether host-plant shifts have impacted both genomic adaptation and species diversification in a butterfly family (Papilionidae) over geological times.
The insect family Papilionidae (the swallowtail butterflies) and the plant family Aristolochiaceae (the birthworts).
The research sample included all species for which we could obtain DNA sequence data such that they could be included in comprehensive phylogenetic trees. The sample was global in scope, and there were no data exclusions.
Sample size was determined by the availability of genetic and geographic data for both focal clades. We used all available data in our study. The sample size used in our study exceeds the vast majority of published genome-wide studies at a macroevolutionary scale.
DNA sequence data were extracted from public DNA sequence databases (GenBank or Ensembl, most of which have been previsously generated by the authors). Species geographic distribution data were extracted from the literature and our previous works. Ecological data for the swallowtails (i.e. host-plant preferences) were also extracted from the literature and our previous works.

Global scale Throughout the Cenozoic
No data were excluded from the analyses.
Our data are not experimental and experiments were thus not replicated. However, we used multiple distinct statistical tests (e.g. BAMM, MuSSE, RevBayes, RPANDA) and all approaches yielded concordant results. We also tested extensively for artifacts that might explain the genomic pattern.
We did not perform an experiment and there was thus no group allocation. We used all species of swallowtail butterflies and birthwort plants for which (1) DNA sequence data were available, and (2) spatial and ecological data were available. There was no further group partitioning of data beyond the natural groupings associated with geography and clade membership.
Blinding was not relevant to our study, because all available data were used (our study did not perform an experiment).