The GAIA project has advanced beyond the state of the art by integrating large-scale comparative genomics and macroevolutionary approaches to investigate the evolutionary dynamics of insect–plant interactions. While host-plant shifts are recognized as key ecological transitions in herbivorous insects, their genomic and diversification impacts remain poorly understood. Previous studies have focused on a narrow set of candidate genes, especially those related to detoxification (e.g. cytochrome P450s), overlooking the broader genomic consequences of such transitions. GAIA addresses this gap by combining high-resolution phylogenies, genome-wide data, and robust statistical frameworks to test whether host-plant shifts drive adaptive evolution and influence diversification.
Using swallowtail butterflies (Papilionidae) as a model, we produced the most comprehensive time-calibrated phylogeny to date—covering nearly two-thirds of described species—through global collaborations and targeted sampling. We sequenced high-quality genomes for all species across all genera and compiled an extensive dataset of life-history traits, host associations, and biogeography. Ancestral state reconstructions enabled us to trace the evolutionary history of host-plant use and identify key ecological transitions.
Initial analyses focused on 28 branches with inferred host-plant shifts. We conducted dN/dS analyses to detect molecular adaptation, revealing that lineages shifting to novel host-plant families harbored significantly more genes under positive selection than non-shifting lineages. These signals remained strong after controlling for environmental variables, suggesting a genomic signature of adaptation linked to host shifts. This work yielded a first list of candidate genes potentially involved in insect–plant coevolution, implicating a wider range of physiological and regulatory pathways than previously recognized.
The project has now reached a major milestone: genome sequencing is complete for all species, allowing us to scale up analyses from 28 to several hundred branches. This will substantially enhance the power and resolution of dN/dS analyses, enabling detection of finer-scale adaptive patterns. The expanded dataset will also improve ancestral state reconstructions and diversification analyses, allowing us to rigorously test whether host-plant shifts consistently correlate with changes in speciation or extinction rates across lineages and through time.
In parallel, we are exploring the evolutionary histories and functional roles of candidate genes under selection, improving understanding of their involvement in host adaptation. Coupling this with transcriptomic data from caterpillar–plant interaction experiments will link gene expression directly to ecological context and function. This integrative approach promises new insights into the molecular basis of the insect–plant arms race.
By the end of the project, we aim to deliver a generalizable framework for understanding how ecological interactions shape genome evolution and diversification in phytophagous insects. This will serve as a proof of concept for application to other insect groups. All genomic resources, trait datasets, and analytical pipelines developed in GAIA will be made publicly available to support further research in evolutionary biology, genomics, and ecology.
