Periodic Reporting for period 4 - GAIA (A Genomic and Macroevolutionary Approach to Studying Diversification in an Insect-Plant Arms Race)
Reporting period: 2024-09-01 to 2025-02-28
The ERC GAIA project is interested in understanding why herbivorous insects exhibit such an exuberant diversity, which is often attributed to their association with plants, making their interactions of particular importance to understanding what is driving their vast diversity. Sixty years ago, biologists exploring the underlying factors proposed the hypothesis of coevolution and the “escape and radiate” model. Despite general support for this hypothesis, the macroevolutionary and genomic consequences of the origins and evolutionary dynamics of host-plant shifts remain elusive. Recent results illustrate the need for a multidisciplinary approach to assessing the role of host plants in shaping insect diversity at macroevolutionary scales. Using the swallowtail butterflies (Papilionidae) and their host plants, the GAIA project is developing a macroevolutionary and genomic framework to studying the origin and evolution of an arms race through time and space. We are building a complete species-level phylogeny for Papilionidae relying on whole-genome sequencing for all species. This time-calibrated phylogeny will be combined with species traits to estimate ancestral host-plant preferences and subsequent host-plant shifts. We are also reconstructing dated phylogenies of the main host-plant families to estimate whether the butterflies and their host plants diversified concurrently through time and space. Diversification rates will be estimated for shifting/non-shifting and prey/non-prey clades. A matching genomic survey will look for genes under positive selection by comparing sets of phylogenetic branches that experienced a host-plant shift versus branches without such a shift. Transcriptomes will be characterized for caterpillars and their plants to identify and pinpoint the genes involved in the arms race, as well as to compare them across the swallowtail tree of life. With this ambitious research proposal, we aim to provide answers to longstanding and fundamental evolutionary questions on the mechanisms behind ecological interactions over long timescales.
A comprehensive, multi-step research strategy was implemented to address the project's core questions, which span taxonomy, trait evolution, genomics, and macroevolution. The work began with global taxon sampling through an extensive network of international collaborations, targeted field expeditions, and visits to major museum collections to ensure broad phylogenetic and geographic coverage. The taxonomic groundwork was solidified by redefining species boundaries, providing a robust framework for compiling a rich, curated dataset of species-level traits. This dataset includes host-plant preferences, biogeographic distributions, and key morphological features, such as color patterns and wing size. To enable genome-wide analyses, high-coverage whole-genome sequencing (>100×) was performed on representative genera, and all sampled species were sequenced at lower coverage (>50×). De novo genome assemblies were generated and rigorously assessed for quality to allow the identification of orthologous genes across taxa. These genomic resources formed the basis for robust phylogenetic reconstructions and molecular dating analyses, which provided estimates of lineage origins and divergence times. Methods for ancestral state reconstruction were employed to infer the evolution of host-plant associations across the phylogeny, revealing patterns of host shifts and conservatism. Macroevolutionary modeling allowed us to estimate speciation and extinction rates in relation to these ecological transitions. Finally, comparative genomic analyses identified molecular signatures associated with host-plant shifts, offering novel insights into the links between ecological diversification, genomic change, and evolutionary dynamics. These results have substantially advanced our understanding of trait evolution and genomic adaptation in relation to ecological specialization. The genomic resources and trait datasets generated will be made available to everyone.
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.
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.