Patterns and processes of horizontal DNA transfer: an in-depth exploration of the host-parasitoid route – Horizon

We developed a dedicated “triplet” pipeline (host–parasitoid–control) to detect HGT signatures (high-identity cross-species hits, phylogenetic validation, contamination control) and to test overrepresentation statistically. We profiled polydnavirus integrations in Lepidoptera (intégration motifs, variability, determinants) and initiated controlled infections with dsDNA viruses (baculo/irido) to probe capture and transfer of mobile elements. A theoretical component formalized how horizontal and vertical inheritance interact to define evolutionary individuals and units of selection. Methods were iteratively improved for scalability, taxonomic breadth and tighter integration of data and models.

Horizon delivered three core advances. (1) Oukkal’s work: tachinid flies, unlike endoparasitic Hymenoptera, do not rely on domesticated viruses—pointing to divergent parasitic trajectories in terms of viral domestication; additionally, a viral relative of ichnoviruses was identified, providing the first direct evidence for their viral origin. (2) Portal’s work: a novel comparative pipeline produced the first large-scale quantitative test of the host–parasitoid HGT hypothesis in the ACG dataset, with preliminary results indicating numerous HGT in parasitized systems. (3) Matrougui’s work: polydnavirus insertions in Lepidoptera are frequent and variable, with determinants mapped; experimental infections were launched to test viral vector roles. Complementary studies (Reiss 2019, Muller 2025, Guinet 2023) broadened scope by documenting HGT patterns, phylogenetic effects and viral endogenization in parasitoid systems. Finally, although somewhat peripheral to the initial objectives, the work of Thomas Kosc on the thermodynamic consistency of autocatalytic cycles (PNAS 2025) illustrates the project’s contribution to a broader theoretical reflection on the foundations of evolutionary processes and on the physical conditions that enable the circulation and stabilization of genetic information.

The outstanding feature of Horizon lies in its integrative design: the project combined a uniquely documented ecological system, large-scale comparative genomics, mechanistic analyses of viral endogenization, and conceptual work on individuality in evolution. Few projects in evolutionary biology have spanned such scales, from integration motifs of viral DNA in host chromosomes to theoretical reflections on what it means to be an evolutionary individual when genomes are porous to external inputs. This breadth gave Horizon a distinctive identity and positioned it at the forefront of research on horizontal DNA transfer (HGT) in animals.

A major achievement was the use of the Área de Conservación Guanacaste dataset, one of the richest ecological–genetic resources worldwide. Horizon developed a novel “triplet pipeline” (host–parasitoid–control) to test whether parasitism increases HGT, producing the first large-scale quantitative evaluation of this long-debated hypothesis. This methodological innovation, with strict contamination control and phylogenetic validation, provides a durable tool for future studies, applicable not only to parasitoid systems but also to other intimate associations such as symbioses or predator–prey interactions.

Horizon also clarified the viral dimension of HGT. The discovery of a close relative of ichnoviruses gave the first direct evidence of their viral origin, filling a longstanding gap in our understanding of polydnavirus domestication. At the same time, characterization of viral integrations in Lepidoptera genomes revealed their frequency, variability, and potential to reach the germ line integrations. These results advance our knowledge of parasitoid biology while illuminating general mechanisms by which viruses mediate genetic exchanges across species boundaries.

Looking forward, Horizon opens several perspectives. Expanding the comparative framework to additional ecological systems and taxa will refine our understanding of how ecological connectivity and phylogenetic distance jointly shape HGT. Targeted metagenomic exploration should reveal new lineages related to polydnaviruses, possibly documenting further domestication events. Continuing experimental infections with large dsDNA viruses, combined with deeper sequencing and multiple infection cycles, could ultimately provide direct demonstrations of virus-mediated HGT.

Conceptually, Horizon invites a reassessment of evolutionary theory. By showing that horizontal flows of DNA are not rare anomalies but integral parts of genome dynamics, the project calls for renewed frameworks where individuality and units of selection are reconsidered in light of porous genomes and ecological networks. This conceptual impact ensures that Horizon’s influence will extend well beyond its immediate findings.

It is now recognised that DNA can move across species barriers, not only in bacteria and archaea, where this has been long-recognised, but also among eukaryotes, including metazoans. In the latter however, Horizontal Transfers (HTs) are only documented from a few case studies, providing us with a highly-fragmented picture of which genetic elements can actually move, and by what processes. Evidence for HT between insect parasitoids and the hosts in which they develop indicates that this tight ecological connectivity can allow the transmission of DNA. Other data sets suggest that Transposable Elements (TEs) tend to be exchanged most frequently between closely related lineages, possibly because of the resemblance between the donor and recipient organisms. Building on these observations, we hypothesize here that ecological connectivity and phylogenetic relatedness represent the major determinants of HT. To test this hypothesis, we will combine full genome sequencing with the results of 40 years of field work in a Costa Rican National Park that have exhaustively documented the network of interactions between Lepidoptera caterpillars and their parasitoids. We take advantage of the DNA-barcoding campaign that has complemented the ecological dataset since 2004, and produced molecular markers and DNA extracts from over 200,000 specimens, distributed across 5000+ species of Lepidoptera and their 2000+ species of parasitoids, both Diptera and Hymenoptera. The available molecular data provides a useful phylogenetic framework which will be used in combination with the ecological network to select 250 species, each represented by two specimens, from which we will produce full genomes. The available DNA extracts are readily usable for full genome sequencing, as demonstrated by a preliminary sequencing experiment that we performed since the submission of our pre-proposal.
In the first year and first Task of the project, we will sequence and assemble the genomes. In the second task, we will document patterns of HT, that is, produce an exhaustive catalogue of transfer events using a combination of two approaches: (1) we will compute the genetic distance at all homologous regions between hosts and parasitoid genomes, to detect very similar sequences, that are indicative of recent host-parasitoid HTs; (2) a more complete picture will be obtained using cophylogenetic approaches (that is, comparisons between species trees and gene-specific trees) that will reveal ancient transfers, as well as transfers between closely related species (e.g. between two hosts or two parasitoids). These analyses will be applied to the various kinds of genetic entities present in our data set: nuclear genomes (distinguishing transposable elements from non-mobile nuclear DNA), intracellular bacteria and viruses. Following this descriptive step of the project, we will be in position to investigate the processes underlying HTs, in the third Task of the project. Specifically, we will test the hypothesis that ecological connectivity and phylogenetic distance are the two major factors affecting the passage of DNA across species. Having assessed the amount of HTs that have occurred between hosts and parasitoids, we will test the correlation between the ecological network and HT patterns. We will also investigate the possibility of HTs between two parasitoids or between two hosts through a shared prey or predator. Using such within-group transfers, we will analyse the relationship between the phylogenetic distance and the rate of HT between lineages. While challenging both in its scale and in the complexity of the questions being addressed, the Horizon project involves a team of highly complementary researchers, datasets and methods, from field ecology to phylogenomics, that will provide major breakthrough in our understanding of horizontal DNA transfer in metazoans, and the possibly vast evolutionary implications of this fascinating phenomenon.