Biology subjects

Pellen, Y.

Publications and source records attributed to Pellen, Y..

4 recordsLinked to original sources

bioRxiv2025

Testing for positive selection in multi-copy gene families using a reconciliation approach

Multi-copy gene families evolve through dynamic processes of duplication, loss, and sequence divergence, often exhibiting complex paralogy and orthology relationships that complicate the detection of adaptive evolution. Traditional dN/dS-based positive selection analyses are typically limited to single-copy genes, overlooking most of the adaptive signal in multi-copy families. We present a novel pipeline that integrates existing tools to map branch-specific positive selection events from gene trees onto species phylogenies. Our approach incorporates a normalization procedure that corrects for biases caused by variable branch lengths, reducing false enrichment signals on longer branches. Applied to the odorant receptor repertoires of ants, the framework successfully identified branches of the species tree enriched for positive selection, revealing clade-specific adaptive patterns obscured by conventional methods. This reconciliation-based strategy enables detection of adaptive hotspots in complex gene families, providing a versatile tool for linking molecular evolution to species-level diversification.

bioinformatics↗

bioRxiv2025

Adaptive evolution of odorant receptors is associated with elaborations of social organization in ants

Cooperation in social insect colonies depends on complex chemical communication, requiring a large array of chemosensory receptors. Ant odorant receptors (ORs) were dramatically expanded compared to other insects, most notably in the "9-exon" subfamily, which was implicated in responding to cuticular hydrocarbons, a major class of signalling compounds. These observations indicate adaptive evolution of olfactory functions, but this process was never studied in the context of the evolution of specific sociobiological traits. The Global Ant Genomics Alliance has compiled 163 high-quality ant genomes, enabling detailed study of OR evolution in unprecedented detail. Analysing 55,068 ORs across the phylogeny, we tested for association between sociobiological traits and adaptive evolution of ORs, including gene duplication and adaptive sequence evolution. We identified strong enrichment of positive selection on 9-exon ORs in the ancestor of the formicoid clade, which evolved larger colonies and greater reproductive division of labour. This result indicates a key role of chemical communication in the early evolution of complex social organization. We also observed enrichment of positive selection on 9-exon ORs associated with the recent evolution of continuous worker polymorphism in multiple lineages. Surprisingly, the evolution of other sociobiological traits was associated with reduced positive selection on ORs. These results suggest that worker polymorphism involves more extensive adaptation of chemical communication compared to other aspects of ant sociobiology. By analysing the most comprehensive OR dataset to date, we provide new insights into the specific context in which ORs played a major role in the elaboration of social traits in ants.

evolutionary biology↗

bioRxiv2025

Genetic basis of cuticular hydrocarbon variation in the desert ant

Cuticluar hydrocarbons (CHCs) are a ubiquitous component of insect cuticles that are used for a wide range of chemical signaling functions, especially recognition. Recognition and other signals are vital for the maintenance of insularity and cooperation in social insect colonies. Therefore, we expect natural selection on the composition and variabitlity of social insect CHC profiles. Selection on these signals may result in the evolution of genetic polymorphism affecting variation in CHC profiles. Here we tested for a genetic basis of CHC variation in the desert ant Cataglyphis niger. We applied a genomic mapping appraoch to a cohort of brothers from the same nest to reduce noise from environmental effects and achieve a clear statistical signal for association between the variation of CHCs and quantitative trait loci (QTL). This analysis identified 19 QTLs associated with 8 out of the 31 CHCs identified, and one QTL associated with total CHC quantity. These QTLs are located on 11 different chromosomes, including two cases where QTLs of different CHCs overlap. Each QTL explains between 13-25% of the variation in a specific CHC. We highlight several candidate genes in the QTLs identified, including fatty acid elongase and reductase genes. Our results reveal a polygenic genomic architecture underlying CHC variation in a population of the desert ant and open new research avenues into the genetic basis and evolution of chemical signaling in social insects.

ecology↗

bioRxiv2024

Repeated evolution of supergenes on an ancient social chromosome

Supergenes are non-recombining chromosomal regions that code for complex polymorphic traits. Advances in population genomics have uncovered supergenes associated with diverse traits, ranging from butterfly wing patterns to floral morphs. In ants, two supergenes on non-homologous "social chromosomes" in Solenopsis and Formica are associated with social polymorphism, with either single queen (monogyne) or multiple queens (polygyne) colonies. We discovered a new supergene associated with similar polymorphism in the desert ant Cataglyphis niger. Despite Cataglyphis being more closely related to Formica than Solenopsis, its social chromosome is homologous to that of Solenopsis, with conservation of synteny in gene content and order. This suggests that the social chromosome is ancient, dating back to the common ancestor of Solenopsis and Cataglyphis, at least 90 million years ago. Low sequence divergence between supergene haplotypes in both Solenopsis and Cataglyphis suggests that the two supergenes evolved recently and independently in the two divergent lineages on this ancient social chromosome. Comparative analysis of hymenopteran genomes further revealed a bee chromosome homologous to the ants social chromosome. The ant social chromosome contains the largest set of genes that are conserved as a linkage group across ant and bee genomes. This conserved gene set is enriched for olfactory functions, most notably a large number of odorant-binding proteins. The conservation of this gene set suggests that this chromosome plays an important role in social behavior across social Hymenoptera. We propose that the conserved gene set in the social chromosome was repeatedly used as a pre-adapted toolkit for the evolution of social traits in general, and specifically in the evolution of polygyne social structure in ants.

evolutionary biology↗