Goncalves, L. T. | Search bioRxiv

bioRxiv2026

A feedback between dispersal and hybridization may facilitate the repeated emergence of flight in field crickets

Dispersal and hybridization can reinforce one another in a feedback loop when species that disperse farther are more likely to encounter and mate with close relatives, resulting in gene flow that can reintroduce dispersal-enhancing alleles in their descendants. This dynamic could help explain why complex dispersal-related traits, such as flight in insects, appear to evolve repeatedly within a clade, but this idea has rarely been tested with genomic data. North American Gryllus field crickets, in which flight capability appears to have been regained from flightless ancestors at least nine independent times, offer a powerful system to do so. Using a genome-wide dataset, we test three predictions about the origins of phylogenetic discordance in Gryllus and the role of dispersal-related traits. First, we find that both incomplete lineage sorting (ILS) and hybridization contribute to extensive gene tree conflict observed across the Gryllus phylogeny, but several conflicting patterns cannot be explained by ILS alone. Multiple lines of evidence reveal introgression at both deep and recent nodes, producing a mosaic evolutionary history with reticulation across many lineages. Second, hybridization is disproportionately concentrated among flight-capable lineages, supporting the idea that dispersal ability increases opportunities for interspecific gene flow. Third, introgression from flight-capable lineages could help explain repeated trait reversal across the phylogeny, suggesting that allele flow may have contributed to the re-emergence of flight in descendants of flightless ancestors. These results are consistent with a dispersal-hybridization feedback shaping both the reticulated phylogenetic history of Gryllus and the repeated emergence of flight. More broadly, models of character evolution built on bifurcating trees may overestimate the number of independent trait origins when reticulate processes are ignored.

evolutionary biology↗

bioRxiv2026

Reference genome choice impacts SNP recovery but not evolutionary inference in young species

Reduced-representation sequencing approaches such as RAD-seq are widely used in population genomics and phylogenetics, particularly for non-model organisms. However, bioinformatics choices during data processing can strongly influence downstream analyses. One key but underexplored factor is the reference genome used for read alignment and SNP discovery. Here, we evaluate the effects of reference genome choice on RAD-seq analyses using multiple datasets spanning recent radiations in Petunia and Calibrachoa, and reference genomes that differ in phylogenetic relatedness. When using congeneric reference genomes, we observed highly consistent mapping rates, SNP recovery, and downstream population genomic patterns. In contrast, mapping to more distantly related genomes resulted in lower mapping rates and stronger effects on summary statistics. Despite these quantitative reductions, broader patterns of genetic structure and diversity, as well as evolutionary relationships, remained largely congruent across reference genomes. Overall, our results indicate that reference genome choice matters most when genomes are distantly related or when analyses target fine-scale genomic signals. For recent radiations with largely conserved genome structure, closely related reference genomes yield comparable SNP datasets and lead to the same biological conclusions regarding population structure and phylogenetic relationships. These findings provide practical guidance for RAD-seq studies in non-model systems, showing that congeneric reference genomes are sufficient for robust population and phylogenetic inference, and that more distantly related genomes can remain informative when no close reference is available.

bioinformatics↗