A reusable neural approach to recombination mapping for model and non-model species

Abstract

Pedigree and crossing experiments can measure crossovers directly and provide the gold standard for recombination mapping, but their cost restricts fine-scale recombination mapping to only a few species. Patterns of linkage disequilibrium (LD) provide an alternative statistical approach for inferring variation in recombination along the genome. LD, however, is confounded by many evolutionary factors, such as demographic changes, life-history traits, and genomic structural variation. We present fastrho, a state-space neural-network estimator trained across a range of simulation-based priors. In simulated bottleneck and expansion scenarios, the fixed checkpoint recovered local map shape without target-specific retraining; comparisons with pyrho used lookup tables constructed under the simulation-generating history. We further evaluated generalizability across multiple species and, to account for additional confounders not represented in the initial training data, designed specialized models for inference in selfing plants, structured Arabis populations, and large- malaria-vector populations. A major biological application of the mosquito model was the construction of a five-arm recombination atlas spanning 13 Ag3 populations, providing a detailed view of recombination-rate variation across the dataset. Recombination maps inferred from Ag3 pedigrees provided independent, coarse-scale support for this atlas. Finally, analyses of resistance loci and redpoll bird supergenes demonstrate how selection and structural variation influence LD. Throughout our study, we use experimental maps for independent validation. Together, our results establish fastrho as a flexible framework for robust recombination mapping across diverse biological systems.