Clean Breaks: Attention Force Field Deconvolution of Recombination Across Sequence Manifolds

Abstract

Homologous recombination and horizontal gene transfer assemble mosaic chromosomes across divergent lineages. Reticulate evolution violates bifurcating trees, yet existing detectors enforce a stark trade-off: phylogenetic changepoint models optimize partitioned topologies at exponential computational cost, whereas sequence triplet heuristics evaluate rapidly but suffer from severe combinatorial event overcounting. We introduce RhizAeon, an open-source platform that deconvolves reticulate evolution through continuous trajectory mechanics across metric embeddings in linear time (O(N K L)). Projecting aligned sequences into canonical metric coordinates and routing lineage-specific rate variation into an unpolarized root sink, the engine iteratively scrubs mosaic tracts and verifies breakpoints through Brownian-bridge statistics, dyadic matched filters, and maximum-likelihood polishing. Across canonical coalescent benchmarks and a continuous parameter sweep of 1,000,000 whole genomes, RhizAeon bounds false-positive rates well below the 5.0% nominal ceiling (0.58% on 1,200 rate-variation nulls and 1.01% across 333,334 continuous sweep nulls). Leave-one-in verification and bidirectional overlap clustering collapse co-recombinant clades into single ancestral reticulations. Empirical analyses across wildlife sarbecovirus Spike chimeras, multidrug-resistant Streptococcus pneumoniae chromosomes (2.22 Mb), and 379 primate HLA Class I alleles reconstruct complex whole-genome mosaicism, cassette exchanges, and micro-conversions in seconds. The core engine compiles to WebAssembly for interactive execution within standard web browsers.