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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.

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