Clean Breaks: Attention Force Field Deconvolution of Recombination Across Sequence Manifolds
- 1Temple University Institute for Genomics and Evolutionary Medicine
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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BibTeX
@misc{pond2026clean,
title = {{Clean Breaks: Attention Force Field Deconvolution of Recombination Across Sequence Manifolds}},
author = {S. L. Kosakovsky Pond and D. Callan and S. Weaver and H. Verdonk and J. Zehr and A. Nekrutenko and T. K. Paisie and D. P. Martin},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.19.760237},
url = {https://www.biorxiv.org/content/10.64898/2026.10.19.760237v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - Clean Breaks: Attention Force Field Deconvolution of Recombination Across Sequence Manifolds
AU - S. L. Kosakovsky Pond
AU - D. Callan
AU - S. Weaver
AU - H. Verdonk
AU - J. Zehr
AU - A. Nekrutenko
AU - T. K. Paisie
AU - D. P. Martin
PY - 2026
DA - 2026/10/19
PB - bioRxiv
DO - 10.64898/2026.10.19.760237
UR - https://www.biorxiv.org/content/10.64898/2026.10.19.760237v1
AB - 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.
ER -