A forest is more than its trees: haplotypes and ancestral recombination graphs.
Foreshadowing haplotype-based methods of the genomics era, it is an old observation that the "junction" between two distinct haplotypes produced by recombination is inherited as a Mendelian marker. In a genealogical context, this recombination-mediated information reflects the persistence of ancestr...
| Publicado en: | Genetics Vol. 232; no. 1; pp. 1 - 13 |
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| Autores principales: | , , , |
| Formato: | algorithm equations & formulas tables/charts Journal Article |
| Publicado: |
Oxford University Press / USA
Jan2026
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| Acceso en línea: | Ver este registro en EBSCOhost |
| fields | @attributes: recordID: 1 pdfLink: plink: https://search.ebscohost.com/login.aspx?direct=true&db=ccm&AN=190773575&site=ehost-live header: @attributes: shortDbName: ccm uiTerm: 190773575 longDbName: CINAHL Complete uiTag: AN controlInfo: bkinfo: dissinfo: jinfo: jid: 00166731 GNT jtl: Genetics issn: 00166731 maglogo: N pubinfo: dt: Jan2026 vid: 232 iid: 1 pid: 622 pub: Oxford University Press / USA artinfo: ui: 190773575 190773575 190773575 10.1093/genetics/iyaf198 190773575 ppf: 1 ppct: 12 formats: tig: atl: A forest is more than its trees: haplotypes and ancestral recombination graphs. aug: au: Fritze, Halley Pope, Nathaniel Kelleher, Jerome Ralph, Peter affil: Department of Mathematics, University of Oregon, Eugene, Oregon 97403, United States sug: subj: Haplotypes Genomics Phylogenetics Bioinformatics DNA, Recombinant Physiology Algorithms Human Funding Source Models, Biological DNA Sequence Analysis Data Analysis, Statistical Genetic Variation Simulations Comparative Studies Nucleotides Genetic Markers Mutation Hereditary Diseases Risk Factors Evolution Molecular Biology ab: Foreshadowing haplotype-based methods of the genomics era, it is an old observation that the "junction" between two distinct haplotypes produced by recombination is inherited as a Mendelian marker. In a genealogical context, this recombination-mediated information reflects the persistence of ancestral haplotypes across local genealogical trees in which they do not represent coalescences. We show how these non-coalescing haplotypes ("locally-unary nodes") may be inserted into ancestral recombination graphs, a compact but information-rich data structure describing the genealogical relationships among recombinant sequences. The resulting ancestral recombination graphs are smaller, faster to compute with, and the additional ancestral information that is inserted is nearly always correct where the initial ancestral recombination graph is correct. We provide efficient algorithms to infer locally-unary nodes within existing ancestral recombination graphs, and explore some consequences for ancestral recombination graphs inferred from real data. To do this, we introduce new metrics of agreement and disagreement between ancestral recombination graphs that, unlike previous methods, consider ancestral recombination graphs as describing relationships between haplotypes rather than just a collection of trees. pubtype: Academic Journal doctype: algorithm equations & formulas tables/charts Journal Article ougenre: Article language: English refInfo: holdings: @attributes: islocal: N |
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