Constructing Minimal Ancestral Recombination Graphs
Abstract
By viewing the ancestral recombination graph as defining a sequence of trees, we show how possible evolutionary histories consistent with given data can be constructed using the minimum number of recombination events. In contrast to previously known methods, which yield only estimated lower bounds, our method of detecting recombination always gives the minimum number of recombination events if the right kind of rooted trees are used in our algorithm. A new lower bound can be defined if rooted trees with fewer constraints are used. As well as studying how often it actually is equal to the minimum, we test how this new lower bound performs in comparison to some other lower bounds. Our study indicates that the new lower bound is an improvement on earlier bounds. Also, using simulated data, we investigate how well our method can recover the actual site-specific evolutionary relationships. In the presence of recombination, using a single tree to describe the evolution of the entire locus clearly leads to lower average recovery percentages than does our method. Our study shows that recovering the actual local tree topologies can be done more accurately than estimating the actual number of recombination events.
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Each ancestral recombination event manifests as a clade of haplotypes that descend from the first ancestral haplotype to have it, moving from one position in the tree upstream of the event to a new position in the downstream tree.
“Each ancestral recombination event manifests as a clade of haplotypes, all of which descend from the first ancestral haplotype to have it, moving from one position in the tree upstream of the event to a new position in the downstream tree (3).”
From An ancestral recombination graph of human, Neanderthal, and Denisovan genomes (2021) · cites this paper as [3]
Under the assumption that every shared derived allele defines a clade, pairs of sites for which the inferred clades share members but for which neither is a superset of the other mark ancestral recombination events, or breakpoints between different trees.
“It has been shown that, under this assumption, pairs of sites for which the inferred clades share members but for which neither is a superset of the other, mark ancestral recombination events, or breakpoints between different trees. This is referred to as the “four-haplotype test” or “four-gamete test” (3, 11).”
From An ancestral recombination graph of human, Neanderthal, and Denisovan genomes (2021) · cites this paper as [3]
An ancestral recombination event can be conceptualized as a branch movement, consisting of a set of haplotypes moving from one clade in an upstream tree into a new clade in a downstream tree.
“An ancestral recombination event can be conceptualized as a branch movement (3) and so each consists of a set of haplotypes moving from one clade in an upstream tree into a new clade in a downstream tree.”
From An ancestral recombination graph of human, Neanderthal, and Denisovan genomes (2021) · cites this paper as [3]
Cites
The Structure of Haplotype Blocks in the Human Genome
Gabriel, S. B., Schaffner, S. F., Nguyen, H., Moore, J. M., Roy, J., Blumenstiel, B., Higgins, J., DeFelice, M., Lochner, A., Faggart, M., et al. (2002) · Science · doi:10.1126/science.1069424 · Cited by 5,863 · see citing works
Mapping Trait Loci by Use of Inferred Ancestral Recombination Graphs
Minichiello, M. J., & Durbin, R. (2006) · The American Journal of Human Genetics · doi:10.1086/508901 · Cited by 115 · see citing works
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Genome-Wide Inference of Ancestral Recombination Graphs
Rasmussen, M. D., Hubisz, M. J., Gronau, I., & Siepel, A. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004342 · Cited by 371 · see citing works
Mapping Trait Loci by Use of Inferred Ancestral Recombination Graphs
Minichiello, M. J., & Durbin, R. (2006) · The American Journal of Human Genetics · doi:10.1086/508901 · Cited by 115 · see citing works
An ancestral recombination graph of human, Neanderthal, and Denisovan genomes
Schaefer, N. K., Shapiro, B., & Green, R. E. (2021) · Science Advances · doi:10.1126/sciadv.abc0776 · Cited by 106 · see citing works
“Each ancestral recombination event manifests as a clade of haplotypes, all of which descend from the first ancestral haplotype to have it, moving from one position in the tree upstream of the event to a new position in the downstream tree (3).”
BackgroundInfluential
- Authors
- Song, Y. S., & Hein, J.
- Affiliations
- University of Oxford (GB)
- Venue
- Journal of Computational Biology
- Publisher
- SAGE Publications
- Published
- 2005-03
- Volume
- 12
- Issue
- 2
- Pages
- 147-169
- ISSN
- 1066-5277 (ISSN-L)
- 1557-8666
- OpenAlex
- W2026152438
- Cited by
- 130
- References
- 2
- Citations by year
- 2025: 1 · 2024: 31 · 2023: 3 · 2022: 1 · 2021: 3 · 2019: 4 · 2018: 3 · 2017: 2 · 2016: 7 · 2015: 3 · 2014: 6 · 2013: 8 · 2012: 2
- FWCI
- 3.49
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Journal of Computational Biology (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Medical Research Council
- Engineering and Physical Sciences Research Council (GR/R51384/01)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Keywords
- ancestral recombination graph, recombination detection, rooted trees, lower bounds, phylogenetic inference, recombination history
- MeSH terms
- Algorithms, Animals, Computer Graphics, Computer Simulation, Haplotypes, Humans, Models, Genetic, Recombination, Genetic, Evolution, Molecular, Computational Biology
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