general and efficient representation of ancestral recombination graphs.

Wong Y., Ignatieva A., Koskela J., Gorjanc G., Wohns AW., Kelleher J.

As a result of recombination, adjacent nucleotides can have different paths of genetic inheritance and therefore the genealogical trees for a sample of DNA sequences vary along the genome. The structure capturing the details of these intricately interwoven paths of inheritance is referred to as an ancestral recombination graph (ARG). Classical formalisms have focused on mapping coalescence and recombination events to the nodes in an ARG. However, this approach is out of step with some modern developments, which do not represent genetic inheritance in terms of these events or explicitly infer them. We present a simple formalism that defines an ARG in terms of specific genomes and their intervals of genetic inheritance, and show how it generalizes these classical treatments and encompasses the outputs of recent methods. We discuss nuances arising from this more general structure, and argue that it forms an appropriate basis for a software standard in this rapidly growing field.

DOI

10.1093/genetics/iyae100

Type

Journal article

Publication Date

2024-09-01T00:00:00+00:00

Volume

228

Addresses

Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7LF, UK.

Keywords

Humans, Evolution, Molecular, Recombination, Genetic, Genome, Models, Genetic, Software

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