Journal article
A general and efficient representation of ancestral recombination graphs
- Abstract:
- 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. This approach is out of step with some modern developments, however, 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 generalises 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.
- Publication status:
- Published
- Peer review status:
- Peer reviewed
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(Preview, Version of record, pdf, 1.3MB, Terms of use)
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- Publisher copy:
- 10.1093/genetics/iyae100
Authors
+ Engineering and Physical Sciences Research Council
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- Funder identifier:
- https://ror.org/0439y7842
- Grant:
- EP/X024881/1
- Publisher:
- Oxford University Press
- Journal:
- Genetics More from this journal
- Volume:
- 228
- Issue:
- 1
- Article number:
- iyae100
- Publication date:
- 2024-06-19
- Acceptance date:
- 2024-06-05
- DOI:
- EISSN:
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1943-2631
- ISSN:
-
0016-6731
- Language:
-
English
- Keywords:
- Pubs id:
-
2009152
- Local pid:
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pubs:2009152
- Deposit date:
-
2024-06-19
- ARK identifier:
Terms of use
- Copyright holder:
- Wong et al.
- Copyright date:
- 2024
- Rights statement:
- © The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
- Licence:
- CC Attribution (CC BY)
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