The era of the ARG: An introduction to ancestral recombination graphs and their significance in empirical evolutionary genomics.
In the presence of recombination, the evolutionary relationships between a set of sampled genomes cannot be described by a single genealogical tree. Instead, the genomes are related by a complex, interwoven collection of genealogies formalized in a structure called an ancestral recombination graph (...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2024-01-01
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| Series: | PLoS Genetics |
| Online Access: | https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1011110&type=printable |
| _version_ | 1797337250419179520 |
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| author | Alexander L Lewanski Michael C Grundler Gideon S Bradburd |
| author_facet | Alexander L Lewanski Michael C Grundler Gideon S Bradburd |
| author_sort | Alexander L Lewanski |
| collection | DOAJ |
| description | In the presence of recombination, the evolutionary relationships between a set of sampled genomes cannot be described by a single genealogical tree. Instead, the genomes are related by a complex, interwoven collection of genealogies formalized in a structure called an ancestral recombination graph (ARG). An ARG extensively encodes the ancestry of the genome(s) and thus is replete with valuable information for addressing diverse questions in evolutionary biology. Despite its potential utility, technological and methodological limitations, along with a lack of approachable literature, have severely restricted awareness and application of ARGs in evolution research. Excitingly, recent progress in ARG reconstruction and simulation have made ARG-based approaches feasible for many questions and systems. In this review, we provide an accessible introduction and exploration of ARGs, survey recent methodological breakthroughs, and describe the potential for ARGs to further existing goals and open avenues of inquiry that were previously inaccessible in evolutionary genomics. Through this discussion, we aim to more widely disseminate the promise of ARGs in evolutionary genomics and encourage the broader development and adoption of ARG-based inference. |
| first_indexed | 2024-03-08T09:06:48Z |
| format | Article |
| id | doaj.art-d3035437510343fbba2687bafec06ede |
| institution | Directory Open Access Journal |
| issn | 1553-7390 1553-7404 |
| language | English |
| last_indexed | 2024-03-08T09:06:48Z |
| publishDate | 2024-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Genetics |
| spelling | doaj.art-d3035437510343fbba2687bafec06ede2024-02-01T05:31:47ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042024-01-01201e101111010.1371/journal.pgen.1011110The era of the ARG: An introduction to ancestral recombination graphs and their significance in empirical evolutionary genomics.Alexander L LewanskiMichael C GrundlerGideon S BradburdIn the presence of recombination, the evolutionary relationships between a set of sampled genomes cannot be described by a single genealogical tree. Instead, the genomes are related by a complex, interwoven collection of genealogies formalized in a structure called an ancestral recombination graph (ARG). An ARG extensively encodes the ancestry of the genome(s) and thus is replete with valuable information for addressing diverse questions in evolutionary biology. Despite its potential utility, technological and methodological limitations, along with a lack of approachable literature, have severely restricted awareness and application of ARGs in evolution research. Excitingly, recent progress in ARG reconstruction and simulation have made ARG-based approaches feasible for many questions and systems. In this review, we provide an accessible introduction and exploration of ARGs, survey recent methodological breakthroughs, and describe the potential for ARGs to further existing goals and open avenues of inquiry that were previously inaccessible in evolutionary genomics. Through this discussion, we aim to more widely disseminate the promise of ARGs in evolutionary genomics and encourage the broader development and adoption of ARG-based inference.https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1011110&type=printable |
| spellingShingle | Alexander L Lewanski Michael C Grundler Gideon S Bradburd The era of the ARG: An introduction to ancestral recombination graphs and their significance in empirical evolutionary genomics. PLoS Genetics |
| title | The era of the ARG: An introduction to ancestral recombination graphs and their significance in empirical evolutionary genomics. |
| title_full | The era of the ARG: An introduction to ancestral recombination graphs and their significance in empirical evolutionary genomics. |
| title_fullStr | The era of the ARG: An introduction to ancestral recombination graphs and their significance in empirical evolutionary genomics. |
| title_full_unstemmed | The era of the ARG: An introduction to ancestral recombination graphs and their significance in empirical evolutionary genomics. |
| title_short | The era of the ARG: An introduction to ancestral recombination graphs and their significance in empirical evolutionary genomics. |
| title_sort | era of the arg an introduction to ancestral recombination graphs and their significance in empirical evolutionary genomics |
| url | https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1011110&type=printable |
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