Homology and linkage in crossover for linear genomes of variable length.
The use of variable-length genomes in evolutionary computation has applications in optimisation when the size of the search space is unknown, and provides a unique environment to study the evolutionary dynamics of genome structure. Here, we revisit crossover for linear genomes of variable length, id...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2019-01-01
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| Series: | PLoS ONE |
| Online Access: | https://doi.org/10.1371/journal.pone.0209712 |
| _version_ | 1819142861675823104 |
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| author | Adriaan Merlevede Henrik Åhl Carl Troein |
| author_facet | Adriaan Merlevede Henrik Åhl Carl Troein |
| author_sort | Adriaan Merlevede |
| collection | DOAJ |
| description | The use of variable-length genomes in evolutionary computation has applications in optimisation when the size of the search space is unknown, and provides a unique environment to study the evolutionary dynamics of genome structure. Here, we revisit crossover for linear genomes of variable length, identifying two crucial attributes of successful recombination algorithms: the ability to retain homologous structure, and to reshuffle variant information. We introduce direct measures of these properties-homology score and linkage score-and use them to review existing crossover algorithms, as well as two novel ones. In addition, we measure the performance of these crossover methods on three different benchmark problems, and find that variable-length genomes out-perform fixed-length variants in all three cases. Our homology and linkage scores successfully explain the difference in performance between different crossover methods, providing a simple and insightful framework for crossover in a variable-length setting. |
| first_indexed | 2024-12-22T12:17:05Z |
| format | Article |
| id | doaj.art-3299757fc9384021a9c3ed600e95b542 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-22T12:17:05Z |
| publishDate | 2019-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-3299757fc9384021a9c3ed600e95b5422022-12-21T18:26:06ZengPublic Library of Science (PLoS)PLoS ONE1932-62032019-01-01141e020971210.1371/journal.pone.0209712Homology and linkage in crossover for linear genomes of variable length.Adriaan MerlevedeHenrik ÅhlCarl TroeinThe use of variable-length genomes in evolutionary computation has applications in optimisation when the size of the search space is unknown, and provides a unique environment to study the evolutionary dynamics of genome structure. Here, we revisit crossover for linear genomes of variable length, identifying two crucial attributes of successful recombination algorithms: the ability to retain homologous structure, and to reshuffle variant information. We introduce direct measures of these properties-homology score and linkage score-and use them to review existing crossover algorithms, as well as two novel ones. In addition, we measure the performance of these crossover methods on three different benchmark problems, and find that variable-length genomes out-perform fixed-length variants in all three cases. Our homology and linkage scores successfully explain the difference in performance between different crossover methods, providing a simple and insightful framework for crossover in a variable-length setting.https://doi.org/10.1371/journal.pone.0209712 |
| spellingShingle | Adriaan Merlevede Henrik Åhl Carl Troein Homology and linkage in crossover for linear genomes of variable length. PLoS ONE |
| title | Homology and linkage in crossover for linear genomes of variable length. |
| title_full | Homology and linkage in crossover for linear genomes of variable length. |
| title_fullStr | Homology and linkage in crossover for linear genomes of variable length. |
| title_full_unstemmed | Homology and linkage in crossover for linear genomes of variable length. |
| title_short | Homology and linkage in crossover for linear genomes of variable length. |
| title_sort | homology and linkage in crossover for linear genomes of variable length |
| url | https://doi.org/10.1371/journal.pone.0209712 |
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