Multiple Loci Selection with Multi-Way Epistasis in Coalescence with Recombination
As studies move into deeper characterization of the impact of selection through non-neutral mutations in whole genome population genetics, modeling for selection becomes crucial. Moreover, epistasis has long been recognized as a significant component in understanding the evolution of complex genetic...
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-04-01
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| Series: | Algorithms |
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| Online Access: | https://www.mdpi.com/1999-4893/14/5/136 |
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| author | Aritra Bose Filippo Utro Daniel E. Platt Laxmi Parida |
| author_facet | Aritra Bose Filippo Utro Daniel E. Platt Laxmi Parida |
| author_sort | Aritra Bose |
| collection | DOAJ |
| description | As studies move into deeper characterization of the impact of selection through non-neutral mutations in whole genome population genetics, modeling for selection becomes crucial. Moreover, epistasis has long been recognized as a significant component in understanding the evolution of complex genetic systems. We present a backward coalescent model, EpiSimRA, that accommodates multiple loci selection, with multi-way (<i>k</i>-way) epistasis for any arbitrary <i>k</i>. Starting from arbitrary extant populations with epistatic sites, we trace the Ancestral Recombination Graph (ARG), sampling relevant recombination and coalescent events. Our framework allows for studying different complex evolutionary scenarios in the presence of selective sweeps, positive and negative selection with multiway epistasis. We also present a forward counterpart of the coalescent model based on a Wright-Fisher (WF) process, which we use as a validation framework, comparing the hallmarks of the ARG between the two. We provide the first framework that allows a nose-to-nose comparison of multiway epistasis in a coalescent simulator with its forward counterpart with respect to the hallmarks of the ARG. We demonstrate, through extensive experiments, that EpiSimRA is consistently superior in terms of performance (seconds vs. hours) in comparison to the forward model without compromising on its accuracy. |
| first_indexed | 2024-03-10T11:58:11Z |
| format | Article |
| id | doaj.art-a7784e066b244a989a5060a1b11a9dab |
| institution | Directory Open Access Journal |
| issn | 1999-4893 |
| language | English |
| last_indexed | 2024-03-10T11:58:11Z |
| publishDate | 2021-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Algorithms |
| spelling | doaj.art-a7784e066b244a989a5060a1b11a9dab2023-11-21T17:07:41ZengMDPI AGAlgorithms1999-48932021-04-0114513610.3390/a14050136Multiple Loci Selection with Multi-Way Epistasis in Coalescence with RecombinationAritra Bose0Filippo Utro1Daniel E. Platt2Laxmi Parida3Computational Genomics, IBM Thomas J. Watson Research Center, Ossining, NY 10562, USAComputational Genomics, IBM Thomas J. Watson Research Center, Ossining, NY 10562, USAComputational Genomics, IBM Thomas J. Watson Research Center, Ossining, NY 10562, USAComputational Genomics, IBM Thomas J. Watson Research Center, Ossining, NY 10562, USAAs studies move into deeper characterization of the impact of selection through non-neutral mutations in whole genome population genetics, modeling for selection becomes crucial. Moreover, epistasis has long been recognized as a significant component in understanding the evolution of complex genetic systems. We present a backward coalescent model, EpiSimRA, that accommodates multiple loci selection, with multi-way (<i>k</i>-way) epistasis for any arbitrary <i>k</i>. Starting from arbitrary extant populations with epistatic sites, we trace the Ancestral Recombination Graph (ARG), sampling relevant recombination and coalescent events. Our framework allows for studying different complex evolutionary scenarios in the presence of selective sweeps, positive and negative selection with multiway epistasis. We also present a forward counterpart of the coalescent model based on a Wright-Fisher (WF) process, which we use as a validation framework, comparing the hallmarks of the ARG between the two. We provide the first framework that allows a nose-to-nose comparison of multiway epistasis in a coalescent simulator with its forward counterpart with respect to the hallmarks of the ARG. We demonstrate, through extensive experiments, that EpiSimRA is consistently superior in terms of performance (seconds vs. hours) in comparison to the forward model without compromising on its accuracy.https://www.mdpi.com/1999-4893/14/5/136coalescent theorynatural selectionepistasisrecombination eventancestral recombination graph |
| spellingShingle | Aritra Bose Filippo Utro Daniel E. Platt Laxmi Parida Multiple Loci Selection with Multi-Way Epistasis in Coalescence with Recombination Algorithms coalescent theory natural selection epistasis recombination event ancestral recombination graph |
| title | Multiple Loci Selection with Multi-Way Epistasis in Coalescence with Recombination |
| title_full | Multiple Loci Selection with Multi-Way Epistasis in Coalescence with Recombination |
| title_fullStr | Multiple Loci Selection with Multi-Way Epistasis in Coalescence with Recombination |
| title_full_unstemmed | Multiple Loci Selection with Multi-Way Epistasis in Coalescence with Recombination |
| title_short | Multiple Loci Selection with Multi-Way Epistasis in Coalescence with Recombination |
| title_sort | multiple loci selection with multi way epistasis in coalescence with recombination |
| topic | coalescent theory natural selection epistasis recombination event ancestral recombination graph |
| url | https://www.mdpi.com/1999-4893/14/5/136 |
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