Gene birth in a model of non-genic adaptation
Abstract Background Over evolutionary timescales, genomic loci can switch between functional and non-functional states through processes such as pseudogenization and de novo gene birth. Particularly, de novo gene birth is a widespread process, and many examples continue to be discovered across diver...
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| Format: | Article |
| Language: | English |
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BMC
2023-11-01
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| Series: | BMC Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12915-023-01745-5 |
| _version_ | 1797556431194423296 |
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| author | Somya Mani Tsvi Tlusty |
| author_facet | Somya Mani Tsvi Tlusty |
| author_sort | Somya Mani |
| collection | DOAJ |
| description | Abstract Background Over evolutionary timescales, genomic loci can switch between functional and non-functional states through processes such as pseudogenization and de novo gene birth. Particularly, de novo gene birth is a widespread process, and many examples continue to be discovered across diverse evolutionary lineages. However, the general mechanisms that lead to functionalization are poorly understood, and estimated rates of de novo gene birth remain contentious. Here, we address this problem within a model that takes into account mutations and structural variation, allowing us to estimate the likelihood of emergence of new functions at non-functional loci. Results Assuming biologically reasonable mutation rates and mutational effects, we find that functionalization of non-genic loci requires the realization of strict conditions. This is in line with the observation that most de novo genes are localized to the vicinity of established genes. Our model also provides an explanation for the empirical observation that emerging proto-genes are often lost despite showing signs of adaptation. Conclusions Our work elucidates the properties of non-genic loci that make them fertile for adaptation, and our results offer mechanistic insights into the process of de novo gene birth. |
| first_indexed | 2024-03-10T17:01:46Z |
| format | Article |
| id | doaj.art-47b6320a4f7a4848b8040bef9b4667d5 |
| institution | Directory Open Access Journal |
| issn | 1741-7007 |
| language | English |
| last_indexed | 2024-03-10T17:01:46Z |
| publishDate | 2023-11-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Biology |
| spelling | doaj.art-47b6320a4f7a4848b8040bef9b4667d52023-11-20T10:55:43ZengBMCBMC Biology1741-70072023-11-0121111810.1186/s12915-023-01745-5Gene birth in a model of non-genic adaptationSomya Mani0Tsvi Tlusty1Center for Soft and Living Matter, Institute for Basic ScienceCenter for Soft and Living Matter, Institute for Basic ScienceAbstract Background Over evolutionary timescales, genomic loci can switch between functional and non-functional states through processes such as pseudogenization and de novo gene birth. Particularly, de novo gene birth is a widespread process, and many examples continue to be discovered across diverse evolutionary lineages. However, the general mechanisms that lead to functionalization are poorly understood, and estimated rates of de novo gene birth remain contentious. Here, we address this problem within a model that takes into account mutations and structural variation, allowing us to estimate the likelihood of emergence of new functions at non-functional loci. Results Assuming biologically reasonable mutation rates and mutational effects, we find that functionalization of non-genic loci requires the realization of strict conditions. This is in line with the observation that most de novo genes are localized to the vicinity of established genes. Our model also provides an explanation for the empirical observation that emerging proto-genes are often lost despite showing signs of adaptation. Conclusions Our work elucidates the properties of non-genic loci that make them fertile for adaptation, and our results offer mechanistic insights into the process of de novo gene birth.https://doi.org/10.1186/s12915-023-01745-5Spontaneous mutationStructural variationMutation rateDistribution of fitness effectsAdaptationDe novo gene birth |
| spellingShingle | Somya Mani Tsvi Tlusty Gene birth in a model of non-genic adaptation BMC Biology Spontaneous mutation Structural variation Mutation rate Distribution of fitness effects Adaptation De novo gene birth |
| title | Gene birth in a model of non-genic adaptation |
| title_full | Gene birth in a model of non-genic adaptation |
| title_fullStr | Gene birth in a model of non-genic adaptation |
| title_full_unstemmed | Gene birth in a model of non-genic adaptation |
| title_short | Gene birth in a model of non-genic adaptation |
| title_sort | gene birth in a model of non genic adaptation |
| topic | Spontaneous mutation Structural variation Mutation rate Distribution of fitness effects Adaptation De novo gene birth |
| url | https://doi.org/10.1186/s12915-023-01745-5 |
| work_keys_str_mv | AT somyamani genebirthinamodelofnongenicadaptation AT tsvitlusty genebirthinamodelofnongenicadaptation |