Pub Date : 2023-01-01Epub Date: 2022-11-30DOI: 10.1007/s11692-022-09579-9
Evgeni Bolotin, Daniel Melamed, Adi Livnat
Cases of parallel or recurrent gene fusions in evolution as well as in genetic disease and cancer are difficult to explain, because unlike point mutations, they can require the repetition of a similar configuration of multiple breakpoints rather than the repetition of a single point mutation. The used-together-fused-together hypothesis holds that genes that are used together repeatedly and persistently in a specific context are more likely to undergo fusion mutation in the course of evolution for mechanistic reasons. This hypothesis offers to explain gene fusion in both evolution and disease under one umbrella. Using bioinformatic data, we tested this hypothesis against alternatives, including that all gene pairs can fuse by random mutation, but among pairs thus fused, those that had interacted previously are more likely to be favored by selection. Results show that across multiple measures of gene interaction, human genes whose orthologs are fused in one or more species are more likely to interact with each other than random pairs of genes of the same genomic distance between pair members; that an overlap exists between genes that fused in the course of evolution in non-human species and genes that undergo fusion in human cancers; and that across six primate species studied, fusions predominate over fissions and exhibit substantial evolutionary parallelism. Together, these results support the used-together-fused-together hypothesis over its alternatives. Multiple implications are discussed, including the relevance of mutational mechanisms to the evolution of genome organization, to the distribution of fitness effects of mutation, to evolutionary parallelism and more.
Supplementary information: The online version contains supplementary material available at 10.1007/s11692-022-09579-9.
{"title":"Genes that are Used Together are More Likely to be Fused Together in Evolution by Mutational Mechanisms: A Bioinformatic Test of the Used-Fused Hypothesis.","authors":"Evgeni Bolotin, Daniel Melamed, Adi Livnat","doi":"10.1007/s11692-022-09579-9","DOIUrl":"10.1007/s11692-022-09579-9","url":null,"abstract":"<p><p>Cases of parallel or recurrent gene fusions in evolution as well as in genetic disease and cancer are difficult to explain, because unlike point mutations, they can require the repetition of a similar configuration of multiple breakpoints rather than the repetition of a single point mutation. The used-together-fused-together hypothesis holds that genes that are used together repeatedly and persistently in a specific context are more likely to undergo fusion mutation in the course of evolution for mechanistic reasons. This hypothesis offers to explain gene fusion in both evolution and disease under one umbrella. Using bioinformatic data, we tested this hypothesis against alternatives, including that all gene pairs can fuse by random mutation, but among pairs thus fused, those that had interacted previously are more likely to be favored by selection. Results show that across multiple measures of gene interaction, human genes whose orthologs are fused in one or more species are more likely to interact with each other than random pairs of genes of the same genomic distance between pair members; that an overlap exists between genes that fused in the course of evolution in non-human species and genes that undergo fusion in human cancers; and that across six primate species studied, fusions predominate over fissions and exhibit substantial evolutionary parallelism. Together, these results support the used-together-fused-together hypothesis over its alternatives. Multiple implications are discussed, including the relevance of mutational mechanisms to the evolution of genome organization, to the distribution of fitness effects of mutation, to evolutionary parallelism and more.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s11692-022-09579-9.</p>","PeriodicalId":50471,"journal":{"name":"Evolutionary Biology","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9925542/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10767184","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-12-30DOI: 10.1007/s11692-022-09590-0
L. Courtenay
{"title":"Can we Restore Balance to Geometric Morphometrics? A Theoretical Evaluation of how Sample Imbalance Conditions Ordination and Classification","authors":"L. Courtenay","doi":"10.1007/s11692-022-09590-0","DOIUrl":"https://doi.org/10.1007/s11692-022-09590-0","url":null,"abstract":"","PeriodicalId":50471,"journal":{"name":"Evolutionary Biology","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2022-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46684337","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-12-02DOI: 10.1007/s11692-022-09589-7
Manuela V. dos Santos, A. Prudente, M. T. Rodrigues, M. Sturaro
{"title":"Correction to: The Role of Vicariance and Paleoclimatic Shifts in the Diversification of Uranoscodon superciliosus (Squamata, Tropiduridae) of the Amazonian Floodplains","authors":"Manuela V. dos Santos, A. Prudente, M. T. Rodrigues, M. Sturaro","doi":"10.1007/s11692-022-09589-7","DOIUrl":"https://doi.org/10.1007/s11692-022-09589-7","url":null,"abstract":"","PeriodicalId":50471,"journal":{"name":"Evolutionary Biology","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2022-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47855252","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-12-01DOI: 10.1007/s11692-022-09587-9
G. Estivals, F. Duponchelle, C. Garcia-Davila, U. Römer, C. Mariac, J. Renno
{"title":"Exceptional Genetic Differentiation at a Micro-geographic Scale in Apistogramma agassizii (Steindachner, 1875) from the Peruvian Amazon: Sympatric Speciation?","authors":"G. Estivals, F. Duponchelle, C. Garcia-Davila, U. Römer, C. Mariac, J. Renno","doi":"10.1007/s11692-022-09587-9","DOIUrl":"https://doi.org/10.1007/s11692-022-09587-9","url":null,"abstract":"","PeriodicalId":50471,"journal":{"name":"Evolutionary Biology","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41539535","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-11-13DOI: 10.1007/s11692-022-09581-1
M. Zelditch, D. L. Swiderski
{"title":"The Predictable Complexity of Evolutionary Allometry","authors":"M. Zelditch, D. L. Swiderski","doi":"10.1007/s11692-022-09581-1","DOIUrl":"https://doi.org/10.1007/s11692-022-09581-1","url":null,"abstract":"","PeriodicalId":50471,"journal":{"name":"Evolutionary Biology","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2022-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43046923","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-11-10DOI: 10.1007/s11692-022-09584-y
Ellen M. Martin, J. Young, C. Fellmann, B. Kraatz, E. Sherratt
{"title":"Anatomical Correlates of Cursoriality are Compromised by Body Size and Propensity to Burrow in a Group of Small Mammals (Lagomorpha)","authors":"Ellen M. Martin, J. Young, C. Fellmann, B. Kraatz, E. Sherratt","doi":"10.1007/s11692-022-09584-y","DOIUrl":"https://doi.org/10.1007/s11692-022-09584-y","url":null,"abstract":"","PeriodicalId":50471,"journal":{"name":"Evolutionary Biology","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2022-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46883122","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-11-08DOI: 10.1007/s11692-022-09583-z
Manuela V. dos Santos, A. Prudente, M. T. Rodrigues, M. Sturaro
{"title":"The Role of Vicariance and Paleoclimatic Shifts in the Diversification of Uranoscodon superciliosus (Squamata, Tropiduridae) of the Amazonian Floodplains","authors":"Manuela V. dos Santos, A. Prudente, M. T. Rodrigues, M. Sturaro","doi":"10.1007/s11692-022-09583-z","DOIUrl":"https://doi.org/10.1007/s11692-022-09583-z","url":null,"abstract":"","PeriodicalId":50471,"journal":{"name":"Evolutionary Biology","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2022-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49522412","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-11-04DOI: 10.1007/s11692-022-09585-x
Martina Muraro, M. Falaschi, G. Ficetola
{"title":"Patterns of Performance Variation Between Animal Hybrids and their Parents: A Meta-analysis","authors":"Martina Muraro, M. Falaschi, G. Ficetola","doi":"10.1007/s11692-022-09585-x","DOIUrl":"https://doi.org/10.1007/s11692-022-09585-x","url":null,"abstract":"","PeriodicalId":50471,"journal":{"name":"Evolutionary Biology","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2022-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45347609","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-10-29DOI: 10.1007/s11692-022-09586-w
M. J. Tulli, A. Manzano, V. Abdala
{"title":"Correction to: Is the Shape of Turtle Claws Driven by Locomotor Modes?","authors":"M. J. Tulli, A. Manzano, V. Abdala","doi":"10.1007/s11692-022-09586-w","DOIUrl":"https://doi.org/10.1007/s11692-022-09586-w","url":null,"abstract":"","PeriodicalId":50471,"journal":{"name":"Evolutionary Biology","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2022-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47083740","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-10-29DOI: 10.1007/s11692-022-09580-2
M. J. Tulli, A. Manzano, V. Abdala
{"title":"Is the Shape of Turtle Claws Driven by Locomotor Modes?","authors":"M. J. Tulli, A. Manzano, V. Abdala","doi":"10.1007/s11692-022-09580-2","DOIUrl":"https://doi.org/10.1007/s11692-022-09580-2","url":null,"abstract":"","PeriodicalId":50471,"journal":{"name":"Evolutionary Biology","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2022-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42413490","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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