A Novel Multi-Scale Modeling Approach to Infer Whole Genome Divergence
We propose a novel and simple approach to elucidate genomic patterns of divergence using principal component analysis (PCA). We applied this methodology to the metric space generated by M. musculus genome-wide SNPs. Distance profiles were computed between M. musculus and its closely related species,...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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SAGE Publishing
2012-01-01
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| Series: | Evolutionary Bioinformatics |
| Online Access: | https://doi.org/10.4137/EBO.S10194 |
| _version_ | 1818512603441266688 |
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| author | Eli Reuveni Alessandro Giuliani |
| author_facet | Eli Reuveni Alessandro Giuliani |
| author_sort | Eli Reuveni |
| collection | DOAJ |
| description | We propose a novel and simple approach to elucidate genomic patterns of divergence using principal component analysis (PCA). We applied this methodology to the metric space generated by M. musculus genome-wide SNPs. Distance profiles were computed between M. musculus and its closely related species, M. spretus , which was used as external reference. While the speciation dynamics were apparent in the first principal component, the within M. musculus differentiation dimensions gave rise to three minor components. We were unable to obtain a clear divergence signature discriminating laboratory strains, suggesting a stronger effect of genetic drift. These results were at odds with wild strains which exhibit defined deterministic signals of divergence. Finally, we were able to rank novel and previously known genes according to their likelihood to be under selective pressure. In conclusion, we posit PCA as a robust methodology to unravel diverging DNA regions without any a priori forcing. |
| first_indexed | 2024-12-10T23:49:16Z |
| format | Article |
| id | doaj.art-80b28a193c2f4a888af7176d4da31786 |
| institution | Directory Open Access Journal |
| issn | 1176-9343 |
| language | English |
| last_indexed | 2024-12-10T23:49:16Z |
| publishDate | 2012-01-01 |
| publisher | SAGE Publishing |
| record_format | Article |
| series | Evolutionary Bioinformatics |
| spelling | doaj.art-80b28a193c2f4a888af7176d4da317862022-12-22T01:28:50ZengSAGE PublishingEvolutionary Bioinformatics1176-93432012-01-01810.4137/EBO.S10194A Novel Multi-Scale Modeling Approach to Infer Whole Genome DivergenceEli Reuveni0Alessandro Giuliani1Mouse Biology Unit, European Molecular Biology Laboratory (EMBL), via Ramarini 32, 00015 Monterotondo, Italy.Istituto Superiore di Sanita', Environment and Health Department, Roma, Italy.We propose a novel and simple approach to elucidate genomic patterns of divergence using principal component analysis (PCA). We applied this methodology to the metric space generated by M. musculus genome-wide SNPs. Distance profiles were computed between M. musculus and its closely related species, M. spretus , which was used as external reference. While the speciation dynamics were apparent in the first principal component, the within M. musculus differentiation dimensions gave rise to three minor components. We were unable to obtain a clear divergence signature discriminating laboratory strains, suggesting a stronger effect of genetic drift. These results were at odds with wild strains which exhibit defined deterministic signals of divergence. Finally, we were able to rank novel and previously known genes according to their likelihood to be under selective pressure. In conclusion, we posit PCA as a robust methodology to unravel diverging DNA regions without any a priori forcing.https://doi.org/10.4137/EBO.S10194 |
| spellingShingle | Eli Reuveni Alessandro Giuliani A Novel Multi-Scale Modeling Approach to Infer Whole Genome Divergence Evolutionary Bioinformatics |
| title | A Novel Multi-Scale Modeling Approach to Infer Whole Genome Divergence |
| title_full | A Novel Multi-Scale Modeling Approach to Infer Whole Genome Divergence |
| title_fullStr | A Novel Multi-Scale Modeling Approach to Infer Whole Genome Divergence |
| title_full_unstemmed | A Novel Multi-Scale Modeling Approach to Infer Whole Genome Divergence |
| title_short | A Novel Multi-Scale Modeling Approach to Infer Whole Genome Divergence |
| title_sort | novel multi scale modeling approach to infer whole genome divergence |
| url | https://doi.org/10.4137/EBO.S10194 |
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