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Estimating true evolutionary distances under rearrangements, duplications, and losses
BACKGROUND: The rapidly increasing availability of whole-genome sequences has enabled the study of whole-genome evolution. Evolutionary mechanisms based on genome rearrangements have attracted much attention and given rise to many models; somewhat independently, the mechanisms of gene duplication an...
Autores principales: | , , , |
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2010
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3009527/ https://www.ncbi.nlm.nih.gov/pubmed/20122229 http://dx.doi.org/10.1186/1471-2105-11-S1-S54 |
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author | Lin, Yu Rajan, Vaibhav Swenson, Krister M Moret, Bernard ME |
author_facet | Lin, Yu Rajan, Vaibhav Swenson, Krister M Moret, Bernard ME |
author_sort | Lin, Yu |
collection | PubMed |
description | BACKGROUND: The rapidly increasing availability of whole-genome sequences has enabled the study of whole-genome evolution. Evolutionary mechanisms based on genome rearrangements have attracted much attention and given rise to many models; somewhat independently, the mechanisms of gene duplication and loss have seen much work. However, the two are not independent and thus require a unified treatment, which remains missing to date. Moreover, existing rearrangement models do not fit the dichotomy between most prokaryotic genomes (one circular chromosome) and most eukaryotic genomes (multiple linear chromosomes). RESULTS: To handle rearrangements, gene duplications and losses, we propose a new evolutionary model and the corresponding method for estimating true evolutionary distance. Our model, inspired from the DCJ model, is simple and the first to respect the prokaryotic/eukaryotic structural dichotomy. Experimental results on a wide variety of genome structures demonstrate the very high accuracy and robustness of our distance estimator. CONCLUSION: We give the first robust, statistically based, estimate of genomic pairwise distances based on rearrangements, duplications and losses, under a model that respects the structural dichotomy between prokaryotic and eukaryotic genomes. Accurate and robust estimates in true evolutionary distances should translate into much better phylogenetic reconstructions as well as more accurate genomic alignments, while our new model of genome rearrangements provides another refinement in simplicity and verisimilitude. |
format | Text |
id | pubmed-3009527 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2010 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-30095272010-12-23 Estimating true evolutionary distances under rearrangements, duplications, and losses Lin, Yu Rajan, Vaibhav Swenson, Krister M Moret, Bernard ME BMC Bioinformatics Research BACKGROUND: The rapidly increasing availability of whole-genome sequences has enabled the study of whole-genome evolution. Evolutionary mechanisms based on genome rearrangements have attracted much attention and given rise to many models; somewhat independently, the mechanisms of gene duplication and loss have seen much work. However, the two are not independent and thus require a unified treatment, which remains missing to date. Moreover, existing rearrangement models do not fit the dichotomy between most prokaryotic genomes (one circular chromosome) and most eukaryotic genomes (multiple linear chromosomes). RESULTS: To handle rearrangements, gene duplications and losses, we propose a new evolutionary model and the corresponding method for estimating true evolutionary distance. Our model, inspired from the DCJ model, is simple and the first to respect the prokaryotic/eukaryotic structural dichotomy. Experimental results on a wide variety of genome structures demonstrate the very high accuracy and robustness of our distance estimator. CONCLUSION: We give the first robust, statistically based, estimate of genomic pairwise distances based on rearrangements, duplications and losses, under a model that respects the structural dichotomy between prokaryotic and eukaryotic genomes. Accurate and robust estimates in true evolutionary distances should translate into much better phylogenetic reconstructions as well as more accurate genomic alignments, while our new model of genome rearrangements provides another refinement in simplicity and verisimilitude. BioMed Central 2010-01-18 /pmc/articles/PMC3009527/ /pubmed/20122229 http://dx.doi.org/10.1186/1471-2105-11-S1-S54 Text en Copyright ©2010 Lin et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Lin, Yu Rajan, Vaibhav Swenson, Krister M Moret, Bernard ME Estimating true evolutionary distances under rearrangements, duplications, and losses |
title | Estimating true evolutionary distances under rearrangements, duplications, and losses |
title_full | Estimating true evolutionary distances under rearrangements, duplications, and losses |
title_fullStr | Estimating true evolutionary distances under rearrangements, duplications, and losses |
title_full_unstemmed | Estimating true evolutionary distances under rearrangements, duplications, and losses |
title_short | Estimating true evolutionary distances under rearrangements, duplications, and losses |
title_sort | estimating true evolutionary distances under rearrangements, duplications, and losses |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3009527/ https://www.ncbi.nlm.nih.gov/pubmed/20122229 http://dx.doi.org/10.1186/1471-2105-11-S1-S54 |
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