MapGL: inferring evolutionary gain and loss of short genomic sequence features by phylogenetic maximum parsimony
Abstract Background Comparative genomics studies are growing in number partly because of their unique ability to provide insight into shared and divergent biology between species. Of particular interest is the use of phylogenetic methods to infer the evolutionary history of cis-regulatory sequence f...
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| Format: | Article |
| Language: | English |
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BMC
2020-09-01
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| Series: | BMC Bioinformatics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12859-020-03742-9 |
| _version_ | 1819010470709821440 |
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| author | Adam G. Diehl Alan P. Boyle |
| author_facet | Adam G. Diehl Alan P. Boyle |
| author_sort | Adam G. Diehl |
| collection | DOAJ |
| description | Abstract Background Comparative genomics studies are growing in number partly because of their unique ability to provide insight into shared and divergent biology between species. Of particular interest is the use of phylogenetic methods to infer the evolutionary history of cis-regulatory sequence features, which contribute strongly to phenotypic divergence and are frequently gained and lost in eutherian genomes. Understanding the mechanisms by which cis-regulatory element turnover generate emergent phenotypes is crucial to our understanding of adaptive evolution. Ancestral reconstruction methods can place species-specific cis-regulatory features in their evolutionary context, thus increasing our understanding of the process of regulatory sequence turnover. However, applying these methods to gain and loss of cis-regulatory features historically required complex workflows, preventing widespread adoption by the broad scientific community. Results MapGL simplifies phylogenetic inference of the evolutionary history of short genomic sequence features by combining the necessary steps into a single piece of software with a simple set of inputs and outputs. We show that MapGL can reliably disambiguate the mechanisms underlying differential regulatory sequence content across a broad range of phylogenetic topologies and evolutionary distances. Thus, MapGL provides the necessary context to evaluate how genomic sequence gain and loss contribute to species-specific divergence. Conclusions MapGL makes phylogenetic inference of species-specific sequence gain and loss easy for both expert and non-expert users, making it a powerful tool for gaining novel insights into genome evolution. |
| first_indexed | 2024-12-21T01:12:47Z |
| format | Article |
| id | doaj.art-c47afe58893b4a1399e733c5112b2cfe |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-21T01:12:47Z |
| publishDate | 2020-09-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-c47afe58893b4a1399e733c5112b2cfe2022-12-21T19:20:54ZengBMCBMC Bioinformatics1471-21052020-09-012111910.1186/s12859-020-03742-9MapGL: inferring evolutionary gain and loss of short genomic sequence features by phylogenetic maximum parsimonyAdam G. Diehl0Alan P. Boyle1Department of Computational Medicine and Bioinformatics, University of MichiganDepartment of Computational Medicine and Bioinformatics, University of MichiganAbstract Background Comparative genomics studies are growing in number partly because of their unique ability to provide insight into shared and divergent biology between species. Of particular interest is the use of phylogenetic methods to infer the evolutionary history of cis-regulatory sequence features, which contribute strongly to phenotypic divergence and are frequently gained and lost in eutherian genomes. Understanding the mechanisms by which cis-regulatory element turnover generate emergent phenotypes is crucial to our understanding of adaptive evolution. Ancestral reconstruction methods can place species-specific cis-regulatory features in their evolutionary context, thus increasing our understanding of the process of regulatory sequence turnover. However, applying these methods to gain and loss of cis-regulatory features historically required complex workflows, preventing widespread adoption by the broad scientific community. Results MapGL simplifies phylogenetic inference of the evolutionary history of short genomic sequence features by combining the necessary steps into a single piece of software with a simple set of inputs and outputs. We show that MapGL can reliably disambiguate the mechanisms underlying differential regulatory sequence content across a broad range of phylogenetic topologies and evolutionary distances. Thus, MapGL provides the necessary context to evaluate how genomic sequence gain and loss contribute to species-specific divergence. Conclusions MapGL makes phylogenetic inference of species-specific sequence gain and loss easy for both expert and non-expert users, making it a powerful tool for gaining novel insights into genome evolution.http://link.springer.com/article/10.1186/s12859-020-03742-9Phylogenetic analysisGenomicsGenome evolutionRegulatory evolutionGenomic algorithmsAncestral reconstruction |
| spellingShingle | Adam G. Diehl Alan P. Boyle MapGL: inferring evolutionary gain and loss of short genomic sequence features by phylogenetic maximum parsimony BMC Bioinformatics Phylogenetic analysis Genomics Genome evolution Regulatory evolution Genomic algorithms Ancestral reconstruction |
| title | MapGL: inferring evolutionary gain and loss of short genomic sequence features by phylogenetic maximum parsimony |
| title_full | MapGL: inferring evolutionary gain and loss of short genomic sequence features by phylogenetic maximum parsimony |
| title_fullStr | MapGL: inferring evolutionary gain and loss of short genomic sequence features by phylogenetic maximum parsimony |
| title_full_unstemmed | MapGL: inferring evolutionary gain and loss of short genomic sequence features by phylogenetic maximum parsimony |
| title_short | MapGL: inferring evolutionary gain and loss of short genomic sequence features by phylogenetic maximum parsimony |
| title_sort | mapgl inferring evolutionary gain and loss of short genomic sequence features by phylogenetic maximum parsimony |
| topic | Phylogenetic analysis Genomics Genome evolution Regulatory evolution Genomic algorithms Ancestral reconstruction |
| url | http://link.springer.com/article/10.1186/s12859-020-03742-9 |
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