Article
Whole genome phylogenies for multiple Drosophila species
BMC Research Notes
(2012)
Abstract
Background: Reconstructing the evolutionary history of organisms using traditional phylogenetic methods may suffer from inaccurate sequence alignment. An alternative approach, particularly effective when whole genome sequences are available, is to employ methods that don’t use explicit sequence alignments. We extend a novel phylogenetic method based on Singular Value Decomposition (SVD) to reconstruct the phylogeny of 12 sequenced Drosophila species. SVD analysis provides accurate comparisons for a high fraction of sequences within whole genomes without the prior identification of orthologs or homologous sites. With this method all protein sequences are converted to peptide frequency vectors within a matrix that is decomposed to provide simplified vector representations for each protein of the genome in a reduced dimensional space. These vectors are summed
together to provide a vector representation for each species, and the angle between these vectors provides distance measures that are used to construct species trees.
Results: An unfiltered whole genome analysis (193,622 predicted proteins) strongly supports the currently accepted phylogeny for 12 Drosophila species at higher dimensions except for the generally accepted but difficult to discern sister relationship between D. erecta and D. yakuba. Also, in accordance with previous studies, many sequences appear to support alternative phylogenies. In this case, we observed grouping of D. erecta with D. sechellia when approximately 55% to 95% of the proteins were removed using a filter based on projection values or by reducing
resolution by using fewer dimensions. Similar results were obtained when just the
melanogaster subgroup was analyzed.
Conclusions: These results indicate that using our novel phylogenetic method, it is possible to consult and interpret all predicted protein sequences within multiple whole genomes to produce accurate phylogenetic estimations of relatedness between Drosophila species. Furthermore, protein filtering can be effectively applied to reduce incongruence in the dataset as well as to generate alternative phylogenies.
Keywords
- Singular value decomposition,
- Phylogenomics,
- Comparative genomics,
- Drosophila phylogeny
Disciplines
Publication Date
2012
DOI
DOI: 10.1186/1756-0500-5-670
Publisher Statement
Copyright 2012 Seetharam and Stuart; licensee BioMed Central Ltd. Posted with permission.
Citation Information
Arun S. Seetharam and Gary W. Stuart. "Whole genome phylogenies for multiple Drosophila species" BMC Research Notes Vol. 5 (2012) p. 670 Available at: http://works.bepress.com/arun-seetharam/3/
Creative Commons license
This work is licensed under a Creative Commons CC_BY International License.