Phylogenetic Inference From Conserved sites Alignments
Molecular sequences provide a rich source of data for inferring the phylogenetic relationships among species. However, recent work indicates that even an accurate multiple alignment of a large sequence set may yield an incorrect phylogeny and that the quality of the phylogenetic tree improves when the input consists only of the highly conserved, motif regions of the alignment. This work introduces two methods of producing multiple alignments that include only the conserved regions of the initial alignment. The first method retains conserved motifs, whereas the second retains individual conserved sites in the initial alignment. Using parsimony analysis on a mitochondrial data set containing 19 species among which the phylogenetic relationships are widely accepted, both conserved alignment methods produce better phylogenetic trees than the complete alignment. Unlike any of the 19 inference methods used before to analyze this data, both methods produce trees that are completely consistent with the known phylogeny. The motif-based method employs far fewer alignment sites for comparable error rates. For a larger data set containing mitochondrial sequences from 39 species, the site-based method produces a phylogenetic tree that is largely consistent with known phylogenetic relationships and suggests several novel placements.
- Research Organization:
- University of California - Santa Cruz (US)
- Sponsoring Organization:
- USDOE Office of Energy Research (ER) (US)
- DOE Contract Number:
- FG03-98ER62648
- OSTI ID:
- 781872
- Journal Information:
- Journal of Experimental Zoology, Vol. 285, Issue 2; Other Information: Published in Journal of Experimental Zoology, Online ISSN 1097-010X and Print ISSN 0022-104X, Volume 285, No.2, 128-139 (15 Aug 1999); PBD: 15 Aug 1999; ISSN 1097-010X / 0022-104X
- Country of Publication:
- United States
- Language:
- English
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