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| Content Provider | PubMed Central |
|---|---|
| Author | Lake, J. A. |
| Abstract | The reconstruction of phylogenetic trees from DNAand protein sequences is confounded by unequal rate effects. These effects cangroup rapidly evolving taxa with other rapidly evolving taxa, whether or notthey are genealogically related. All algorithms are sensitive to these effectswhenever the assumptions on which they are based are not met. The algorithmpresented here, called paralinear distances, is valid for a much broader classof substitution processes than previous algorithms and is accordingly lessaffected by unequal rate effects. It may be used with all nucleic acid, protein,or other sequences, provided that their evolution may be modeled as a successionof Markov processes. The properties of the method have been proven bothanalytically and by computer simulations. Like all other methods, paralineardistances can fail when sequences are misaligned or when site-to-site sequencevariation of rates is extensive. To examine the usefulness of paralineardistances, the "origin of the eukaryotes" has been investigated by theanalysis of elongation factor Tu sequences with a variety of sequencealignments. It has been found that the order in which sequences are pairwisealigned strongly determines the topology which is reconstructed by paralineardistances (as it does for all other reconstruction methods tested). When theparts of the alignment that are unaffected by alignment order are analyzed,paralinear distances strongly select the eocyte topology. This provides evidencethat the eocyte prokaryotes are the closest prokaryotic relatives of theeukaryotes. |
| Starting Page | 1455 |
| File Format | |
| ISSN | 10916490 |
| e-ISSN | 10916490 |
| Journal | Proceedings of the National Academy of Sciences of the United States of America |
| Issue Number | 4 |
| Volume Number | 91 |
| Language | English |
| Publisher Date | 1994-02-15 |
| Access Restriction | Open |
| Subject Keyword | Research in Higher Education |
| Content Type | Text |
| Resource Type | Article |
| Subject | Multidisciplinary |
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