Topological Bias in Distance-Based Phylogenetic Methods: Problems with Over- and Underestimated Genetic Distances
I show several types of topological biases in distance-based methods that use the least-squares method to evaluate branch lengths and the minimum evolution (ME) or the Fitch-Margoliash (FM) criterion to choose the best tree. For a 6-species tree, there are two tree shapes, one with three cherries (a...
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| Format: | Article |
| Language: | English |
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SAGE Publishing
2006-01-01
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| Series: | Evolutionary Bioinformatics |
| Online Access: | https://doi.org/10.1177/117693430600200034 |
| _version_ | 1818240151450550272 |
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| author | Xuhua Xia |
| author_facet | Xuhua Xia |
| author_sort | Xuhua Xia |
| collection | DOAJ |
| description | I show several types of topological biases in distance-based methods that use the least-squares method to evaluate branch lengths and the minimum evolution (ME) or the Fitch-Margoliash (FM) criterion to choose the best tree. For a 6-species tree, there are two tree shapes, one with three cherries (a cherry is a pair of adjacent leaves descending from the most recent common ancestor), and the other with two. When genetic distances are underestimated, the 3-cherry tree shape is favored with either the ME or FM criterion. When the genetic distances are overestimated, the ME criterion favors the 2-cherry tree, but the direction of bias with the FM criterion depends on whether negative branches are allowed, i.e. allowing negative branches favors the 3-cherry tree shape but disallowing negative branches favors the 2-cherry tree shape. The extent of the bias is explored by computer simulation of sequence evolution. |
| first_indexed | 2024-12-12T13:08:53Z |
| format | Article |
| id | doaj.art-e22b63fd43c0429fa8ead370b90cee60 |
| institution | Directory Open Access Journal |
| issn | 1176-9343 |
| language | English |
| last_indexed | 2024-12-12T13:08:53Z |
| publishDate | 2006-01-01 |
| publisher | SAGE Publishing |
| record_format | Article |
| series | Evolutionary Bioinformatics |
| spelling | doaj.art-e22b63fd43c0429fa8ead370b90cee602022-12-22T00:23:35ZengSAGE PublishingEvolutionary Bioinformatics1176-93432006-01-01210.1177/117693430600200034Topological Bias in Distance-Based Phylogenetic Methods: Problems with Over- and Underestimated Genetic DistancesXuhua Xia0Department of Biology, University of Ottawa, Ottawa, Ontario, Canada.I show several types of topological biases in distance-based methods that use the least-squares method to evaluate branch lengths and the minimum evolution (ME) or the Fitch-Margoliash (FM) criterion to choose the best tree. For a 6-species tree, there are two tree shapes, one with three cherries (a cherry is a pair of adjacent leaves descending from the most recent common ancestor), and the other with two. When genetic distances are underestimated, the 3-cherry tree shape is favored with either the ME or FM criterion. When the genetic distances are overestimated, the ME criterion favors the 2-cherry tree, but the direction of bias with the FM criterion depends on whether negative branches are allowed, i.e. allowing negative branches favors the 3-cherry tree shape but disallowing negative branches favors the 2-cherry tree shape. The extent of the bias is explored by computer simulation of sequence evolution.https://doi.org/10.1177/117693430600200034 |
| spellingShingle | Xuhua Xia Topological Bias in Distance-Based Phylogenetic Methods: Problems with Over- and Underestimated Genetic Distances Evolutionary Bioinformatics |
| title | Topological Bias in Distance-Based Phylogenetic Methods: Problems with Over- and Underestimated Genetic Distances |
| title_full | Topological Bias in Distance-Based Phylogenetic Methods: Problems with Over- and Underestimated Genetic Distances |
| title_fullStr | Topological Bias in Distance-Based Phylogenetic Methods: Problems with Over- and Underestimated Genetic Distances |
| title_full_unstemmed | Topological Bias in Distance-Based Phylogenetic Methods: Problems with Over- and Underestimated Genetic Distances |
| title_short | Topological Bias in Distance-Based Phylogenetic Methods: Problems with Over- and Underestimated Genetic Distances |
| title_sort | topological bias in distance based phylogenetic methods problems with over and underestimated genetic distances |
| url | https://doi.org/10.1177/117693430600200034 |
| work_keys_str_mv | AT xuhuaxia topologicalbiasindistancebasedphylogeneticmethodsproblemswithoverandunderestimatedgeneticdistances |