دورية أكاديمية
Difficulties in testing for covarion-like properties of sequences under the confounding influence of changing proportions of variable sites
| العنوان: | Difficulties in testing for covarion-like properties of sequences under the confounding influence of changing proportions of variable sites |
|---|---|
| المؤلفون: | Gruenheit, Nicole, Lockhart, Peter J., Steel, Mike, Martin, William |
| المصدر: | Gruenheit , N , Lockhart , P J , Steel , M & Martin , W 2008 , ' Difficulties in testing for covarion-like properties of sequences under the confounding influence of changing proportions of variable sites ' Molecular Biology and Evolution , vol 25 , no. 7 , pp. 1512-1520 . DOI:10.1093/molbev/msn098 |
| بيانات النشر: | University of Canterbury. Mathematics and Statistics |
| سنة النشر: | 2008 |
| مصطلحات موضوعية: | Chloroplast proteins, Contingency test, Covarion, Phylogenetics, /dk/atira/pure/subjectarea/asjc/1300/1311, Genetics, /dk/atira/pure/subjectarea/asjc/1300/1303, Biochemistry, /dk/atira/pure/subjectarea/asjc/2700/2716, Genetics(clinical), /dk/atira/pure/subjectarea/asjc/1300, Genetics and Molecular Biology(all), /dk/atira/pure/subjectarea/asjc/1100/1105, Ecology, Evolution, Behavior and Systematics, /dk/atira/pure/subjectarea/asjc/1100/1101, Agricultural and Biological Sciences (miscellaneous), /dk/atira/pure/subjectarea/asjc/1300/1312, Molecular Biology, stat, envir |
| الوصف: | The covarion (COV)-like properties of sequences are poorly described and their impact on phylogenetic analyses poorly understood. We demonstrate using simulations that, under an evolutionary model where the proportion of variable sites changes in nonadjacent lineages, log likelihood values for rates across site (RAS) and COV models become similar, making models difficult to distinguish. Further, although COV and RAS models provide a great improvement in likelihood scores over a homogeneous model with these simulated data, reconstruction accuracy of tree building is low, suggesting caution when it is suspected that proportions of variable sites differ in different evolutionary lineages. We study the performance of a recently developed contingency test that detects the presence of COV-type evolution modified for protein data. We report that if proportions of variable sites (pvar) change in a lineage-specific manner such that their distributions in different lineages become sufficiently nonoverlapping, then the contingency test can incorrectly suggest a homogeneous model. Also of concern is the possibility of different proportions of variable sites between the groups being studied. In a study of chloroplast proteins, interpretation of the test is found to be susceptible to different partitioning of taxon groups, making the test very subjective in its implementation. Extreme intergroup differences in the extent of divergence and difference in proportions of variable sites could be contributing to this effect. © The Author 2008. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. |
| نوع الوثيقة: | article in journal/newspaper |
| اللغة: | English |
| العلاقة: | https://www.research.manchester.ac.uk/portal/en/publications/difficulties-in-testing-for-covarionlike-properties-of-sequences-under-the-confounding-influence-of-changing-proportions-of-variable-sitesTest(a480c777-cc29-4102-91ff-617b4c3cbadb).html |
| الإتاحة: | https://doi.org/10.1093/molbev/msn098Test https://www.research.manchester.ac.uk/portal/en/publications/difficulties-in-testing-for-covarionlike-properties-of-sequences-under-the-confounding-influence-of-changing-proportions-of-variable-sitesTest(a480c777-cc29-4102-91ff-617b4c3cbadb).html |
| حقوق: | undefined |
| رقم الانضمام: | edsbas.FA866275 |
| قاعدة البيانات: | BASE |
| الوصف غير متاح. |