Microsatellite Behavior with Range Constraints: Parameter Estimation and Improved Distances for Use in Phylogenetic Reconstruction |
| |
Authors: | David D. Pollock Aviv Bergman Marcus W. Feldman David B. Goldstein |
| |
Affiliation: | aInterval Research Corporation, Palo Alto, California, 94304;bDepartment of Mathematical Biology, National Institute for Medical Research, Mill Hill, London, NW7 1AA, United Kingdom;cInterval Research Corporation, Palo Alto, CA, 94304;dInterval Research Corporation, Palo Alto, California, 94304;eDepartment of Biological Sciences, Stanford Unviversity, Stanford, California, 94304;fInterval Research Corporation, Palo Alto, CA, 94304;gDepartment of Zoology, University of Oxford, OX1 3PS, United Kingdom |
| |
Abstract: | A symmetric stepwise mutation model with reflecting boundaries is employed to evaluate microsatellite evolution under range constraints. Methods of estimating range constraints and mutation rates under the assumptions of the model are developed. Least squares procedures are employed to improve molecular distance estimation for use in phylogenetic reconstruction in the case where range constraints and mutation rates vary across loci. The bias and accuracy of these methods are evaluated using computer simulations, and they are compared to previously existing methods which do not assume range constraints. Range constraints are seen to have a substantial impact on phylogenetic conclusions based on molecular distances, particularly for more divergent taxa. Results indicate that if range constraints are in effect, the methods developed here should be used in both the preliminary planning and final analysis of phylogenetic studies employing microsatellites. It is also seen that in order to make accurate phylogenetic inferences under range constraints, a larger number of loci are required than in their absence. |
| |
Keywords: | microsatellite evolution phylogenetics least squares |
本文献已被 ScienceDirect 等数据库收录! |
|