MICROSATELLITE BEHAVIOR WITH RANGE CONSTRAINTS - PARAMETER-ESTIMATIONAND IMPROVED DISTANCES FOR USE IN PHYLOGENETIC RECONSTRUCTION

A symmetric stepwise mutation model with reflecting boundaries is empl oyed to evaluate microsatellite evolution under range constraints. Met hods of estimating range constraints and mutation rates under the assu mptions of the model are developed. Least squares procedures are emplo yed to improve molecular distance estimation for use in phylogenetic r econstruction in the case where range constraints and mutation rates v ary across loci. The bias and accuracy of these methods are evaluated using computer simulations, and they are compared to previously existi ng methods which do not assume range constraints. Range constraints ar e seen to have a substantial impact on phylogenetic conclusions based on molecular distances, particularly for more divergent tars. Results indicate that if range constraints are in effect, the methods develope d here should be used in both the preliminary planning and final analy sis of phylogenetic studies employing microsatellites. it is also seen that in order to make accurate phylogenetic inferences under range co nstraints, a larger number of loci are required than in their absence, (C) 1998 Academic Press.