Microsatellite behavior with range constraints

Parameter estimation and improved distances for use in phylogenetic reconstruction

David D. Pollock, Aviv Bergman, Marcus W. Feldman, David B. Goldstein

Research output: Contribution to journalArticle

36 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)256-271
Number of pages16
JournalTheoretical Population Biology
Volume53
Issue number3
DOIs
StatePublished - Jun 1998
Externally publishedYes

Fingerprint

Microsatellite Repeats
microsatellite repeats
phylogenetics
mutation
phylogeny
Mutation Rate
loci
methodology
computer simulation
least squares
Least-Squares Analysis
planning
Computer Simulation
parameter estimation
method
Mutation
rate

Keywords

  • Evolution
  • Least squares
  • Microsatellite
  • Phylogenetics

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Ecology, Evolution, Behavior and Systematics

Cite this

Microsatellite behavior with range constraints : Parameter estimation and improved distances for use in phylogenetic reconstruction. / Pollock, David D.; Bergman, Aviv; Feldman, Marcus W.; Goldstein, David B.

In: Theoretical Population Biology, Vol. 53, No. 3, 06.1998, p. 256-271.

Research output: Contribution to journalArticle

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