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Keywords:

  • imperfect microsatellites;
  • phylogenetic reconstructions

This study explores the effects of microsatellite size homoplasies on the reconstruction of phylogenetic relationships and estimates of population parameters as the fixation index (FST) using as a case study a truncated microsatellite from the picote splitfin Zoogoneticus quitzeoensis. The results suggest that the use of imperfect microsatellites may have only a minor effect in phylogenetic and population studies.