title: Are microsatellite fragment lengths useful for population-level studies? The case of Polygala lewtonii (Polygalaceae).
abstract: OBJECTIVE
  Microsatellites, despite being commonly used population-level markers, contain biases because scoring relies solely on fragment length. Their complexity can lead to homoplasy, the effects of which are poorly understood. We investigated the impact of using fragment lengths, repeats, or flanking region sequences on common population-level analyses.
  
  
  METHODS
  Five polymorphic microsatellite markers amplified across the central Florida scrub endemic Polygala lewtonii (Polygalaceae) and its close, widespread congener P. polygama. We genotyped 147 individuals of P. lewtonii and 156 of P. polygama, and sequenced the amplicons of four markers across all individuals. We ran basic statistics, spatial clustering analysis, historical demographics, and migration tests.
  
  
  RESULTS
  One population of intermediate morphology was genetically clearly identified as P. polygama, making it the southernmost population of this species. Statistics were comparable between the fragment length and repeat numbers, with some notable differences. Flanking regions exhibited surprisingly high polymorphism between species, and between geographically distant conspecific populations.
  
  
  CONCLUSIONS
  The increasing use of markers developed in one species and amplified in another is only a good practice if precautions are taken, notably the sequencing of the fragments between species and populations. Flanking region sequences are a useful marker at the interspecific level.
authors.affiliation: Department of Biology, University of Florida, Gainesville, Florida 32611 USA; Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA.
authors.forename: Charlotte C
authors.initials: CC
authors.lastname: Germain-Aubrey
authors.affiliation: College of Medicine, University of Florida, Gainesville, Florida 32603 USA.
authors.forename: Cory
authors.initials: C
authors.lastname: Nelson
authors.affiliation: Department of Biology, University of Florida, Gainesville, Florida 32611 USA; Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA; UF Genetics Institute, University of Florida, Gainesville, Florida 32608 USA.
authors.forename: Douglas E
authors.initials: DE
authors.lastname: Soltis
authors.affiliation: Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA; UF Genetics Institute, University of Florida, Gainesville, Florida 32608 USA.
authors.forename: Pamela S
authors.initials: PS
authors.lastname: Soltis
authors.affiliation: Department of Biology, University of Florida, Gainesville, Florida 32611 USA; Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA; UF Genetics Institute, University of Florida, Gainesville, Florida 32608 USA.
authors.forename: Matthew A
authors.initials: MA
authors.lastname: Gitzendanner
keywords: Polygala lewtonii; Polygalaceae; flanking regions; microsatellites; population-level sequence markers