title: A 10-gene phylogeny of Solanum section Herpystichum (Solanaceae) and a comparison of phylogenetic methods.
abstract: OBJECTIVE
  Solanum section Herpystichum is a lineage that comprises both widespread and very narrowly distributed species. This study investigates the phylogenetic relationships of sect. Herpystichum and evaluates several phylogenetic methods for analysis of multiple sequences.
  
  
  METHODS
  Sequence data from seven nuclear (ITS, GBSSI, and five COSII) and three plastid (psbA-trnH, trnT-trnF, and trnS-trnG) regions were concatenated and analyzed under maximum parsimony and Bayesian criteria. In addition, we used two analytical methods that take into account differences in topologies resulting from the analyses of the individual markers: Bayesian Estimation of Species Trees (BEST) and supertree analysis.
  
  
  RESULTS
  The monophyletic Solanum sect. Herpystichum was resolved with moderate support in the concatenated maximum parsimony and Bayesian analyses and the supertree analysis, and relationships within the section were well-resolved and strongly supported. The BEST topology, however, was poorly resolved. Also, because of how BEST deals with missing sequences, >25% of our accessions, including two species, had to be excluded from the analyses. Our results indicate a progenitor-descendent relationship with two species nested within the widespread S. evolvulifolium.
  
  
  CONCLUSIONS
  Analytical methods that consider individual topologies are important for studies based on multiple molecular markers. On the basis of analyses in this study, BEST had the serious shortcoming that taxa with missing sequences must be removed from the analysis or they can produce spurious topologies. Supertree analysis provided a good alternative for our data by allowing the inclusion of all 10 species of sect. Herpystichum.
authors.affiliation: Department of Biology, 257 South 1400 East, University of Utah, Salt Lake City, Utah 84112, USA. eric.tepe@gmail.com
authors.forename: Eric J
authors.initials: EJ
authors.lastname: Tepe
authors.forename: Frank T
authors.initials: FT
authors.lastname: Farruggia
authors.forename: Lynn
authors.initials: L
authors.lastname: Bohs
mesh_terms: D001483:Base Sequence; D002467:Cell Nucleus / Q000235:genetics; D021901:DNA, Intergenic / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics*; D019143:Evolution, Molecular; D017343:Genes, Plant; D005819:Genetic Markers; D014644:Genetic Variation; D008957:Models, Genetic; D010802:Phylogeny; D018515:Plant Leaves / Q000235:genetics; D010940:Plant Proteins / Q000235:genetics; D018087:Plastids / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*; D019657:Solanaceae / Q000145:classification / Q000235:genetics*
chemical_list: D021901:DNA, Intergenic; D018744:DNA, Plant; D005819:Genetic Markers; D010940:Plant Proteins