title: Advances in the use of DNA barcodes to build a community phylogeny for tropical trees in a Puerto Rican forest dynamics plot.
abstract: BACKGROUND
  Species number, functional traits, and phylogenetic history all contribute to characterizing the biological diversity in plant communities. The phylogenetic component of diversity has been particularly difficult to quantify in species-rich tropical tree assemblages. The compilation of previously published (and often incomplete) data on evolutionary relationships of species into a composite phylogeny of the taxa in a forest, through such programs as Phylomatic, has proven useful in building community phylogenies although often of limited resolution. Recently, DNA barcodes have been used to construct a robust community phylogeny for nearly 300 tree species in a forest dynamics plot in Panama using a supermatrix method. In that study sequence data from three barcode loci were used to generate a well-resolved species-level phylogeny.
  
  
  RESULTS
  Here we expand upon this earlier investigation and present results on the use of a phylogenetic constraint tree to generate a community phylogeny for a diverse, tropical forest dynamics plot in Puerto Rico. This enhanced method of phylogenetic reconstruction insures the congruence of the barcode phylogeny with broadly accepted hypotheses on the phylogeny of flowering plants (i.e., APG III) regardless of the number and taxonomic breadth of the taxa sampled. We also compare maximum parsimony versus maximum likelihood estimates of community phylogenetic relationships as well as evaluate the effectiveness of one- versus two- versus three-gene barcodes in resolving community evolutionary history.
  
  
  CONCLUSIONS
  As first demonstrated in the Panamanian forest dynamics plot, the results for the Puerto Rican plot illustrate that highly resolved phylogenies derived from DNA barcode sequence data combined with a constraint tree based on APG III are particularly useful in comparative analysis of phylogenetic diversity and will enhance research on the interface between community ecology and evolution.
authors.affiliation: Department of Botany, National Museum of Natural History Smithsonian Institution, Washington, DC, United States of America. kressj@si.edu
authors.forename: W John
authors.initials: WJ
authors.lastname: Kress
authors.forename: David L
authors.initials: DL
authors.lastname: Erickson
authors.forename: Nathan G
authors.initials: NG
authors.lastname: Swenson
authors.forename: Jill
authors.initials: J
authors.lastname: Thompson
authors.forename: Maria
authors.initials: M
authors.lastname: Uriarte
authors.forename: Jess K
authors.initials: JK
authors.lastname: Zimmerman
mesh_terms: D058893:DNA Barcoding, Taxonomic / Q000379:methods*; D018744:DNA, Plant / Q000737:chemistry / Q000235:genetics*; D021903:DNA, Ribosomal Spacer / Q000235:genetics; D017753:Ecosystem; D004722:Endoribonucleases / Q000235:genetics; D014644:Genetic Variation; D009713:Nucleotidyltransferases / Q000235:genetics; D010802:Phylogeny; D011647:Puerto Rico; D012273:Ribulose-Bisphosphate Carboxylase / Q000235:genetics; D017422:Sequence Analysis, DNA; D013045:Species Specificity; D014197:Trees / Q000145:classification / Q000235:genetics*; D014329:Tropical Climate
chemical_list: D018744:DNA, Plant; D021903:DNA, Ribosomal Spacer; D009713:Nucleotidyltransferases; C034038:mRNA maturase; D004722:Endoribonucleases; C101625:RbcL protein, plastid; D012273:Ribulose-Bisphosphate Carboxylase