title: Assessing the impact of phylogenetic incongruence on taxonomy, floral evolution, biogeographical history, and phylogenetic diversity.
abstract: OBJECTIVE
  Phylogenetic incongruence between "gene trees" and "species trees" has been widely acknowledged in phylogenetic research. Conflicts may emerge from several processes including paralogy, hybridization, and incomplete lineage sorting. Although phylogenetic incongruence appears common, its impact on many phylogeny-based analyses remains poorly understood.
  
  
  METHODS
  We examined the occurrence of phylogenetic conflict between nuclear (ribosome ITS) and plastid (rbcL, trnL-F, rpl20-rps12, and rps16 intron) loci in the ancient angiosperm family Chloranthaceae. Then we investigated how phylogenetic conflict bears on taxonomic classification within the family as well as on inferences on biogeographical history, floral evolution, and measures of phylogenetic diversity (PD).
  
  
  RESULTS
  We found evidence for significant phylogenetic incongruence between plastid and nuclear data in the genus Hedyosmum. Within Hedyosmum, our results did not support previous subgeneric classification of the genus. Division of sections within subgenus Tafalla was supported by the ITS data but not by the plastid data set. As a consequence, we showed that inferring the evolution of key floral characters and geographical history within Hedyosmum depends on the phylogenetic data used. Both data sets yielded similar PD measures across genera, but we found contrasting PD measures in Hedyosmum, even after correcting for rate heterogeneity.
  
  
  CONCLUSIONS
  Our study demonstrated that phylogenetic conflict not only affects the inference of organismal relationships but also impacts our understanding of biogeographical history, morphological evolution, and phylogenetic diversity.
authors: Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences 541006, Guilin, China.
authors: Qiang
authors: Q
authors: Zhang
authors: College of Marine and Environmental Sciences, James Cook University, Townsville, Queensland, Australia.
authors: Taylor S
authors: TS
authors: Feild
authors: Gothenburg Botanical Garden and Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden.
authors: Alexandre
authors: A
authors: Antonelli
mesh_terms: D002467:Cell Nucleus / Q000235:genetics / Q000378:metabolism; D060365:Chloroplast Proteins / Q000235:genetics* / Q000378:metabolism; D019143:Evolution, Molecular; D035264:Flowers; D019684:Magnoliopsida / Q000145:classification* / Q000235:genetics* / Q000378:metabolism; D008969:Molecular Sequence Data; D010802:Phylogeny; D063148:Plant Dispersal; D017422:Sequence Analysis, DNA
chemical_list: D060365:Chloroplast Proteins
keywords: Chloranthaceae; Hedyosmum; biogeography; phylogenetic conflict; phylogenetics; species trees