title: Detecting the symplesiomorphy trap: a multigene phylogenetic analysis of terebelliform annelids.
abstract: BACKGROUND
  For phylogenetic reconstructions, conflict in signal is a potential problem for tree reconstruction. For instance, molecular data from different cellular components, such as the mitochondrion and nucleus, may be inconsistent with each other. Mammalian studies provide one such case of conflict where mitochondrial data, which display compositional biases, support the Marsupionta hypothesis, but nuclear data confirm the Theria hypothesis. Most observations of compositional biases in tree reconstruction have focused on lineages with different composition than the majority of the lineages under analysis. However in some situations, the position of taxa that lack compositional bias may be influenced rather than the position of taxa that possess compositional bias. This situation is due to apparent symplesiomorphic characters and known as "the symplesiomorphy trap".
  
  
  RESULTS
  Herein, we report an example of the sympleisomorphy trap and how to detect it. Worms within Terebelliformia (sensu Rouse & Pleijel 2001) are mainly tube-dwelling annelids comprising five 'families': Alvinellidae, Ampharetidae, Terebellidae, Trichobranchidae and Pectinariidae. Using mitochondrial genomic data, as well as data from the nuclear 18S, 28S rDNA and elongation factor-1α genes, we revealed incongruence between mitochondrial and nuclear data regarding the placement of Trichobranchidae. Mitochondrial data favored a sister relationship between Terebellidae and Trichobranchidae, but nuclear data placed Trichobranchidae as sister to an Ampharetidae/Alvinellidae clade. Both positions have been proposed based on morphological data.
  
  
  CONCLUSIONS
  Our investigation revealed that mitochondrial data of Ampharetidae and Alvinellidae exhibited strong compositional biases. However, these biases resulted in a misplacement of Trichobranchidae, rather than Alvinellidae and Ampharetidae. Herein, we document that Trichobranchidae was apparently caught in the symplesiomorphy trap suggesting that in certain situations even homologies can be misleading.
authors.affiliation: Auburn University, Department of Biological Sciences, 101 Life Science Building, Auburn, AL 36849, USA.
authors.forename: Min
authors.initials: M
authors.lastname: Zhong
authors.forename: Benjamin
authors.initials: B
authors.lastname: Hansen
authors.forename: Maximilian
authors.initials: M
authors.lastname: Nesnidal
authors.forename: Anja
authors.initials: A
authors.lastname: Golombek
authors.forename: Kenneth M
authors.initials: KM
authors.lastname: Halanych
authors.forename: Torsten H
authors.initials: TH
authors.lastname: Struck
mesh_terms: D000818:Animals; D000845:Annelida / Q000166:cytology* / Q000235:genetics; D059001:Aquatic Organisms / Q000145:classification / Q000235:genetics; D001499:Bayes Theorem; D005075:Biological Evolution; D002467:Cell Nucleus / Q000235:genetics; D004272:DNA, Mitochondrial / Q000235:genetics; D004275:DNA, Ribosomal / Q000235:genetics; D016013:Likelihood Functions; D008957:Models, Genetic; D010802:Phylogeny; D017422:Sequence Analysis, DNA
chemical_list: D004272:DNA, Mitochondrial; D004275:DNA, Ribosomal