title: Multi-locus phylogeny of dolphins in the subfamily Lissodelphininae: character synergy improves phylogenetic resolution.
abstract: BACKGROUND
  Dolphins of the genus Lagenorhynchus are anti-tropically distributed in temperate to cool waters. Phylogenetic analyses of cytochrome b sequences have suggested that the genus is polyphyletic; however, many relationships were poorly resolved. In this study, we present a combined-analysis phylogenetic hypothesis for Lagenorhynchus and members of the subfamily Lissodelphininae, which is derived from two nuclear and two mitochondrial data sets and the addition of 34 individuals representing 9 species. In addition, we characterize with parsimony and Bayesian analyses the phylogenetic utility and interaction of characters with statistical measures, including the utility of highly consistent (non-homoplasious) characters as a conservative measure of phylogenetic robustness. We also explore the effects of removing sources of character conflict on phylogenetic resolution.
  
  
  RESULTS
  Overall, our study provides strong support for the monophyly of the subfamily Lissodelphininae and the polyphyly of the genus Lagenorhynchus. In addition, the simultaneous parsimony analysis resolved and/or improved resolution for 12 nodes including: (1) L. albirostris, L. acutus; (2) L. obscurus and L. obliquidens; and (3) L. cruciger and L. australis. In addition, the Bayesian analysis supported the monophyly of the Cephalorhynchus, and resolved ambiguities regarding the relationship of L. australis/L. cruciger to other members of the genus Lagenorhynchus. The frequency of highly consistent characters varied among data partitions, but the rate of evolution was consistent within data partitions. Although the control region was the greatest source of character conflict, removal of this data partition impeded phylogenetic resolution.
  
  
  CONCLUSIONS
  The simultaneous analysis approach produced a more robust phylogenetic hypothesis for Lagenorhynchus than previous studies, thus supporting a phylogenetic approach employing multiple data partitions that vary in overall rate of evolution. Even in cases where there was apparent conflict among characters, our data suggest a synergistic interaction in the simultaneous analysis, and speak against a priori exclusion of data because of potential conflicts, primarily because phylogenetic results can be less robust. For example, the removal of the control region, the putative source of character conflict, produced spurious results with inconsistencies among and within topologies from parsimony and Bayesian analyses.
authors.affiliation: Department of Zoology, 203 Natural Sciences Building, Michigan State University, East Lansing, Michigan, 48823, USA. cognatoa@msu.edu
authors.forename: April D
authors.initials: AD
authors.lastname: Harlin-Cognato
authors.forename: Rodney L
authors.initials: RL
authors.lastname: Honeycutt
mesh_terms: D000199:Actins / Q000235:genetics; D000818:Animals; D001499:Bayes Theorem; D045303:Cytochromes b / Q000235:genetics; D004272:DNA, Mitochondrial / Q000235:genetics; D004268:DNA-Binding Proteins / Q000235:genetics; D003661:Decision Support Techniques; D004289:Dolphins / Q000145:classification* / Q000235:genetics; D019143:Evolution, Molecular; D005819:Genetic Markers; D008969:Molecular Sequence Data; D010802:Phylogeny; D013045:Species Specificity
chemical_list: D000199:Actins; D004272:DNA, Mitochondrial; D004268:DNA-Binding Proteins; D005819:Genetic Markers; C064655:V(D)J recombination activating protein 2; D045303:Cytochromes b