title: A new perspective on phylogeny and evolution of tetraodontiform fishes (Pisces: Acanthopterygii) based on whole mitochondrial genome sequences: basal ecological diversification?
abstract: BACKGROUND
  The order Tetraodontiformes consists of approximately 429 species of fishes in nine families. Members of the order exhibit striking morphological diversity and radiated into various habitats such as freshwater, brackish and coastal waters, open seas, and deep waters along continental shelves and slopes. Despite extensive studies based on both morphology and molecules, there has been no clear resolution except for monophyly of each family and sister-group relationships of Diodontidae + Tetraodontidae and Balistidae + Monacanthidae. To address phylogenetic questions of tetraodontiform fishes, we used whole mitochondrial genome (mitogenome) sequences from 27 selected species (data for 11 species were newly determined during this study) that fully represent all families and subfamilies of Tetraodontiformes (except for Hollardinae of the Triacanthodidae). Partitioned maximum likelihood (ML) and Bayesian analyses were performed on two data sets comprising concatenated nucleotide sequences from 13 protein-coding genes (all positions included; third codon positions converted into purine [R] and pyrimidine [Y]), 22 transfer RNA and two ribosomal RNA genes (total positions = 15,084).
  
  
  RESULTS
  The resultant tree topologies from the two data sets were congruent, with many internal branches showing high support values. The mitogenomic data strongly supported monophyly of all families and subfamilies (except the Tetraodontinae) and sister-group relationships of Balistidae + Monacanthidae and Tetraodontidae + Diodontidae, confirming the results of previous studies. However, we also found two unexpected basal splits into Tetraodontoidei (Triacanthidae + Balistidae + Monacanthidae + Tetraodontidae + Diodontidae + Molidae) and Triacanthodoidei (Ostraciidae + Triodontidae + Triacanthodidae).
  
  
  CONCLUSIONS
  This basal split into the two clades has never been reported and challenges previously proposed hypotheses based on both morphology and nuclear gene sequences. It is likely that the basal split had involved ecological diversification, because most members of Tetraodontoidei exclusively occur in shallow waters (freshwater, brackish and coastal waters, and open seas), while those of Triacanthodoidei occur mainly in relatively deep waters along continental shelves and slopes except for more derived ostraciids. This suggests that the basal split between the two clades led to subsequent radiation into the two different habitats.
authors.affiliation: Ocean Research Institute, University of Tokyo, 1-15-1 Minamidai, Nakano-ku, Tokyo 164-8639, Japan. ayyamano@mail.ecc.u-tokyo.ac.jp
authors.forename: Yusuke
authors.initials: Y
authors.lastname: Yamanoue
authors.forename: Masaki
authors.initials: M
authors.lastname: Miya
authors.forename: Keiichi
authors.initials: K
authors.lastname: Matsuura
authors.forename: Masaya
authors.initials: M
authors.lastname: Katoh
authors.forename: Harumi
authors.initials: H
authors.lastname: Sakai
authors.forename: Mutsumi
authors.initials: M
authors.lastname: Nishida
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D004272:DNA, Mitochondrial / Q000235:genetics; D019143:Evolution, Molecular; D014644:Genetic Variation; D054629:Genome, Mitochondrial; D016013:Likelihood Functions; D010802:Phylogeny; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D023721:Tetraodontiformes / Q000145:classification / Q000235:genetics*
chemical_list: D004272:DNA, Mitochondrial