title: Mitochondrial genomic investigation of flatfish monophyly.
abstract: We present the first study to use whole mitochondrial genome sequences to examine phylogenetic affinities of the flatfishes (Pleuronectiformes). Flatfishes have attracted attention in evolutionary biology since the early history of the field because understanding the evolutionary history and patterns of diversification of the group will shed light on the evolution of novel body plans. Because recent molecular studies based primarily on DNA sequences from nuclear loci have yielded conflicting results, it is important to examine phylogenetic signal in different genomes and genome regions. We aligned and analyzed mitochondrial genome sequences from thirty-nine pleuronectiforms including nine that are newly reported here, and sixty-six non-pleuronectiforms (twenty additional clade L taxa [Carangimorpha or Carangimorpharia] and forty-six secondary outgroup taxa). The analyses yield strong support for clade L and weak support for the monophyly of Pleuronectiformes. The suborder Pleuronectoidei receives moderate support, and as with other molecular studies the putatively basal lineage of Pleuronectiformes, the Psettodoidei is frequently not most closely related to other pleuronectiforms. Within the Pleuronectoidei, the basal lineages in the group are poorly resolved, however several flatfish subclades receive consistent support. The affinities of Lepidoblepharon and Citharoides among pleuronectoids are particularly uncertain with these data.
authors.affiliation: Department of Biology and Wildlife, PO Box 756100, Fairbanks, AK 99775-6100, USA. Electronic address: m.campbell1@massey.ac.nz.
authors.forename: Matthew A
authors.initials: MA
authors.lastname: Campbell
authors.affiliation: University of Alaska Museum, 907 Yukon Drive, Fairbanks, AK 99775, USA; Fisheries Division, School of Fisheries and Ocean Sciences, University of Alaska Fairbanks, 905 N. Koyukuk Drive, Fairbanks, AK 99775-7220, USA. Electronic address: jalopez2@alaska.edu.
authors.forename: J Andrés
authors.initials: JA
authors.lastname: López
authors.affiliation: National Museum of Nature and Science, Collection Center, 4-1-1 Amakubo, Tsukuba City, Ibaraki 305-0005, Japan. Electronic address: satotaka@kahaku.go.jp.
authors.forename: Takashi P
authors.initials: TP
authors.lastname: Satoh
authors.affiliation: Institute of Oceanography, National Taiwan University, No. 1 Sec. 4 Roosevelt Rd., Taipei 10617, Taiwan. Electronic address: wjchen.actinops@gmail.com.
authors.forename: Wei-Jen
authors.initials: WJ
authors.lastname: Chen
authors.affiliation: Natural History Museum and Institute, 955-2 Aoba-cho, Chuo-Ku, Chiba 260-8682, Japan. Electronic address: miya@chiba-muse.or.jp.
authors.forename: Masaki
authors.initials: M
authors.lastname: Miya
mesh_terms: D000818:Animals; D004272:DNA, Mitochondrial / Q000737:chemistry / Q000145:classification / Q000235:genetics*; D005412:Flatfishes / Q000235:genetics*; D054629:Genome, Mitochondrial / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D013045:Species Specificity
chemical_list: D004272:DNA, Mitochondrial
keywords: Carangimorpharia; Incomplete lineage sorting; Mitogenomes; Partitioned analysis; Phylogeny; Pleuronectiformes