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Mitochondrial genomic investigation of flatfish monophyly
Authors:Matthew A Campbell  J Andrés López  Takashi P Satoh  Wei-Jen Chen  Masaki Miya
Institution:1. Department of Biology and Wildlife, PO Box 756100, Fairbanks, AK 99775-6100, USA;2. University of Alaska Museum, 907 Yukon Drive, Fairbanks, AK 99775, USA;3. Fisheries Division, School of Fisheries and Ocean Sciences, University of Alaska Fairbanks, 905 N. Koyukuk Drive, Fairbanks, AK 99775-7220, USA;4. National Museum of Nature and Science, Collection Center, 4-1-1 Amakubo, Tsukuba City, Ibaraki 305-0005, Japan;5. Institute of Oceanography, National Taiwan University, No. 1 Sec. 4 Roosevelt Rd., Taipei 10617, Taiwan;6. Natural History Museum and Institute, 955-2 Aoba-cho, Chuo-Ku, Chiba 260-8682, Japan
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.
Keywords:1  first codon positions of aligned proteins  2  second codon positions of aligned proteins  3  third codon positions of aligned proteins  DDBJ  DNA Data Bank of Japan  DNA  deoxyribonucleic acid  EMBL  European Molecular Biology Laboratory  Γ  four-category gamma distributed rate variation among sites  GTR  general time reversible model of nucleotide evolution  ML  maximum likelihood  MSA  multiple sequence alignment  n  nucleotide  ND6  NADH-ubiquinone oxidoreductase chain 6  PCR  polymerase chain reaction  R  ribosomal RNA  RNA  ribonucleic acid  rRNA  ribosomal RNA  RY  purine and pyrimidine recoding  T  transfer RNA  tRNA  transfer RNA
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