Open Access Research article

Mitogenomic sequences and evidence from unique gene rearrangements corroborate evolutionary relationships of myctophiformes (Neoteleostei)

Jan Y Poulsen1*, Ingvar Byrkjedal1, Endre Willassen1, David Rees1, Hirohiko Takeshima2, Takashi P Satoh3, Gento Shinohara3, Mutsumi Nishida2 and Masaki Miya4

Author Affiliations

1 Natural History Collections, University Museum of Bergen, University of Bergen, Allégaten 41, P.O. Box 7800, Bergen N-5020, Norway

2 Department of Marine Bioscience, Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8564, Japan

3 National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba, Ibaraki 305-0005, Japan

4 Department of Zoology, Natural History Museum and Institute, 955-2 Aoba-cho, Chuo-ku, Chiba 260-8682, Japan

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BMC Evolutionary Biology 2013, 13:111  doi:10.1186/1471-2148-13-111

Published: 3 June 2013

Additional files

Additional file 1:

Table T2. Partitioning schemes used in the present study suggested by PartitionFinder.

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Additional file 2:

Saturation plots of pairwise distances of 1st, 2nd and 3rd codon positions in the 12 protein coding genes employed in the analyses. Vertical axis shows p-distance for each codon position against total p-distance (horizontal axis). Saturation from RY-coding of the 3rd codon positions included (only transversions valued) although not used in the present study from early onset of saturation.

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Additional file 3: Figure S1:

Secondary structure of INC-regions. Sequence alignments and secondary tRNA structures of INC-regions are shown for synapomorphic spacers pertaining to gene order rearrangements 1, 3, 5 and 8 presented in Figure 3. The remaining INC-regions presented in Figure 3 are relatively short sequences and are not included.

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Additional file 4: Table T1:

Base pair details of INC-regions found in Myctophidae. Eight mt regions correspond to gene order and INC-region synapomorphies presented in Figure 3 with slash (/) denoting bordering genes. The last column includes mt information from the polymorphic region from tRNA-Thr and downstream towards the control region (CR). Numbers of INC-sequence base pairs are parenthesized next to flanking genes. Greater-than sign (>) and hyphen (−) denote partial and no sequence, respectively, from failure to complete the sequences.

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Additional file 5:

IMQMψ gene order in a clade of scarid parrotfishes. Taxa constituting a monophyletic clade in Scaridae all show similar patterns in the IMQ-region as observed within Diaphini. Grey areas show INC-regions with number of base pairs noted for each taxon and the arrow indicates possible gradual removal of INC-regions.

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