Mitochondrial DNA of the Co-1 gene region was sequenced for 8 fish species (in total 17 sequences of at least 532 bp) from the far east of Russia and compared to 3 other perciform sequences, altogether comprising 20 perch-like fish sequences and 2 outgroup sequences (Cypriniformes). The analysis of the protein-coding Co-1 gene revealed a statistically substantiated bias in the (T+C):(A+G) content, confirming the basic findings on the pyrimidines-prunes ratio. The average scores of p-distances for different scales of the evolutionary history of the Co-1 gene revealed a pattern of increased nucleotide diversity at 4 different levels: (1) intraspecies, (2) intragenus, (3) intrafamily and (4) intraorder. The scores of the average p-distances of the 4 categories of comparison were: (1) 0.11 ± 0.04%, (2) 1.87 ± 0.68%, (3) 12.67 ± 0.28%, and (4) 16.52 ± 0.10%, respectively (mean ± SE). These data support the concept that speciation in the order Perciformes in most cases follows a geographic mode through accumulation of numerous small genetic changes over a long time. The phylogenetic trees for 18 and 21 sequences of perch-like fishes together with 2 other fishes belonging to the ray-finned fishes (Actinopterygii) were developed using the Co-1 gene and 4 different analytical approaches: neighbour-joining (NJ), maximum likelihood (ML), Bayesian (BA) and maximum parsimony (MP). The analysis revealed a monophyletic origin for the representatives of the Stichaeidae, which was the principal percoid family investigated (86, 96 and 100% support in our NJ, ML and BA analyses, respectively). Species identification on a per individual basis or Co-1-based DNA barcoding was high.
The analysis of variation among 203 nucleotide sequences of Co-1 gene (DNA-barcode) for 45 species, 31 genera and 7 families of the order Perciformes from the Far Eastern seas of Russia has been performed. As a result, 42 species (93.3%) can be unambiguously identified using molecular DNA-barcode at Co-1, whereas more variable markers are required for other species (6.7%): Stichaeus grigorjewi, S. nozawae, and Lumpenus sagitta. The latter includes as well 2 morphologically distinct (by number of vertebrae) but genetically unresolved species, L. sagitta (Sea of Okhotsk) and L. fabricii (Bering Sea). In addition, within this genus morphologically poorly characterized but genetically well-distinguished cryptic species has been detected. Amphi-Pacific distribution is in question relative to L. sagitta. Cryptic diversity was observed in the genus Ammodytes.
A total of 95 nucleotide sequences of a Co 1 gene fragment of approximately 650 bp were analyzed for fishes of the orders Perciformes and Scorpaeniformes (outgroup). Gene trees based on four algorithms (BA, NJ, MP, and ML) were similar in topology of solved branches. An emphasis was placed on the species and generic levels, but a significant phylogenetic signal was obtained for higher taxonomic ranks as well. For instance, a monophyletic origin was confirmed for the family Zoarcidae and the subfamily Opisthocentrinae (Stichaeidae). The proportion of different nucleotides in the sequences compared (p distances) significantly increased with increasing taxonomic rank. The p distances were estimated for four hierarchic levels and were (1) 0.15 ± 0.06% for the within species hierarchic level, (2) 6.33 ± 0.37% for the within genus level, (3) 11.83 ± 0.06% for the within family level, and (4) 15.22 ± 0.05% for the within order level. The difference in the Co 1 gene fragments between levels (1) and (2) allows almost errorless species identification on the basis of this kind of a molecular bar code.
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