Molecular phylogenetics of pricklebacks and other percoid fishes from the Sea of Japan

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.