Molecular systematics and DNA barcoding of Altai osmans, oreoleuciscus (pisces, cyprinidae, and leuciscinae), and their nearest relatives, inferred from sequences of cytochrome b (Cyt-b), cytochrome oxidase c (Co-1), and complete mitochondrial genome

Abstract

Mitochondrial DNA (mtDNA) at the protein-coding Cyt-b gene along with data retrieved from GenBank for Co-1 gene fragments and complete mitochondrial genome (mitogenome) of Altai osmans and the nearest relatives of Leuciscinae fish species were compared for the estimation of variability and phylogenetic tree building. Phylogenetic trees were built by four techniques: Bayesian (BA), maximum likelihood (ML), maximum parsimony (MP), and neighbor-joining (NJ). Resolution of Cyt-b trees for species of two genera (Oreoleuciscus and Phoxinus) was quite distinct at all the approaches. For Tribolodon, the single gene trees were not well resolved; however, the mitogenome tree was resolved. Species identification on per individual basis (DNA barcoding) was high for both Cyt-b and Co-1 genes. The trees built using the data for 13 protein mitochondrial genes revealed a complicated phylogenetic pattern within the subfamily Leuciscinae. Scores of the average p-distances at three taxonomic levels were considerably different: (1) 1.16 ± 0.96, (2) 8.21 ± 1.01, and (3) 16.41 ± 0.85 for Cyt-b and (1) 1.04 ± 0.78, (2) 8.30 ± 0.92, and (3) 10.74 ± 0.79 for 13 protein genes of mitogenome, where (1) is intraspecies, (2) is intragenus, and (3) is intrasubfamily levels. Data on mitogenome distances were summarized for the taxonomic hierarchy for the first time. A concordant increase in distance score with growth of the rank of taxa (having the minimum score at the intraspecies level), both for a single gene and the whole mitogenome, substantiates the concept that speciation in the subfamily Leuciscinae in most cases follows the geographic mode. The distinct clustering of Altai osmans, Oreoleuciscus potanini and O. humilis, in the Cyt-b and Co-1 gene trees with small overall genetic distances, obtained for both genes, allows us to consider these taxa as separate but genetically sister species.

Keywords:

• Co-1
• Cyt-b
• DNA barcoding
• fish evolution
• molecular phylogeny
• mtDNA
• nucleotide composition
• p-distance
• sequence divergence
• taxonomy

Acknowledgements

The authors sincerely thank the director, the scientific secretary, and the staff of the Altai State Reserve for their support of the expedition. The authors are grateful to Dr. A. V. Naseka for the fish specimens from Tuva, provided earlier for the research. The authors are very thankful as well to Drs. S. N. Sharina and S. V. Turanov for their help in this research and for fruitful discussion. The authors acknowledge English revision of the manuscript and useful comments made by Mr. E. P. Shvetsov.

Disclosure statement

Two authors, Yu. Ph. Kartavtsev and A. O. Katugina, appreciate the financial support received from the Russian Science Fund, Agreement #14-50-00034 (biodiversity and genetic identification of commercial species). All authors also acknowledge the support from the Russian Foundation for Basic Research, Grant #15-29-02456 (DNA barcoding and molecular phylogenetics of Far Eastern aquatic organisms). Funding was partly provided as well by the Federal program for basic research of the Far East Branch of Russian Academy of Sciences, Grant #15-I-6-014 o as it connected to speciation. No other financial, consulting, or personal relationships have influenced this work, and no writing assistance was obtained.