Complete mitochondrial DNA sequence analysis of Ponto-Caspian sturgeon species

We present an analysis of sequence variation across complete mitochondrial (mt) genomes of eleven sturgeon species. We have sequenced five mt-genomes from four Ponto-Caspian species: Acipenser gueldenstaedtii (Russian sturgeon), Acipenser persicus (Persian sturgeon), Acipenser naccarii (Adriatic sturgeon), and Acipenser baerii (Siberian sturgeon). Two specimens of A. gueldenstaedtii were included representing the gueldenstaedtii-like haplotype and the baerii-like haplotype. Phylogenetic information content of each gene, clusters of genes sharing similar functions (tRNAs, protein coding sequences) and of the entire mitochondrial DNA genome was evaluated using the Shimodaira and Hasegawa test. Based on their suitability to reconstruct sturgeon phylogeny, mitochondrial genes were ranked between 'very good' (ND5, cytb - large agreement between phylogenies based on these genes and the phylogeny calculated on the entire mt genome), 'good' (COI, ND4, ATP6), 'medium' (ATP8, COII, COIII, ND1, ND2, ND3, ND4L) and 'weak' (ND6 - tree topology is significantly deviated from the expected one). The maximum parsimony (MP) tree based on entire mt genomes showed that Scaphirinchus is a sister clade of the genera Acipencer and Huso. However, maximum likelihood (ML) algorithm with the most suitable nucleotide evolution model (GTR+I+G) places Scaphyrinchus within Acipenser as a sister branch to Ponto-Caspian species. Both algorithms (MP, ML) agreed in the following points: (i) Atlantic and Pacific species are separated in different clades, Huso huso is basal with the Atlantic species and (ii) all species of the gueldenstadetii-complex are closely related. Finally, eight substitutions between A. baerii and the baerii-like specimen of A. gueldenstaedtii were found overall protein coding sequences, and 131 substitutions were detected between the gueldenstaedtii-like and baerii-like haplotype over the entire mt genome. Taking the small sample size under consideration, these differences have to be handled with care and should be addressed in further studies.