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The enigmatic and poorly studied sturgeon genus  Pseudoscaphirhynchus  (Scaphirhynchinae: Acipenseridae) comprises three species: the Amu Darya shovelnose sturgeon ( Pseudoscaphirhynchus kaufmanni  (Bogdanow)), dwarf Amu Darya shovelnose sturgeon  P .  hermanni  (Kessler), and Syr Darya shovelnose sturgeon ( P .  fedtschenkoi  (Bogdanow). Two species –  P .  hermanni  and  P .  kaufmanni  – are critically endangered due to the Aral Sea area ecological disaster, caused by massive water use for irrigation to support cotton agriculture, subsequent pesticide pollution and habitat degradation. For another species –  P .  fedtschenkoi  – no sightings have been reported since 1960-s and it is believed to be extinct, both in nature and in captivity. In this study, complete mitochondrial (mt) genomes of these three species of  Pseudoscaphirhynchus  were characterized using Illumina and Sanger sequencing platforms. Phylogenetic analyses showed the significant divergence between Amu Darya and Syr Darya freshwater sturgeons and supported the monophyletic origin of the  Pseudoscaphirhynchus  species. We confirmed that two sympatric Amu Darya species  P .  kaufmanni  and  P .  hermanni  form a single genetic cluster, which may require further morphological and genetic study to assess possible hybridization, intraspecific variation and taxonomic status and to develop conservation measures to protect these unique fishes.

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Molecular phylogeny of one extinct and two critically endangered Central Asian sturgeon species (genus Pseudoscaphirhynchus) based on their mitochondrial genomes