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High-throughput sequencing of the mitochondrial genomes from archived fish scales: an example of the endangered putative species flock of Sevan trout Salmo ischchan

Abstract

Sevan trout, Salmo ischchan, dwelling in the mountain Lake Sevan (Caucasus) is a unique species complex. Four sympatric forms of Sevan trout were divergent in both their phenotypes and ecologies. Three forms were lacustrine spawners but were unique in their spawning times and the type of substrate. The fish community of Lake Sevan was strongly impacted by human activity in twentieth century. Two forms of Sevan trout went extinct in the 1980s and the other two forms are at the brink of extinction. The present study demonstrated that archived/historical scales of extinct forms stored at room temperature for up to 44 years are a suitable source of DNA for high-throughput sequencing and for the reconstruction of mitochondrial genomes. In addition, we obtained the mitochondrial genomes of the extant forms for comparison to the extinct forms and reconstruction of a mitogenomic phylogeny of all forms of Sevan trout. The mitogenome gene arrangement was identical in all individuals studied with structure similar to other Salmo spp. The nucleotide sequence divergence between sympatric forms was shallow (P-distance = 0.0003–0.0012). A phylogenetic tree based on mitogenomes confirmed sister position of Sevan trout to the Caspian trout, Salmo trutta caspius (P-distance = 0.0049).

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Acknowledgements

The authors are grateful to Mikhail V. Kovalchuk (National Research Centre “Kurchatov Institute,” Moscow, Russia) for his ongoing support, and Professor Yuri Gerassimov for logistics. We would like to thank Professor Nikolay Kolchanov, Dr. Alexander Pilipenko, and Dr. Rostislav Trapezov for permission to use the Interinstitutional Center of Molecular Paleogenetics infrastructure for DNA manipulations and helpful support. We are thankful to Dr. Alexander Golubtsov and three anonymous reviewers for their valuable comments on manuscript. We also appreciate the thoughtful discussions with Professor Axel Meyer and Professor Michael Mina on the concept of a species flock. This study was funded by the Russian Science Foundation, Grant No. 15-14-10020 (sampling and partially bioinformatics) and the National Research Centre “Kurchatov Institute” (DNA extraction, preparation of libraries, NGS-sequencing, and partially bioinformatics).

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Levin, B., Simonov, E., Rastorguev, S. et al. High-throughput sequencing of the mitochondrial genomes from archived fish scales: an example of the endangered putative species flock of Sevan trout Salmo ischchan. Hydrobiologia 822, 217–228 (2018). https://doi.org/10.1007/s10750-018-3688-7

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Keywords

  • Historical DNA samples
  • Salmonidae
  • Species complex
  • Genomics
  • Mitogenome
  • Phylogeny