Volkov
@vniro.ru
Molecular genetics
VNIRO
Scopus Publications
Scopus Publications
A. A. Volkov, S. M. Rastorguev, E. D. Vasil’eva, and V. P. Vasil’ev
Pleiades Publishing Ltd
Abstract We have analyzed the polymorphism of ISSR fragments of DNA by polymerase chain reaction in spined loaches for the first time. The analysis has made it possible to successfully differentiate the genomes, which were presumably involved in the formation of polyploid forms of hybrid origin: Cobitis taenia; spined loaches from the Danube River basin, which are diagnosed as C. elongatoides; C. tanaitica from the Don River basin and spined loaches from Lake Sinoe, which are also assigned to the species C. tanaitica by a number of authors. The following conclusions have been made based on comparative morphological studies of previously undifferentiated forms: (1) spined loaches from Central Europe with karyotype 2n = 50, NF = 96 correspond to the diagnosis of the species C. elongatoides; this species also differs from a number of closely related species and polyploid forms in the origin of the dorsal fin in front of the base of the pelvic fins, as well as in the presence of a spot in the lower half of the caudal fin base; (2) spined loaches from Lake Sinoe and other populations of Central Europe with karyotype 2n = 50, NF = 86 are nonconspecific to C. tanaitica and should apparently be ranked as an independent species, C. megaspila.
O. N. Melkova, E. V. Kulyabina, S. Yu. Fomina, and A. A. Volkov
Springer Science and Business Media LLC
E. V. Ponomareva, A. A. Volkov, M. V. Ponomareva, and E. A. Shubina
Pleiades Publishing Ltd
G. M. Shalgimbaeva, N. S. Mugue, K. B. Isbekov, A. A. Volkov, and E. V. Mikodina
Pleiades Publishing Ltd
Alexander G. Osinov, Alexander A. Volkov, and Dimitri A. Pavlov
Springer Science and Business Media LLC
John Gilbey, Valeriia A. Soshnina, Alexander A. Volkov, and Daria A. Zelenina
Wiley
Trans-oceanic movement, stocking, and subsequent establishment of Pacific pink salmon (Oncorhynchus gorbuscha) into the Atlantic White Sea area has resulted in their spreading further across the northern Atlantic, with spawning being reported in a number of regions within this area. Such expansions of non-native species bring potential risks to the ecosystems in question. It has not yet been established if the spawning events of pink salmon observed are the result of self-sustaining populations in these areas, or are due to repeated invasions of strayers from the White Sea stocks. In 2017 pink salmon were observed in a number of Scottish rivers in historically large numbers. This study set out to examine genetic variation in these fish and compare this to fish in Pacific founder regions and the White Sea translocated populations. A total of 286 samples from Scotland, the Atlantic White Sea, the Pacific Okhotsk region, and Northern Pacific Bering Sea were screened using a 1018 bp sequenced region of the Cytochrome b mtDNA gene and 205 of these samples for 13 microsatellites. Significant bottleneck and founder effects were observed in the White Sea stocks in both mitochondrial and nuclear DNA, including loss of diversity and changes in haplotype and allele proportions. Scottish fish were indistinguishable from White Sea populations and as such it was not possible to determine if the fish were strayers from this region or returning fish from previous spawning events in Scotland. Therefore, while the fish caught in Scotland have their origins in the White Sea population, it may not be easy to determine whether self-sustaining populations have, or are becoming, established in the UK using genetic analysis and other techniques may need to be employed. This article is protected by copyright. All rights reserved.
D. V. Bocharova, Ya. I. Alekseev, A. A. Volkov, G. S. Lavrov, A. G. Plugov, I. A. Volkov, A. A. Chemigov, B. V. Bardin, and V. E. Kurochkin
Pleiades Publishing Ltd
DNA sequencing is an essential task of modern molecular genetic research. Its fundamental parameter is the accuracy of decoding. In this work, we determined the maximum lengths of DNA fragments, obtained by the Sanger method and sequenced with an accuracy of 99%, in a polymer based on linear poly(N,N-dimethylacrylamide) PDMA-6 for capillaries 50 cm long to the optical window of the detector of a Nanophore 05 domestic genetic analyzer and an imported GA 3500xL genetic analyzer. The results of DNA sequencing obtained by various analysis algorithms were compared. The parameters of the analysis algorithms were selected, ensuring best results of DNA sequencing in using the PDMA-6 polymer.
Artem V. Nedoluzhko, Maria V. Gladysheva-Azgari, Gulmira M. Shalgimbayeva, Alexander A. Volkov, Natalia V. Slobodova, Svetlana V. Tsygankova, Eugenia S. Boulygina, Van Q. Nguyen, The T. Pham, Duc T. Nguyen,et al.
Elsevier BV
Abstract At least three subspecies of the common carp, namely, Cyprinus carpio carpio, C. carpio haematopterus, and C. carpio viridiviolaceus, have been described to date. These subspecies natively inhabit Ponto-Caspian and Far Eastern regions, as well as northern Vietnam, but they have also been introduced into aquaculture in almost every region of the world where the environmental conditions are suitable. Moreover, common carp is one of the most widely cultured freshwater fish species in the world. In northern Vietnam, common carp fisheries and aquacultural production are of great economic importance. Investigation of the subspecies distribution among aquacultured and wild common carps is important for understanding the impact of human economic activity, such as aquaculture production, on the environment. In the present study, double-digest restriction site-associated DNA sequencing (ddRAD-seq) was used to estimate the genetic impact of aquaculture carps on the wild common carp populations of northern Vietnam. Our work reveals that a part of wild carp populations has a significant contribution to farmed fish ancestry. For some populations, this contribution exceeds 25% of the population ancestry, but the ancestry value is distributed across most specimens of the populations, whereas pure aquaculture specimens are quite uncommon for wild habitats.
Alexei M. Orlov, Maxim O. Rybakov, Elena V. Vedishcheva, Alexander A. Volkov, and Svetlana Yu. Orlova
MDPI AG
The first records of walleye pollock Gadus chalcogrammus Pallas, 1814 in the seas of the Siberian Arctic (the Laptev Sea, the Kara Sea, the southeastern Barents Sea), are documented. Information about the external morphology (morphometric and meristic characters), photos of sagittal otoliths and fish, and data on the sequences of the CO1 mtDNA gene are presented. The results of a comparative analysis indicate that walleye pollock caught in the Siberian Arctic do not differ in principle from North Pacific and North Atlantic individuals. Previous conclusions about the conspecificity of the walleye and Norwegian pollock Theragra finnmarchica are confirmed. New captures of walleye pollock in the Siberian Arctic allow us to formulate a hypothesis about its continuous species’ range from the coasts of Norway in the North Atlantic to the coasts of Korea, Japan, and California in the North Pacific. The few records of walleye pollock in the North Atlantic originate from the North Pacific due to the transport of early pelagic juveniles to the Arctic by currents through the Bering Strait and further active westward migrations of individuals which have switched to the bentho-pelagic mode of life.
Gulmira Shalgimbayeva, Alexander Volkov, Natalia Slobodova, Fedor Sharko, Svetlana Tsygankova, Eugenia Boulygina, Van Q. Nguyen, The T. Pham, Duc T. Nguyen, Saule Zh. Assylbekova,et al.
MDPI AG
Common carp (Cyprinus carpio) is a widespread freshwater fish species of the Cyprinidae family, one of the largest and most diverse fish families. The natural habitats of C. carpio extend from Western Europe to South-East Asia. Common carp has remained an economically important fish species in aquaculture for many centuries and its production nowadays exceeds 4 million tons worldwide and continues to grow. The taxonomy of C. carpio is complicated, since this species is usually distinguished in two, three, and even four distinct subspecies. In the present study, we used ddRAD-sequencing to genotype 30 specimens from five wild common carp populations from the Ponto-Caspian, Balkhash-Ile, and Aral Sea geographical regions. It is demonstrated that they differ at the population level according to F-statistics analysis. At the same time, the subspecies status of C. carpio aralensis has not yet been confirmed. We found several loci that can be used as a discriminant for Aral and Ponto-Caspian wild common carp populations. It is suggested that Aral carp (C. carpio aralensis), which inhabits Balkhash-Ile and Aral Sea basins, is related to Ponto-Caspian or European carp (C. carpio carpio). Moreover, Aral carp might be the ancestor for European carp subspecies. Our results can be used to develop population-specific, high-density SNP marker panels, allowing the trade control of common carp production in the Eurasian Economic Union.
Ekaterina V. Mikodina, Gulmira M. Shalgimbaeva, and Alexander A. Volkov
EDP Sciences
Geoecology of the Ural River: landscape, climate, flora, and ichthyofaunal are given. Features of air and water temperature, winds, water sources, and balance are detailed. Information about Sturgeon fishes of the Acipenseridae family, the number of which is critical, is presented. The interaction of natural conditions and anthropogenic factors in the creature of spawning biotopes is described.
A. A. Volkov, I. A. Volkov, A. G. Plugov, E. V. Kulyabina, O. N. Melkova, G. S. Lavrov, D. V. Bocharova, and Ya. I. Alekseev
Springer Science and Business Media LLC
Metrological support for DNA sequencing has been developed. Sequencing of a standard sample of a human mitochondrial DNA sequence was performed by the Sanger method on domestic capillary electrophoresis genetic analyzers Nanofor 05. The results of the work performed were used to approve the type of standard sample of human mitochondrial DNA sequence and the DNA sequence measuring instrument.
Alexander G. Osinov, Alexander A. Volkov, and Nikolai S. Mugue
Springer Science and Business Media LLC
Evolutionary history, systematics and taxonomy of charrs of the genus Salvelinus and especially of the representatives of the S. alpinus–S. malma species complex remain confused that is connected with a substantial ecological and morphological flexibility of this group and with supposed ancient hybridization between some taxa. For the analysis of phylogenetic relationships and introgressive hybridization between the species of the genus Salvelinus including three endemic species from Lake El’gygytgyn and all main representatives of the S. alpinus–S. malma species complex, nucleotide sequences of the mtDNA control region and two nuclear genes (ITS1 and RAG1) were analyzed. The differences in the topologies of individual gene trees, among other reasons, were connected with incomplete lineage sorting and historical introgressive hybridization between certain taxa. Several cases of mtDNA capture by different taxa and phylogenetic groups were proposed. Main phylogenetic groups of the S. alpinus–S. malma species complex were revised. The origin and phylogenetic relationships of southern Dolly Varden from North America were not unambiguously defined. We proposed that introgressive hybridization had an important role in the evolutionary history of charrs, in particular, in the appearance of a high level of morphological, ecological and taxonomical diversity.
A. G. Osinov and A. A. Volkov
Pleiades Publishing Ltd
To test the reliability of Restriction Fragment Length Polymorphism data for ATPase6–NADH4L region of mitochondrial DNA (2162 bp), which unambiguously support the allopatric origin of the small-mouth charr Salvelinus elgyticus and “Boganida” charr S. “boganidae” in Lake Elgygytgyn, this region was sequenced in some members of the S. alpinus–S. malma complex. It is shown that RFLP data on the number of restriction sites and the size of restriction fragments for the 2162 bp region are poorly consistent with data on nucleotide sequences for the majority of forms and species of charr. Based on the identified errors, data on the MvaI restriction sites for ATPase6–NADH4L region of mitochondrial DNA cannot be considered as unambiguous evidence in favor of the allopatric origin of the two charr species in Lake Elgygytgyn. Nevertheless, the nucleotide data for this fragment suggest with a high probability that the small-mouth and “Boganida” charrs of Lake Elgygytgyn have an allopatric origin.
Artem V. Nedoluzhko, Natalia V. Slobodova, Fedor Sharko, Gulmira M. Shalgimbayeva, Svetlana V. Tsygankova, Eugenia S. Boulygina, Zsigmond Jeney, Van Q. Nguyen, Thế T. Pham, Đức T. Nguyen,et al.
Wiley
Abstract Common carp (Cyprinus carpio) has an outstanding economic importance in freshwater aquaculture due to its high adaptive capacity to both food and environment. In fact, it is the third most farmed fish species worldwide according to the Food and Agriculture Organization. More than four million tons of common carp are produced annually in aquaculture, and more than a hundred thousand tons are caught from the wild. Historically, the common carp was also the first fish species to be domesticated in ancient China, and now, there is a huge variety of domestic carp strains worldwide. In the present study, we used double digestion restriction site‐associated DNA sequencing to genotype several European common carp strains and showed that they are divided into two distinct groups. One of them includes central European common carp strains as well as Ponto–Caspian wild common carp populations, whereas the other group contains several common carp strains that originated in the Soviet Union, mostly as cold‐resistant strains. We believe that breeding with wild Amur carp and subsequent selection of the hybrids for resistance to adverse environmental conditions was the attribute of the second group. We assessed the contribution of wild Amur carp inheritance to the common carp strains and discovered discriminating genes, which differed in allele frequencies between groups. Taken together, our results improve our current understanding of the genetic variability of common carp, namely the structure of natural and artificial carp populations, and the contribution of wild carp traits to domestic strains.
M. A. Gruzdeva, A. V. Semenova, K. V. Kuzishchin, E. V. Ponomareva, A. A. Volkov, and D. S. Pavlov
Pleiades Publishing Ltd
The genetic variability of Dolly Varden, white-spotted char, and their interspecific hybrids for nine nuclear DNA microsatellite loci and the mtDNA CO1 gene was investigated. Significant genetic divergence between the two species of char for all microsatellite loci was shown (FST = 0.529; p < 0.001). Dolly Varden was characterized by significantly greater genetic variability compared to white-spotted char in terms of the average expected heterozygosity (HE) and allelic richness (AR). Hybrids had intermediate HE and AR values compared to their parents. Three haplotypes in the CO1 gene were revealed. All phenotypic white-spotted char individuals and the hybrids had one haplotype that was specific to S. leucomaenis. Specimens that were phenotypically identified as Dolly Varden had two haplotypes related to S. malma. Thus, the hybrids were produced by males of Dolly Varden and females of white-spotted char. The individuals with hybrid genotypes, except for one, were the first generation hybrids (F1). One char may be a descendant of a hybrid crossbreeding with one of the parental species or a second-generation hybrid F2, indicating that hybridization between the species studied is introgressive.
Einar E. Nielsen, , Alessia Cariani, Eoin Mac Aoidh, Gregory E. Maes, Ilaria Milano, Rob Ogden, Martin Taylor, Jakob Hemmer-Hansen, Massimiliano Babbucci,et al.
Springer Science and Business Media LLC
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
S. Yu. Orlova, A. A. Volkov, D. M. Shcepetov, O. A. Maznikova, N. V. Chernova, E. A. Chikurova, I. I. Glebov, and A. M. Orlov
Pleiades Publishing Ltd
Samples of Greenland halibut Reinhardtius hippoglossoides (Jordan and Snyder, 1901) from the Atlantic, Arctic, and Pacific Oceans were compared using eight microsatellite loci and the Cyt b mtDNA gene. The data obtained revealed a population connectivity of the Greenland halibut from the Laptev Sea to those from the Atlantic Ocean that is result of considerable eastward range extension due to recent climate change. Genetic differences between the Greenland halibut groupings of the Atlantic and Pacific Oceans, according to Fst values (0.141–0.197), reach a high level. Given the genetic differences revealed by both nuclear and mitochondrial markers, the taxonomic status of the Greenland halibut inhabiting the Pacific Ocean requires reevaluation at least to the rank of subspecies. It is suggested that the Greenland halibut populations of the Atlantic Ocean basin originated from those of the North Pacific. The time and conditions of Greenland halibut penetration from the North Pacific to the Atlantic Ocean are discussed.
M. A. Gruzdeva, K. V. Kuzishchin, A. V. Semenova, E. V. Ponomareva, A. A. Volkov, and D. S. Pavlov
Pleiades Publishing Ltd
Hybrids between the whitespotted char Salvelinus leucomaenis and the northern Dolly Varden S. malma malma have been found to regularly occur and exist in the Utkholok River in western Kamchatka and constitute a significant part of the local char stock. Initially, hybrids were recorded in 1970–1971; however, a detailed description is provided for the first time. The diagnosis, description, morphometry, and skull morphology, as well as an analysis of the mtDNA CO1 gene and nuclear TNFα gene sequences and variation in six microsatellite loci, are considered. It has been established that in some of the craniological and meristic morphological traits and genetic markers the hybrids hold an intermediate position between the whitespotted char and northern Dolly Varden, whereas in other traits they are closer to whitespotted char or northern Dolly Varden. According to data of the genetic marker analysis, the hybrids are produced by female whitespotted char and male northern Dolly Varden. It has been shown that in the Utkholok River hybridization occurs constantly due to the disruption of the prezygotic isolation mechanism. A hypothesis is made that the process of permanent hybridization and the large number of hybrids are caused by the close proximity of the spawning grounds of the whitespotted char and northern Dolly Varden in the river tributaries. During the spawning of the whitespotted char, anadromous males, as well as mature male parr of both the whitespotted char and northern Dolly Varden, form a “gamete cloud” resulting in fertilization of whitespotted char eggs.
S. Yu. Orlova, A. A. Volkov, I. I. Gordeev, A. A. Baitaliuk, and A. M. Orlov
Pleiades Publishing Ltd
The frequency of occurrence of the COI gene of mitochondrial DNA in the Pacific flatnose Antimora microlepis and blue antimora Antimora rostrata (Moridae, Gadiformes) was analyzed in samples collected in different areas of the World Ocean. The revealed maximum haplotype diversity of COI in the blue antimora in the North Atlantics may indicate that this species emerged in this region, from which it widely distributed in the World Ocean. The Pacific flatnose Antimora microlepis originated from Antimora rostrata. Antimora might penetrate into the North Pacific by several routes: through the Panama Strait, along the coast of Antarctica, or through the Indian Ocean along the coast of Australia.
A. G. Osinov, D. A. Pavlov, and A. A. Volkov
Pleiades Publishing Ltd
Morphological and genetic characteristics are used for the analysis of the origin of charrs from the lakes of the Kolyma basin (Chuk, Gek, Gulyaevskoe-4, Gulyaevskoe-6, and Lenkovoe) and the Sea of Okhotsk basin (Lake Chistoe). In addition to these samples, the fragments of the control region of mitochondrial DNA (CR mtDNA, 550-bp) and exon 2 of recombination activating gene 1 (RAG1, 899-bp) are sequenced in the charrs from lakes Dzhul’etta and Cherechen’ (Kolyma basin) and lakes Elikchanskie, Bol’shoi Mak-Mak, Ueginskoe (Sea of Okhotsk basin), Ulakhan-Silyan-Kyuel’ (Yana River basin) as well as in northern Dolly Varden from the Kamchatka River. The charr from Lake Chistoe is represented by northern Dolly Varden. In the charrs from lakes Chuk, Gek, Gulyaevskoe-4, Gulyaevskoe-6, Lenkovoe, Cherechen’, Elikchanskie, Bol’shoi Mak-Mak, and Ueginskoe, the haplotypes of mtDNA of the Bering group (a haplogroup of northern Dolly Varden) are revealed. Based on the morphological and RAG1 data, populations of charrs from these lakes belong to the Salvelinus alpinus complex. A transfer of mtDNA of northern Dolly Varden to the charrs from the Kolyma and Sea of Okhotsk basins occurred during the last postglacial expansion and subsequent hybridization. Based on the results of morphological and genetic analysis, the charrs from the Kolyma and Sea of Okhotsk basins cannot be unambiguously referred to the phylogenetic groups of Eurasian Arctic charr or Taranets charr. The presence of mtDNA haplotypes of the Arctic group (a haplogroup of Taranets charr) in the populations of lakes Dzhul’etta, Maksi, and Ueginskoe shows a possibility of their belonging to the group of Taranets charr.
Ekaterina S. Bocharova, Alexey A. Sergeev, and Aleksandr A. Volkov
F1000 Research Ltd
From the DNA libraries enriched by the repeat motifs (AAAC)6, (AATC)6, (ACAG)6, (ACCT)6, (ACTC)6, ACTG)6, (AAAT)8, (AACT)8, (AAGT)8, (AGAT)8, for two viviparous sea anemones Aulactinia stella and Cribrinopsis albopunctata, 41 primer pairs were developed. These primer pairs resulted in the identification of 41 candidate microsatellite loci in either A. stella or C. albopunctata. Polymorphic loci were identified in both sea anemone species for 13 of the primer pairs and can be applicable for population genetics researches.
S. Yu. Orlova, A. A. Volkov, O. A. Maznikova, N. V. Chernova, I. I. Glebov, and A. M. Orlov
Pleiades Publishing Ltd
This is the first study to perform a comparative genetic analysis of Greenland halibut in the samples from the Atlantic (waters of west and east of Greenland), Arctic (Laptev Sea), and Pacific (the western part of the Bering Sea) ocean basins using seven microsatellite loci. The obtained data clearly demonstrate that the Greenland halibut population in the Laptev Sea belongs to the groups of the Atlantic Ocean basin. Apparently, the Greenland halibut of the Laptev Sea is represented by a dependent population, which is replenished due to the drift of immatures from the spawning grounds in the Barents Sea with the transformed Atlantic water flow along the continental slope. In addition, the Arctic population can be partially replenished due to the breeding of the halibut in local spawning grounds.