Alexey Veselov

Footprints of directional selection in wild Atlantic salmon populations: evidence for parasite-driven evolution?

Mechanisms of host-parasite co-adaptation have long been of interest in evolutionary biology; however, determining the genetic basis of parasite resistance has been challenging. Current advances in genome technologies provide new opportunities for obtaining a genome-scale view of the action of parasite-driven natural selection in wild populations and thus facilitate the search for specific genomic regions underlying inter-population differences in pathogen response. European populations of Atlantic salmon (Salmo salar L.) exhibit natural variance in susceptibility levels to the ectoparasite Gyrodactylus salaris Malmberg 1957, ranging from resistance to extreme susceptibility, and are therefore a good model for studying the evolution of virulence and resistance. However, distinguishing the molecular signatures of genetic drift and environment-associated selection in small populations such as land-locked Atlantic salmon populations presents a challenge, specifically in the search for pathogen-driven selection. We used a novel genome-scan analysis approach that enabled us to i) identify signals of selection in salmon populations affected by varying levels of genetic drift and ii) separate potentially selected loci into the categories of pathogen (G. salaris)-driven selection and selection acting upon other environmental characteristics. A total of 4631 single nucleotide polymorphisms (SNPs) were screened in Atlantic salmon from 12 different northern European populations. We identified three genomic regions potentially affected by parasite-driven selection, as well as three regions presumably affected by salinity-driven directional selection. Functional annotation of candidate SNPs is consistent with the role of the detected genomic regions in immune defence and, implicitly, in osmoregulation. These results provide new insights into the genetic basis of pathogen susceptibility in Atlantic salmon and will enable future searches for the specific genes involved.

Temporal variation of genetic composition in Atlantic salmon populations from the Western White Sea Basin: influence of anthropogenic factors?

BackgroundStudies of the temporal patterns of population genetic structure assist in evaluating the consequences of demographic and environmental changes on population stability and persistence. In this study, we evaluated the level of temporal genetic variation in 16 anadromous and 2 freshwater salmon populations from the Western White Sea Basin (Russia) using samples collected between 1995 and 2008. To assess whether the genetic stability was affected by human activity, we also evaluated the effect of fishing pressure on the temporal genetic variation in this region.ResultsWe found that the genetic structure of salmon populations in this region was relatively stable over a period of 1.5 to 2.5 generations. However, the level of temporal variation varied among geographical regions: anadromous salmon of the Kola Peninsula exhibited a higher stability compared to that of the anadromous and freshwater salmon from the Karelian White Sea coast. This discrepancy was most likely attributed to the higher census, and therefore effective, population sizes of the populations inhabiting the rivers of the Kola Peninsula compared to salmon of the Karelian White Sea coast. Importantly, changes in the genetic diversity observed in a few anadromous populations were best explained by the increased level of fishing pressure in these populations rather than environmental variation or the negative effects of hatchery escapees. The observed population genetic patterns of isolation by distance remained consistent among earlier and more recent samples, which support the stability of the genetic structure over the period studied.ConclusionsGiven the increasing level of fishing pressure in the Western White Sea Basin and the higher level of temporal variation in populations exhibiting small census and effective population sizes, further genetic monitoring in this region is recommended, particularly on populations from the Karelian rivers.

Activity of enzymes involved in the energy and carbohydrate metabolism and the level of some molecular-genetic characteristics in young salmons (Salmo salar L.) with different age and weight

In order to investigate the metabolic regulation in Atlantic salmon fries (Salmo salar L.) during their growth, development, and in the course of size divergence, age-related changes in the activity of enzymes involved in the energy and carbohydrate metabolism, including myosin heavy chain isoform expression, RNA/DNA ratio in the white muscles and liver of specimens at ages of 0+, 1+, and 2+, as well as correlations of these characteristics with the body weight of fish specimens were analyzed. Multidirectional changes in the activity of enzymes taking part in aerobic and anaerobic energy metabolism, as well as a decrease in the protein synthesis with age, were revealed. There was a positive correlation between the activities of cytochrome c oxidase, lactate dehydrogenase, aldolase, and myosin gene expression in the muscles, cytochrome c oxidase activity, glucose-6-phosphate dehydrogenase, and glycerol-3-phosphate dehydrogenase in the liver with the body weight of salmon within the age groups.

Features in the Lipid Status of Two Generations of Fingerlings (0+) of Atlantic Salmon (Salmo salar L.) Inhabiting the Arenga River (Kola Peninsula)

The present research focused on determining the lipid status of salmon fingerlings (0+) in early development after dispersal form groups of spawning nests in biotopes of different hydrological conditions. The revealed qualitative and quantitative differences in the levels of phospholipids and fatty acids among two generations of Atlantic salmon fingerlings (0+) living in different biotopes of the Arenga River (a tributary of the Varzuga River) may be associated with the peculiarities of their genetically determined processes of the biosynthesis and modification of individual lipid classes and trophoecological factors (food spectrum, quality and availability of food objects, and hydrological regime). The research was organized to observe the dynamics of these developmental changes from ages 0+ to 2+.

Age-Specific Lipid and Fatty Acid Profiles of Atlantic Salmon Juveniles in the Varzuga River

The age-specific lipid and fatty acid profiles of juvenile Atlantic salmon at different ages (0+, 1+, and 2+ years) after hatching from nests located in the mainstream of a large Arctic River, the Varzuga River, and resettling to the favorable Sobachji shoal in autumn before overwinter are herein presented. The contemporary methods of the lipid analysis were used: thin layer chromatography and gas chromatography. The results show that the stability of the regulation of important functions in developing organisms is maintained through structural alterations in lipids. These alterations can be considered as a sequence of the modifications and changes in the ratios of certain lipid classes and fatty acids constituents. In general, changes in the lipids and fatty acids (FAs) maintained the physiological limits and controls through the adaptive systems of the organism. The mechanisms of juvenile fish biochemical adaptation to the environmental conditions in the studied biotope include the modification of the energy metabolism and anabolism, and here belongs to the energy characteristics of metabolic processes.

Description of the European river lamprey Lampetra fluviatilis (L., 1758) from the Lososinka River (Onega Lake Basin).

124 Representatives of the species European river lamm prey Lampetra fluviatilis (Linnaeus, 1758) signifii cantly differ in their morphological characters and produce forms with different life strategies [1] whose relationships are unclear. Parasitic representatives of this species (L. fluviatilis sensu stricto) migrating from rivers to lakes and seas for feeding and returning back to the rivers for spawning are of special interest. They are recorded in the IUCN Red Data Book (protection status LC) as species that are still rare in some parts of their ranges but the state of whose populations has been considerably improved [2]. Recently, in Russia and Baltic states, the fishery for lamprey has been resumed. The lampreys feeding in lakes Ladoga and Onega have not been investigated yet. There is only a study [3] whose author identified the lamprey living in Lake Ladoga as L. fluviatiis forma ladogensis, providd ing no diagnostic characters differing the Ladoga form from the typical migratory lamprey (forma typica), except for the total body length. There is no information on the morphology of lamm prey living in Lake Onega, connected with Lake Ladoga by the Svir River. Berg [4], having compared morphological characters of large migratory lampreys (forma typica) and small lacustrine parasitic lamprey caught in lakes Ladoga and Onega, assumed the latter to be the rapidly maturing form, forma praecox. In spite of publication of this book by Berg [4] in 1948, it contains data of the 1930s, i.e., those collected before the construction of the first dam on the Svir River (1936), which has become an insurmountable barrier for the anadromous spawners. Here, we present the first detailed morphological description of the Onega lamprey. The data of this study may be then compared with other representaa tives of the genus Lampetra: typical anadromous, anadromous praecox, resident (at present considered to be an independent species, the European brook lamprey L. planeri). drainage area is 322.5 km 2 , the fall of stream is 153 m, and the average annual water discharge in the mouth is estimated at 3.66 m 3 /s [5]. At a distance of 380 m from the river mouth, there is a dam which is the limit for the lampreys swimming from the lake for spawning. This short estuarine stretch is a spawning ground for freshwater salmon, trout, and grayling. Collection and storage of the material, and investigaa tion methods. The material was collected when lamm …

Protein degradation systems in the skeletal muscles of parr and smolt Atlantic salmon Salmo salar L. and brown trout Salmo trutta L.

Although protein degradation limits the rate of muscle growth in fish, the role of proteolytic systems responsible for degrading myofibrillar proteins in skeletal muscle is not well defined. The study herein aims to evaluate the role of calpains (calcium-activated proteases) and proteasomes (ATP-dependent proteases) in mediating muscle protein turnover at different life stages in wild salmonids. Protease activities were estimated in Atlantic salmon (Salmo salar L.) and brown trout (Salmo trutta L.) parr and smolts from the Indera River (Kola Peninsula, Russia). Calpain and proteasome activities in Atlantic salmon skeletal muscles were lower in smolts as compared with parr. Reduced muscle protein degradation accompanying Atlantic salmon parr-smolt transformation appeared to provide intense muscle growth essential for a minimum threshold size achievement that is required for smoltification. Calpain and proteasome activities in brown trout parr and smolts at age 3+ did not significantly differ. However, calpain activity was higher in smolts brown trout 4+ as compared with parr, while proteasome activity was lower. Results suggest that brown trout smoltification does not correspond with intense muscle growth and is more facultative and plastic in comparison with Atlantic salmon smoltification. Obtained data on muscle protein degradation capacity as well as length-weight parameters of fish reflect differences between salmon and trout in growth and smoltification strategies.

Comparative characteristics of the lipid and fatty acid status of eyed-stage atlantic salmon embryos reared in natural and artificial environments

The lipid status of Atlantic salmon (Salmo salar L.) embryos has been compared between embryos developing in incubator nests installed in the natural environment (Umba River, Kola Peninsula) and those developing in a laboratory (in aquaria). The developmental stage of eye pigmentation selected for comparison is characterized by the highest sensitivity of the embryos to environmental factors. The content of certain classes of total lipids and fatty acids was different between the two groups of embryos, and the ratios between the relative content values for some of the compounds were different as well. The difference may be due to environmental factors (temperature, oxygen levels, running water in the nests, etc.) affecting the developing embryos, and they may determine the subsequent embryonic and postembryonic development of the fish.

Genomic signatures of parasite-driven natural selection in north European Atlantic salmon ( Salmo salar )

Understanding the genomic basis of host-parasite adaptation is important for predicting the long-term viability of species and developing successful management practices. However, in wild populations, identifying specific signatures of parasite-driven selection often presents a challenge, as it is difficult to unravel the molecular signatures of selection driven by different, but correlated, environmental factors. Furthermore, separating parasite-mediated selection from similar signatures due to genetic drift and population history can also be difficult. Populations of Atlantic salmon (Salmo salar L.) from northern Europe have pronounced differences in their reactions to the parasitic flatworm Gyrodactylus salaris Malmberg 1957 and are therefore a good model to search for specific genomic regions underlying inter-population differences in pathogen response. We used a dense Atlantic salmon SNP array, along with extensive sampling of 43 salmon populations representing the two G. salaris response extremes (extreme susceptibility vs resistant), to screen the salmon genome for signatures of directional selection while attempting to separate the parasite effect from other factors. After combining the results from two independent genome scan analyses, 57 candidate genes potentially under positive selection were identified, out of which 50 were functionally annotated. This candidate gene set was shown to be functionally enriched for lymph node development, focal adhesion genes and anti-viral response, which suggests that the regulation of both innate and acquired immunity might be an important mechanism for salmon response to G. salaris. Overall, our results offer insights into the apparently complex genetic basis of pathogen susceptibility in salmon and highlight methodological challenges for separating the effects of various environmental factors.

Variation in the COI gene of the freshwater pearl mussel Margaritifera margaritifera from River Vuokkijoki

The freshwater pearl mussel Margaritifera margaritifera L. is one of the most endangered freshwater mussels in the world. Effective conservation of threatened species requires not only ecological, but also genetic information from the target species and populations. Since low genetic diversity can reduce the ability of a species to adapt to environmental changes, maintaining genetic diversity has been identified as one of the key elements in successful conservation programs. We examined genetic variation of the freshwater pearl mussel from the River Vuokkijoki, Karelia, Russia. We sequenced a fragment of the cytochrome c oxidase subunit I gene (COI) from 22 individuals and compared the data to 32 previously published COI sequences available in GenBank. We identified 10 different COI haplotypes in the sequenced samples, three of which had not been previously reported. Our results show that the River Vuokkijoki has high genetic diversity and suggest that the colonization of this northern freshwater pearl mussel population might have occurred from multiple and even distant refugia. Therefore, the freshwater pearl mussel population of the River Vuokkijoki is valuable for the conservation of the whole species.