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

Abstract 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.Peer reviewe

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

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

Comparison of anadromous and landlocked Atlantic salmon genomes reveals signatures of parallel and relaxed selection across the Northern Hemisphere

Most Atlantic salmon (Salmo salarL.) populations follow an anadromous life cycle, spending early life in freshwater, migrating to the sea for feeding, and returning to rivers to spawn. At the end of the last ice age similar to 10,000 years ago, several populations of Atlantic salmon became landlocked. Comparing their genomes to their anadromous counterparts can help identify genetic variation related to either freshwater residency or anadromy. The objective of this study was to identify consistently divergent loci between anadromous and landlocked Atlantic salmon strains throughout their geographical distribution, with the long-term aim of identifying traits relevant for salmon aquaculture, including fresh and seawater growth, omega-3 metabolism, smoltification, and disease resistance. We used a Pool-seq approach (n = 10-40 individuals per population) to sequence the genomes of twelve anadromous and six landlocked Atlantic salmon populations covering a large part of the Northern Hemisphere and conducted a genomewide association study to identify genomic regions having been under different selection pressure in landlocked and anadromous strains. A total of 28 genomic regions were identified and includedcadm1on Chr 13 andppargc1aon Chr 18. Seven of the regions additionally displayed consistently reduced heterozygosity in fish obtained from landlocked populations, including the genes gpr132, cdca4, and sertad2 on Chr 15. We also found 16 regions, includingigf1on Chr 17, which consistently display reduced heterozygosity in the anadromous populations compared to the freshwater populations, indicating relaxed selection on traits associated with anadromy in landlocked salmon. In conclusion, we have identified 37 regions which may harbor genetic variation relevant for improving fish welfare and quality in the salmon farming industry and for understanding life-history traits in fish.Peer reviewe

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+

Synergetic Synthesis of Nonlinear Laws of Throttle Control of a Pneumatic Drive

Currently, a significant trend in control in robotic systems is developing and improving linear and nonlinear control algorithms to improve the overall quality of production with high accuracy and adaptability. The present study considers a synergistic synthesis of throttle control of a pneumatic distributor valve and backpressure control for piston rod positioning. The article presents the synthesis of control laws for the position of a pneumatic cylinder piston using the method of analytical design of aggregated regulators (ADAR) of synergetic control theory (STC), which allows operation with nonlinear mathematical models, eliminating the loss of information about the object during linearization. A comparative calculation of the energy efficiency of backpressure control and throttle control methods was carried out, while the numerical value of the total airflow with throttle control is 0.0569 m3⁄s and, with backpressure control, it is 0.0337 m3⁄s. Using a P controller in a linear model gives a transient oscillatory process damped in 2–2.5 s. When using a PID controller, the process has an overshoot equal to 11.5%, while the synergistic controller allows you to smoothly move the drive stem to a given position without overshoot. The parametric uncertainty analysis of the considered mathematical model is carried out. The model’s main parameters are identified, which change the actual functioning of the system under study. The inconsistency of applying classical control laws based on typical controllers to parametrically indeterminate mathematical models is shown

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

Pink salmon in Norway: the reluctant invader

In 2017, Norway experienced an invasion of the Pacific salmonid pink salmon (Oncorhynchus gorbuscha) in numbers never before seen in rivers all along the coast. Significant numbers were also caught in other parts of northwestern Europe. Pink salmon has been observed in variable numbers in Norwegian waters in the summer and autumn of most years since 1960, after the first successful Russian introduction of pink salmon fry in rivers draining to the White Sea in northwest Russia in 1959. With the exception of 1960, pink salmon have been most abundant in odd years, based on the odd-year broodline of the 2-year life salmonid. Even-year fish has generally been less abundant, but in recent years, significant numbers of this broodline have also been caught. In this paper we review the available information on pink salmon in Norwegian rivers and discuss (1) to what extent the presence of this species in Norway has been driven by Russian introductions and natural reproduction in Russian, and lately in Norwegian, rivers, and (2) the likelihood of reproducing populations of pink salmon being established in more Norwegian rivers. Considering the continued propagule pressure in terms of adult pink salmon entering and spawning in Norwegian rivers, it is puzzling that self-propagating populations apparently only have been established in some rivers in the northernmost part of the country. The potential impact of pink salmon on native salmonids and river ecosystems is discussed briefly. Extensive research is required to understand the mechanisms that determine the fate of pink salmon as an alien species, and specifically the possible impact of pink salmon on native salmonids and the environment in the recipient rivers and in the ocean

Pink salmon in Norway: the reluctant invader

In 2017, Norway experienced an invasion of the Pacific salmonid pink salmon (Oncorhynchus gorbuscha) in numbers never before seen in rivers all along the coast. Significant numbers were also caught in other parts of northwestern Europe. Pink salmon has been observed in variable numbers in Norwegian waters in the summer and autumn of most years since 1960, after the first successful Russian introduction of pink salmon fry in rivers draining to the White Sea in northwest Russia in 1959. With the exception of 1960, pink salmon have been most abundant in odd years, based on the odd-year broodline of the 2-year life salmonid. Even-year fish has generally been less abundant, but in recent years, significant numbers of this broodline have also been caught. In this paper we review the available information on pink salmon in Norwegian rivers and discuss (1) to what extent the presence of this species in Norway has been driven by Russian introductions and natural reproduction in Russian, and lately in Norwegian, rivers, and (2) the likelihood of reproducing populations of pink salmon being established in more Norwegian rivers. Considering the continued propagule pressure in terms of adult pink salmon entering and spawning in Norwegian rivers, it is puzzling that self-propagating populations apparently only have been established in some rivers in the northernmost part of the country. The potential impact of pink salmon on native salmonids and river ecosystems is discussed briefly. Extensive research is required to understand the mechanisms that determine the fate of pink salmon as an alien species, and specifically the possible impact of pink salmon on native salmonids and the environment in the recipient rivers and in the ocean