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Most population genomic tools rely on accurate single nucleotide polymorphism (SNP) calling and filtering to meet their underlying assumptions. However, genomic complexity, resulting from structural variants, paralogous sequences, and repetitive elements, presents significant challenges in assembling contiguous reference genomes. Consequently, short-read resequencing studies can encounter mismapping issues, leading to SNPs that deviate from Mendelian expected patterns of heterozygosity and allelic ratio. In this study, we employed the ngsParalog software to identify such deviant SNPs in whole-genome sequencing (WGS) data with low (1.5×) to intermediate (4.8×) coverage for four species: Arctic Char (Salvelinus alpinus), Lake Whitefish (Coregonus clupeaformis), Atlantic Salmon (Salmo salar), and the American Eel (Anguilla rostrata). The analyses revealed that deviant SNPs accounted for 22% to 62% of all SNPs in salmonid datasets and approximately 11% in the American Eel dataset. These deviant SNPs were particularly concentrated within repetitive elements and genomic regions that had recently undergone rediploidization in salmonids. Additionally, narrow peaks of elevated coverage were ubiquitous along all four reference genomes, encompassed most deviant SNPs, and could be partially associated with transposons and tandem repeats. Including these deviant SNPs in genomic analyses led to highly distorted site frequency spectra, underestimated pairwise FST values, and overestimated nucleotide diversity. Considering the widespread occurrence of deviant SNPs arising from a variety of sources, their important impact in estimating population parameters, and the availability of effective tools to identify them, we propose that excluding deviant SNPs from WGS datasets is required to improve genomic inferences for a wide range of taxa and sequencing depths. [ABSTRACT FROM AUTHOR]

The "genomics era" has allowed questions to be asked about genome organization and genome architecture of non-model species at a rate not previously seen. Analyses of these genome-wide datasets have documented many examples of novel structural variants (SVs) such as chromosomal inversions, copy number variants, and chromosomal translocations, many of which have been linked to adaptation. The salmonids are a taxonomic group with abundant genome-wide datasets due to their importance in aquaculture and fisheries. However, the number of documented SVs in salmonids is surprisingly low and is most likely due to removing loci in high linkage disequilibrium when analyzing structure and gene flow. Here we re-analyze RAD-seq data from several populations of Arctic charr (Salvelinus alpinus) and document a novel ~1.2 MB SV at the distal end of LG12. This variant contains 15 protein-coding genes connected to a wide-range of functions including cell adhesion and signal transduction. Interestingly, we studied the frequency of this polymorphism in four disjointed populations of charr--one each from Nunavut, Newfoundland, Eastern Russia, and Scotland--and found evidence of the variant only in Nunavut, Canada, suggesting the polymorphism is novel and recently evolved. [ABSTRACT FROM AUTHOR]

Salmon farming has multiplied from a side business of coastal farmers to one of the world's major aquaculture species. This has dramatically altered the disease dynamics between farmed and wild salmonids. As salmon fish farming has increased, new restrictions have been enforced to combat emerging density-dependent impacts of pathogen spillover. In most northern and arctic regions, the effects of pathogens from fish farms on wild salmonids have been minimal for two key reasons: (i) relative low density of fish farms in the north and (ii) cold water temperatures. However, both factors are set to change dramatically. On one side, there is an increasing interest in utilizing northern areas for fish farming due to limited capacity for expansion in mid-latitude regions. On the other side, climate change is rapidly changing these northern ecosystems. High-latitude regions inhabit some of the largest remaining wild Atlantic salmon populations in the world along with sea trout and Arctic charr. Wild salmonids in the north have most likely seldom been exposed to high infection pressure, and we question how these populations will cope with changes that are coming. We identify 12 research questions emerging from these imminent changes and discuss methodologies for addressing them. We conclude that policies related to fish farming must consider uncertainties with respect to pathogen dynamics in the north until these research questions are fully addressed. [ABSTRACT FROM AUTHOR]

Arctic charr (Salvelinus alpinus) is a species of high economic value for the aquaculture industry, and of high ecological value due to its Holarctic distribution in both marine and freshwater environments. Novel genome sequencing approaches enable the study of population and quantitative genetic parameters even on species with limited or no prior genomic resources. Low coverage genotyping by sequencing (GBS) was applied in a selected strain of Arctic charr in Sweden originating from a landlocked freshwater population. For the needs of the current study, animals from year classes 2013 (171 animals, parental population) and 2017 (759 animals; 13 full sib families) were used as a template for identifying genome wide single nucleotide polymorphisms (SNPs). GBS libraries were constructed using the PstI and MspI restriction enzymes. Approximately 14.5K SNPs passed quality control and were used for estimating a genomic relationship matrix. Thereafter a wide range of analyses were conducted in order to gain insights regarding genetic diversity and investigate the efficiency of the genomic information for parentage assignment and breeding value estimation. Heterozygosity estimates for both year classes suggested a slight excess of heterozygotes. Furthermore, FST estimates among the families of year class 2017 ranged between 0.009 - 0.066. Principal components analysis (PCA) and discriminant analysis of principal components (DAPC) were applied aiming to identify the existence of genetic clusters among the studied population. Results obtained were in accordance with pedigree records allowing the identification of individual families. Additionally, DNA parentage verification was performed, with results in accordance with the pedigree records with the exception of a putative dam where full sib genotypes suggested a potential recording error. Breeding value estimation for juvenile growth through the usage of the estimated genomic relationship matrix clearly outperformed the pedigree equivalent in terms of prediction accuracy (0.51 opposed to 0.31). Overall, low coverage GBS has proven to be a cost-effective genotyping platform that is expected to boost the selection efficiency of the Arctic charr breeding program. [ABSTRACT FROM AUTHOR]

Understanding the genomic basis of adaptative intraspecific phenotypic variation is a central goal in conservation genetics and evolutionary biology. Lake trout (Salvelinus namaycush) are an excellent species for addressing the genetic basis for adaptive variation because they express a striking degree of ecophenotypic variation across their range; however, necessary genomic resources are lacking. Here we utilize recently-developed analytical methods and sequencing technologies to (1) construct a high-density linkage and centromere map for lake trout, (2) identify loci underlying variation in traits that differentiate lake trout ecophenotypes and populations, (3) determine the location of the lake trout sex determination locus, and (4) identify chromosomal homologies between lake trout and other salmonids of varying divergence. The resulting linkage map contains 15,740 single nucleotide polymorphisms (SNPs) mapped to 42 linkage groups, likely representing the 42 lake trout chromosomes. Female and male linkage group lengths ranged from 43.07 to 134.64 centimorgans, and 1.97 to 92.87 centimorgans, respectively. We improved the map by determining coordinates for 41 of 42 centromeres, resulting in a map with 8 metacentric chromosomes and 34 acrocentric or telocentric chromosomes. We use the map to localize the sex determination locus and multiple quantitative trait loci (QTL) associated with intraspecific phenotypic divergence including traits related to growth and body condition, patterns of skin pigmentation, and two composite geomorphometric variables quantifying body shape. Two QTL for the presence of vermiculations and spots mapped with high certainty to an arm of linkage group Sna3, growth related traits mapped to two QTL on linkage groups Sna1 and Sna12, and putative body shape QTL were detected on six separate linkage groups. The sex determination locus was mapped to Sna4 with high confidence. Synteny analysis revealed that lake trout and congener Arctic char (Salvelinus alpinus) are likely differentiated by three or four chromosomal fissions, possibly one chromosomal fusion, and 6 or more large inversions. Combining centromere mapping information with putative inversion coordinates revealed that the majority of detected inversions differentiating lake trout from other salmonids are pericentric and located on acrocentric and telocentric linkage groups. Our results suggest that speciation and adaptive divergence within the genus Salvelinus may have been associated with multiple pericentric inversions occurring primarily on acrocentric and telocentric chromosomes. The linkage map presented here will be a critical resource for advancing conservation oriented genomic research on lake trout and exploring chromosomal evolution within and between salmonid species. [ABSTRACT FROM AUTHOR]

The cardiovascular system is a major limiting system in thermal adaptation, but the exact physiological mechanisms underlying responses to thermal stress are still not completely understood. Recent studies have uncovered the possible role of reactive oxygen species production rates of heart mitochondria in determining species' upper thermal limits. The present study examines the relationship between individual response to a thermal challenge test (CTmax), susceptibility to peroxidation of membrane lipids, heart fatty acid profiles and cardiac antioxidant enzyme activities in two salmonid species from different thermal habitats (Salvelinus alpinus , Salvelinus fontinalis) and their hybrids. The susceptibility to peroxidation of membranes in the heart was negatively correlated with individual thermal tolerance. The same relationship was found for arachidonic and eicosapentaenoic acid. Total H2O2 buffering activity of the heart muscle was higher for the group with high thermal resistance. These findings underline a potential general causative relationship between sensitivity to oxidative stress, specific fatty acids, antioxidant activity in the cardiac muscle and thermal tolerance in fish and likely other ectotherms. Heart fatty acid profile could be indicative of species resilience to global change, and more importantly the plasticity of this trait could predict the adaptability of fish species or populations to changes in environmental temperature. [ABSTRACT FROM AUTHOR]

Heat waves are threatening fish around the world, leading sometimes to mass mortality events. One crucial function of fish failing in high temperatures is oxygen delivery capacity, i.e. cardiovascular function. For anadromous salmonids, increased temperature could be especially detrimental during upstream migration since they need efficiently working oxygen delivery system in order to cross the river rapids to reach upstream areas. The migration also occurs during summer and early autumn exposing salmonids to peak water temperatures, and in shallow rivers there is little availability for thermal refuges as compared to thermally stratified coastal and lake habitats. In order to shed light on the mechanisms underpinning the capacity of migrating fish to face high environmental temperatures, we applied a physiological and molecular approach measuring cardiovascular capacities of migrating and resident Arctic char (Salvelinus alpinus) and brown trout (Salmo trutta) in Northern Norway. The maximum cardiovascular capacity of migrating fish was significantly lower compared to the resident conspecifics. The onset of cardiac impairment started only 2°C higher than river temperature, meaning that even a small increase in water temperature may already compromise cardiac function. The migrating fish were also under significant cellular stress, expressing increased level of cardiac heat shock proteins. We consider these findings highly valuable when addressing climate change effect on migrating fish and encourage taking action in riverine habitat conservation policies. The significant differences in upper thermal tolerance of resident and migrating fish could also lead changes in population dynamics, which should be taken into account in future conservation plans. [ABSTRACT FROM AUTHOR]

Despite immense concern over amplified warming in the Arctic, physiological research to address related conservation issues for valuable cold-adapted fish, such as the Arctic char (Salvelinus alpinus), is lacking. This crucial knowledge gap is largely attributable to the practical and logistical challenges of conducting sensitive physiological investigations in remote field settings. Here, we used an innovative, mobile aquatic-research laboratory to assess the effects of temperature on aerobic metabolism and maximum heart rate (f Hmax) of upriver migrating Arctic char in the Kitikmeot region of Nunavut in the central Canadian Arctic. Absolute aerobic scope was unchanged at temperatures from 4 to 16°C, while f Hmax increased with temperature (Q 10 = 2.1), as expected. However, f Hmax fell precipitously below 4°C and it began to plateau above ~ 16°C, reaching a maximum at ~ 19°C before declining and becoming arrhythmic at ~ 21°C. Furthermore, recovery from exhaustive exercise appeared to be critically impaired above 16°C. The broad thermal range (~4–16°C) for increasing f Hmax and maintaining absolute aerobic scope matches river temperatures commonly encountered by migrating Arctic char in this region. Nevertheless, river temperatures can exceed 20°C during warm events and our results confirm that such temperatures would limit exercise performance and thus impair migration in this species. Thus, unless Arctic char can rapidly acclimatize or alter its migration timing or location, which are both open questions, these impairments would likely impact population persistence and reduce lifetime fitness. As such, future conservation efforts should work towards quantifying and accounting for the impacts of warming, variable river temperatures on migration and reproductive success. [ABSTRACT FROM AUTHOR]

Diploidization, which follows whole genome duplication events, does not occur evenly across the genome. In salmonid fishes, certain pairs of homeologous chromosomes preserve tetraploid loci in higher frequencies toward the telomeres due to residual tetrasomic inheritance. Research suggests this occurs only in homeologous pairs where one chromosome arm has undergone a fusion event. We present a linkage map for Arctic charr (Salvelinus alpinus), a salmonid species with relatively fewer chromosome fusions. Genotype by sequencing identified 19,418 SNPs, and a linkage map consisting of 4508 markers was constructed from a subset of high quality SNPs and microsatellite markers that were used to anchor the new map to previous versions. Both male- and female-specific linkage maps contained the expected number of 39 linkage groups. The chromosome type associated with each linkage group was determined, and 10 stable metacentric chromosomes were identified, along with a chromosome polymorphism involving the sex chromosome AC04. Two instances of a weak form of pseudolinkage were detected in the telomeric regions of homeologous chromosome arms in both female and male linkage maps. Chromosome arm homologies within the Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss) genomes were determined. Paralogous sequence variants (PSVs) were identified, and their comparative BLASTn hit locations showed that duplicate markers exist in higher numbers on seven pairs of homeologous arms, previously identified as preserving tetrasomy in salmonid species. Homeologous arm pairs where neither arm has been part of a fusion event in Arctic charr had fewer PSVs, suggesting faster diploidization rates in these regions. [ABSTRACT FROM AUTHOR]

Sperm production and sperm swimming speed, which most likely affect fertilization under sperm competition, are modified by proximate mechanisms. In a comprehensive observational study of free-living and reproductively active Arctic charr (Salvelinus alpinus), we examined the possible modulating effects of male social status (including ornamental development), parasite intensities, and immunity on novel traits indicative of ejaculate quality (e.g., Adenosine triphosphate (ATP) in sperm cells, levels of immunoglobulins attached to sperm cells, and the degree of DNA fragmentation in sperm cells). A multiple regression model showed no relationship between DNA fragmentation in sperm cells and abdominal coloration of charr, suggesting that sperm of colorful males are not better protected against oxidative stress. We found, however, that males with traits indicative of high social status had low amounts of ATP in sperm cells and also sperm cells with low swimming speed. Sperm production, on the other hand, was strongly predicted by parasite intensities only and these associations were mainly positive. Our results suggest that the presence of parasites seems to stimulate sperm production similar to what is observed among males entering subordinate reproductive roles. Thus, if resistance toward parasites is influencing parasite intensities, resistance may also indirectly be important for the “choice” of reproductive role and in turn investment in primary sex traits. [ABSTRACT FROM PUBLISHER]

Dyck and Kebreab (2009) analyzed the required summer intake of arctic char, ringed seal blubber, and berries that polar bears must consume to maintain their body mass during a summer ice-free period. Their calculations of required intake were based on the amount of body mass lost by fasting bears in western Hudson Bay. However, fasting polar bears are in a low metabolic state with energetic requirements less than those of an active, feeding bear. Estimates of energy consumed by captive brown bears were 4-4.5 times higher than the estimates used by Dyck and Kebreab for similar diets. Furthermore, the authors' portrayal of the availability of these resources is misleading because they do not acknowledge limited accessibility of arctic char due to their limited anadromy and predominant occurrence in streams too deep to facilitate efficient capture by polar bears; effects of large interannual fluctuations in the availability of berries or competition with other frugivores; high energetic requirements associated with lengthy foraging times required to locate and consume sufficient fruit; and data from southern Hudson Bay, western Hudson Bay, and the southern Beaufort Sea that document continued declines in several biological indices over the past several decades despite the authors' suggested availability of terrestrially based food resources. Based on current information, arctic char, berries, and ringed seals in open water do not appear to be food sources with the potential to offset the nutritional consequences of an extended ice-free period. [ABSTRACT FROM AUTHOR]

Bjørn, P-A., Finstad, B., Kristoffersen, R., Rikardsen, A. H., and McKinley, R. S. 2007. Differences in risks and consequences of salmon louse, Lepeophtheirus salmonis (Krøyer), infestation on sympatric populations of Atlantic salmon, brown trout, and Arctic charr within northern fjords. – ICES Journal of Marine Science, 64: 386–393. Differences in salmon louse (Lepeophtheirus salmonis) infestation on sympatric populations of fjord-migrating, Atlantic salmon post-smolts (Salmo salar), brown trout (Salmo trutta) (sea trout), and Arctic charr (Salvelinus alpinus) were studied in three fjords with fish-farming activity in northern Norway during the period June–August 2000. Atlantic salmon post-smolts were only captured in the fjords during late June and early July, and probably left them subsequently. No fish were infested with salmon lice. In contrast, brown trout and Arctic charr had similar infection patterns during their sampling periods, with very low prevalence and mean infection intensity during June (0–21% and 0–6 lice per fish, respectively), slightly increasing in July (8–70% and 6–12 lice per fish, respectively), and peaking in August (80–88% and 19–27 lice per fish, respectively). The chalimus stages dominated during June and July, with a few pre-adult and adult stages observed in July, and all stages were found frequently during August. The observations indicate that Atlantic salmon may have a mismatch between the time of louse infestation and their post-smolt fjord migration in northern fjords. In contrast, brown trout and Arctic charr feed within the fjords throughout summer and have a higher risk of harmful infestation in years with suitable environmental conditions for salmon louse development, especially in fish‐farming areas. Arctic charr usually spend the shortest time at sea of the three species, and the salmon lice may not have time to develop to the adult stage on this species. [ABSTRACT FROM PUBLISHER]

We report on the construction of a linkage map for brown trout (Salmo trutta) and its comparison with those of other tetraploid-derivative fish in the family Salmonidae, including Atlantic salmon (Salmo salar), rainbow trout (Oncorhynchus mykiss), and Arctic char (Salvelinus alpinus). Overall, we identified 37 linkage groups (2n = 80) from the analysis of 288 microsatellite polymorphisms, 13 allozyme markers, and phenotypic sex in four backcross families. Additionally, we used gene-centromere analysis to approximate the position of the centromere for 20 linkage groups and thus relate linkage arrangements to the physical morphology of chromosomes. Sex-specific maps derived from multiple parents were estimated to cover 346.4 and 912.5 cM of the male and female genomes, respectively. As previously observed in other salmonids, recombination rates showed large sex differences (average female-to-male ratio was 6.4), with male crossovers generally localized toward the distal end of linkage groups. Putative homeologous regions inherited from the salmonid tetraploid ancestor were identified for 10 pairs of linkage groups, including five chromosomes showing evidence of residual tetrasomy (pseudolinkage). Map alignments with orthologous regions in Atlantic salmon, rainbow trout, and Arctic char also revealed extensive conservation of syntenic blocks across species, which was generally consistent with chromosome divergence through Robertsonian translocations. [ABSTRACT FROM AUTHOR]

We searched for quantitative trait loci (QTL) affecting upper temperature tolerance (UTT) in crosses between the Nauyuk Lake and Fraser River strains of Arctic charr (Salvelinus alpinus) using survival analysis. Two QTL were detected by using two microsatellite markers after correcting for experiment-wide error. A comparative mapping approach localized these two QTL to homologous linkage groups containing UTT QTL in rainbow trout (Oncorhynchus mykiss). Additional marginal associations were detected in several families in regions homologous to those with QTL in rainbow trout. Thus, the genes underlying UTT QTL may antedate the divergence of these two species, which occurred by ∼16 MYA. The data also indicate that one pair of homeologs (ancestrally duplicated chromosomal segments) have contained QTL in Arctic charr since the evolution of salmonids from a tetraploid ancestor 25-100 MYA. This study represents one of the first examples of comparative QTL mapping in an animal polyploid group and illustrates the fate of QTL after genome duplication and reorganization. [ABSTRACT FROM AUTHOR]

Presents several abstracts of different articles related to biology. 'Hormonal Control of Hepatocyte Metabolism in Arctic Charr,' by O. Aas-Hansen, E.H. Jorgensen, and M.M. Vijayan; 'New Insight Into Brain Evolution: Viewpoint From Planarian,' by K. Agata, Y. Umesono, S. Koinuma, K. Okamoto, H. Itoh, and T. Inoue; 'In Vivo and In Vitro Heterogeneity of Segment Length Changes in the Toad Semimembranosus,' by A.N. Ahn, R.J. Monti, and A.A. Biewener.

The abundance of salmon lice was examined in two stocks of sympatric anadromous Arctic char and sea trout in sub-Arctic regions in northern Norway in June, July, and August 1992 and 1993. One stock feeds in a coastal area exposed to moderate salmon farming activity (exposed area), while the other feed in a region without salmon farms (unexposed area). The salmon lice infestation on both species differed significantly between the exposed and unexposed area as well as between years and also between weeks within the same year. We did not detect, however, any clear significant differences in salmon lice abundance between sympatric populations of Arctic char and sea trout, or between different size groups of the species. The 1992 and 1993 infestation pattern in the exposed area showed an epidemic tendency in both Arctic char and sea trout, characterised by a sudden increase in both prevalence and abundance of lice larvae in July 1992 (23.6±25.7 lice/fish) and August 1993 (19.9±20.8 lice/fish). We therefore suggest that salmon lice epidemics, previously only observed on sea trout, may also occur in populations of Arctic char, and that fish farming contributes to the elevated lice level in wild fish. The fish in the unexposed area were also infested, although at significantly lower levels than fish from the exposed area. The infestation peaked in August 1992 at 13.0±18.1 lice/fish and August 1993 at 3.9±4.5 lice/fish, suggested that lice originating on ascending wild Atlantic salmon, or lice larvae drifting from farming areas, may infest Arctic char and sea trout also in unexposed localities in Subarctic areas. [Copyright &y& Elsevier]

Deals with a study which evaluated mitochondrial DNA sequence variation in a 552-base pair fragment of the control region of Arctic charr of the Salmonidae species. Taxonomic status of the Salvelinus alpinus complex; Materials and methods; Results of the study; Discussion on mitochondrial DNA diversity and population structure.