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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]

We evaluated hypotheses of intralacustrine diversification and plastic responses to two diet environments in Icelandic Arctic charr ( Salvelinus alpinus). Full-sib families of progeny of wild polymorphic charr from two lakes where morphs vary in their degree of phenotypic and ecological divergence were split, with half of the offspring reared on a benthic and half on a limnetic type of diet to estimate family norms of reaction. We focused on variation in craniofacial traits because they are probably functionally related to diet and complement a previous study of body shape in these charr. A hierarchical analysis of phenotypic variation between lakes, pairs of morphs within each lake, and two families within each morph found that phenotypic variation partitioned between families relative to morphs was reduced in the more ecologically diversified population, which is consistent with adaptive diversification. The effect size of plastic responses between lake populations was similar, suggesting little difference in the degree of canalization in contrast to a previous analysis of body form plasticity. Thus, the role that plastic morphological responses play in the adaptive diversification of morphs and different lake populations of Arctic charr may depend on the trait. © 2013 The Linnean Society of London [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]