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The lumpfish Cyclopterus lumpus is commercially exploited in numerous areas of its range in the North Atlantic Ocean, and is important in salmonid aquaculture as a biological agent for controlling sea lice. Despite the economic importance, few genetic resources for downstream applications, such as linkage mapping, parentage analysis, marker-assisted selection (MAS), quantitative trait loci (QTL) analysis, and assessing adaptive genetic diversity are currently available for the species. Here, we identify both genome- and transcriptome-derived microsatellites loci from C. lumpus to facilitate such applications. Across 2,346 genomic contigs, we detected a total of 3,067 microsatellite loci, of which 723 were the most suitable ones for primer design. From 116,555 transcriptomic unigenes, we identified a total of 231,556 microsatellite loci, which may indicate a high coverage of the available STRs. Out of these, primer pairs could only be designed for 6,203 loci. Dinucleotide repeats accounted for 89 percent and 52 percent of the genome- and transcriptome-derived microsatellites, respectively. The genetic composition of the dominant repeat motif types showed differences from other investigated fish species. In the genome-derived microsatellites AC/GT (67.8 percent), followed by AG/CT (15.1 percent) and AT/AT (5.6 percent) were the major motifs. Transcriptome-derived microsatellites showed also most dominantly the AC/GT repeat motif (33 percent), followed by A/T (26.6 percent) and AG/CT (11 percent). Functional annotation of microsatellite-containing transcriptomic sequences showed that the majority of the expressed sequence tags encode proteins involved in cellular and metabolic processes, binding activity and catalytic reactions. Importantly, STRs linked to genes involved in immune system process, growth, locomotion and reproduction were discovered in the present study. The extensive genomic marker information reported here will facilitate molecular ecology studies, conservation initiatives and will benefit many aspects of the breeding programmes of C. lumpus.

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Members of the smoothhound shark genus Mustelus display a widespread distribution pattern across ocean basins with a high degree of sub-regional endemism. The patterns and processes that resulted in smoothhound biodiversity and present-day distribution remain largely unknown. We infer the phylogenetic relationships of the genus Mustelus, based on sequence data (3474 bp) from three mitochondrial genes (CR, NADH-2 and 12S-16SrRNA) and a nuclear gene (KBTBD2) from seven species of Mustelus distributed across the eastern Atlantic- and Indo-Pacific oceans. Using the CR and KBTBD2 dataset, we infer the phylogeographic placement of Old World Mustelus, with particular reference to species from southern Africa. Using a near-complete phylogeny of the genus including Old World and New World species of Mustelus and publicly available sequences of the NADH-2 gene, we found supporting evidence indicating a major cladogenic event separating placental and aplacental species. Biogeographical analyses further revealed that the radiation of Mustelus in the southern African region was driven primarily by long-distance dispersal during the upper Miocene to lower Pleistocene. The placement of the placental blackspotted smoothhound Mustelus punctulatus at the base of the placental non-spotted clade suggests the secondary loss of black spots in the genus, and this was also supported by the ancestral state reconstruction. The results furthermore suggest that the Southern Hemisphere species of the genus arose from multiple separate dispersal events from the Northern Hemisphere which is in line with the earliest record of Mustelus in the Northern Hemisphere.

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The blacktip shark Carcharhinus limbatus is a cosmopolitan species found in warm-temperate, subtropical and tropical waters around the world. The research here aimed to assess whether multiple paternity exists in South African C. limbatus and to confirm phylogeographic patterns previously observed within the species. A minimum and maximum frequency of 50% and 71% multiple paternity, respectively, were observed in 14 litters genotyped with five microsatellite markers. Based on the mitochondrial control region, relatively high nucleotide and haplotype diversity characterised the South African sampling population, and pairwise φST values indicated that it significantly differed from the populations of the Pacific and the western Atlantic oceans. The haplotype network showed that the South African samples were grouped closely with the Australian, Indo-Pacific and West African C. limbatus samples, which is suggestive of an Indo-Pacific origin for this population. This study is the first to report multiple paternity in this species. Furthermore, the results reveal that C. limbatus from South Africa is genetically diverse and phylogeographically distinct from most other C. limbatus populations.

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Habitat discontinuity, anthropogenic disturbance, and overharvesting have led to population fragmentation and decline worldwide. Preservation of remaining natural genetic diversity is crucial to avoid continued genetic erosion. Brown trout (Salmo trutta L.) is an ideal model species for studying anthropogenic influences on genetic integrity, as it has experienced significant genetic alterations throughout its natural distribution range due to habitat fragmentation, overexploitation, translocations, and stocking. The Pasvik River is a subarctic riverine system shared between Norway, Russia, and Finland, subdivided by seven hydroelectric power dams that destroyed about 70% of natural spawning and nursing areas. Stocking is applied in certain river parts to support the natural brown trout population. Adjacent river segments with different management strategies (stocked vs. not stocked) facilitated the simultaneous assessment of genetic impacts of dams and stocking based on analyses of 16 short tandem repeat loci. Dams were expected to increase genetic differentiation between and reduce genetic diversity within river sections. Contrastingly, stocking was predicted to promote genetic homogenization and diversity, but also potentially lead to loss of private alleles and to genetic erosion. Our results showed comparatively low heterozygosity and clear genetic differentiation between adjacent sections in nonstocked river parts, indicating that dams prevent migration and contribute to genetic isolation and loss of genetic diversity. Furthermore, genetic differentiation was low and heterozygosity relatively high across stocked sections. However, in stocked river sections, we found signatures of recent bottlenecks and reductions in private alleles, indicating that only a subset of individuals contributes to reproduction, potentially leading to divergence away from the natural genetic state. Taken together, these results indicate that stocking counteracts the negative fragmentation effects of dams, but also that stocking practices should be planned carefully in order to ensure long‐term preservation of natural genetic diversity and integrity in brown trout and other species in regulated river systems.