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      Half a century of genetic interaction between farmed and wild Atlantic salmon: Status of knowledge and unanswered questions

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          Genome-wide genetic marker discovery and genotyping using next-generation sequencing.

          The advent of next-generation sequencing (NGS) has revolutionized genomic and transcriptomic approaches to biology. These new sequencing tools are also valuable for the discovery, validation and assessment of genetic markers in populations. Here we review and discuss best practices for several NGS methods for genome-wide genetic marker development and genotyping that use restriction enzyme digestion of target genomes to reduce the complexity of the target. These new methods -- which include reduced-representation sequencing using reduced-representation libraries (RRLs) or complexity reduction of polymorphic sequences (CRoPS), restriction-site-associated DNA sequencing (RAD-seq) and low coverage genotyping -- are applicable to both model organisms with high-quality reference genome sequences and, excitingly, to non-model species with no existing genomic data.
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            Rapid worldwide depletion of predatory fish communities.

            Serious concerns have been raised about the ecological effects of industrialized fishing, spurring a United Nations resolution on restoring fisheries and marine ecosystems to healthy levels. However, a prerequisite for restoration is a general understanding of the composition and abundance of unexploited fish communities, relative to contemporary ones. We constructed trajectories of community biomass and composition of large predatory fishes in four continental shelf and nine oceanic systems, using all available data from the beginning of exploitation. Industrialized fisheries typically reduced community biomass by 80% within 15 years of exploitation. Compensatory increases in fast-growing species were observed, but often reversed within a decade. Using a meta-analytic approach, we estimate that large predatory fish biomass today is only about 10% of pre-industrial levels. We conclude that declines of large predators in coastal regions have extended throughout the global ocean, with potentially serious consequences for ecosystems. Our analysis suggests that management based on recent data alone may be misleading, and provides minimum estimates for unexploited communities, which could serve as the 'missing baseline' needed for future restoration efforts.
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              Adaptive versus non-adaptive phenotypic plasticity and the potential for contemporary adaptation in new environments

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                Author and article information

                Journal
                Fish and Fisheries
                Fish Fish
                Wiley-Blackwell
                14672960
                September 2017
                September 2017
                : 18
                : 5
                : 890-927
                Article
                10.1111/faf.12214
                © 2017

                http://doi.wiley.com/10.1002/tdm_license_1.1

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