Adaptation to Low Salinity Promotes Genomic Divergence in Atlantic Cod (Gadus morhua L.)
Paul R. Berg,Sissel Jentoft,Bastiaan Star,Kristoffer Hofaker Ring,Halvor Knutsen,Sigbjørn Lien,Kjetill S. Jakobsen,Carl André +7 more
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TLDR
The data suggest that adaptive responses to the environmental conditions in the Baltic Sea may contribute to a strong and effective reproductive barrier, and that Baltic cod can be viewed as an example of ongoing speciation.Abstract:
How genomic selection enables species to adapt to divergent environments is a fundamental question in ecology and evolution. We investigated the genomic signatures of local adaptation in Atlantic cod (Gadus morhua L.) along a natural salinity gradient, ranging from 35% in the North Sea to 7% within the Baltic Sea. By utilizing a 12 K SNPchip, we simultaneously assessed neutral and adaptive genetic divergence across the Atlantic cod genome. Combining outlier analyses with a landscape genomic approach, we identified a set of directionally selected loci that are strongly correlated with habitat differences in salinity, oxygen, and temperature. Our results show that discrete regions within the Atlantic cod genome are subject to directional selection and associated with adaptation to the local environmental conditions in the Baltic- and the North Sea, indicating divergence hitchhiking and the presence of genomic islands of divergence. We report a suite of outlier single nucleotide polymorphisms within or closely located to genes associated with osmoregulation, as well as genes known to play important roles in the hydration and development of oocytes. These genes are likely to have key functions within a general osmoregulatory framework and are important for the survival of eggs and larvae, contributing to the buildup of reproductive isolation between the low-salinity adapted Baltic cod and the adjacent cod populations. Hence, our data suggest that adaptive responses to the environmental conditions in the Baltic Sea may contribute to a strong and effective reproductive barrier, and that Baltic cod can be viewed as an example of ongoing speciation.read more
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Finding the Genomic Basis of Local Adaptation: Pitfalls, Practical Solutions, and Future Directions.
Sean Hoban,Joanna L. Kelley,Katie E. Lotterhos,Michael F. Antolin,Gideon S. Bradburd,David B. Lowry,Mary L. Poss,Laura K. Reed,Andrew Storfer,Michael C. Whitlock +9 more
TL;DR: The promises and challenges of these genome scan methods are reviewed, including correcting for the confounding influence of a species’ demographic history, biases caused by missing aspects of the genome, matching scales of environmental data with population structure, and other statistical considerations.
Detecting selection along environmental gradients: analysis of eight methods and their effectiveness for outbreeding and selfing populations : [W633]
Stéphane De Mita,Anne-Céline Thuillet,Nourollah Ahmadi,Stéphanie Manel,Joëlle Ronfort,Yves Vigouroux +5 more
TL;DR: In this article, the authors provide guidelines for the use of popular or recently developed statistical methods to detect footprints of selection, and investigate the power and robustness of eight methods to identify loci potentially under selection.
Journal ArticleDOI
Variation in recombination frequency and distribution across eukaryotes: patterns and processes
Jessica Stapley,Philine G. D. Feulner,Philine G. D. Feulner,Susan E. Johnston,Anna W. Santure,Carole M. Smadja +5 more
TL;DR: The patterns of, and processes governing recombination in eukaryotes are explored, and how variation in rate and distribution relates to genome architecture, genetic and epigenetic mechanisms, sex, environmental perturbations and variable selective pressures is discussed.
Journal ArticleDOI
Harnessing the Power of Genomics to Secure the Future of Seafood
Louis Bernatchez,Maren Wellenreuther,Maren Wellenreuther,Cristian Araneda,David T. Ashton,Julia Maria Isis Barth,Terry D. Beacham,Gregory E. Maes,Gregory E. Maes,Jann T. Martinsohn,Kristina M. Miller,Kerry A. Naish,Jennifer R. Ovenden,Craig R. Primmer,Ho Young Suk,Nina Overgaard Therkildsen,Ruth E. Withler +16 more
TL;DR: The value of genomic information towards securing the future of seafood does not need to be further demonstrated and immediate efforts are needed to remove structural roadblocks and focus on ways that support integration of genomic-informed methods into management and production practices.
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