ALBERT

Description: In several species genetic differentiation across environmental gradients or between geographically separate populations has been reported to center at "genomic islands of divergence," resulting in heterogeneous differentiation patterns across genomes. Here, genomic regions of elevated divergence were observed on three chromosomes of the highly mobile fish Atlantic cod ( Gadus morhua ) within geographically fine-scaled coastal areas. The "genomic islands" extended at least 5, 9.5, and 13 megabases on linkage groups 2, 7, and 12, respectively, and coincided with large blocks of linkage disequilibrium. For each of these three chromosomes, pairs of segregating, highly divergent alleles were identified, with little or no gene exchange between them. These patterns of recombination and divergence mirror genomic signatures previously described for large polymorphic inversions, which have been shown to repress recombination across extensive chromosomal segments. The lack of genetic exchange permits divergence between noninverted and inverted chromosomes in spite of gene flow. For the rearrangements on linkage groups 2 and 12, allelic frequency shifts between coastal and oceanic environments suggest a role in ecological adaptation, in agreement with recently reported associations between molecular variation within these genomic regions and temperature, oxygen, and salinity levels. Elevated genetic differentiation in these genomic regions has previously been described on both sides of the Atlantic Ocean, and we therefore suggest that these polymorphisms are involved in adaptive divergence across the species distributional range.

Description: Great genetic variability among teleost immunomes, with gene losses and expansions of central adaptive and innate components, has been discovered through genome sequencing over the last few years. Here, we demonstrate that the innate Myxovirus resistance gene ( Mx ) is lost from the ancestor of Gadiformes and the closely related Stylephorus chordatus , thus predating the loss of Major Histocompatibility Complex class II ( MHCII ) in Gadiformes. Although the functional implication of Mx loss is still unknown, we demonstrate that this loss is one of several ancient events appearing in successive order throughout the evolution of teleost immunity. In particular, we find that the loss of Toll-like receptor 5 predates the loss of Mx involving the entire Paracanthopterygii lineage. Using a time-calibrated phylogeny, we show that loss of MHCII and Mx overlap with major paleoclimatic and geological events indicating that these genetic changes were adaptive responses to the changing environment at the time.

Description: Atlantic cod (Gadus morhua) is a large, cold-adapted teleost that sustains long-standing commercial fisheries and incipient aquaculture. Here we present the genome sequence of Atlantic cod, showing evidence for complex thermal adaptations in its haemoglobin gene cluster and an unusual immune architecture compared to other sequenced vertebrates. The genome assembly was obtained exclusively by 454 sequencing of shotgun and paired-end libraries, and automated annotation identified 22,154 genes. The major histocompatibility complex (MHC) II is a conserved feature of the adaptive immune system of jawed vertebrates, but we show that Atlantic cod has lost the genes for MHC II, CD4 and invariant chain (Ii) that are essential for the function of this pathway. Nevertheless, Atlantic cod is not exceptionally susceptible to disease under natural conditions. We find a highly expanded number of MHC I genes and a unique composition of its Toll-like receptor (TLR) families. This indicates how the Atlantic cod immune system has evolved compensatory mechanisms in both adaptive and innate immunity in the absence of MHC II. These observations affect fundamental assumptions about the evolution of the adaptive immune system and its components in vertebrates.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3537168/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3537168/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Star, Bastiaan -- Nederbragt, Alexander J -- Jentoft, Sissel -- Grimholt, Unni -- Malmstrom, Martin -- Gregers, Tone F -- Rounge, Trine B -- Paulsen, Jonas -- Solbakken, Monica H -- Sharma, Animesh -- Wetten, Ola F -- Lanzen, Anders -- Winer, Roger -- Knight, James -- Vogel, Jan-Hinnerk -- Aken, Bronwen -- Andersen, Oivind -- Lagesen, Karin -- Tooming-Klunderud, Ave -- Edvardsen, Rolf B -- Tina, Kirubakaran G -- Espelund, Mari -- Nepal, Chirag -- Previti, Christopher -- Karlsen, Bard Ove -- Moum, Truls -- Skage, Morten -- Berg, Paul R -- Gjoen, Tor -- Kuhl, Heiner -- Thorsen, Jim -- Malde, Ketil -- Reinhardt, Richard -- Du, Lei -- Johansen, Steinar D -- Searle, Steve -- Lien, Sigbjorn -- Nilsen, Frank -- Jonassen, Inge -- Omholt, Stig W -- Stenseth, Nils Chr -- Jakobsen, Kjetill S -- 098051/Wellcome Trust/United Kingdom -- England -- Nature. 2011 Aug 10;477(7363):207-10. doi: 10.1038/nature10342.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Ecological and Evolutionary Synthesis, Department of Biology, University of Oslo, PO Box 1066, Blindern, N-0316 Oslo, Norway.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21832995" target="_blank"〉PubMed〈/a〉

Description: The whole-genome duplication 80 million years ago of the common ancestor of salmonids (salmonid-specific fourth vertebrate whole-genome duplication, Ss4R) provides unique opportunities to learn about the evolutionary fate of a duplicated vertebrate genome in 70 extant lineages. Here we present a high-quality genome assembly for Atlantic salmon (Salmo salar), and show that large genomic reorganizations, coinciding with bursts of transposon-mediated repeat expansions, were crucial for the post-Ss4R rediploidization process. Comparisons of duplicate gene expression patterns across a wide range of tissues with orthologous genes from a pre-Ss4R outgroup unexpectedly demonstrate far more instances of neofunctionalization than subfunctionalization. Surprisingly, we find that genes that were retained as duplicates after the teleost-specific whole-genome duplication 320 million years ago were not more likely to be retained after the Ss4R, and that the duplicate retention was not influenced to a great extent by the nature of the predicted protein interactions of the gene products. Finally, we demonstrate that the Atlantic salmon assembly can serve as a reference sequence for the study of other salmonids for a range of purposes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lien, Sigbjorn -- Koop, Ben F -- Sandve, Simen R -- Miller, Jason R -- Kent, Matthew P -- Nome, Torfinn -- Hvidsten, Torgeir R -- Leong, Jong S -- Minkley, David R -- Zimin, Aleksey -- Grammes, Fabian -- Grove, Harald -- Gjuvsland, Arne -- Walenz, Brian -- Hermansen, Russell A -- von Schalburg, Kris -- Rondeau, Eric B -- Di Genova, Alex -- Samy, Jeevan K A -- Olav Vik, Jon -- Vigeland, Magnus D -- Caler, Lis -- Grimholt, Unni -- Jentoft, Sissel -- Inge Vage, Dag -- de Jong, Pieter -- Moen, Thomas -- Baranski, Matthew -- Palti, Yniv -- Smith, Douglas R -- Yorke, James A -- Nederbragt, Alexander J -- Tooming-Klunderud, Ave -- Jakobsen, Kjetill S -- Jiang, Xuanting -- Fan, Dingding -- Hu, Yan -- Liberles, David A -- Vidal, Rodrigo -- Iturra, Patricia -- Jones, Steven J M -- Jonassen, Inge -- Maass, Alejandro -- Omholt, Stig W -- Davidson, William S -- England -- Nature. 2016 Apr 18;533(7602):200-5. doi: 10.1038/nature17164.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, As NO-1432, Norway. ; Department of Biology, University of Victoria, Victoria, British Columbia V8W 3N5, Canada. ; J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, Maryland 20850, USA. ; Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, As NO-1432 Norway. ; Department of Plant Physiology, Umea Plant Science Centre, Umea University, Umea 90187, Sweden. ; Institute for Physical Sciences and Technology, University of Maryland, College Park, Maryland 20742-2431, USA. ; Department of Molecular Biology, University of Wyoming, Laramie, Wyoming 82071, USA. ; Center for Computational Genetics and Genomics, Temple University, Philadelphia, Pennsylvania 19122-6078, USA. ; Department of Biology, Temple University, Philadelphia, Pennsylvania 19122-6078, USA. ; Center for Mathematical Modeling, University of Chile, Santiago 8370456, Chile. ; Center for Genome Regulation, University of Chile, Santiago 8370415, Chile. ; Medical Genetics, Oslo University Hospital and University of Oslo, Oslo NO-0424, Norway. ; Department of Virology, Norwegian Veterinary Institute, Oslo NO-0454, Norway. ; Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo NO-0316, Norway. ; CHORI, Oakland, California 94609, USA. ; AquaGen, Trondheim NO-7462, Norway. ; Nofima, Tromso NO-9291, Norway. ; National Center for Cool and Cold Water Aquaculture, ARS-USDA, Kearneysville, West Virginia 25430, USA. ; Beckman Genomics, Danvers, Massachusetts 01923, USA. ; Courtagen Life Sciences, Woburn, Massachusetts 01801, USA. ; BGI-Shenzhen, Shenzhen 518083, China. ; Laboratory of Molecular Ecology, Genomics, and Evolutionary Studies, Department of Biology, University of Santiago, Santiago 9170022, Chile. ; Faculty of Medicine, University of Chile, Santiago 8380453, Chile. ; Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada. ; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada. ; Department of Informatics, University of Bergen, Bergen NO-6020, Norway. ; Centre for Biodiversity Dynamics, Department of Biology, NTNU - Norwegian University of Science and Technology, Trondheim NO-7491, Norway.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/27088604" target="_blank"〉PubMed〈/a〉

Description: 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.