| 1. |
- Andersen, Øivind, et al.
(author)
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The conserved Phe GH5 of importance for hemoglobin intersubunit contact is mutated in gadoid fish
- 2014
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In: BMC Evolutionary Biology. - 1471-2148. ; 14:1
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Journal article (peer-reviewed)abstract
- Abstract Background Functionality of the tetrameric hemoglobin molecule seems to be determined by a few amino acids located in key positions. Oxygen binding encompasses structural changes at the interfaces between the α1β2 and α2β1 dimers, but also subunit interactions are important for the oxygen binding affinity and stability. The latter packing contacts include the conserved Arg B12 interacting with Phe GH5, which is replaced by Leu and Tyr in the α A and α D chains, respectively, of birds and reptiles. Results Searching all known hemoglobins from a variety of gnathostome species (jawed vertebrates) revealed the almost invariant Arg B12 coded by the AGG triplet positioned at an exon-intron boundary. Rare substitutions of Arg B12 in the gnathostome β globins were found in pig, tree shrew and scaled reptiles. Phe GH5 is also highly conserved in the β globins, except for the Leu replacement in the β1 globin of five marine gadoid species, gilthead seabream and the Comoran coelacanth, while Cys and Ile were found in burbot and yellow croaker, respectively. Atlantic cod β1 globin showed a Leu/Met polymorphism at position GH5 dominated by the Met variant in northwest-Atlantic populations that was rarely found in northeast-Atlantic cod. Site-specific analyses identified six consensus codons under positive selection, including 122β(GH5), indicating that the amino acid changes identified at this position may offer an adaptive advantage. In fact, computational mutation analysis showed that the replacement of Phe GH5 with Leu or Cys decreased the number of van der Waals contacts essentially in the deoxy form that probably causes a slight increase in the oxygen binding affinity. Conclusions The almost invariant Arg B12 and the AGG codon seem to be important for the packing contacts and pre-mRNA processing, respectively, but the rare mutations identified might be beneficial. The Leu122β1(GH5)Met and Met55β1(D6)Val polymorphisms in Atlantic cod hemoglobin modify the intradimer contacts B12-GH5 and H2-D6, while amino acid replacements at these positions in avian hemoglobin seem to be evolutionary adaptive in air-breathing vertebrates. The results support the theory that adaptive changes in hemoglobin functions are caused by a few substitutions at key positions.
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| 2. |
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| 3. |
- Barth, Julia M.I., et al.
(author)
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Disentangling structural genomic and behavioural barriers in a sea of connectivity
- 2019
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In: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 28:6, s. 1394-1411
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Journal article (peer-reviewed)abstract
- © 2019 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd Genetic divergence among populations arises through natural selection or drift and is counteracted by connectivity and gene flow. In sympatric populations, isolating mechanisms are thus needed to limit the homogenizing effects of gene flow to allow for adaptation and speciation. Chromosomal inversions act as an important mechanism maintaining isolating barriers, yet their role in sympatric populations and divergence with gene flow is not entirely understood. Here, we revisit the question of whether inversions play a role in the divergence of connected populations of the marine fish Atlantic cod (Gadus morhua), by exploring a unique data set combining whole-genome sequencing data and behavioural data obtained with acoustic telemetry. Within a confined fjord environment, we find three genetically differentiated Atlantic cod types belonging to the oceanic North Sea population, the western Baltic population and a local fjord-type cod. Continuous behavioural tracking over 4year revealed temporally stable sympatry of these types within the fjord. Despite overall weak genetic differentiation consistent with high levels of gene flow, we detected significant frequency shifts of three previously identified inversions, indicating an adaptive barrier to gene flow. In addition, behavioural data indicated that North Sea cod and individuals homozygous for the LG12 inversion had lower fitness in the fjord environment. However, North Sea and fjord-type cod also occupy different depths, possibly contributing to prezygotic reproductive isolation and representing a behavioural barrier to gene flow. Our results provide the first insights into a complex interplay of genomic and behavioural isolating barriers in Atlantic cod and establish a new model system towards an understanding of the role of genomic structural variants in adaptation and diversification.
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| 4. |
- Barth, Julia M.I., et al.
(author)
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Genome architecture enables local adaptation of Atlantic cod despite high connectivity
- 2017
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In: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 26:17, s. 4452-4466
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Journal article (peer-reviewed)abstract
- Adaptation to local conditions is a fundamental process in evolution; however, mechanisms maintaining local adaptation despite high gene flow are still poorly understood. Marine ecosystems provide a wide array of diverse habitats that frequently promote ecological adaptation even in species characterized by strong levels of gene flow. As one example, populations of the marine fish Atlantic cod (Gadus morhua) are highly connected due to immense dispersal capabilities but nevertheless show local adaptation in several key traits. By combining population genomic analyses based on 12K single nucleotide polymorphisms with larval dispersal patterns inferred using a biophysical ocean model, we show that Atlantic cod individuals residing in sheltered estuarine habitats of Scandinavian fjords mainly belong to offshore oceanic populations with considerable connectivity between these diverse ecosystems. Nevertheless, we also find evidence for discrete fjord populations that are genetically differentiated from offshore populations, indicative of local adaptation, the degree of which appears to be influenced by connectivity. Analyses of the genomic architecture reveal a significant overrepresentation of a large ~5 Mb chromosomal rearrangement in fjord cod, previously proposed to comprise genes critical for the survival at low salinities. This suggests that despite considerable connectivity with offshore populations, local adaptation to fjord environments may be enabled by suppression of recombination in the rearranged region. Our study provides new insights into the potential of local adaptation in high gene flow species within fine geographical scales and highlights the importance of genome architecture in analyses of ecological adaptation.
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| 5. |
- Knutsen, Halvor, et al.
(author)
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Combining population genomics with demographic analyses highlights habitat patchiness and larval dispersal as determinants of connectivity in coastal fish species
- 2022
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In: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 31:9, s. 2562-2577
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Journal article (peer-reviewed)abstract
- Gene flow shapes spatial genetic structure and the potential for local adaptation. Among marine animals with non-migratory adults, the presence or absence of a pelagic larval stage is thought to be a key determinant in shaping gene flow and the genetic structure of populations. In addition, the spatial distribution of suitable habitats is expected to influence the distribution of biological populations and their connectivity patterns. We used whole genome sequencing to study demographic history and reduced representation (ddRAD) sequencing data to analyze spatial genetic structure in broadnosed pipefish (Syngnathus typhle). Its main habitat is eelgrass beds, which are patchily distributed along the study area in southern Norway. Demographic connectivity among populations was inferred from long-term (~30 year) population counts that uncovered a rapid decline in spatial correlations in abundance with distance as short as ~2 km. These findings were contrasted with data for two other fish species that have a pelagic larval stage (corkwing wrasse, Symphodus melops; black goby, Gobius niger). For these latter species, we found wider spatial scales of connectivity and weaker genetic isolation-by-distance patterns, except where both species experienced a strong barrier to gene flow, seemingly due to lack of suitable habitat. Our findings verify expectations that a fragmented habitat and absence of a pelagic larval stage promote genetic structure, while presence of a pelagic larvae stage increases demographic connectivity and gene flow, except perhaps over extensive habitat gaps.
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| 7. |
- Lien, Sigbjorn, et al.
(author)
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The Atlantic salmon genome provides insights into rediploidization
- 2016
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In: Nature. - : Nature Publishing Group. - 0028-0836 .- 1476-4687. ; 533:7602, s. 200-205
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Journal article (peer-reviewed)abstract
- 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.
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| 8. |
- Musilova, Zuzana, et al.
(author)
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Vision using multiple distinct rod opsins in deep-sea fishes
- 2019
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In: Science. - Washington : American Association of Advanced Science. - 0036-8075 .- 1095-9203. ; 364:6440, s. 588-
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Journal article (peer-reviewed)abstract
- Vertebrate vision is accomplished through light-sensitive photopigments consisting of an opsin protein bound to a chromophore. In dim light, vertebrates generally rely on a single rod opsin [rhodopsin 1 (RH1)] for obtaining visual information. By inspecting 101 fish genomes, we found that three deep-sea teleost lineages have independently expanded their RH1 gene repertoires. Among these, the silver spinyfin (Diretmus argenteus) stands out as having the highest number of visual opsins in vertebrates (two cone opsins and 38 rod opsins). Spinyfins express up to 14 RH1s (including the most blueshifted rod photopigments known), which cover the range of the residual daylight as well as the bioluminescence spectrum present in the deep sea. Our findings present molecular and functional evidence for the recurrent evolution of multiple rod opsin-based vision in vertebrates.
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| 9. |
- Svedäng, Henrik, et al.
(author)
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Local cod (Gadus morhua) revealed by egg surveys and population genetic analysis after longstanding depletion on the Swedish Skagerrak coast
- 2019
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In: ICES Journal of Marine Science. - : Oxford University Press (OUP). - 1054-3139 .- 1095-9289. ; 76:2, s. 418-429
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Journal article (peer-reviewed)abstract
- Dramatic and persistent reductions in Atlantic cod (Gadus morhua) are common in many coastal areas. While offshore cod stocks still were abundant and productive, the Swedish west coast showed signs of diminishing adult cod abundance at the beginning of the 1980s, where the local cod component was considered to be extirpated. To survey the present cod spawning activity and stock composition, we initiated egg trawling over two consecutive years (203 hauls in total) in combination with population genetic analyses (425 individually genotyped eggs). Here, we provide evidence of cod spawning at the Swedish Skagerrak coast, suggesting recolonization or that local cod has recovered from a nearly depleted state. Early stage eggs were found inside fjords too far to have been transported by oceanic drift from offshore spawning areas. The cod eggs were genetically similar in early to late life-stages and cluster mainly with the local adult cod, indicating that eggs and adults belong to the same genetic unit. The cod eggs were genetically differentiated from adult North Sea cod, and, to a lesser degree, also from the Kattegat and Öresund cod, i.e. indicating a possible recovery of local coastal stock.The patterns of the genetic structure in the inshore areas are, however, difficult to fully disentangle, as Atlantic cod in the North Sea-Skagerrak area seem to be a mixture of co-existing forms: local cod completing their entire life cycle in fjords and sheltered areas, and oceanic populations showing homing behaviours. The egg abundances are considerably lower compared with what is found in similar studies along the Norwegian Skagerrak coast. Nevertheless, the discovery of locally spawning cod along the Swedish west coast—although at low biomasses—is an encouraging finding that highlights the needs for endurance in protective measures and of detailed surveys to secure intraspecific biodiversity and ecosystem services.
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| 10. |
- Theissinger, Kathrin, et al.
(author)
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How genomics can help biodiversity conservation
- 2023
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In: Trends in Genetics. - : Elsevier. - 0168-9525 .- 1362-4555. ; 39:7, s. 545-559
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Research review (peer-reviewed)abstract
- The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics.
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| 11. |
- Varadharajan, Srinidhi, et al.
(author)
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The Grayling Genome Reveals Selection on Gene Expression Regulation after Whole-Genome Duplication
- 2018
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In: Genome Biology and Evolution. - : Oxford University Press. - 1759-6653. ; 10:10, s. 2785-2800
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Journal article (peer-reviewed)abstract
- Whole-genome duplication (WGD) has been a major evolutionary driver of increased genomic complexity in vertebrates. One such event occurred in the salmonid family ∼80 Ma (Ss4R) giving rise to a plethora of structural and regulatory duplicate-driven divergence, making salmonids an exemplary system to investigate the evolutionary consequences of WGD. Here, we present a draft genome assembly of European grayling (Thymallus thymallus) and use this in a comparative framework to study evolution of gene regulation following WGD. Among the Ss4R duplicates identified in European grayling and Atlantic salmon (Salmo salar), one-third reflect nonneutral tissue expression evolution, with strong purifying selection, maintained over ∼50 Myr. Of these, the majority reflect conserved tissue regulation under strong selective constraints related to brain and neural-related functions, as well as higher-order protein–protein interactions. A small subset of the duplicates have evolved tissue regulatory expression divergence in a common ancestor, which have been subsequently conserved in both lineages, suggestive of adaptive divergence following WGD. These candidates for adaptive tissue expression divergence have elevated rates of protein coding- and promoter-sequence evolution and are enriched for immune- and lipid metabolism ontology terms. Lastly, lineage-specific duplicate divergence points toward underlying differences in adaptive pressures on expression regulation in the nonanadromous grayling versus the anadromous Atlantic salmon. Our findings enhance our understanding of the role of WGD in genome evolution and highlight cases of regulatory divergence of Ss4R duplicates, possibly related to a niche shift in early salmonid evolution.
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