[Show abstract][Hide abstract] ABSTRACT: During a recent marine biological expedition to the Northeast Greenland shelf break (latitudes 74–77 °N), we made the first discovery of Atlantic cod (Gadus morhua), beaked redfish (Sebastes mentella) and capelin (Mallotus villosus). Our novel observations shift the distribution range of Atlantic cod >1000 km further north in East Greenland waters. In light of climate change, we discuss physical forcing and putative connections between the faunas of the Northeast Greenland shelf and the Barents Sea. We emphasise the importance of using real data in spread scenarios for understudied Arctic seas.
Full-text · Article · Jan 2016 · The Science of Nature
[Show abstract][Hide abstract] ABSTRACT: Polar cod, Boreogadus
saida, is a key species in Arctic marine ecosystems; however, its genetic population structure is largely undescribed. The population genetic structure of 472 B.
saida specimens among nine locations in the north-east Atlantic was revealed using 12 microsatellite loci. Pairwise F
comparisons showed significant population differentiation between B.
saida sampled inside fjords in Svalbard and north-east Greenland, as compared to B.
saida from the shelf. The observed genetic variation was not a function of isolation by distance, and it is speculated that B.
saida populations inhabiting fjords may have become reproductively isolated from shelf-dwelling B.
saida during the last post-glacial recolonization.
[Show abstract][Hide abstract] ABSTRACT: The identification of isolated populations in widely distributed marine species is often impeded by low levels of genetic
differentiation. However, modern genetic approaches now allow for the efficient detection of potentially large numbers of
novel genetic variations, thereby improving the power to identify biologically meaningful management units. To investigate
the genetic structuring of saithe (Pollachius virens L.), we applied seascape genetic approaches to 131 single nucleotide polymorphism loci genotyped in 584 fish collected from
11 locations across the North Atlantic. Wombling analysis and the Monmonier algorithm revealed four genetic clusters (Barents
Sea, Central Northeast Atlantic, Rockall, and Canada) across the species distribution range. These results imply that genetic
structuring in saithe may be influenced by abiotic factors such as geographical distance, and bathymetry as well as biotic
factors such as sex-biased migration, and natal homing. The results suggest a potential mismatch between management and biological
units across the Northeast Atlantic, which may have implications for sustainable exploitation of the species.
Full-text · Article · Oct 2015 · ICES Journal of Marine Science
[Show abstract][Hide abstract] ABSTRACT: Invasion of exotic species has caused the loss of biodiversity and imparts evolutionary and ecological changes in the introduced systems. In northern Fennoscandia, European whitefish (Coregonus lavaretus (L.)) is a highly polymorphic species displaying adaptive radiations into partially reproductively isolated and thus genetically differentiated sympatric morphs utilizing the planktivorous and benthivorous food niche in many lakes. In 1993, Lake Skrukkebukta was invaded by vendace (Coregonus albula (L.)) which is a zooplanktivorous specialist. The vendace displaced the densely rakered whitefish from its preferred pelagic niche to the benthic habitat harbouring the large sparsely rakered whitefish. In this study, we investigate the potential influence of the vendace invasion on the breakdown of reproductive isolation between the two whitefish morphs. We inferred the genotypic and phenotypic differentiation between the two morphs collected at the arrival (1993) and 15 years after (2008) the vendace invasion using 16 microsatellite loci and gill raker numbers, the most distinctive adaptive phenotypic trait between them. The comparison of gill raker number distributions revealed two modes growing closer over 15 years following the invasion. Bayesian analyses of genotypes revealed that the two genetically distinct whitefish morphs that existed in 1993 had collapsed into a single population in 2008. The decline in association between the gill raker numbers and admixture values over 15 years corroborates the findings from the Bayesian analysis. Our study thus suggests an apparent decrease of reproductive isolation in a morph-pair of European whitefish within 15 years (≃ 3 generations) following the invasion of a superior trophic competitor (vendace) in a subarctic lake, reflecting a situation of "speciation in reverse".
[Show abstract][Hide abstract] ABSTRACT: Understanding how a monophyletic lineage of a species diverges into several adaptive forms has received increased attention in recent years, but the underlying mechanisms in this process are still under debate. Postglacial fishes are excellent model organisms for exploring this process, especially the initial stages of ecological speciation, as postglacial lakes represent replicated discrete environments with variation in available niches. Here, we combine data of niche utilization, trophic morphology, and 17 microsatellite loci to investigate the diversification process of three sympatric European whitefish morphs from three northern Fennoscandian lakes. The morphological divergence in the gill raker number among the whitefish morphs was related to the utilization of different trophic niches and was associated with reproductive isolation within and across lakes. The intralacustrine comparison of whitefish morphs showed that these systems represent two levels of adaptive divergence: (1) a consistent littoral-pelagic resource axis; and (2) a more variable littoral-profundal resource axis. The results also indicate that the profundal whitefish morph has diverged repeatedly from the ancestral littoral whitefish morph in sympatry in two different watercourses. In contrast, all the analyses performed revealed clustering of the pelagic whitefish morphs across lakes suggesting parallel postglacial immigration with the littoral whitefish morph into each lake. Finally, the analyses strongly suggested that the trophic adaptive trait, number of gill rakers, was under diversifying selection in the different whitefish morphs. Together, the results support a complex evolutionary scenario where ecological speciation acts, but where both allopatric (colonization history) and sympatric (within watercourse divergence) processes are involved.
Full-text · Article · Dec 2013 · Ecology and Evolution
[Show abstract][Hide abstract] ABSTRACT: Coregonids constitute one of the most diverse fi sh families in the northern freshwater systems and several species are highly endangered mainly due to anthropogenic pressure. Cost effective and powerful polymerase chain reaction (PCR) microsatellite multiplex assays were established for genetic studies of the population structure, hybridization and conservation status of European whitefish (Coregonus lavaretus (L.)) and vendace (C. albula (L.)). An assay containing four PCR multiplexes for co-amplification of 9, 5, 3, and 4 loci was developed for C. lavaretus. Cross-species amplification and rearrangement of the same loci resulted in an assay containing three multiplex reactions of 6, 3, and 4 loci for C. albula. Highly significant pair-wise FST - estimates were obtained between C. albula from L. Vaggatem (Norway) and L. Palojärvi (Finland) (FST = 0.301, p < 0.001), between C. lavaretus from L. Skrukkebukta (Norway) and L. Stuorajavri (Norway) (FST = 0.161, p < 0.001), and between morphpairs occurring in the two latter lakes (FST = 0.0135-0.043, p < 0.001). The multiplex assays provided a 100% correct assignment success for discriminating C. lavaretus and C. albula and hence provide a powerful diagnostic tool for the future management of these species.
Full-text · Article · Nov 2013 · Advances in Limnology
[Show abstract][Hide abstract] ABSTRACT: Three methods for extracting DNA were tested on otoliths, scales, fins, and gill tissue from European whitefish [Coregonus lavaratus (L.)]. The aim was to find time-efficient and affordable ways to simultaneously extract DNA suitable for conservation genetic studies from a large number of samples and different tissues. A rapid low-cost method led to 97 % success of microsatellite amplification in otoliths and 100 % in scales. High amplification success was achieved with fin (97 %) and gill (99 %) tissue using a salt lysis-based protocol. A commercial extraction kit delivered good results with all tissues. The findings are useful for conservation genetic studies using both contemporary and archived samples.
[Show abstract][Hide abstract] ABSTRACT: Capelin (Mallotus villosus) displays alterna-tive reproductive modes throughout its circumpolar dis-tribution. This predicts divergent thermohaline tolerance of eggs because they are incubated in either a steady offshore or variable intertidal environment. We investi-gate herein thermohaline tolerance of eggs from the offshore spawning Barents Sea capelin. Subsequently, we compare our data with those previously published on other offshore and intertidal spawning capelin popula-tions across the Northeast Atlantic Ocean, with the aim of determining possible patterns in the thermohaline tolerance of eggs from the alternative reproductive modes. In a 2×4 factorial design various combinations of salinities and temperatures had only negligible effect on the survival of eggs until first hatch. The embryonic development rate from fertilisation until first hatch across populations and between the two reproductive modes suggested non-local thermohaline tolerance to-wards the physical factors during development. Finally, no differences were observed in salinity tolerance from fertilisation to first hatch between populations represent-ing different reproductive modes. The present findings demonstrate wide thermohaline tolerance of capelin eggs regardless of population origin and reproductive mode.
Full-text · Article · Jun 2013 · Environmental Biology of Fishes
[Show abstract][Hide abstract] ABSTRACT: Here we provide the first karyological characterization of the Arctic gadoid fish Gaidropsarus argentatus (Arctic rockling), through conventional and molecular cytogenetics. The analysis of six specimens collected along the coasts of Greenland during TUNU-MAFIG (Marine Fishes of North East Greenland – diversity and adaptation) expeditions, consistently indicated 48 chromosomes, with the karyotypic formula 12 m/sm+36 st/t and Fundamental Number (FN)=60. The description of the species-specific karyotype for a fish living in Arctic marine waters per se adds a significant piece of information to the necessary biological baseline for monitoring of biodiversity changes in polar regions. In addition, comparison of our data on the Arctic G. argentatus with those of the Mediterranean co-generic G. mediterraneus revealed a surprisingly high level of cytogenetic diversity between the two species (2n=48 vs. 2n=28), laying the basis for future analyses aimed at tracing the chromosomal evolution and diversification within this geographically widespread genus.
No preview · Article · Dec 2012 · Marine Biology Research
[Show abstract][Hide abstract] ABSTRACT: Highly repetitive sequences are the bane of genome sequence assembly, and the short read lengths produced by current next generation sequencing technologies further exacerbates this obstacle. An adopted practice is to exclude repetitive sequences in genome data assembly, as the majority of repeats lack protein-coding genes. However, this could result in the exclusion of important genotypes in newly sequenced non-model species. The absence of the antifreeze glycoproteins (AFGP) gene family in the recently sequenced Atlantic cod genome serves as an example.
The Atlantic cod (Gadus morhua) genome was assembled entirely from Roche 454 short reads, demonstrating the feasibility of this approach. However, a well-known major adaptive trait, the AFGP, essential for survival in frigid Arctic marine habitats was absent in the annotated genome. To assess whether this resulted from population difference, we performed Southern blot analysis of genomic DNA from multiple individuals from the North East Arctic cod population that the sequenced cod belonged, and verified that the AFGP genotype is indeed present. We searched the raw assemblies of the Atlantic cod using our G. morhua AFGP gene, and located partial AFGP coding sequences in two sequence scaffolds. We found these two scaffolds constitute a partial genomic AFGP locus through comparative sequence analyses with our newly assembled genomic AFGP locus of the related polar cod, Boreogadus saida. By examining the sequence assembly and annotation methodologies used for the Atlantic cod genome, we deduced the primary cause of the absence of the AFGP gene family from the annotated genome was the removal of all repetitive Roche 454 short reads before sequence assembly, which would exclude most of the highly repetitive AFGP coding sequences. Secondarily, the model teleost genomes used in projection annotation of the Atlantic cod genome have no antifreeze trait, perpetuating the unawareness that the AFGP gene family is missing.
We recovered some of the missing AFGP coding sequences and reconstructed a partial AFGP locus in the Atlantic cod genome, bringing to light that not all repetitive sequences lack protein coding information. Also, reliance on genomes of model organisms as reference for annotating protein-coding gene content of a newly sequenced non-model species could lead to omission of novel genetic traits.
[Show abstract][Hide abstract] ABSTRACT: Nucleotide sequence alignment of the Gm1-1 AFGP gene [GenBank:AF529262] from the Øresund, Denmark Atlantic cod and six of the seven AFGP genes we identified from Atlantic cod genome data []. ATLCOD1A_AFGP7 was not included in the alignment due to long insertions in the putative intron region at 5′ of the sequence (given in lower case). ‘N’s represent gaps in the Atlantic cod sequence assembly . Dashed lines indicate gaps introduced by the alignment. Asterisks indicate nucleotide identity in the column disregarding “N”. Single-letter amino acid translation of Gm1-1 is given in red, below the first nucleotide of each codon in the nucleotide alignment. ATLCOD1A_AFGP1 has the most number of amino acid substitutions (first line below Gm1-1 aa sequence), while all other ATLCOD1A AFGP sequences have few substitutions (second line below Gm1-1 amino acid sequence). Substitutions given in green would disrupt the regular (Ala/Pro-Ala-Thr) tripeptide units, and those given in blue would not. ATLCOD1A_AFGP1 has a reading frame shift at the 5′ to AFGP coding region, which would render it a pseudogene unless the frame shift reflects sequencing or assembly error. ATLCOD1A_AFGP5 and Gm1-1 are very likely counterparts in the respective individuals as their aligned sequences are 99.8% identical. The grey shaded sequences in ALTCOD1A AFGP genes were identified and masked by Star et al. using RepeatMasker with RepBase Update (teleost) TE library, and a custom library created de novo with RepeatModeler to identify novel repeats in the Atlantic cod genome (Supplementary Note 16 and Supplementary Table 6 of ). The repeat masking eliminated almost all partial AFGP coding sequences that remained after the initial removal of highly repetitive sequences from the Roche 454 reads prior to sequence assembly.
[Show abstract][Hide abstract] ABSTRACT: be used for research, teaching and private study purposes. Any substantial or systematic reproduction, re-distribution, re-selling, loan or sub-licensing, systematic supply or distribution in any form to anyone is expressly forbidden. The publisher does not give any warranty express or implied or make any representation that the contents will be complete or accurate or up to date. The accuracy of any instructions, formulae and drug doses should be independently verified with primary sources. The publisher shall not be liable for any loss, actions, claims, proceedings, demand or costs or damages whatsoever or howsoever caused arising directly or indirectly in connection with or arising out of the use of this material.
Full-text · Article · Sep 2009 · Marine Biology Research
[Show abstract][Hide abstract] ABSTRACT: Correct phenotypical identification of and discrimination between Boreogadus saida and Arctogadus glacialis is challenging, especially for larvae and young fish. We propose the use of a single microsatellite genetic marker, Gmo8,
to distinguish between the two gadoid fish species. Amplified allele frequencies differed considerably, with B. saida (n=97) being almost exclusively monomorphic at this locus, whereas A. glacialis (n=136) is highly polymorphic. There was a clear separation between the amplified allele ranges for the two species. The species
specific properties of Gmo8 enables the use of this marker to distinguish between B. saida and A. glacialis.
[Show abstract][Hide abstract] ABSTRACT: The Atlantic cod (Gadus morhua) is a groundfish of great economic value in fisheries and an emerging species in aquaculture. Genetic markers are needed to identify wild stocks in order to ensure sustainable management, and for marker-assisted selection and pedigree determination in aquaculture. Here, we report on the development and evaluation of a large number of Single Nucleotide Polymorphism (SNP) markers from the alignment of Expressed Sequence Tag (EST) sequences in Atlantic cod. We also present basic population parameters of the SNPs in samples of North-East Arctic cod and Norwegian coastal cod obtained from three different localities, and test for SNPs that may have been targeted by natural selection.
A total of 17,056 EST sequences were used to find 724 putative SNPs, from which 318 segregating SNPs were isolated. The SNPs were tested on Atlantic cod from four different sites, comprising both North-East Arctic cod (NEAC) and Norwegian coastal cod (NCC). The average heterozygosity of the SNPs was 0.25 and the average minor allele frequency was 0.18. FST values were highly variable, with the majority of SNPs displaying very little differentiation while others had FST values as high as 0.83. The FST values of 29 SNPs were found to be larger than expected under a strictly neutral model, suggesting that these loci are, or have been, influenced by natural selection. For the majority of these outlier SNPs, allele frequencies in a northern sample of NCC were intermediate between allele frequencies in a southern sample of NCC and a sample of NEAC, indicating a cline in allele frequencies similar to that found at the Pantophysin I locus.
The SNP markers presented here are powerful tools for future genetics work related to management and aquaculture. In particular, some SNPs exhibiting high levels of population divergence have potential to significantly enhance studies on the population structure of Atlantic cod.
[Show abstract][Hide abstract] ABSTRACT: Atlantic cod (Gadus morhua) encompasses many different populations or stocks, which in part are managed separately. In the northeast Atlantic cod is
divided into two main management units; northeast Arctic cod and coastal cod. These two groups have traditionally been separated
by otolith classification. In this study, the power of different classes of genetic markers in separating the two cod groups
was investigated. The variation in thirteen genetic markers, including allozymes, haemoglobin, the scDNA locus Pantophysin
(Pan I) and a number of microsatellites was investigated, and mixed stock analysis and individual assignment tests were performed
on samples comprising a mixture of individuals of putative coastal and oceanic type cod. The genetic analyses showed a large
genetic differentiation between outer stations and stations located closer to the mainland shore. Mixed stock analysis and
individual assignment tests used for estimation of stock proportions gave results similar to those obtained by otolith classification.
[Show abstract][Hide abstract] ABSTRACT: A large majority of Atlantic cod (Gadus morhua) found all year round in outer parts of fjords and along outer coastal areas in general in northern Norway have a genetic signature at the pantophysin (Pan I) locus that distinguish them from Norwegian coastal cod (NCC) found further inside fjords in the same areas. The identity of these fish has been controversial and to examine if they represent a distinct coastal cod group, or are identical to the migratory North East Arctic cod (NEAC) of the Barents Sea, a comparison was conducted at 10 microsatellite loci for 15 samples comprising each of the three groups inner coastal NCC, outer coastal cod and NEAC. Spatial analysis of molecular variance revealed that the outer coastal samples cannot be discriminated from NEAC by means of microsatellite markers, supporting the similarity of the two groups at the Pan I locus. This implies that a portion of the otherwise migratory NEAC, at least in its premature stage, remains in coastal areas in close contact with the genetically quite distinct NCC group. Both the coalescent-based simulation approach and the lnRH test for selective sweeps proved two of the microsatellite loci, GMO 34 and GMO 132 to be non-neutral. Notwithstanding, these two loci, together with the acknowledged non-neutral Pan I locus, which displayed profound linkage disequilibrium to GMO 34 within NEAC, are as yet the only nuclear markers which unambiguously discriminate between NEAC and NCC. Although the relative contribution of restricted gene flow versus selection as a causative agent for the divergence between NEAC and NCC has not been assessed, we believe the magnitude of differentiation at the three loci provides rational for maintaining NEAC and NCC as separate management units.
Full-text · Article · Jul 2007 · Fisheries Research
[Show abstract][Hide abstract] ABSTRACT: The walleye pollock (Theragra chalcogramma) and Norwegian pollock (T. finnmarchica) are confined to the North Pacific and North Atlantic Oceans, respectively, and considered as distinct species within the family Gadidae. We have determined the complete mtDNA nucleotide sequence of two specimens of Norwegian pollock and compared the sequences to that of 10 specimens of walleye pollock representing stocks from the Sea of Japan and the Bering Sea, 2 specimens of Atlantic cod (Gadus morhua), and 2 specimens of haddock (Melanogrammus aeglefinus).
A total number of 204 variable positions were identified among the 12 pollock specimens, but no specific substitution pattern could be identified between the walleye and Norwegian pollocks. Phylogenetic analysis using 16,500 homologous mtDNA nucleotide positions clearly identify the Norwegian pollock within the walleye pollock species cluster. Furthermore, the Norwegian pollock sequences were most similar to mitochondrial genotypes present in walleye pollock specimens from the Sea of Japan, an observation supported both by neighbor-joining, maximum parsimony, and maximum likelihood analyses.
We infer that walleye pollock and Norwegian pollock represent one single species and that Norwegian pollock has been recently introduced from the Pacific to the Atlantic Oceans.
Full-text · Article · Feb 2007 · BMC Evolutionary Biology
[Show abstract][Hide abstract] ABSTRACT: Population structure, growth and body composition (wet-, dry-, ash weight and total lipid) of the Arctic pelagic amphipod Themisto libellula were studied in four fjords on West Spitsbergen, Svalbard, from July to December 2000 and in April 2002. In one of the fjords, Kongsfjorden, growth of T. libellula was calculated as the change in mean length of the 0+ cohort from July to December. The young were released from the brood pouches in early spring (March–April). Summer growth was 3.5mmmonth−1, whereas growth during the autumn was only 0.6mmmonth−1. The size frequency distributions indicated a 2–2.5year life-span. The size structure of the population in Hornsund, the southernmost fjord on Spitsbergen, indicated a delayed time of spawning. The storage of lipids in T. libellula occurred during late summer and towards the winter, when the food items contain the maximum amount of stored lipids.
[Show abstract][Hide abstract] ABSTRACT: The genetic population structure of Atlantic cod in Ullsfjord, north Norway, was studied by analysing allele frequencies at the scnDNA locus pantophysin (Pan I) in 2597 fish. The Pan I frequencies displayed distinct horizontal stratification within the fjord, which persisted over seasons and years. In the spring spawning season, mature cod predominated by the Pan IA allele typical for Norwegian coastal cod, inhabited the inner, more isolated part of the fjord, whereas immature cod predominated by the north-east Arctic cod typical Pan IB allele were found in the outer part open to Barents Sea water. Young of the year caught in the autumn displayed a predominance of the Pan IA allele throughout the fjord. The present study provides evidence for the existence of a local stock of breeding coastal cod in the inner part of Ullsfjord, whereas the outer part is likely to represent feeding grounds for young year classes of north-east Arctic cod. Comparisons with previous studies indicate, however, that there is temporal variation in the relative abundance of north-east Arctic cod and Norwegian coastal cod in the outer part of the fjord.
No preview · Article · Dec 2005 · Fisheries Research