Genetic divergence at the synaptophysin (Syp I) locus among Norwegian coastal and north-east Arctic populations of Atlantic cod

Several nuclear RFLP loci have been discovered recently that exhibit extensive allele frequency variation among Norwegian coastal and north-east Arctic populations of Atlantic cod Gadus morhua. One of these polymorphisms was detected by hybridizing an anonymous cDNA clone (GM798) against genomic DNA digested with the restriction enzyme DraI. This cDNA clone has now been sequenced and identified as synaptophysin (Syp I), an integral synaptic vesicle membrane protein. Primers were constructed that amplify an intron of the Syp I gene that is polymorphic for the DraI site, thus making it possible to use a PCR-based assay to score the polymorphism. A total of 965 individuals sampled from the Barents Sea, coastal areas and fjords in northern Norway have been analysed for this polymorphism. The results confirm that highly significant differences exist between NE Arctic and coastal cod at the Syp I locus. A cluster analysis revealed a deep split between coastal and Arctic populations and hierarchical F-statistics indicated that about 40% of the total variation was attributable to differences between Arctic and coastal groups. The temporal stability of allele frequencies was assessed by comparing Syp I allele frequencies among samples of juveniles (0 group) captured at specific locations in fjords in consecutive years and among samples of adults and juveniles collected from the same fjord. Samples of juveniles collected in 1994 and 1995 in Malangen were genetically indistinguishable whereas juveniles sampled from Dønnesfjord and Ullsfjorden over the same 2-year period exhibited significant differences. Adults and 0-group individuals collected from the same fjord were found to be genetically indistinguishable in Malangen, but not in Balsfjorden. In addition to detecting large differences among Arctic and coastal groups, the Syp I locus suggests that genetic heterogeneity exists among resident populations of cod in different fjords and that gene flow among populations throughout northern Norway may be considerably lower than previously believed.     

High gene flow in polar cod (Boreogadus saida) from West-Svalbard and the Eurasian Basin

The current and projected environmental change of the Arctic Ocean contrasts sharply with the limited knowledge of its genetic biodiversity. Polar cod Boreogadus saida (Lepechin, 1774) is an abundant circumpolar marine fish and ecological key species. The central role of polar cod in the Arctic marine food web warrants a better understanding of its population structure and connectivity. In this study, the genetic population structure of 171 juveniles, collected from several fjords off West-Svalbard (Billefjorden, Hornsund and Kongsfjorden), the northern Sophia Basin and the Eurasian Basin of the Arctic Ocean, was analysed using nine DNA microsatellite loci. Genetic analyses indicated moderate to high genetic diversity, but absence of spatial population structure and isolation-by-distance, suggesting ongoing gene flow between the studied sampling regions. High levels of connectivity may be key for polar cod to maintain populations across wide spatial scales. The adaptive capacity of the species will be increasingly important to face challenges such as habitat fragmentation, ocean warming and changes in prey composition. In view of a limited understanding of the population dynamics and evolution of polar cod, a valuable next step to predict future developments should be an integrated biological evaluation, including population genomics, a life-history approach, and habitat and biophysical dispersal modelling.     

Mitochondrial cytochrome b DNA sequence variation of Atlantic cod from Iceland and Greenland

Sequence variation of a 250–bp (base pair) fragment of the mitochondrial cytochrome b gene has been studied using polymerase chain reaction and direct sequencing of 519 Atlantic cod Gadus morhua from Iceland and 78 cod from Greenland. Twenty-four variable nucleotide sites, mostly silent, define 34 haplotypes. The amount of variation is high ( ĥC =0·73, π=0·52 per 100 bp) with five haplotypes at polymorphic frequencies in Iceland and a number of widely dispersed rather rare haplotypes. A tree of genetic relationships among haplotypes has considerable homoplasy yet it is relatively shallow implying a high turnover of variants of the polymorphism. Net nucleotide genetic divergences among localities are nil. Geographic locality overall area, and inshore/offshore comparison explain none of the variation in an AMOVA, all the variation is among individuals and a null hypothesis of non-differentiation of haplotype frequencies among localities or overall areas cannot be rejected. A temporal year-class effect is found. The evolutionary difference between Greenland and Iceland cod is not significant and the percentage of variation accounted for by the Greenland/Iceland difference is half of what a temporal effect within Iceland explains. There is no evidence for considering the cod at Greenland and Iceland to consist of separate evolutionary units and the question of separate management units must address the lack of diagnostic genotypes and evidence for gene flow from clinal variation.     

Biomarkers in fish from dioxin-contaminated fjords

The Grenland fjords, southern Norway, have been heavily contaminated by dibenzo-p-dioxins and dibenzofurans (dioxins) over decades through inputs from a magnesium smelter. Despite radically decreased inputs since 1990, there are still high levels of dioxins in both biotic and abiotic components of the fjords. The aim of the study was to establish whether biomarkers' responses in three fish species, Atlantic cod (Gadus morhua L.), sea-trout (anadromous brown trout, Salmo trutta L.) and flounder (Platichthys flesus L.), could be used to discern the effects in the most contaminated ecosystem, Frierfjord, from the effects in the adjacent, less-contaminated ecosystem, Eidangerfjord. Biomarker responses clearly indicated that the three fish species were affected by dioxin exposure. Phase I responses in cod and trout could be used to differentiate exposure in the two fjord ecosystems. Phase II responses (glutathione S-transferase) in cod and trout similarly indicated a higher dioxin exposure in Frierfjord compared with Eidangerfjord. Results for glutathione S-transferase and glutathione reductase indicated different exposure levels in the two fjords, but also showed seasonal variability, and the results highlighted the need for baseline data for these biomarkers.     

Pantophysin (Pan I) locus divergence between inshore v. offshore and northern v. southern populations of Atlantic cod in the north‐east Atlantic

More than 6000 cod Gadus morhua , sampled in coastal and offshore waters stretching from the Barents Sea down to the North Sea, were analysed for frequencies of alleles at the scnDNA pantophysin locus ( Pan I)[formerly called synaptophysin ( Syp I)]. The significant allele frequency difference between the two major stocks of cod in Norway, north‐east Arctic cod (NEAC) and Norwegian coastal cod (NCC), was upheld in all years of the investigation (1993 to 2001), and applied both to larval cod and post‐juveniles of various ages. On a north‐south axis, the appearance of a latitudinal cline of post‐juvenile (≥1 year) allele frequencies was exposed. The intermediate allele frequencies in coastal areas of northern Norway, seem to a large extent to be caused by intermingling of the two stocks, although the existence of populations of coastal cod with alternative Pan I frequencies could not be ruled out. The role of selection is yet unresolved. Depth of the sampling location seemed to have an effect on the allele frequencies and their temporal stability, while there was no indication of seasonal variation in the frequencies. Breeding structure was the most likely cause for upholding the extreme divergence in Pan I frequencies between NEAC and NCC.     

Population genetics of drifting (Calanus spp.) and resident (Acartia clausi) plankton in Norwegian fjords

Kaartvedt distinguished between drifting and resident planktonand hypothesized that the latter were distinguished by theirability to maintain their horizontal position in desired habitats(Kaartvedt, 1993). In this study, we examined the populationgenetic consequences of these two lifestyles for copepods infour fjords of western Norway (Lurefjorden, Masfjorden, Sognefjordenand Sørfjorden) and one fjord in eastern Norway (Oslofjorden).Based on DNA sequence variation of a region of mitochondrial16S rRNA, we contrasted population genetic diversity and structurein drifting populations of Calanus spp. with that of residentpopulations of Acartia clausi. With the exception of Sørfjorden(where Calanus spp. were rare), two or three species of Calanusco-occurred in significantly different proportions in the fjords.Based on a 350 base-pair region of mitochondrial 16S rRNA, Calanusspp. varied in molecular genetic diversity, with the highestvalues for C.helgolandicus. There was no evidence of significantgenetic structure of fjord populations for either C.finmarchicusor C.helgolandicus; the population structure of C.glacialiscould not be evaluated as the species was only abundant in Lurefjorden.Acartia clausi was abundant in all five fjords sampled for thisstudy. Molecular genetic diversity of A.clausi, based on a 220bp region of mt 16S rRNA, was within the range of Calanus spp.values. Populations of A.clausi showed significant genetic structure(i.e. haplotype frequencies differed markedly) among the fjords.The results of this study indicated that little exchange (geneflow) occurs between populations of A.clausi in different fjords,and suggested that the populations are long-term residents ofa fjord. In contrast, most Calanus spp. fjord populations maybe replaced periodically, as they drift with currents flowingto and from coastal and fjord environments.     

Evidence for Two Highly Differentiated Herring Groups at Goose Bank in the Barents Sea and the Genetic Relationship to Pacific Herring, Clupea pallasi

Genetic studies on Atlantic herring, Clupea harengus, have generally revealed a low level of genetic variation over large geographic areas. Genetically distinct herring populations in some of the Norwegian fjords are exceptions, and juvenile herring from the large oceanic herring, Norwegian Spring Spawners (NSS), are often found in mixture with local fjord populations as well as widely distributed in the Barents Sea. Research surveys in the eastern Barents Sea (Goose Bank) in 1993, 1994 and 2001 included collection of herring samples for allozyme analyses. As expected the results identified juveniles from NSS stock, but an additional unique group of herring (low vertebrae number), being almost fixed for alternative alleles at several allozyme loci, was detected. In some cases, the two groups of herring were taken in the same trawl catches as documented by highly significant departure from Hardy—Weinberg expectation with large excess of homozygotes providing evidence for population mixing. Large genetic differences (Nei's genetic distance = 1.53; F_ST = 0.754) were detected in pairwise comparisons based on five allozyme loci. The two herring groups were also compared with reference samples of Pacific herring, Clupea pallasi, including one sample from Japan Sea and three Alaskan samples. UPGMA dendrogram based on five allozyme loci revealed a close genetic relationship between the low vertebrae herring in the Barents Sea and the group of samples of Pacific herring. Although significant different in allele frequencies, one of the herring samples clustered together with the reference sample from Bering Sea with genetic distance of 0.008 and F_ST value of 0.032. The close genetic relationship found in this paper, suggest a re-evaluation of the taxonomic status of the Barents Sea herring populations investigated.     

Biomarkers in fish from dioxin-contaminated fjords

Abstract

The Grenland fjords, southern Norway, have been heavily contaminated by dibenzo-p-dioxins and dibenzofurans (dioxins) over decades through inputs from a magnesium smelter. Despite radically decreased inputs since 1990, there are still high levels of dioxins in both biotic and abiotic components of the fjords. The aim of the study was to establish whether biomarkers’ responses in three fish species, Atlantic cod (Gadus morhua L.), sea-trout (anadromous brown trout, Salmo trutta L.) and flounder (Platichthys flesus L.), could be used to discern the effects in the most contaminated ecosystem, Frierfjord, from the effects in the adjacent, less-contaminated ecosystem, Eidangerfjord. Biomarker responses clearly indicated that the three fish species were affected by dioxin exposure. Phase I responses in cod and trout could be used to differentiate exposure in the two fjord ecosystems. Phase II responses (glutathione S-transferase) in cod and trout similarly indicated a higher dioxin exposure in Frierfjord compared with Eidangerfjord. Results for glutathione S-transferase and glutathione reductase indicated different exposure levels in the two fjords, but also showed seasonal variability, and the results highlighted the need for baseline data for these biomarkers.     

The demography of a haemoglobin polymorphism in the Atlantic cod, Gadus morhua L.

Genetic stability was investigated at a polymorphic haemoglobin gene-locus in 13 124 Atlantic cod, Gadus morhua L. A total of 30 year-classes, sampled over 18 years, were variously sampled in 33 named localities. Regional populations showed distinctive allele frequencies, and each major cod fishery showed some degree of genetic imbalance, which was expressed as excessive numbers of homozygotes. This imbalance occurred seasonally in a proportion of the population samples in each of the major cod fisheries. The findings are attributable to migrations of distinctive genetic populations.     

Pattern of genetic differentiation in the Maculinea alcon species group (Lepidoptera, Lycaenidae) in Central Europe

The taxonomic status of Alcon Blues living in Central and Western Europe (conventionally: Maculinea alcon and Maculinea rebeli ) is quite confused. Some authors distinguish them as separate species of the M. alcon species group, while others consider them as subspecies or simply ecological forms. Our aim was to study the pattern of genetic differentiation among several populations of these taxa with reference to their taxonomic position. Imagoes were collected from 27 localities in Central Europe between 1999 and 2003. Samples originated from four regions: northern Hungary, central Hungary, Romania: Transylvania and Slovenia. Enzyme polymorphism was analysed using polyacrylamide gel electrophoresis. In all samples 16 enzyme loci were studied. In the analysis of the data, F -statistics was computed and the total genetic variation was partitioned into within and between population components. Nei's genetic distances were calculated and UPGMA dendrogram was constructed on the basis of the distance matrix. Hierarchical F -statistics and amova was computed to study the pattern of genetic differentiation among the samples. Principal component analysis (PCA) was also carried out using the allele frequencies of the samples. The results of all analyses indicated a high level of differentiation among the samples. The differences among the samples collected in different years from the same population accounted for a considerable amount of the between sample variation. The distribution of the between sample variation did not exhibit a species pattern. The results of amova and PCA indicated that the geographic pattern was slightly more expressed in the between sample variation compared with the species pattern of it. These results seem to contradict with the conventional taxonomical subdivision.     

Population genetic analysis of Euro-Arctic polar cod <Emphasis Type="Italic">Boreogadus saida</Emphasis> suggests fjord and oceanic structuring

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 _ST 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.     

利用SSR标记对新疆主栽玉米杂交种SC704及其亲本的遗传变异检测

玉米杂交种SC704多年来一直是新疆玉米生产的主栽品种。为了评估不同地区品种的遗传变异程度,本研究利用SSR标记时来自全疆各玉米主要生产地的SC704及其亲本共46份材料分别进行了检测。结果表明,父本ZPL717中存在一定程度的杂合、变异等现象,而大部分母本ZPL773和杂交种的遗传一致性较好,但存在个别疑似混杂的材料。另外,在SSR扩增位点中,ZPL773与B73有94％一致,而ZPL717与M017之间只有41％是一致的。自然变异的累积和天然异交可能是导致SC704及其亲本遗传变异的主要原因。     

Patterns of differentiation in a colour polymorphism and in neutral markers reveal rapid genetic changes in natural damselfly populations

The existence and mode of selection operating on heritable adaptive traits can be inferred by comparing population differentiation in neutral genetic variation between populations (often using F(ST) values) with the corresponding estimates for adaptive traits. Such comparisons indicate if selection acts in a diversifying way between populations, in which case differentiation in selected traits is expected to exceed differentiation in neutral markers [F(ST )(selected) > F(ST )(neutral)], or if negative frequency-dependent selection maintains genetic polymorphisms and pulls populations towards a common stable equilibrium [F(ST) (selected) < F(ST) (neutral)]. Here, we compared F(ST) values for putatively neutral data (obtained using amplified fragment length polymorphism) with estimates of differentiation in morph frequencies in the colour-polymorphic damselfly Ischnura elegans. We found that in the first year (2000), population differentiation in morph frequencies was significantly greater than differentiation in neutral loci, while in 2002 (only 2 years and 2 generations later), population differentiation in morph frequencies had decreased to a level significantly lower than differentiation in neutral loci. Genetic drift as an explanation for population differentiation in morph frequencies could thus be rejected in both years. These results indicate that the type and/or strength of selection on morph frequencies in this system can change substantially between years. We suggest that an approach to a common equilibrium morph frequency across all populations, driven by negative frequency-dependent selection, is the cause of these temporal changes. We conclude that inferences about selection obtained by comparing F(ST) values from neutral and adaptive genetic variation are most useful when spatial and temporal data are available from several populations and time points and when such information is combined with other ecological sources of data.     

Differences in Salinity Tolerance and Gene Expression Between Two Populations of Atlantic Cod (Gadus morhua) in Response to Salinity Stress

Populations of marine fish, even from contrasting habitats, generally show low genetic differentiation at neutral genetic markers. Nevertheless, there is increasing evidence for differences in gene expression among populations that may be ascribed to adaptive divergence. Studying variation in salinity tolerance and gene expression among Atlantic cod (Gadus morhua) from two populations distributed across a steep salinity gradient, we observed high mortality (45% North Sea cod and 80% Baltic Sea cod) in a reciprocal common garden setup. Quantitative RT-PCR assays for expression of hsp70 and Na/K-ATPase α genes demonstrated significant differences in gene regulation within and between populations and treatment groups despite low sample sizes. Most interesting are the significant differences observed in expression of the Na/K-ATPase α gene in gill tissue between North Sea and Baltic cod. The findings strongly suggest that Atlantic cod are adapted to local saline conditions, despite relatively low levels of neutral genetic divergence between populations.     

Gene flow and lack of population differentiation in Atlantic cod, Gadus morhua L., from Iceland, and comparison of cod from Norway and Newfoundland

Restriction analysis of mitochondrial DNA was used to study genetic variation and geographic population structure of Atlantic cod from localities around Iceland. Gene phylogenies were constructed and geographic locations superimposed on these. The variation was not localized. Estimated gene flow was large. Thus, Atlantic cod in Iceland belong to a single genetic population. Analyses of published sequence variation of cod from Norway and Newfoundland showed that the extensive continuity of intraspecific phylogeny of cod in Iceland, which is very similar to other marine organisms with a similar life history, extends from Norway to Newfoundland and possibly to larger areas of the Atlantic.     

Genetic response to human‐induced habitat changes in the marine environment: A century of evolution of European sprat in Landvikvannet,Norway

Habitat changes represent one of the five most pervasive threats to biodiversity. However, anthropogenic activities also have the capacity to create novel niche spaces to which species respond differently. In 1880, one such habitat alterations occurred in Landvikvannet, a freshwater lake on the Norwegian coast of Skagerrak, which became brackish after being artificially connected to the sea. This lake is now home to the European sprat, a pelagic marine fish that managed to develop a self‐recruiting population in barely few decades. Landvikvannet sprat proved to be genetically isolated from the three main populations described for this species; that is, Norwegian fjords, Baltic Sea, and the combination of North Sea, Kattegat, and Skagerrak. This distinctness was depicted by an accuracy self‐assignment of 89% and a highly significant F _ST between the lake sprat and each of the remaining samples (average of ≈0.105). The correlation between genetic and environmental variation indicated that salinity could be an important environmental driver of selection (3.3% of the 91 SNPs showed strong associations). Likewise, Isolation by Environment was detected for salinity, although not for temperature, in samples not adhering to an Isolation by Distance pattern. Neighbor‐joining tree analysis suggested that the source of the lake sprat is in the Norwegian fjords, rather than in the Baltic Sea despite a similar salinity profile. Strongly drifted allele frequencies and lower genetic diversity in Landvikvannet compared with the Norwegian fjords concur with a founder effect potentially associated with local adaptation to low salinity. Genetic differentiation (F _ST) between marine and brackish sprat is larger in the comparison Norway‐Landvikvannet than in Norway‐Baltic, which suggests that the observed divergence was achieved in Landvikvannet in some 65 generations, that is, 132 years, rather than gradually over thousands of years (the age of the Baltic Sea), thus highlighting the pace at which human‐driven evolution can happen.     

Spatial and temporal stability of mtDNA haplogroup frequencies in native North America

Mitochondrial DNA lineage frequencies in prehistoric Aleut, eastern Utah Fremont, Southwestern Anasazi, Pyramid Lake, and Stillwater Marsh skeletal samples from northwest Nevada and the Oneota of western Illinois are compared with those in 41 contemporary aboriginal populations of North America. The ancient samples range in age from 300 years to over 6,000 years. The results indicate that the prehistoric inhabitants of North America exhibit the same level of mtDNA variability as contemporary populations of the continent. Variation in modern mtDNA haplogroup frequencies is highly geographically structured, and the prehistoric samples exhibit the same geographic pattern of variation. This indicates that differentiation of regional patterns of mtDNA lineage variation occurred early in North American prehistory (much more than 2,000 years B.P.), has remained relatively stable since its origin, and was little influenced by the disruptions hypothesized for other genetic systems as a result of population declines and relocations at contact.     

Long-term studies on genetic interaction between wild and ranched cod Gadus morhua by use of a genetic marked strain

Releases of farmed fish, whether accidental from commercial aquaculture facilities or intentional as part of stock enhancement/ranching activities, are considered to pose a risk to native gene pools. Stock enhancement studies of Atlantic cod, Gadus morhua , based on artificially produced juveniles, were initiated in 1984 in western Norway, and genetic aspects were incorporated. In order to investigate potential interbreeding between released and wild cod, a genetically marked cod strain was developed, being homozygotic for a rare allele ( GPI‐1*30 ) expressed in white muscle tissue. In the period from 1990 to 1994, juveniles from the genetic marked strain were released in large quantities in three locations (Masfjord, Øygarden, Heimarkspollen), giving a significant increase of the marker allele in the local wild cod populations. Recently, studies have been conducted in the same areas to estimate the extent of interbreeding between the wild and released cod. The results, however, revealed no permanent increase of the frequency of the marker allele and/or GPI‐1*30 heterozygotes as would be expected from interbreeding. The recent data are compared with comprehensive genetic data of the cod populations in the areas before the actual releases, covering the full period from 1994 to 2003. The present results are also discussed in relation to fishing pressure on coastal cod, migration information and reproductive success of released, genetically marked cod.     

Comparing microsatellite variation in north-east Atlantic cod (Gadus morhua L.) to genetic structuring as revealed by the pantophysin (Pan I) locus

Variation at seven microsatellite loci was compared with variation observed at Pan I, a single copy nuclear DNA gene coding for pantophysin, in 14 samples of Atlantic cod ( Gadus morhua ) stretching from Spitsbergen to the North Sea. Population structuring indicated by the two types of markers was concordant and in agreement with the traditional grouping of cod in the study area into three main populations: north-east Arctic cod (NEAC), Norwegian coastal cod (NCC) and North Sea cod (NSC). Microsatellites, however, revealed genetic heterogeneity not only within NCC, as did Pan I, but also within NEAC and NSC, which appeared to be homogenous when analysed for Pan I. Moreover, microsatellites displayed lower levels of differentiation than Pan I between NEAC and two other groups. Differences in the magnitude of differentiation for the two types of markers may be attributable to higher levels of polymorphism and alleged selective neutrality of microsatellites. Isolation by distance was clearly apparent for microsatellites but was less evident for Pan I, indicating that environmentally induced selection appears to shape the patterns of genetic differentiation for this marker. Even though the population structure of north-east Atlantic cod, as revealed by microsatellites and Pan I, appears to be maintained largely by restricted gene flow, selection acting on a recent historical time scale probably contributes to the observed geographic pattern of Pan I frequencies.     

Mitochondrial DNA in the Atlantic cod, Gadus morhua: lack of genetic divergence between eastern and western populations

Mitochondrial DNA variation was examined in two populations of Atlantic cod from the North Sea and the Grand Banks of Newfoundland. Eight restriction enzymes revealed no major genetic difference between these eastern and western populations. These results are discussed in relation to earlier electrophoretic studies on this species.