Einar E. Nielsen

Technical University of Denmark, København, Capital Region, Denmark

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Publications (56)243.16 Total impact

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    ABSTRACT: Shallow population structure is generally reported for most marine fish and explained as a consequence of high dispersal, connectivity and large population size. Targeted gene analyses and more recently genome-wide studies have challenged such view, suggesting that adaptive divergence might occur even when neutral markers provide genetic homogeneity across populations. Here, 381 SNPs located in transcribed regions were used to assess large- and fine-scale population structure in the European hake (Merluccius merluccius), a widely distributed demersal species of high priority for the European fishery. Analysis of 850 individuals from 19 locations across the entire distribution range showed evidence for several outlier loci, with significantly higher resolving power. While 299 putatively neutral SNPs confirmed the genetic break between basins (FCT = 0.016) and weak differentiation within basins, outlier loci revealed a dramatic divergence between Atlantic and Mediterranean populations (FCT range 0.275–0.705) and fine-scale significant population structure. Outlier loci separated North Sea and Northern Portugal populations from all other Atlantic samples and revealed a strong differentiation among Western, Central and Eastern Mediterranean geographical samples. Significant correlation of allele frequencies at outlier loci with seawater surface temperature and salinity supported the hypothesis that populations might be adapted to local conditions. Such evidence highlights the importance of integrating information from neutral and adaptive evolutionary patterns towards a better assessment of genetic diversity. Accordingly, the generated outlier SNP data could be used for tackling illegal practices in hake fishing and commercialization as well as to develop explicit spatial models for defining management units and stock boundaries.
    Molecular Ecology 01/2014; 23(1). DOI:10.1111/mec.12568 · 5.84 Impact Factor
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    ABSTRACT: An essential prerequisite of sustainable fisheries is the match between biologically relevant processes and management action. Various populations may however co-occur on fishing grounds, although they might not belong to the same stock, leading to poor performance of stock assessment and management. Plaice in Kattegat and Skagerrak have traditionally been considered as one stock unit. Current understanding indicates that several plaice components may exist in the transition area between the North Sea and the Baltic Sea. A comprehensive review of all available biological knowledge on plaice in this area is performed, including published and unpublished literature together with the analyses of commercial and survey data and historical tagging data. The results suggest that plaice in Skagerrak is closely associated with plaice in the North Sea, although local populations are present in the area. Plaice in Kattegat, the Belts Sea and the Sound can be considered a stock unit, as is plaice in the Baltic Sea. The analyses revealed great heterogeneity in the dynamics and productivity of the various local components, and suggested for specific action to maintain biodiversity.
    Journal of Sea Research 11/2013; 84:40-48. DOI:10.1016/j.seares.2013.04.007 · 1.86 Impact Factor
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    ABSTRACT: The genomic architecture underlying ecological divergence and ecological speciation with gene flow is still largely unknown for most organisms. One central question is whether divergence is genome-wide or localized in ‘genomic mosaics’ during early stages when gene flow is still pronounced. Empirical work has so far been limited, and the relative impacts of gene flow and natural selection on genomic patterns have not been fully explored. Here, we use ecotypes of Atlantic cod to investigate genomic patterns of diversity and population differentiation in a natural system characterized by high gene flow and large effective population sizes, properties which theoretically could restrict divergence in local genomic regions. We identify a genomic region of strong population differentiation, extending over approximately 20 cM, between pairs of migratory and stationary ecotypes examined at two different localities. Furthermore, the region is characterized by markedly reduced levels of genetic diversity in migratory ecotype samples. The results highlight the genomic region, or ‘genomic island’, as potentially associated with ecological divergence and suggest the involvement of a selective sweep. Finally, we also confirm earlier findings of localized genomic differentiation in three other linkage groups associated with divergence among eastern Atlantic populations. Thus, although the underlying mechanisms are still unknown, the results suggest that ‘genomic mosaics’ of differentiation may even be found under high levels of gene flow and that marine fishes may provide insightful model systems for studying and identifying initial targets of selection during ecological divergence.
    Molecular Ecology 04/2013; 22(10):2653-2667. DOI:10.1111/mec.12284 · 5.84 Impact Factor
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    ABSTRACT: Landscape genetics, which considers genetic population structure in the context of spatially referenced parameters in the surrounding landscape, has been shown to be extremely useful for wildlife management. Unfortunately its widespread uptake beyond the research community is hampered due to a lack of effective communication of usable information in a suitable format for application by stakeholders such as wildlife regulators or managers. To improve the communication of suitable information, geovisualization of results should be facilitated in a comprehensible format for stakeholders without GIS or genetic expertise. While specialist applications exist, alternative accessible solutions do not provide adequate support for the visualization of multi-attribute spatially referenced genetic population structure information. As a solution, we document our exploration for an appropriate symbology to communicate landscape genetic information through an accessible, web-based interface. A full problem description, review of available technologies, development rationale, and discussion of the symbology exploration are provided.
    Transactions in GIS 04/2013; 17(2). DOI:10.1111/j.1467-9671.2012.01349.x · 0.54 Impact Factor
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    ABSTRACT: Little is known about how quickly natural populations adapt to changes in their environment and how temporal and spatial variation in selection pressures interact to shape patterns of genetic diversity. We here address these issues with a series of genome scans in four overfished populations of Atlantic cod (Gadus morhua) studied over an 80-year period. Screening of >1000 gene-associated single-nucleotide polymorphisms (SNPs) identified 77 loci that showed highly elevated levels of differentiation, likely as an effect of directional selection, in either time, space or both. Exploratory analysis suggested that temporal allele frequency shifts at certain loci may correlate with local temperature variation and with life history changes suggested to be fisheries induced. Interestingly, however, largely nonoverlapping sets of loci were temporal outliers in the different populations and outliers from the 1928 to 1960 period showed almost complete stability during later decades. The contrasting microevolutionary trajectories among populations resulted in sequential shifts in spatial outliers, with no locus maintaining elevated spatial differentiation throughout the study period. Simulations of migration coupled with observations of temporally stable spatial structure at neutral loci suggest that population replacement or gene flow alone could not explain all the observed allele frequency variation. Thus, the genetic changes are likely to at least partly be driven by highly dynamic temporally and spatially varying selection. These findings have important implications for our understanding of local adaptation and evolutionary potential in high gene flow organisms and underscore the need to carefully consider all dimensions of biocomplexity for evolutionarily sustainable management.
    Molecular Ecology 03/2013; DOI:10.1111/mec.12260 · 5.84 Impact Factor
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    ABSTRACT: High gene flow is considered the norm for most marine organisms and is expected to limit their ability to adapt to local environments. Few studies have directly compared the patterns of differentiation at neutral and selected gene loci in marine organisms. We analysed a transcriptome-derived panel of 281 SNPs in Atlantic herring (Clupea harengus), a highly migratory small pelagic fish, for elucidating neutral and selected genetic variation among populations and to identify candidate genes for environmental adaptation. We analysed 607 individuals from 18 spawning locations in the northeast Atlantic, including two temperature clines (5-12 °C) and two salinity clines (5-35‰). By combining genome scan and landscape genetic analyses, four genetically distinct groups of herring were identified: Baltic Sea, Baltic-North Sea transition area, North Sea/British Isles and North Atlantic; notably, samples exhibited divergent clustering patterns for neutral and selected loci. We found statistically strong evidence for divergent selection at 16 outlier loci on a global scale, and significant correlations with temperature and salinity at nine loci. On regional scales, we identified two outlier loci with parallel patterns across temperature clines and five loci associated with temperature in the North Sea/North Atlantic. Likewise, we found seven replicated outliers, of which five were significantly associated with low salinity across both salinity clines. Our results reveal a complex pattern of varying spatial genetic variation among outlier loci, likely reflecting adaptations to local environments. In addition to disclosing the fine scale of local adaptation in a highly vagile species, our data emphasize the need to preserve functionally important biodiversity.
    Molecular Ecology 06/2012; 21(15):3686-703. DOI:10.1111/j.1365-294X.2012.05639.x · 5.84 Impact Factor
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    ABSTRACT: Illegal, Unreported and Unregulated fishing has had a major role in the overexploitation of global fish populations. In response, international regulations have been imposed and many fisheries have been 'eco-certified' by consumer organizations, but methods for independent control of catch certificates and eco-labels are urgently needed. Here we show that, by using gene-associated single nucleotide polymorphisms, individual marine fish can be assigned back to population of origin with unprecedented high levels of precision. By applying high differentiation single nucleotide polymorphism assays, in four commercial marine fish, on a pan-European scale, we find 93-100% of individuals could be correctly assigned to origin in policy-driven case studies. We show how case-targeted single nucleotide polymorphism assays can be created and forensically validated, using a centrally maintained and publicly available database. Our results demonstrate how application of gene-associated markers will likely revolutionize origin assignment and become highly valuable tools for fighting illegal fishing and mislabelling worldwide.
    Nature Communications 05/2012; 3:851. DOI:10.1038/ncomms1845 · 10.74 Impact Factor
  • Einar E Nielsen, Dorte Bekkevold
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    ABSTRACT: Few species worldwide have attracted as much attention in relation to conservation and sustainable management as Pacific salmon. Most populations have suffered significant reductions, many have disappeared, and even entire evolutionary significant units (ESUs) are believed to have been lost. Until now, no 'smoking gun' in terms of direct genetic evidence of the loss of a salmon ESU has been produced. In this issue of Molecular Ecology, Iwamoto et al. (2012) use microsatellite analysis of historical scale samples of Columbia River sockeye salmon (Oncorhynchus nerka) from 1924 (Fig. 1) to ask the pertinent question: Do the historical samples contain salmon from extirpated populations or ESUs? They identified four genetic groups in the historical samples of which two were almost genetically identical to contemporary ESUs in the river, one showed genetic relationship with a third ESU, but one group was not related to any of the contemporary populations. In association with ecological data, the genetic results suggest that an early migrating Columbia River headwater sockeye salmon ESU has been extirpated. The study has significant importance for conservation and reestablishment of sockeye populations in the Columbia River, but also underpins the general significance of shifting baselines in conservation biology, and how to assess loss of genetic biodiversity. The results clearly illustrate the huge and versatile potential of using historical DNA in population and conservation genetics. Because of the extraordinarily plentiful historical samples and rapid advances in fish genomics, fishes are likely to spearhead future studies of temporal ecological and population genomics in non-model organisms. [Figure: see text].
    Molecular Ecology 04/2012; 21(7):1539-41. DOI:10.1111/j.1365-294X.2012.05498.x · 5.84 Impact Factor
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    ABSTRACT: Widespread environmental changes including climate change, selective harvesting and landscape alterations now greatly affect selection regimes for most organisms. How animals and plants can adapt to these altered environments via contemporary evolution is thus of strong interest. We discuss how to use genetic monitoring to study adaptive responses via repeated analysis of the same populations over time, distinguishing between phenotypic and molecular genetics approaches. After describing monitoring designs, we develop explicit criteria for demonstrating adaptive responses, which include testing for selection and establishing clear links between genetic and environmental change. We then review a few exemplary studies that explore adaptive responses to climate change in Drosophila, selective responses to hunting and fishing, and contemporary evolution in Daphnia using resurrected resting eggs. We further review a broader set of 44 studies to assess how well they meet the proposed criteria, and conclude that only 23% fulfill all criteria. Approximately half (43%) of these studies failed to rule out the alternative hypothesis of replacement by a different, better-adapted population. Likewise, 34% of the studies based on phenotypic variation did not test for selection as opposed to drift. These shortcomings can be addressed via improved experimental designs and statistical testing. We foresee monitoring of adaptive responses as a future valuable tool in conservation biology, for identifying populations unable to evolve at sufficiently high rates and for identifying possible donor populations for genetic rescue. Technological advances will further augment the realization of this potential, especially next-generation sequencing technologies that allow for monitoring at the level of whole genomes.
    Molecular Ecology 03/2012; 21(6):1311-29. DOI:10.1111/j.1365-294X.2011.05463.x · 5.84 Impact Factor
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    ABSTRACT: 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.
    Biochemical Genetics 12/2011; 50(5-6):454-66. DOI:10.1007/s10528-011-9490-0 · 0.82 Impact Factor
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    ABSTRACT: The classical paradigm of marine fish that inhabit a realm with relatively few natural boundaries, exhibit extremely large effective population sizes, and with a potential for high dispersal, predicts high population connectivity, low genetic differentiation, and slow rates of genetic change. With marked improvements in the design of population genetic sampling programmes and the availability of a plethora of advanced molecular tools enabling direct analysis of ecologically significant divergence across fine spatial and temporal scales, it is evident that the evolutionary world of marine fish deviates frequently from such “open-system – low divergence” models. Increasing evidence of genetic divergence across relatively small spatial scales, sometimes in conjunction with rapid phenotypic and genetic shifts, highlights the potential for local adaptation in marine fish. Importantly, advances in genomic tools, such as transcriptomics, high throughput SNP platforms and next generation sequencing now enable empirical determination of genes under selection and the provision of extensive repositories of sequence information. Such data allows the generation of hypotheses and tests of adaptive dynamics in the field. Here, with reference to genome scans and exploration of candidate genes, we examine how such tools can be integrated with field and laboratory studies to explore the extent and significance of local adaptation in marine fish.
    American Fisheries Society 140th Annual Meeting; 09/2011
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    ABSTRACT: The importance of marine organisms for both economical and ecological reasons is enormous; and knowledge of population structure and connectivity is crucial for the sustainable utilisation and conservation of exploited fish stocks. However in most cases our understanding of these spatial patterns of natural variation, both neutral and adaptive, is limited. For marine fish, the maintenance of local stocks containing adaptive diversity is associated with the sustainability and resilience of marine fisheries in the face of climatic and anthropogenic threats. However, many previous studies with genetic markers such as microsatellites have observed weak genetic structure in marine fish and combined with a pelagic larval stage, this has supported the hypothesis that gene flow is extensive and that there is little opportunity for differentiation on local scales. A consequence of the limited opportunity for divergence is the associated assumption that local adaptation would be similarly restricted, except perhaps at macrogeographic levels. However, the application of Single Nucleotide Polymorphisms (SNPs) has the potential to demonstrate previously undetected spatial and temporal population structuring and signatures of adaptive variation. Additionally, SNPs are uniquely applicable for the identification and monitoring of wild fish populations and the traceability of products throughout the food supply chain, allowing effective enforcement of fisheries regulations. Here we demonstrate the utility of SNP panels developed in a European Commission-funded consortium, FishPopTrace, to scenarios that are relevant for the identification of potential illegal fishing and/or mislabeling for two commercially important Atlantic species; cod (Gadus morhua) and herring (Clupea harengus). Markers under selection are typically inappropriate for assessing demographic processes such as gene flow. However, the broad distribution of SNP loci throughout the genome, together with the potential to score large numbers using high throughout approaches, allows for the additional flexibility in traceability studies to establish marker panels with loci that vary in their evolutionary dynamics. Strategies for optimizing population assignment in relation to SNP characteristics and target species biology across various spatial scales will be discussed.
    American Fisheries Society 140th Annual Meeting; 09/2011
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    ABSTRACT: Elucidating the relative roles of dispersal and retention of juvenile stages is an important issue for understanding population structure and evolution in marine organisms. We investigated the genetic population structure of juvenile Atlantic cod (Gadus morhua) within the transition zone between the North Sea and the Baltic Sea, employing nine microsatellite loci, and compared our data with adult cod data from the same area. Small but statistically significant overall differentiation (Fst = 0.003) was found among juvenile samples. Samples of juveniles grouped genetically with adult samples from the same geographical regions. Individual admixture analysis of a large sample of juveniles taken within the transition zone showed that the patterns of genetic differentiation could not be explained by mixing of pure North Sea and Baltic Sea individuals. Instead, the high number of juveniles with intermediate genotypes was compatible with a scenario of exclusive local (transition zone) origin. The results support the hypothesis that population structure in marine fishes is maintained by the retention of juveniles.
    Canadian Journal of Fisheries and Aquatic Sciences 04/2011; 62(10):2219-2225. DOI:10.1139/f05-139 · 2.28 Impact Factor
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    ABSTRACT: Recent improvements in the speed, cost and accuracy of next generation sequencing are revolutionizing the discovery of single nucleotide polymorphisms (SNPs). SNPs are increasingly being used as an addition to the molecular ecology toolkit in nonmodel organisms, but their efficient use remains challenging. Here, we discuss common issues when employing SNP markers, including the high numbers of markers typically employed, the effects of ascertainment bias and the inclusion of nonneutral loci in a marker panel. We provide a critique of considerations specifically associated with the application and population genetic analysis of SNPs in nonmodel taxa, focusing specifically on some of the most commonly applied methods.
    Molecular Ecology Resources 03/2011; 11 Suppl 1:123-36. DOI:10.1111/j.1755-0998.2010.02943.x · 5.63 Impact Factor
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    ABSTRACT: Microsatellite genotyping is a common DNA characterization technique in population, ecological and evolutionary genetics research. Since different alleles are sized relative to internal size-standards, different laboratories must calibrate and standardize allelic designations when exchanging data. This interchange of microsatellite data can often prove problematic. Here, 16 microsatellite loci were calibrated and standardized for the Atlantic salmon, Salmo salar, across 12 laboratories. Although inconsistencies were observed, particularly due to differences between migration of DNA fragments and actual allelic size (‘size shifts’), inter-laboratory calibration was successful. Standardization also allowed an assessment of the degree and partitioning of genotyping error. Notably, the global allelic error rate was reduced from 0.05 ± 0.01 prior to calibration to 0.01 ± 0.002 post-calibration. Most errors were found to occur during analysis (i.e. when size-calling alleles; the mean proportion of all errors that were analytical errors across loci was 0.58 after calibration). No evidence was found of an association between the degree of error and allelic size range of a locus, number of alleles, nor repeat type, nor was there evidence that genotyping errors were more prevalent when a laboratory analyzed samples outside of the usual geographic area they encounter. The microsatellite calibration between laboratories presented here will be especially important for genetic assignment of marine-caught Atlantic salmon, enabling analysis of marine mortality, a major factor in the observed declines of this highly valued species. Electronic supplementary material The online version of this article (doi:10.1007/s10709-011-9554-4) contains supplementary material, which is available to authorized users.
    Genetica 02/2011; 139(3):353-67. DOI:10.1007/s10709-011-9554-4 · 1.75 Impact Factor
  • P F Larsen, P M Schulte, E E Nielsen
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    ABSTRACT: In recent years, variation in gene expression has been recognized as an important component of environmental adaptation in multiple model species, including a few fish species. There is, however, still little known about the genetic basis of adaptation in gene expression resulting from variation in the aquatic environment (e.g. temperature, salinity and oxygen) and the physiological effect and costs of such differences in gene expression. This review presents and discusses progress and pitfalls of applying gene expression analyses to fishes and suggests simple frameworks to get started with gene expression analysis. It is emphasized that well-planned gene expression studies can serve as an important tool for the identification of selection in local populations of fishes, even for non-traditional model species where limited genomic information is available. Recent studies focusing on gene expression variation among natural fish populations are reviewed, highlighting the latest applications that combine genetic evidence from neutral markers and gene expression data.
    Journal of Fish Biology 01/2011; 78(1):1-22. DOI:10.1111/j.1095-8649.2010.02834.x · 1.73 Impact Factor
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    ABSTRACT: The factors that drive partial migration in organisms are not fully understood. Roach (Rutilus rutilus), a freshwater fish, engage in partial migration where parts of populations switch between summer habitats in lakes and winter habitats in connected streams. To test if the partial migration trait is phenotypically plastic or has genetic components, we translocated roach from 2 populations with different opportunities for migration to a lake with migration opportunity, containing a local roach population. This enabled monitoring of partial migration of fish in 3 different situations: 1) previous opportunity for migration, migrating in a familiar environment (the local population); 2) previous opportunity for migration, migrating in an unfamiliar environment; and 3) no previous opportunity for seasonal migration, migrating in an unfamiliar environment. In addition, we evaluated the migration patterns of roach in the lake with migration opportunity wherefrom group 2 fish were translocated. Directional migration in and out of the lakes was monitored using Passive Integrated Transponder technology. Translocated fish with previous migration opportunity showed migration patterns more similar to local fish than to their home lake population, and individuals translocated from the lake without migration opportunity migrated when given the opportunity, suggesting that partial migration is phenotypically plastic and triggered by lake-specific environmental cues. We found temperature to be a proximate cue for migration decisions. Individuals without previous migration opportunity migrated at a lower proportion and with different small-scale migration patterns, suggesting that also genetic components are involved in the expression of the partial migration trait. Copyright 2010, Oxford University Press.
    Behavioral Ecology 11/2010; 21(6):1140-1146. DOI:10.1093/beheco/arq121 · 3.16 Impact Factor
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    ABSTRACT: Worldwide, many commercial fish stocks have experienced dramatic declines due to overfishing. Such fisheries-induced population reductions could potentially erode the genetic diversity of marine fish populations. Based on analyses of DNA extracted from archived and contemporary samples, this paper compares the genetic variability at nine microsatellite loci in a Canadian population of Atlantic cod (Gadus morhua) over 80 years, spanning from before the fishery intensified to now when the population is at historically low abundance. Extensively validated genetic data from the temporally spaced samples were used to estimate the effective population size. Over the period, we observed no loss of either heterozygosity or allelic diversity. Several of the estimation methods applied could not distinguish the effective population size from infinity, and the lower 95% confidence limit on estimates was generally >500, suggesting that the effective population size is probably considerably larger than this. Hence, it appears that the southern Gulf of St. Lawrence cod stock has maintained genetic variability to sustain future evolution despite a dramatic population decline.
    Canadian Journal of Fisheries and Aquatic Sciences 09/2010; 67(10):1585-1595. DOI:10.1139/F10-084 · 2.28 Impact Factor

Publication Stats

3k Citations
243.16 Total Impact Points

Institutions

  • 2007–2014
    • Technical University of Denmark
      København, Capital Region, Denmark
  • 1999–2008
    • Danish Institute for Health Services Research
      København, Capital Region, Denmark
  • 1997–2005
    • Aarhus University
      • Department of Ecology and Genetics
      Aars, Region North Jutland, Denmark