Einar E Nielsen

Publications (18)81.71 Total impact

• Article: The memory remains: application of historical DNA for scaling biodiversity loss.

  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. · 5.52 Impact Factor
• Source

  Available from: Don Waller

  Article: Monitoring adaptive genetic responses to environmental change.

  Michael M Hansen, Isabelle Olivieri, Donald M Waller, Einar E Nielsen
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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. · 5.52 Impact Factor
• Article: Population genomics of marine fishes: identifying adaptive variation in space and time.

  Einar E Nielsen, Jakob Hemmer-Hansen, Peter Foged Larsen, Dorte Bekkevold
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  ABSTRACT: Studies of adaptive evolution have experienced a recent revival in population genetics of natural populations and there is currently much focus on identifying genomic signatures of selection in space and time. Insights into local adaptation, adaptive response to global change and evolutionary consequences of selective harvesting can be generated through population genomics studies, allowing the separation of the effects invoked by neutral processes (drift-migration) from those due to selection. Such knowledge is important not only for improving our basic understanding of natural as well as human-induced evolutionary processes, but also for predicting future trajectories of biodiversity and for setting conservation priorities. Marine fishes possess a number of features rendering them well suited for providing general insights into adaptive genomic evolution in natural populations. These include well-described population structures, substantial and rapidly developing genomic resources and abundant archived samples enabling temporal studies. Furthermore, superior possibilities for conducting large-scale experiments under controlled conditions, due to the economic resources provided by the large and growing aquaculture industry, hold great promise for utilizing recent technological developments. Here, we review achievements in marine fish genomics to date and highlight potential avenues for future research, which will provide both general insights into evolution in high gene flow species, as well as specific knowledge which can lead to improved management of marine organisms.
  Molecular Ecology 08/2009; 18(15):3128-50. · 5.52 Impact Factor
• Source

  Available from: PubMed Central

  Article: Interpopulation differences in expression of candidate genes for salinity tolerance in winter migrating anadromous brown trout (Salmo trutta L.).

  Peter F Larsen, Einar E Nielsen, Anders Koed, Dennis S Thomsen, Pål A Olsvik, Volker Loeschcke
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  ABSTRACT: Winter migration of immature brown trout (Salmo trutta) into freshwater rivers has been hypothesized to result from physiologically stressful combinations of high salinity and low temperature in the sea. We sampled brown trout from two Danish populations entering different saline conditions and quantified expression of the hsp70 and Na/K-ATPases alpha 1b genes following acclimation to freshwater and full-strength seawater at 2 degrees C and 10 degrees C. An interaction effect of low temperature and high salinity on expression of both hsp70 and Na/K-ATPase alpha 1b was found in trout from the river entering high saline conditions, while a temperature independent up-regulation of both genes in full-strength seawater was found for trout entering marine conditions with lower salinities. Overall our results support the hypothesis that physiologically stressful conditions in the sea drive sea-run brown trout into freshwater rivers in winter. However, our results also demonstrate intra-specific differences in expression of important stress and osmoregulative genes most likely reflecting adaptive differences between trout populations on a regional scale, thus strongly suggesting local adaptations driven by the local marine environment.
  BMC Genetics 02/2008; 9:12. · 2.47 Impact Factor
• Article: Adaptive differences in gene expression in European flounder (Platichthys flesus).

  Peter F Larsen, Einar E Nielsen, Timothy D Williams, Jakob Hemmer-Hansen, James K Chipman, Mogens Kruhøffer, Peter Grønkjaer, Stephen G George, Lars Dyrskjøt, Volker Loeschcke
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  ABSTRACT: Population structure was previously believed to be very limited or absent in classical marine fishes, but recently, evidence of weakly differentiated local populations has been accumulating using noncoding microsatellite markers. However, the evolutionary significance of such minute genetic differences remains unknown. Therefore, in order to elucidate the relationship between genetic markers and adaptive divergence among populations of marine fishes, we combined cDNA microarray and microsatellite analysis in European flounders (Platichthys flesus). We demonstrate that despite extremely low levels of neutral genetic divergence, a high number of genes were significantly differentially expressed between North Sea and Baltic Sea flounders maintained in a long-term reciprocal transplantation experiment mimicking natural salinities. Several of the differentially regulated genes could be directly linked to fitness traits. These findings demonstrate that flounders, despite little neutral genetic divergence between populations, are differently adapted to local environmental conditions and imply that adaptation in gene expression could be common in other marine organisms with similar low levels of population subdivision.
  Molecular Ecology 12/2007; 16(22):4674-83. · 5.52 Impact Factor
• Article: Historical analysis of Pan I in Atlantic cod (Gadus morhua): temporal stability of allele frequencies in the southeastern part of the species distribution

  Einar E. Nielsen, Brian R. MacKenzie, Eydfinn Magnussen, Dorte Meldrup
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  ABSTRACT: We investigated temporal genetic differentiation at the pantophysin (Pan I) locus in four Atlantic cod (Gadus morhua) populations from the southeastern part of the species distribution: the Baltic Sea, the North Sea, the Faroe Plateau, and the Faroe Bank. Historical otolith collections enabled investigation of allele frequency variation over time periods up to 69 years employing Pan I primers specifically designed for partially degraded DNA. Small and nonsignificant temporal changes in Pan I allele frequencies were observed in the four populations. Simultaneous microsatellite analysis revealed similar temporal genetic stability with temporal FST values ranging from 0 to 0.006, suggesting limited demographic changes. Sea surface temperature, which has been suggested as the primary driver for the geographical distribution of Pan I alleles in cod, showed no long-term trend although temperature has increased since the mid-1990s. Our study demonstrates that populations in the southeastern part of the species range has been characterized by very high frequencies of the Pan IA allele for many decades, and accordingly, Pan I serves as a reliable marker for genetic stock identification on a macrogeographical scale.Nous étudions la différenciation génétique au locus Pan I chez quatre populations de morues franche (Gadus morhua) du sud-est de l'aire de répartition de l'espèce, soit celles de la Baltique, de la Mer du Nord, du plateau de Féroé et du banc de Féroé. Des collections historiques d'otolithes ont permis d'analyser la variation de la fréquence des allèles sur des périodes pouvant atteindre 69 ans à l'aide d'amorces Pan I spécialement conçues pour l'ADN partiellement dégradé. Nous observons des changements temporels faibles et non significatifs dans la fréquence des allèles de Pan I dans les quatre populations. Des analyses simultanées des microsatellites montrent aussi une stabilité génétique temporelle, les valeurs temporelles de FST variant de 0-0,006, ce qui indique de faibles changements démographiques. La température de surface de la mer, qu'on a suggéré comme principal facteur explicatif de la répartition géographique des allèles de Pan I chez la morue, ne montre aucune tendance à long terme, bien que la température ait augmenté depuis le milieu des années 1990. Notre étude démontre que les populations du sud-est de l'aire de répartition de l'espèce sont caractérisées depuis plusieurs décennies par de hautes fréquences de l'allèle Pan IA; c'est pourquoi Pan I peut servir de marqueur fiable de l'identification génétique des stocks à l'échelle macrogéographique.[Traduit par la Rédaction]
  Canadian Journal of Fisheries and Aquatic Sciences 09/2007; 64(10):1448-1455. · 2.21 Impact Factor
• Article: Evidence of microsatellite hitch-hiking selection in Atlantic cod (Gadus morhua L.): implications for inferring population structure in nonmodel organisms.

  Einar E Nielsen, Michael M Hansen, Dorte Meldrup
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  ABSTRACT: Microsatellites have gained wide application for elucidating population structure in nonmodel organisms. Since they are generally noncoding, neutrality is assumed but rarely tested. In Atlantic cod (Gadus morhua L.), microsatellite studies have revealed highly heterogeneous estimates of genetic differentiation among loci. In particular one locus, Gmo 132, has demonstrated elevated genetic differentiation. We investigated possible hitch-hiking selection at this and other microsatellite loci in Atlantic cod. We employed 11 loci for analysing samples from the Baltic Sea, North Sea, Barents Sea and Newfoundland covering a large part of the species' distributional range. The 'classical' Lewontin-Krakauer test for selection based on variance in estimates of F(ST) and (standardized genetic differentiation) revealed only one significant pairwise test (North Sea-Barents Sea), and the source of the elevated variance could not be ascribed exclusively to Gmo 132. In contrast, different variants of the recently developed ln Rtheta test for selective sweeps at microsatellite loci revealed a high number of significant outcomes of pair-wise tests for Gmo 132. Further, the presence of selection was indicated in at least one other locus. The results suggest that many previous estimates of genetic differentiation in cod based on microsatellites are inflated, and in some cases relationships among populations are obscured by one or more loci being the subject to hitch-hiking selection. Likewise, temporal estimates of effective population sizes in Atlantic cod may be flawed. We recommend, generally, to use a higher number of microsatellite loci to elucidate population structure in marine fishes and other nonmodel species to allow for identification of outlier loci that are subject to selection.
  Molecular Ecology 11/2006; 15(11):3219-29. · 5.52 Impact Factor
• Article: Genetic restoration of a stocked brown trout Salmo trutta population using microsatellite DNA analysis of historical and contemporary samples

  MICHAEL M. HANSEN, DORTE BEKKEVOLD, LASSE F. JENSEN, KAREN-LISE D. MENSBERG, EINAR E. NIELSEN
  Journal of Applied Ecology 05/2006; 43(4):669 - 679. · 5.05 Impact Factor
• Article: Underwater but not out of sight: genetic monitoring of effective population size in the endangered North Sea houting (Coregonus oxyrhynchus)

  Einar E. Nielsen, Michael M. Hansen, Karen-Lise D. Mensberg
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  ABSTRACT: We analysed 12 microsatellite DNA loci in temporal samples (1980, 1994, and 2002) from the only remaining indigenous population of the North Sea houting (Coregonus oxyrhynchus) in the Vidaa River, Denmark. Using a novel temporal method, we estimated effective population size (Ne) to be 577.4 (90% highest posterior density limits 297.2–3719.8). The same method was used to estimate Ne at the beginning and end of the sampled time interval, and the results were indicative of a relatively stable population. In contrast, tests for recent bottlenecks suggested population declines in the 1980 and 1994 samples, possibly reflecting declines prior to 1980 in the total North Sea houting population. To evaluate the usefulness of the two methods for routine genetic monitoring, we simulated population declines corresponding to reproduction by only 20 or 50 parents in 2002. For both simulated samples, the temporal method provided evidence for a population decline, whereas the test for bottlenecks did not suggest population decline. We conclude that the North Sea houting in the Vidaa River is not immediately threatened by inbreeding or loss of evolutionary potential, and the applied temporal method appears very useful for genetic monitoring of effective population size in endangered, isolated fish populations.Nous avons analysé 12 locus microsatellites d'ADN dans des échantillons répartis dans le temps (1980, 1994 et 2002) provenant de la seule population indigène survivante du houting de la mer du Nord (Coregonus oxyrhynchus) dans la Vidaa, Danemark. À l'aide d'une méthode temporelle nouvelle, nous avons estimé la taille effective de la population (Ne) à 577,4 (limites à 90 % de la densité a posteriori la plus élevée, 297,2–3719,8). La même méthode a servi à estimer Ne au début et à la fin de l'intervalle d'échantillonnage et les résultats indiquent que la population est relativement stable. En revanche, des tests pour l'existence de goulots d'étranglement récents laissent croire à des déclins de population dans les échantillons de 1980 et de 1994, qui reflètent peut-être des déclins dans l'ensemble de la population de houtings de la mer du Nord avant les années 1980. Afin d'évaluer l'utilité des deux méthodes pour une surveillance génétique de routine, nous avons simulé des déclins de population correspondant à une reproduction par seulement 20 ou 50 parents en 2002. Dans les deux échantillons simulés, la méthode temporelle fournit des indices d'un déclin de population, alors que le test pour les goulots d'étranglement n'indique aucun déclin. Nous en concluons que le houting de la mer du Nord de la Vidaa n'est pas menacé dans l'immédiat par la consanguinité ou par la perte de potentiel évolutif et que la méthode temporelle utilisée semble très commode pour suivre la taille effective des populations de poissons isolées et menacées.[Traduit par la Rédaction]
  Canadian Journal of Fisheries and Aquatic Sciences 03/2006; 63(4):780-787. · 2.21 Impact Factor
• Article: Long-term stability and effective population size in North Sea and Baltic Sea cod (Gadus morhua).

  Nina A A Poulsen, Einar E Nielsen, Mikkel H Schierup, Volker Loeschcke, Peter Grønkjaer
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  ABSTRACT: DNA from archived otoliths was used to explore the temporal stability of the genetic composition of two cod populations, the Moray Firth (North Sea) sampled in 1965 and 2002, and the Bornholm Basin (Baltic Sea) sampled in 1928 and 1997. We found no significant changes in the allele frequencies for the Moray Firth population, while subtle but significant genetic changes over time were detected for the Bornholm Basin population. Estimates of the effective population size (Ne) generally exceeded 500 for both populations when employing a number of varieties of the temporal genetic method. However, confidence intervals were very wide and Ne's most likely range in the thousands. There was no apparent loss of genetic variability and no evidence of a genetic bottleneck for either of the populations. Calculations of the expected levels of genetic variability under different scenarios of Ne showed that the number of alleles commonly reported at microsatellite loci in Atlantic cod is best explained by Ne's exceeding thousand. Recent fishery-induced bottlenecks can, however, not be ruled out as an explanation for the apparent discrepancy between high levels of variability and recently reported estimates of Ne < 1000. From life history traits and estimates of survival rates in the wild, we evaluate the compatibility of the species' biology and extremely low Ne/N ratios. Our data suggest that very small Ne's are not likely to be of general concern for cod populations and, accordingly, most populations do not face any severe threat of losing evolutionary potential due to genetic drift.
  Molecular Ecology 02/2006; 15(2):321-31. · 5.52 Impact Factor
• Article: Genetic population structure of turbot (Scophthalmus maximus L.) supports the presence of multiple hybrid zones for marine fishes in the transition zone between the Baltic Sea and the North Sea.

  Einar E Nielsen, Peter H Nielsen, Dorte Meldrup, Michael M Hansen
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  ABSTRACT: Genetic population structure of turbot (Scophthalmus maximus L.) in the Northeast Atlantic was investigated using eight highly variable microsatellite loci. In total 706 individuals from eight locations with temporal replicates were assayed, covering an area from the French Bay of Biscay to the Aaland archipelago in the Baltic Sea. In contrast to previous genetic studies of turbot, we found significant genetic differentiation among samples with a maximum pairwise FST of 0.032. Limited or no genetic differentiation was found among samples within the Atlantic/North Sea area and within the Baltic Sea, suggesting high gene flow among populations in these areas. In contrast, there was a sharp cline in genetic differentiation going from the low saline Baltic Sea to the high saline North Sea. The data were explained best by two divergent populations connected by a hybrid zone; however, a mechanical mixing model could not be ruled out. A significant part of the genetic variance could be ascribed to variation among years within locality. Nevertheless, the population structure was relatively stable over time, suggesting that the observed pattern of genetic differentiation is biologically significant. This study suggests that hybrid zones are a common phenomenon for marine fishes in the transition area between the North Sea and the Baltic Sea and highlights the importance of using interspecific comparisons for inferring population structure in high gene flow species such as most marine fishes.
  Molecular Ecology 04/2004; 13(3):585-95. · 5.52 Impact Factor
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  Available from: dtu.dk

  Article: Long-term temporal changes of genetic composition in brown trout (Salmo trutta L.) populations inhabiting an unstable environment.

  Siri Østergaard, Michael M Hansen, Volker Loeschcke, Einar E Nielsen
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  ABSTRACT: The genetic structure of brown trout (Salmo trutta) populations inhabiting rivers on the island of Bornholm in the Baltic Sea was studied on a spatial and temporal scale. Low water levels in the rivers during the summer period are assumed to have a significant impact on the persistence of local populations, possibly resulting in a metapopulation structure. Extinctions may, however, also be buffered by a remnant strategy, whereby juveniles escape to river outlets during periods of drought. We compared polymorphism at seven microsatellite DNA loci in contemporary and past samples collected from 1944 to 1997. A principal component analysis, a hierarchical gene diversity analysis and assignment tests showed that the genetic composition of populations was not temporally stable, and that temporal genetic differentiation was much stronger than spatial differentiation. Genetic variability was high and stable over time. Effective population sizes (Ne) and migration rate (m) were estimated using a maximum-likelihood-based implementation of the temporal method. Ne estimates were low (ranging from 8.3 to 22.9) and estimates of m were high (between 0.23 and 0.99), in contrast to other Danish trout populations inhabiting larger and more environmentally stable rivers (Ne between 39.2 and 289.9 and m between 0.01 and 0.09). Thus, the observed spatio-temporal patterns of genetic differentiation can be explained by drift in small persisting populations, where levels of genetic variation are maintained by strong gene flow. However, observations of rivers devoid of trout suggested that population turnover also takes place. We suggest that Bornholm trout represent a metapopulation where the genetic structure primarily reflects strong drift and gene flow, combined with occasional extinction-recolonization events.
  Molecular Ecology 12/2003; 12(11):3123-35. · 5.52 Impact Factor
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  Available from: webcluster.sitecore.dtu.dk

  Article: Fragmentation by weirs in a riverine system: A study of genetic variation in time and space among populations of European grayling ( Thymallus thymallus ) in a Danish river system

  Torben Meldgaard, Einar E. Nielsen, Volker Loeschcke
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  ABSTRACT: Human induced habitat alterations affect the genetic structure of many fish populations. Weirs in particular have caused fragmented populations previously connected by gene-flow. We studied the effects of weirs on the distribution of genetic variation within European grayling (Thymallus thymallus) populations from the Skjern River, Denmark. We compared microsatellite data from DNA extracted from historic scale samples collected 60 years ago with data from contemporary samples. Pairwise multilocus F ST estimates between all contemporary population samples were significant as well as exact tests for population differentiation. Assignment tests of individuals to a set of baseline samples showed correct assignment to the population of origin of between 54 and 79%. Assignment of individuals from recent samples to the historic population samples showed highly variable results (3–83%) of correct assignment suggesting different population histories. Pairwise multilocus F ST estimates were significantly correlated with the number of intervening weirs but not with waterway distance. A simulation procedure was used to estimate differences in relative population sizes, which indicated that the main river population was approximately three times larger than those of the tributaries. There were no signs of any loss of genetic variation for the river system as a whole during these 60 years. The results show that weirs can be an important factor for creating the current distribution patterns of genetic variation among grayling populations, most likely by only allowing passive downstream drift of fry and obstructing active upstream migration.
  Conservation Genetics 10/2003; 4(6):735-747. · 1.61 Impact Factor
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  Available from: Daniel Ruzzante

  Article: Evidence of a hybrid-zone in Atlantic cod (Gadus morhua) in the Baltic and the Danish Belt Sea revealed by individual admixture analysis.

  Einar E Nielsen, Michael M Hansen, Daniel E Ruzzante, Dorte Meldrup, Peter Grønkjaer
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  ABSTRACT: The study of hybrid zones is central to our understanding of the genetic basis of reproductive isolation and speciation, yet very little is known about the extent and significance of hybrid zones in marine fishes. We examined the population structure of cod in the transition area between the North Sea and the Baltic Sea employing nine microsatellite loci. Genetic differentiation between the North Sea sample and the rest increased along a transect to the Baltic proper, with a large increase in level of differentiation occurring in the Western Baltic area. Our objective was to determine whether this pattern was caused purely by varying degrees of mechanical mixing of North Sea and Baltic Sea cod or by interbreeding and formation of a hybrid swarm. Simulation studies revealed that traditional Hardy-Weinberg analysis did not have sufficient power for detection of a Wahlund effect. However, using a model-based clustering method for individual admixture analysis, we were able to demonstrate the existence of intermediate genotypes in all samples from the transition area. Accordingly, our data were explained best by a model of a hybrid swarm flanked by pure nonadmixed populations in the North Sea and the Baltic Sea proper. Significant correlation of gene identities across loci (gametic phase disequilibrium) was found only in a sample from the Western Baltic, suggesting this area as the centre of the apparent hybrid zone. A hybrid zone for cod in the ecotone between the high-saline North Sea and the low-saline Baltic Sea is discussed in relation to its possible origin and maintenance, and in relation to a classical study of haemoglobin variation in cod from the Baltic Sea/Danish Belt Sea, suggesting mixing of two divergent populations without interbreeding.
  Molecular Ecology 07/2003; 12(6):1497-508. · 5.52 Impact Factor
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  Available from: Daniel Ruzzante

  Article: Long-term effective population sizes, temporal stability of genetic composition and potential for locl adaptation in anadromous brown trout (Salmo trutta) populations.

  Michael M Hansen, Daniel E Ruzzante, Einar E Nielsen, Dorte Bekkevold, Karen-Lise D Mensberg
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  ABSTRACT: We examined the long-term temporal (1910s to 1990s) genetic variation at eight microsatellite DNA loci in brown trout (Salmo trutta L) collected from five anadromous populations in Denmark to assess the long-term stability of genetic composition and to estimate effective population sizes (Ne). Contemporary and historical samples consisted of tissue and archived scales, respectively. Pairwise thetaST estimates, a hierarchical analysis of molecular variance (amova) and multidimensional scaling analysis of pairwise genetic distances between samples revealed much closer genetic relationships among temporal samples from the same populations than among samples from different populations. Estimates of Ne, using a likelihood-based implementation of the temporal method, revealed Ne >or= 500 in two of three populations for which we have historical data. A third population in a small (3 km) river showed Ne >or= 300. Assuming a stepping-stone model of gene flow we considered the relative roles of gene flow, random genetic drift and selection to assess the possibilities for local adaptation. The requirements for local adaptation were fulfilled, but only adaptations resulting from strong selection were expected to occur at the level of individual populations. Adaptations resulting from weak selection were more likely to occur on a regional basis, i.e. encompassing several populations. Ne appears to have declined recently in at least one of the studied populations, and the documented recent declines of many other anadromous brown trout populations may affect the persistence of local adaptation.
  Molecular Ecology 01/2002; 11(12):2523-35. · 5.52 Impact Factor
• Article: Looking for a needle in a haystack: Discovery of indigenous Atlantic salmon (Salmo salar L.) in stocked populations

  Einar E. Nielsen, Michael M. Hansen, Lars A. Bach
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  ABSTRACT: Microsatellite analysis of Atlantic salmon fromfive Danish rivers was performed to determinethe stocked or indigenous status ofindividuals. Genetic variation at six highlypolymorphic microsatellite loci was assayed andused for individual based analyses (assignmenttests). Contemporary samples of adult returningspawners and fry were compared to baseline datafrom: 1) historical DNA samples (from oldscales) representing the indigenouspopulations, 2) samples from another Danishpopulation (Skjern River) used for stocking,and 3) five exogenous populations used forstocking. Assignment power was high. Thepercent of stocked salmon correctly assigned topopulation of origin ranged from 83% to 99%and the percent of indigenous salmon correctlyassigned to population of origin ranged from83% to 90%. For two of the riverssignificantly more individuals were assigned tothe indigenous populations than expected frommisclassification alone, suggesting that someremains of the indigenous populations hadpersisted. Still, many fish were of exogenousorigin. Simulated hybrids among releasedexogenous salmon and between exogenous andreleased Danish salmon (Skjern River) revealedthat natural hybridisation among released fishwas not likely to be the source of the fryclassified as indigenous, however, thepossibility of hybridisation among indigenousand released fish could not be dismissed.Several full sib groups were found amongindigenous natural fry ruling out one or a fewmatings as the source of the indigenous fry.These results show that some native populationsmay persist even after years of introductionand environmental perturbation; geneticinformation can be used to identify thesepopulations and identify individualsrepresenting these populations for use inrestoration programs.
  Conservation Genetics 08/2001; 2(3):219-232. · 1.61 Impact Factor
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  Available from: Ellen L. Rice Kenchington

  Article: Assigning individual fish to populations using microsatellite DNA markers

  Michael M. Hansen, Ellen Kenchington, Einar E. Nielsen
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  ABSTRACT: New statistical developments combined with the use of highly polymorphic microsatellite DNA markers enable the determination of the population of origin of single fish, resulting in numerous new research possibilities and applications in practical management of fish populations. We first describe three main categories of methods available, i.e. (i) assignment tests and related methods, (ii) discriminant function analysis and (iii) artificial neural networks. In all these, individuals can be assigned to the population from which their multilocus genotypes are most likely to be derived. Assignment tests are based on calculations of the likelihood of multilocus genotypes in populations, based on allele frequencies. Discriminant function analysis is based on multivariate statistics, whereas artificial neural networks formulate predictions through exposure to correct solutions. Assignment tests are the methods of choice when considering genetic data alone, whereas discriminant function analysis and artificial neural networks may be useful when genetic data are combined with, for instance, morphological and ecological data. Assignment tests can be used to assess the genetic distinctness of populations, for discriminating among closely related species and to directly identify immigrants or individuals of immigrant ancestry, and thereby study patterns of dispersal among populations, including sex-biased dispersal. In a conservation context, assignment tests can be used to assess the genetic impact of domesticated fish on wild populations and for determining if extant fish populations are in fact indigenous or descendants from stocked fish or strayers, and they can be applied in forensics, for instance to reveal poaching. Assignment tests are at present most useful for studies of freshwater and anadromous fishes owing to stronger genetic differentiation among populations than in marine fishes. However, some genetically divergent populations of marine fishes have been discovered, which could be used as natural laboratories for studying dispersal and gene flow. It is foreseen that ongoing developments in statistical methods, combined with improved techniques for screening large numbers of loci, will permit assignment methods to become standard tools in studies on the biology of fishes.
  Fish and Fisheries 05/2001; 2(2):93 - 112. · 5.80 Impact Factor
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  Available from: Daniel Ruzzante

  Article: Microsatellite and mitochondrial DNA polymorphism reveals life‐history dependent interbreeding between hatchery and wild brown trout (Salmo trutta L.)

  Michael M. Hansen, Daniel E. Ruzzante, Einar E. Nielsen, Karen‐lise D. Mensberg
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  ABSTRACT: The effects of stocking hatchery trout into wild populations were studied in a Danish river, using microsatellite and mitochondrial DNA (mtDNA) markers. Baseline samples were taken from hatchery trout and wild trout assumed to be unaffected by previous stocking. Also, samples were taken from resident and sea trout from a stocked section of the river. Genetic differentiation between the hatchery strain and the local wild population was modest (microsatellite FST = 0.06). Using assignment tests, more than 90% of individuals from the baseline samples were classified correctly. Assignment tests involving samples from the stocked river section suggested that the contribution by hatchery trout was low among sea trout (< 7%), but high (46%) among resident trout. Hybrid index analysis and a high percentage of mtDNA haplotypes specific to indigenous trout observed among resident trout that were assigned to the hatchery strain suggested that interbreeding took place between hatchery and wild trout. The latter result also indicated that male hatchery trout contributed more to interbreeding than females. We suggest that stronger selection acts against stocked hatchery trout that become anadromous compared to hatchery trout that become resident. As most resident trout are males this could also explain why gene flow from hatchery to wild trout appeared to be male biased. The results show that even despite modest differentiation at neutral loci domesticated trout may still perform worse than local populations and it is important to be aware of differential survival and reproductive success both between life-history types and between sexes.
  Molecular Ecology 04/2000; 9(5):583 - 594. · 5.52 Impact Factor