My research interests are within the fields of population genetics and genomics, evolutionary biology and conservation genetics. I work mainly on freshwater, anadromous and marine fish species.
The current topics of my research include the following:
-Detecting and analysing local adaptation in fish populations, using molecular and quantitative genetics approaches.
-Detecting and analysing selection at the molecular level, using e.g. genome scans.
-The use of historical and contemporary samples for obtaining data on past and present genetic population structure and for estimating demographical parameters such as effective population size and gene flow.
Abstract: European eels (Anguilla anguilla) undertake spawning migrations of more than 5000 kilometres from continental Europe and North Africa to frontal zones in the Sargasso Sea. Subsequently, the larval offspring are advected by large-scale eastward ocean currents towards continental waters. However, the Sargasso Sea is oligotrophic, with generally low plankton biomass, and the feeding biology of eel larvae has so far remained a mystery, hampering understanding of this peculiar life history. DNA barcoding of gut contents of 61 genetically identified A. anguilla larvae caught in the Sargasso Sea showed that even the smallest larvae feed on a striking variety of plankton organisms, and that gelatinous zooplankton is of fundamental dietary importance. Hence, the specific plankton composition seems essential for eel larval feeding and growth, suggesting a linkage between eel survival and regional plankton productivity. These novel insights into the prey of Atlantic eels may furthermore facilitate eel larval rearing in aquaculture, which ultimately may replace the unsustainable use of wild-caught glass eels.
Abstract: Anguillid freshwater eels show remarkable life histories. In the Atlantic, the European eel (Anguilla anguilla) and American eel (A. rostrata) undertake extensive migrations to spawn in the oceanic Sargasso Sea, and subsequently the offspring drift to foraging areas in Europe and North America, first as leaf-like leptocephali larvae which later metamorphose into glass eels. Since recruitment of European and American glass eels has declined drastically during the last decades there is a strong demand for further understanding of the early, oceanic phase of their life-cycle. Consequently, during a field expedition to the eel spawning sites in the Sargasso Sea, we carried out a wide range of dedicated bio-physical studies across areas of eel larval distribution. Our findings suggest a key role of oceanic frontal processes, retaining eel larvae within a zone of enhanced feeding conditions and steering their drift. The majority of the more westerly distributed American eel larvae are likely to follow a westerly/northerly drift route entrained in the Antilles/Florida Currents. European eel larvae are generally believed to initially follow the same route, but their more easterly distribution close to the eastward flowing Subtropical Counter Current indicates that these larvae could follow a shorter, eastward route towards the Azores and Europe. The findings emphasise the significance of oceanic physical-biological linkages in the life-cycle closure of Atlantic eels.
Abstract: Studies of interactions between farmed and wild salmonid fishes have suggested reduced fitness of farmed strains in the wild, but evidence for selection at the genic level is lacking. We studied three brown trout populations in Denmark which have been significantly admixed with stocked hatchery trout (19 to 64%), along with two hatchery strains used for stocking. The wild populations were represented by contemporary samples (2000-2006) and two of them by historical samples (1943-1956). We analyzed 61 microsatellite loci, nine of which showed putative functional relationships (EST-linked or quantitative trait loci). FST based outlier tests provided support for diversifying selection at chromosome regions marked by three loci, two anonymous and one EST-linked. Patterns of differentiation suggested that the loci were candidates for being under diversifying hitch-hiking selection in hatchery versus wild environments. Analysis of hatchery strain admixture proportions showed that in one wild population, two of the loci showed significantly lower admixture proportions than the putatively neutral loci, implying contemporary selection against alleles introduced by hatchery strain trout. In the most strongly admixed population, however, there was no evidence for selection, possibly due to immigration by stocked trout overcoming selection against hatchery-derived alleles or supportive breeding practices allowing hatchery strain trout to escape natural selection. To our knowledge, this is the first study demonstrating footprints of selection in wild salmonid populations subject to spawning intrusion by farmed fish.
Abstract: Farmed Atlantic salmon escapees represent a significant threat to the genetic integrity of natural populations. Not all escapement events are reported, and consequently, there is a need to develop an effective tool for the identification of escapees. In this study, >2200 salmon were collected from 44 cages located on 26 farms in the Hardangerfjord, western Norway. This fjord represents one of the major salmon farming areas in Norway, with a production of 57,000t in 2007. Based upon genetic data from 17 microsatellite markers, significant but highly variable differentiation was observed among the 44 samples (cages), with pair-wise FST values ranging between 0.000-0.185. Bayesian clustering of the samples revealed five major genetic groups, into which the 44 samples were re-organised. Bayesian clustering also identified two samples consisting of fish with mixed genetic background. Performing self-assignment simulations with the data divided into different sub-sets, overall accuracy of assignment was 44% within the entire material (44 samples), 44% for the 28 spring samples, 59% for the 16 autumn samples, and 70% for 8 autumn samples collected from a geographically restricted area. Accuracy of assignment varied greatly among the individual samples. For the Bayesian clustered data set consisting of five genetic groups, overall accuracy of self-assignment was 99%, demonstrating the effectiveness of this strategy to significantly increase accuracy of assignment, albeit at the expense of precision. This study demonstrates the potential to identify the farm of origin for escapees in a region with a large number of salmon farms. The approaches described here will be of relevance to a range of other species reared in culture where identification of escapees may be required.
Abstract: Analyses of historical samples can provide invaluable information on changes to the genetic composition of natural populations resulting from human activities. Here, we analyze 21 microsatellite loci in historical (archived scales from 1927-1956) and contemporary samples of brown trout (Salmo trutta) from six neighbouring rivers in Denmark, to compare the genetic structure of wild populations before and after population declines and stocking with non-local strains of hatchery trout. We show that all populations have been strongly affected by stocking, with admixture proportions ranging from 14 to 64%. Historical population genetic structure was characterized by isolation-by-distance and by positive correlations between historical effective population sizes and habitat area within river systems. Contemporary population genetic structure still showed isolation-by-distance, but also reflected differences among populations in hatchery trout admixture proportions. Despite significant changes to the genetic composition within populations over time, dispersal rates among populations were roughly similar before and after stocking. We also assessed whether population declines or introgression by hatchery strain trout should be the most significant conservation concern in this system. Based on theoretical considerations, we argue that population declines have had limited negative effects for the persistence of adaptive variation, but admixture with hatchery trout may have resulted in reduced local adaptation. Collectively, our study demonstrates the usefulness of analyzing historical samples for identifying the most important consequences of human activities on the genetic structure of wild populations.
Notes: See also the News & Views article: Quinn, T.P. & Seamons, T.D. (2009) Tales from scales: old DNA yields insights into contemporary evolutionary processes affecting fishes. Molecular Ecology, 18, 2545-2546. DOI: 10.1111/j.1365-294X.2009.04199.x
Abstract: Admixture between wild and captive populations is an increasing concern in conservation biology. Understanding the extent of admixture and the processes involved requires identification of admixed and non-admixed individuals. This can be achieved by statistical methods employing Bayesian clustering, but resolution is low if genetic differentiation is weak. Here, we analyze stocked brown trout populations represented by historical (1943-56) and contemporary (2000s) samples, where genetic differentiation between wild populations and stocked trout is weak (pairwise FST of 0.047 and 0.053). By analyzing a high number of microsatellite DNA markers (50) and making use of linkage map information, we achieve clear identification of admixed and non-admixed trout. Moreover, despite strong population-level admixture by hatchery strain trout in one of the populations (70.8%), non-admixed individuals nevertheless persist (7 out of 53 individuals). These remnants of the indigenous population are characterized by later spawning time than the majority of the admixed individuals. We hypothesize that isolation-by-time mediated by spawning time differences between wild and hatchery strain trout is a major factor rescuing a part of the indigenous population from introgression.
Abstract: A total of 929 polymorphic SNPs in EB (out of 54,000 SNPs screened using a BovineSNP50 Illumina Genotyping BeadChip), and 1,524 and 1,403 polymorphic SNPs in WB and PB, respectively, were analysed. EB, WB and PB have all undergone recent drastic reductions in population size. Accordingly, they exhibited extremely depauperate genomes, deviations from genetic equilibrium and a genome organization consisting of a mosaic of haplotype blocks: regions with low haplotype diversity and high levels of linkage disequilibrium. No evidence for positive or stabilizing selection was found in EB, WB and PB, likely reflecting drift overwhelming selection. We suggest that utilization of genome-wide screening technologies, followed by utilization of less expensive techniques (e.g. VeraCode and Fluidigm EP1), holds large potential for genetic monitoring of populations. Additionally, these techniques will allow radical improvements of breeding practices in captive or managed populations, otherwise hampered by the limited availability of polymorphic markers. This result in improved possibilities for 1) estimating genetic relationships among individuals and 2) designing breeding strategies which attempt to preserve or reduce polymorphism in ecologically relevant genes and/or entire blocks. Reviewers: This article was reviewed by: Fyodor Kondrashov and Shamil Sunyaev.
Abstract: In this study, we demonstrate the power of applying complementary DNA (cDNA) microarray technology to identifying candidate loci that exhibit subtle differences in expression levels associated with a complex trait in natural populations of a nonmodel organism. Using a highly replicated experimental design involving 180 cDNA microarray experiments, we measured gene-expression levels from 1098 transcript probes in 90 individuals originating from six brown trout (Salmo trutta) and one Atlantic salmon (Salmo salar) population, which follow either a migratory or a sedentary life history. We identified several candidate genes associated with preparatory adaptations to different life histories in salmonids, including genes encoding for transaldolase 1, constitutive heat-shock protein HSC70-1 and endozepine. Some of these genes clustered into functional groups, providing insight into the physiological pathways potentially involved in the expression of life-history related phenotypic differences. Such differences included the down-regulation of genes involved in the respiratory system of future migratory individuals. In addition, we used linear discriminant analysis to identify a set of 12 genes that correctly classified immature individuals as migratory or sedentary with high accuracy. Using the expression levels of these 12 genes, 17 out of 18 individuals used for cross-validation were correctly assigned to their respective life-history phenotype. Finally, we found various candidate genes associated with physiological changes that are likely to be involved in preadaptations to seawater in anadromous populations of the genus Salmo, one of which was identified to encode for nucleophosmin 1. Our findings thus provide new molecular insights into salmonid life-history variation, opening new perspectives in the study of this complex trait.
Abstract: 1. The present study was designed to characterize the genetic structure of brown trout (Salmo trutta) populations from the southern Balkans and to assess the spread of non-native strains and their introgression into native trout gene pools. We analysed polymorphism at nine microsatellite loci in seven supposedly non-admixed and three stocked brown trout populations.
2. The analyses confirmed the absence of immigration and extraordinarily strong genetic differentiation among the seven non-introgressed populations in parallel with low levels of intrapopulation genetic variability. In contrast, analyses of the stocked populations revealed that the genetic integrity of the local populations had been substantially changed, and the populations must be characterized as hybrid swarms. The pattern of population differentiation observed at microsatellites contrasted to that depicted previously by mtDNA variation. However, the close relationships between populations from the Danube and Axios river systems proposed solely by microsatellites could be explained by palaeogeographic events.
3. Our research showed that most of the populations examined represent unique gene pools, whose existence is critically compromised. Therefore, appropriate management and conservation strategies should be developed urgently in order to protect the subspecific biodiversity and to reverse currently negative trends.
Abstract: Baltic Sea herring (Clupea harengus) have been shown to exhibit morphological differences across the marked salinity and temperature gradients in the region. Here we analyse genetic (nine microsatellite loci), morpho metric (skull shape), and meristic (pectoral fin rays and number of vertebrae) variations across seven samples of spawning herring collected from four spawning locations in the Baltic Sea to examine whether morphological variation correlates with genetic and (or) environmental factors. Results suggest that herring is adapting to its environment through a combination of selection and plastic responses. Skull shape, including and excluding size variation, differed significantly among samples, both temporally and spatially. Genetic and morphometric distances were correlated, especially when size variation was excluded from the analysis. When size variation was included, skull shape variation was more closely correlated with environmental distances among spawning locations. Vertebrate number differed among samples and was correlated with environmental distances, whereas the number of fin rays was not. Genetic and geographic distances among samples were not correlated.
Abstract: BACKGROUND:
Adaptive radiation within fishes of the Coregonus lavaretus complex has created numerous morphs, posing significant challenges for taxonomy and conservation priorities. The highly endangered North Sea houting (C. oxyrhynchus; abbreviated NSH) has been considered a separate species from European lake whitefish (C. lavaretus; abbreviated ELW) due to morphological divergence and adaptation to oceanic salinities. However, its evolutionary and taxonomic status is controversial. We analysed microsatellite DNA polymorphism in nine populations from the Jutland Peninsula and the Baltic Sea, representing NSH (three populations, two of which are reintroduced) and ELW (six populations). The objectives were to: 1) analyse postglacial recolonization of whitefish in the region; 2) assess the evolutionary distinctiveness of NSH, and 3) apply several approaches for defining conservation units towards setting conservation priorities for NSH.
RESULTS:
Bayesian cluster analyses of genetic differentiation identified four major groups, corresponding to NSH and three groups of ELW (Western Jutland, Central Jutland, Baltic Sea). Estimates of historical migration rates indicated recolonization in a north-eastern direction, suggesting that all except the Baltic Sea population predominantly represent postglacial recolonization via the ancient Elbe River. Contemporary gene flow has not occurred between NSH and ELW, with a divergence time within the last 4,000 years suggested from coalescence methods. NSH showed interbreeding with ELW when brought into contact by stocking. Thus, reproductive isolation of NSH was not absolute, although possible interbreeding beyond the F1 level could not be resolved.
CONCLUSIONS:
Fishes of the C. lavaretus complex in the Jutland Peninsula originate from the same recolonization event. NSH has evolved recently and its species status may be questioned due to incomplete reproductive isolation from ELW, but it was shown to merit consideration as an independent conservation unit. Yet, application of several approaches for defining conservation units generated mixed outcomes regarding its conservation priority. Within the total species complex, it remains one among many recently evolved unique forms. Its uniqueness and high conservation priority is more evident at a local geographical scale, where conservation efforts will also benefit populations of a number of other endangered species.
Abstract: Knowledge of the role of landscapes in shaping genetic connectivity and divergence is essential for understanding patterns of biogeography and diversity. This is particularly relevant for the Andes region, a major biodiversity hotspot of relatively recent origin. We examined the phylogeography and landscape genetics of the Andean wax palm Ceroxylon echinulatum (Arecaceae) that occurs in two narrow bands of montane forests on each side of the Andes in Ecuador and northeastern Peru. First, we tested the hypothesis of C. echinulatum being a geographic cline species crossing the Andes in the Amotape–Huancabamba zone (AHZ) of southern Ecuador/northern Peru, as indicated by observations on fruit morphology. Second, we assessed the timeframe of cross-Andean divergence, and third, we investigated the impact of contemporary and historical landscape features on observed spatio-genetic patterns. Individual-based Bayesian clustering (BC) identified a northeastern, southeastern, southwestern, and northwestern cluster, with areas of genetic discontinuity coinciding with the Andes and the Giron–Paute deflection. F-statistics derived from BC suggested an east-to-west dispersal history. Population-based analyses revealed strong genetic structuring at both small and large geographic scales. Interpopulation relationships and Mantel tests strongly supported the cline model with cross-Andean dispersal in the AHZ. Along the cline, gene flow measured as FST was mainly limited by distance, with less but significant impact of climatic friction. Coalescent analysis revealed that cross-Andean divergence took place during the Quaternary. Significant historical isolation (RST > FST) was found in the southwestern population. The current study illustrates a joint effect of founder dynamics, divergence by distance and historical isolation on patterns of Andean diversity and distribution.
Abstract: Archived scales and otoliths constitute a unique source of DNA that potentially enables extension of the temporal scale of genetic studies of fish populations by decades and even centuries. We review recent insights into fish population and conservation genetics obtained using analysis of DNA from archived samples. This involves both new knowledge about demographic parameters and population structure in wild populations and insights into consequences of anthropogenic pressure resulting from over-harvesting, habitat degradation and stocking. We show that the latter category of studies have led to significant changes of management practices. Ongoing improvement of genetic methods will undoubtedly further expand the ability to utilize historical DNA samples. We envisage that temporal comparisons of large numbers of coding genes will lead to novel insights into selective responses of fish populations to anthropogenic challenges, particularly fisheries-induced selection and global warming. However, both acquisition and storage of historical DNA samples can be hurdles to temporal genetic analyses, while degradation and low copy number in historical DNA samples render genetic data from such sources prone to technical artefacts. We summarize recommendations for storage of samples and DNA extraction and provide checklists for validation of genotyping results. Finally, we stress that validation procedures also involve documentation of the time and population of origin of historical samples, and the inferences drawn should account for the technical and statistical uncertainties associated with historical DNA analysis.
Abstract: Knowledge of local adaptation and adaptive potential of natural populations is becoming increasingly relevant due to anthropogenic changes of the environment, such as climate change. The concern is that populations will be negatively affected by increasing temperatures without the capacity to adapt. Temperature-related adaptability in traits related to phenology and early life-history are expected to be particularly important in salmonid fishes. We focused on the latter and investigated if four populations of brown trout (Salmo trutta) are locally adapted in early life-history traits. These populations spawn in rivers that experience different temperature conditions during the time of incubation of eggs and embryos. The populations were reared in a common garden experiment at three different temperatures. Quantitative genetic differentiation (QST) exceeded neutral molecular differentiation (FST) for two traits, indicating local adaptation. A temperature effect was observed for three traits. However, this effect varied among populations due to locally adapted reaction norms, corresponding to the temperature regimes experienced by the populations in their native environments. Additive genetic variance and heritable variation in phenotypic plasticity suggest that although increasing temperatures are likely to affect some populations negatively, they may have the potential to adapt to changing temperature regimes.
Abstract: Temporal samples of Danish brown trout (Salmo trutta) from populations representing varying geographical scales were analysed using eight putatively neutral microsatellite loci and two microsatellite loci embedded in TAP genes (Transporter associated with Antigen Processing). These genes encode molecules that are central to the major histocompatibility complex (MHC) class I restricted antigen presentation and thus integral components in the adaptive immune system. As such, they could be influenced by selection, driven by pathogens and parasites in a manner similar to MHC genes. Analysis of allele frequencies at presumably neutral microsatellite loci revealed a temporally unstable population structure within regions, while the population structure was stable over time among regions. Analyses of the two TAP markers indicated an effect of selection at both a regional and micro-geographical spatial scale. Moreover, signals of divergent selection among temporal samples within localities suggest that selection also might fluctuate at a temporal scale. These results suggest that immune genes other than the classical MHC class I and II might be subject to selection and warrant further studies of functional polymorphism of such genes in natural populations.Heredity (2008) 100, 79-91; doi:10.1038/sj.hdy.6801067; published online 7 November 2007.
Abstract: Brown trout populations in the Hardanger Fjord, Norway, have declined drastically due to increased exposure to salmon lice from salmonid aquaculture. We studied contemporary samples from seven populations and historical samples (1972 and 1983) from the two largest populations, one of which has declined drastically whereas the other remains stable. We analysed 11 microsatellite loci, including one tightly linked to the UBA gene of the major histocompatibility class I complex (MHC) and another locus linked to the TAP2A gene, also associated with MHC. The results revealed asymmetric gene flow from the two largest populations to the other, smaller populations. This has important conservation implications, and we predict that possible future population recoveries will be mediated primarily by the remaining large population. Tests for selection suggested diversifying selection at UBA, whereas evidence was inconclusive for TAP2A. There was no evidence for temporally fluctuating selection. We assessed the distribution of adaptive divergence among populations. The results showed the most pronounced footprints of selection between the two largest populations subject to the least immigration. We suggest that asymmetric gene flow has an important influence on adaptive divergence and constrains local adaptive responses in the smaller populations. Even though UBA alleles may not affect salmon louse resistance, the results bear evidence of adaptive divergence among populations at immune system genes. This suggests that similar genetic differences could exist at salmon louse resistance loci, thus rendering it a realistic scenario that differential population declines could reflect differences in adaptive variation.
Abstract: ABSTRACT: A recent study revealing geographical and environmental barriers to gene flow in the harbour porpoise shows the great potential of 'landscape genetics' when applied to marine organisms.
Abstract: Estimation of effective population sizes (N(e)) and temporal gene flow (N(e)m, m) has many implications for understanding population structure in evolutionary and conservation biology. However, comparative studies that gauge the relative performance of N(e), N(e)m or m methods are few. Using temporal genetic data from two salmonid fish population systems with disparate population structure, we (i) evaluated the congruence in estimates and precision of long- and short-term N(e), N(e)m and m from six methods; (ii) explored the effects of metapopulation structure on N(e) estimation in one system with spatiotemporally linked subpopulations, using three approaches; and (iii) determined to what degree interpopulation gene flow was asymmetric over time. We found that long-term N(e) estimates exceeded short-term N(e) within populations by 2-10 times; the two were correlated in the system with temporally stable structure (Atlantic salmon, Salmo salar) but not in the highly dynamic system (brown trout, Salmo trutta). Four temporal methods yielded short-term N(e) estimates within populations that were strongly correlated, and these were higher but more variable within salmon populations than within trout populations. In trout populations, however, these short-term N(e) estimates were always lower when assuming gene flow than when assuming no gene flow. Linkage disequilibrium data generally yielded short-term N(e) estimates of the same magnitude as temporal methods in both systems, but the two were uncorrelated. Correlations between long- and short-term geneflow estimates were inconsistent between methods, and their relative size varied up to eightfold within systems. While asymmetries in gene flow were common in both systems (58-63% of population-pair comparisons), they were only temporally stable in direction within certain salmon population pairs, suggesting that gene flow between particular populations is often intermittent and/or variable. Exploratory metapopulation N(e) analyses in trout demonstrated both the importance of spatial scale in estimating N(e) and the role of gene flow in maintaining genetic variability within subpopulations. Collectively, our results illustrate the utility of comparatively applying N(e), N(e)m and m to (i) tease apart processes implicated in population structure, (ii) assess the degree of continuity in patterns of connectivity between population pairs and (iii) gauge the relative performance of different approaches, such as the influence of population subdivision and gene flow on N(e) estimation. They further reiterate the importance of temporal sampling replication in population genetics, the value of interpreting N(e)or m in light of species biology, and the need to address long-standing assumptions of current N(e), N(e)m or m models more explicitly in future research.
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 (N-e) 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
Abstract: 1. Gene flow from domesticated to wild populations is a major threat to wild salmonid fish. However, few studies have addressed how populations could be restored after admixture has occurred. We analysed the prospects for restoring the previously intensively stocked brown trout population of the Skjern River, Denmark, by identifying remaining non-admixed individuals to be used for supportive breeding.
2. We analysed microsatellite DNA markers in historical (1940–50s) and contemporary (1992–2004) samples from the Skjern River system, from the strain of domesticated trout previously used for stocking, and from the neighbouring Storå River. We analysed admixture proportions to estimate the genetic contribution by domesticated trout. We identified non-admixed trout using assignment tests, and further analysed the possible sources of indigenous trout by estimating contemporary migration among populations.
3. Genetic differentiation between the historical Storå and Skjern river populations was low (θST = 0·004), suggesting considerable gene flow in the past. The contemporary Skjern and Storå river populations and a supportive breeding brood stock were strongly admixed, but some non-admixed individuals nevertheless remained in the wild-caught samples. In addition, two resident populations in isolated tributaries were found to be indigenous. The indigenous anadromous individuals from the Skjern River were unlikely to have been recruited from either the isolated tributary populations or the neighbouring Storå River and were presumably derived from unidentified spawning sites in the river system.
4. All but one non-admixed anadromous Skjern River trout were females, which we ascribed to sampling bias. Moreover, all non-admixed fish were late-spawning (January–February) whereas the majority of all trout caught for the study were ripe by November–December. The difference in spawning time could be an important factor delaying complete admixture of domesticated and indigenous trout.
5. Synthesis and applications. This study demonstrates the feasibility of restoring populations that have been admixed with exogenous individuals, by identifying non-admixed individuals using genetic markers. However, the results also highlight the problem that numbers of identified non-admixed individuals may be small, necessitating identification of nearby, closely related populations that can be incorporated into breeding programmes.
Abstract: Little is known about the effects of ranched gadoids escaping into wild populations, and plans for substantial up-scaling of gadoid mariculture raise concerns about detrimental effects on local gene pools. Genetic studies from salmonid populations subjected to intentional or unintentional releases of hatchery-produced fish suggest that wild gene pools are affected by introgression, but that the genetic impact can be minor relative to expectations from the often substantial numbers of released hatchery fish. However, even if resilience to introgression is a general trend, wild population fitness is still predicted to be jeopardized by releases. In this paper, we review theoretical genetic effects of escapes of cultivated individuals and the empirical evidence for introgression effects, which are based mainly on salmonid studies. Based on knowledge of gadoid population structure and life history traits, we make predictions for effects of gadoid mariculture on wild populations and discuss approaches for monitoring and minimizing introgression effects. (c) 2005 International Council for the Exploration of the Sea. Published by Elsevier Ltd. All rights reserved
Abstract: The hypothesis that effective population sizes are low in hatchery-reared catla (Catla catla) from Bangladesh, possibly leading to inbreeding and loss of variation, was tested. The study was based on analysis of seven microsatellite loci in three samples of hatchery-reared catla and four samples representing wild populations. Pair-wise estimates of genetic differentiation between samples were low between wild samples (θ ranging from 0·012 to 0·034), but high between hatchery samples (θ ranging from 0·153 to 0·185), suggesting strong genetic drift in hatcheries. Genetic variation, both in terms of expected heterozygosity and allelic richness, was significantly lower in hatchery samples than in samples of wild catla. Application of a method for reconstructing families among offspring without parental genetic data showed that the hatchery samples consisted of very few half- and full-sib families, whereas the wild samples consisted of a high number of families, suggesting that most individuals were unrelated. Finally, estimation of the effective number of parents (Nb) in the largest sample of hatchery fish confirmed that effective population size was low (Nb = 14·9 for multiallelic loci and Nb = 10·6 if alleles were pooled into two composite alleles). The results show that low effective population sizes leading to loss of variation and possibly inbreeding depression should be a matter of serious concern in aquaculture production of catla.
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.
Abstract: During the past 50 years the number of badgers (Meles meles) in Denmark has declined by c. 50%. To assess the genetic consequences of the demographic decline, six DNA-microsatellite loci were used to analyse 139 badger tissue-samples, which were collected in 1995-98 from three zones (1, 2 and 3) in Jutland (Denmark). Results from contemporary samples were compared to data obtained from DNA extracted from teeth belonging to 39 badgers collected from zones 1 and 2 in 1957-66. The microsatellites showed a low to moderate polymorphism, and the within area genetic diversity (H-E) was relatively low (0.308 <= H-E <= 0.441) as compared to other carnivores and mustelids. Genetic differentiation among the three recent sampling zones was significant (F-ST = 0.072, P < 0.0001). The F-ST values between the two recent (F-ST = 0.092, P < 0.0001) and the two historical samples (zones 1 and 2; F-ST = 0.073, P < 0.0001) were significant and similar. The H-E and F-ST of the recent and historical zones were not significantly different (P > 0.05). Despite the drastic recent decline, Danish badgers did not show apparent signs of genetic bottlenecks in both recent and historical samples. The use of molecular techniques which allowed us to work with small amounts of degraded DNA extracted from old teeth, allowed us to exclude the hypothesis that genetic differentiation between zones 1 and 2 was owing to a barrier, which has appeared in the last 50 years. Furthermore, the low genetic variability and therefore the relatively high genetic differentiation shown by Danish badgers were also shown not to be the result of the recent drastic population decline
Abstract: Twentyâ€one allozyme loci in samples of wildâ€caught and hatcheryâ€reared Indian major carps from Bangladesh were analysed. Bayesian modelâ€based clustering analysis revealed the presence of four taxa, corresponding to the three known species along with a fourth unknown taxon present in two hatchery samples. Individual admixture coefficients showed that 24% of all hatcheryâ€reared fishes were hybrids, whereas a single hybrid was observed in the wildâ€caught samples. Only catla Catla catla× rohu Labeo rohita and mrigal Cirrhinus cirrhosus× rohu hybrids were observed, the vast majority of which were F1 hybrids, though five individuals represented putative backcrosses. Mitochondrial DNA analysis revealed that catla × rohu hybridization primarily involved catla males and rohu females, whereas mrigal × rohu hybrids primarily resulted from rohu males and mrigal females. Despite the high percentage of F1â€hybrids in hatchery samples, reproductive barriers among species have so far precluded widespread introgression. Continued hybridization may eventually lead to a breakdown of species barriers, thereby compromising the genetic integrity of the species in the wild, and leading to production losses in aquaculture.
Abstract: The northern pike Esox lucius L. is a freshwater fish exhibiting pronounced population subdivision and low genetic variability. However, there is limited knowledge on phylogeographical patterns within the species, and it is not known whether the low genetic variability reflects primarily current low effective population sizes or historical bottlenecks. We analysed six microsatellite loci in ten populations from Europe and North America. Genetic variation was low, with the average number of alleles within populations ranging from 2.3 to 4.0 per locus. Genetic differentiation among populations was high (overall theta(ST) = 0.51; overall rho(ST) = 0.50). Multidimensional scaling analysis of genetic distances between populations and spatial analysis of molecular variance suggested a single phylogeographical race within the sampled populations from northern Europe, whereas North American and southern European populations were highly distinct. A population from Ireland was monomorphic at all loci, presumably reflecting founder events associated with introduction of the species to the island in the sixteenth century. Bayesian analysis of demographic parameters showed differences in theta (a product of effective population size and mutation rate) among populations from large and small water bodies, but the relative differences in theta were smaller than expected, which could reflect population subdivision within the larger water bodies. Finally, the analyses showed drastic population declines on a time scale of several thousand years within European populations, which we ascribe to either glacial bottlenecks or postglacial founder events. (C) 2005 The Linnean Society of London
Abstract: We analysed family relationships among brown trout from two small tributary populations that have been suggested as a source of individuals for supportive breeding, using variation at eight microsatellite loci. As a control, we analysed a sample of supposedly unrelated individuals representing a large anadromous population, and we simulated unrelated individuals based on the allelic distributions in all three samples. Two different approaches were used: (1) pairwise estimates of relatedness between individuals and (2) a method for partitioning individuals into half-sib and full-sib families. The anadromous population did not show evidence of a significant number of closely related individuals. In both tributary populations, however, the distributions of pairwise relatedness estimates suggested the presence of several related individuals, and sibship reconstruction suggested fewer families consisting of more individuals than were observed for the simulated individuals. The expected increase of inbreeding coefficient in the two samples due to family structure was 0.026 and 0.030 respectively. Moreover, tests for recent bottlenecks yielded significant outcomes in both populations suggesting a history of low effective population sizes. Depending on the effective population size of captive spawners and past effective population sizes in the populations it could be beneficial to conduct sib-avoidance matings, though this cannot eliminate inbreeding but only delay it. Alternatively, individuals from different populations could be crossed. Sibship reconstruction provided the clearest evidence for family structure, but pairwise relatedness is the best measure for designing mating schemes, as it allows for mating as unrelated individuals as possible rather than just avoiding mating between sibs
Abstract: Temporal sampling within the spring-spawning season has revealed differentiation in length-at-age in herring at Rugen and differentiation in, e.g., Anisakis infestation rate, otolith microstructure, and gillraker counts in Gdansk Bay, leading to the expectation that spawning waves consist of distinct herring populations. We tested this expectation by analysing genetic variation at nine microsatellite loci in samples collected at different times during the March to May spawning season in 2 consecutive years, 2002 and 2003. Length-at-age, mean length, and age distributions were compared among samples within locations but did not show consistent temporal patterns. Pairwise genetic differentiation among temporal samples within season was low and non-significant in the Gdansk Bay (0 < F-ST < 0,0025) but higher among Rugen samples (0.0008 < F-ST < 0.0113). Samples from Rugen collected in 2002 differed significantly from each other, and individual assignment tests showed increased divergence with time. Differentiation was not confounded by effects of age class or sex. We conclude that spawning waves are not genetically differentiated among Gdansk samples based on factors analysed in this study, whereas genetically distinct but sympatric spawning populations may be found at Rugen. (c) 2005 International Council for the Exploration of the Sea. Published by Elsevier Ltd. All rights reserved
Abstract: During the last decade, brackish northern pike populations in Denmark have been subject to stocking programmes, using nonindigenous pike from freshwater lakes, in order to compensate for drastic population declines. The present study was designed to investigate the genetic impact of stocking freshwater pike into a brackish pike population in Stege Nor, Denmark. We analysed polymorphism at eight microsatellite loci in samples representing the indigenous Stege Nor population prior to stocking (ie from 1956 to 1957), along with a sample of the contemporary Stege Nor population and samples from the three populations used for stocking. Despite large numbers of stocked fry, the results from both individual and population level admixture analyses demonstrated extremely poor performance and <1% introgression of stocked freshwater pike into the brackish pike population. Furthermore, pairwise F(ST) estimates between samples demonstrated close genetic relationship among temporal samples from Stege Nor, indicating temporal stability over the last 45 years. We also estimated the effective population size (N(e)) of pike in Stege Nor and applied a test for recent population bottlenecks. The harmonic mean of N(e) was relatively high (>250), but there were indications of bottlenecks in all samples and populations. We ascribe this finding to historical rather than recent bottlenecks, possibly dating back to founder events associated with postglacial recolonisation.
Abstract: Numerically small but statistically significant genetic differentiation has been found in many marine fish species despite very large census population sizes and absence of obvious barriers to migrating individuals. Analyses of morphological traits have previously identified local spawning groups of herring (Clupea harengus L.) in the environmentally heterogeneous Baltic Sea, whereas allozyme markers have not revealed differentiation. We analysed variation at nine microsatellite loci in 24 samples of spring-spawning herring collected at 11 spawning locations throughout the Baltic Sea. Significant temporal differentiation was observed at two locations, which we ascribe to sympatrically spawning but genetically divergent 'spawning waves'. Significant differentiation was also present on a geographical scale, though pairwise F(ST) values were generally low, not exceeding 0.027. Partial Mantel tests showed no isolation by geographical distance, but significant associations were observed between genetic differentiation and environmental parameters (salinity and surface temperature) (0.001 < P < or = 0.099), though these outcomes were driven mainly by populations in the southwestern Baltic Sea, which also exhibits the steepest environmental gradients. Application of a novel method for detecting barriers to gene flow by combining geographical coordinates and genetic differentiation allowed us to identify two zones of lowered gene flow. These zones were concordant with the separation of the Baltic Sea into major basins, with environmental gradients and with differences in migration behaviour. We suggest that similar use of landscape genetics approaches may increase the understanding of the biological significance of genetic differentiation in other marine fishes.
Abstract: The spatial and temporal genetic structure of brown trout populations from three small tributaries of Lake Hald, Denmark, was studied using analysis of variation at eight microsatellite loci. From two of the populations temporal samples were available, separated by up to 13 years (3.7 generations). Significant genetic differentiation was observed among all samples, however, hierarchical analysis of molecular variance (AMOVA) showed that differentiation among populations accounted for a non-significant amount of the genetic differentiation, whereas differentiation among temporal samples within populations was highly significant (0.0244, P<0.001). Estimates of effective population size (N e) using a maximum-likelihood based implementation of the temporal method, yielded small values (N e ranging from 33 to 79). When a model was applied that allows for migration among populations, N e estimates were even lower (24–54), and migration rates were suggested to be high (0.13–0.36). All samples displayed a clear signal of a recent bottleneck, probably stemming from a period of unfavourable conditions due to organic pollution in the 1970–1980’s. By comparison to other estimates of N e in brown trout, Lake Hald trout represent a system of small populations linked by extensive gene flow, whereas other populations in larger rivers exhibit much higher N e values and experience lower levels of immigration. We suggest that management considerations for systems like Lake Hald brown trout should focus both on a regional scale and at the level of individual populations, as the future persistence of populations depends both on maintaining individual populations and ensuring sufficient migration links among these populations.
Abstract: The study of sex-biased dispersal has attracted considerable attention in birds and mammals, but less in other taxa, including fishes. We analysed sex-specific dispersal in historical (1910s and 1950s) and contemporary (1990s) samples of anadromous brown trout Salmo trutta. We tested the hypothesis that dispersal is unbiased using information from microsatellite DNA and applying an assignment index for 11 temporally and spatially separated samples. Our results are most consistent with brown trout dispersal being male biased, and provide no evidence of female bias. We found no evidence that dispersal patterns changed over time, indicating that stocking with hatchery strains did not affect sex-specific dispersal.
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.
Abstract: We examined polymorphism at seven microsatellite loci among sea trout (Salmo trutta) (n = 846) collected from three areas in the Limfjord (Denmark). We then assessed their potential population source by comparing, using a mixed stock analysis (MSA) Bayesian framework, their genetic composition to that of brown trout collected from 32 tributaries pooled into nine geographical regions (n = 3801) and two hatcheries (n = 222) used for stocking. For each of the three regional sea trout groups (western, central and eastern Limfjord, n = 91, n = 426, n = 329, respectively), MSA was conducted with (i) all individuals in the group, (ii) with the subset of spawning sea trout only and (iii) with the subset of foraging, nonspawning individuals only, a subset that consisted primarily of sea trout caught during their first year at sea. For all three regional sea trout groups, a higher proportion of individuals (regardless of whether they were foraging or spawning) appear to have originated from the rivers that drain locally, than from the rivers that drain in other parts of the Limfjord. This suggests (1) that sea trout, at least during their first year at sea, undertake limited migrations within the Limfjord system and (2) that sea trout on their spawning run were caught close to their natal rivers. The proportion of sea trout of hatchery origin varied widely among all three Limfjord areas and broadly reflected regional stocking histories, with high proportions of sea trout of domestic origin in the east (39.3%), where stocking with domestic trout was practised intensely at the time of sampling, and in the west (57.2%), where a programme of coastal stocking of post smolts took place over several years in the early 1990s. In contrast, in the central Limfjord, where stocking with domestic trout was largely abandoned in the early 1990s, the proportion of sea trout of domestic origin was only 8.5%. Interestingly, for all three regional sea trout groups, virtually no sea trout of hatchery origin were found among the spawning individuals, which were on average larger than the nonspawning sea trout. These results suggest that stocked domestic brown trout that become anadromous experience high mortality at sea and are therefore largely absent among the larger, spawning individuals. We conclude that sea trout of domestic origin exhibit much reduced ability to reproduce and are unlikely to contribute significantly to the local gene pool largely because of a relatively high mortality at sea before the onset of maturity.
Abstract: In the north Adriatic basin, a morphologically and genetically distinct lineage of grayling is found, designated as the Adriatic grayling. In Slovenia, the Adriatic grayling is restricted to the Soca river system, where it is critically endangered. The most pertinent threat is stocking with non-native, highly divergent Sava (Danubian) drainage stock, and this activity has been going on for more than four decades. The present study was designed to characterise the genetic structure of the Adriatic grayling in Slovenia, with particular emphasis on estimating the degree of introgression with non-indigenous stocked grayling. We analysed polymorphism at 154 microsatellite loci in samples representing grayling from the Adriatic and Danubian drainage stock. A relatively high number (12) of alleles, diagnostic for the Adriatic grayling, were identified. However, a correspondence analysis based on individual multilocus genotypes also revealed that there is no distinctive Adriatic group but rather a dispersed multitude of individuals that cannot be unambiguously distinguished from the more homogenous Danubian population. A Bayesian analysis of individual admixture coefficients confirmed this pattern and revealed extensive introgression between the Adriatic grayling and stocked grayling of Danubian origin. Average individual admixture coefficients showed that only between 50 and 60% of the original gene pools remained, and only few non-introgressed indigenous individuals could be identified. Microsatellite-based individual admixture analysis appear to be an important tool for identifying remaining non-introgressed indigenous individuals that could be used for restoring the original populations.
Abstract: A wide range of animals have been reported to show kin-biased behaviours, such as reduced aggressiveness and increased food sharing among relatives. However, less is known about whether wild animals also associate with relatives under natural conditions, which is a prerequisite to facilitate kin-biased behaviours and hence kin selection. We tested, by means of microsatellite polymorphism, correlations between pair-wise relatedness and pair-wise metric distance in wild brown trout (Salmo trutta L.) under natural conditions in two streams. Our data show that young-of-the-year as well as older trout found close together also had a higher genetic relatedness in one of the two streams, whereas no relationship was found in the other stream. Very few half and full siblings were found in the second stream and under these conditions it is unlikely that kin-biased behaviours will receive positive selection. We discuss the underlying mechanisms for the observed structure and we specifically address the issue of whether the grouping of related individuals could reflect dispersal from the same spawning redds, or if it reflects active association with relatives, possibly conferring kin-selected advantages.
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.
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.
Abstract: The metapopulation concept is appearing with increasing frequency in the marine population dynamics and genetics literature, though its applicability to marine systems remains an open question. Moreover, in recent years, the meaning of the term â€metapopulation’ has become blurred, concomitant with its increasing use. In this paper, we summarize the concept of metapopulation dynamics and the associated theoretical assumptions. We call for a stricter definition and use of the term â€metapopulation’, critically evaluate the applicability of metapopulation theory to marine population dynamics and its use in the related literature, and consider two published case-studies that investigate metapopulation structuring in specific marine populations. Finally, we urge scientists to carefully articulate what is meant by the term â€metapopulation’ and to use appropriate citations in the primary literature to circumvent the potential for nebulous (and possibly damaging) conclusions in the future.
Abstract: Reproductive competition may lead to a large skew in reproductive success among individuals. Very few studies have analysed the paternity contribution of individual males in spawning aggregations of fish species with huge census population sizes. We quantified the variance in male reproductive success in spawning aggregations of cod under experimental conditions over an entire spawning season. Male reproductive success was estimated by microsatellite-based parentage analysis of offspring produced in six separate groups of spawning cod. In total, 1340 offspring and 102 spawnings distributed across a spawning season were analysed. Our results show that multiple males contributed sperm to most spawnings but that paternity frequencies were highly skewed among males, with larger males on average siring higher proportions of offspring. It was further indicated that male reproductive success was dependent on the magnitude of the size difference between a female and a male. We discuss our results in relation to the cod mating system. Finally, we suggest that the highly skewed distribution of paternity success observed in cod may be a factor contributing to the low effective population size/census population size ratios observed in many marine organisms.
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.
Abstract: Indigenous salmonid fish gene pools are affected by domesticated conspecifics, derived from aquaculture escapes and deliberate releases. Variability was examined at nine microsatellite loci in order to assess the long-term impact of stocking domesticated trout in two brown trout populations. The study was based on analysis of two historical samples (1945-56), represented by old scale collections, and seven contemporary samples (1986-2000). In one population historical and contemporary samples were remarkably genetically similar despite more than a decade of intense stocking. Estimation of admixture proportions showed a small genetic contribution from domesticated trout (approximately 6%), and individual admixture analysis demonstrated a majority of nonadmixed individuals. The expected genetic contribution by domesticated trout was 64%, assessed from the number of stocked trout and assuming equal survival and reproductive performance of wild and domesticated trout. This demonstrates poor performance and low fitness of domesticated trout in the wild. In another population there was a strong genetic contribution from domesticated trout (between 57% and 88% in different samples), both in samples from a broodstock thought to represent the indigenous population and in a sample of wild spawners. Survival of domesticated trout and admixture with indigenous fish in the broodstock and subsequent stocking into the river, combined with a low population size of native trout relative to the number of stocked trout, could explain the observed introgression. Few nonadmixed individuals remained in the introgressed population, and I discuss how individual admixture analysis can be used to identify and conserve nonintrogressed remains of the population.
Abstract: The European otter (Lutra lutra) was common in Denmark until the 1960s, but its present distribution encompasses only a minor part of the country. The aim of this study was to assess whether the recent population decline has resulted in loss of genetic variability and to gain further insight into the dynamics of the population decline. This was done by analysing microsatellite DNA variation in contemporary and historical samples, the latter encompassing DNA samples extracted from museum specimens covering a time-span from the 1880s to the 1960s. Tests for differences in expected heterozygosity and the numbers of alleles in contemporary versus historical samples and a test for detecting population bottlenecks provided few indications of a recent bottleneck and loss of variability. However, a procedure for detecting population expansions and declines, based on the genealogical history of microsatellite alleles, suggested that a drastic long-term population decline has taken place, which could have started more than 2000 years ago, possibly due to ancient anthropogenic pressure. Finally, assignment tests and pairwise F(ST) values suggested weak but statistically significant genetic differentiation between the extant population and historical samples of otters from other regions in Denmark, more likely reflecting differentiation among original populations rather than recent drift.
Abstract: Most of the world's cod (Gadus morhua) fisheries are now tightly regulated or closed altogether. Being able to link individual fish to their population of origin would assist enormously in policing regulations and in identifying poachers. Here we show that microsatellite genetic markers can be used to assign individual cod from three different populations in the northeastern Atlantic Ocean to their population of origin.
Abstract: Based on estimates of genetic differentiation between populations, assignment tests and analysis of isolation by distance, stocked populations of brown trout Salmo trutta of Funen Island, Denmark, had been genetically affected by domesticated trout, whereas the stocking of wild exogenous trout into one of the rivers had little or no impact. At the same time, there were clear indications of remaining indigenous gene pools in the Funen populations. The management implications of these findings are discussed and changes in trout release activity are recommended to avoid further mixing of trout gene pools. (C) 2001 The Fisheries Society of the British Isles
Abstract: We examined polymorphism at seven microsatellite loci in 4023 brown trout (Salmo trutta) collected from 32 tributaries to the Limfjord, Denmark (approximately 200 km) and from two hatcheries used for stocking. Populations differ in their estimated sizes and stocking histories. Mean individual inbreeding coefficients do not differ among locations within rivers. Relatedness varies between sites within rivers indicating varied local dynamics at a very small geographical scale. Relatedness is sometimes lower than expected among an equal number of simulated individuals with randomized genotypes, suggesting structure within locations. Five per cent of the genetic variance is distributed among rivers (F(ST) = 0.049), but in the western, less heavily stocked, area of the Limfjord a higher proportion of the genetic variance is distributed among rivers than among locations within rivers. The reverse is true of the eastern, more heavily stocked, area of the Limfjord. Here, a higher proportion of the genetic variance is distributed among locations within rivers than among rivers. Assignment tests reveal that the majority of trout (mean 77% of all fish) are more probably of local origin than hatchery origin but this proportion varies regionally, with rivers in the western area of the Limfjord showing a relatively high (mean 88%) and those in the eastern area showing a relatively low (mean 72%) proportion of locally assigned trout. These results can be interpreted as reflecting stocking impact. Also, the proportion of locally assigned trout correlates with the populations' stocking histories, with rivers presently subjected to stocking (hatchery trout) showing low (mean approximately 0.73), and rivers where stocking was discontinued showing high (mean approximately 0.84) proportions of local fish, probably reflecting lower survival of hatchery than of wild trout. There is evidence for isolation by distance at a large geographical scale when individual river populations are pooled into nine geographical regions but not at a small geographical scale when populations are considered individually. We reject the null hypothesis that stocking has had no impact on population structure but the relatively high proportion of locally assigned trout in populations where stocking with domestic fish no longer takes place suggests limited long-term success of stocking.
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.
Abstract: The hypothesis that stream-resident females of brown trout Salmo trutta occurring in sympatry with sea-migrant females in a small stream were immigrants from an up-stream allopatric landlocked population was rejected. Genetic differentiation was not detected between the sympatric forms whereas they both diverged significantly from the land-locked population. suggesting a common gene-pool for the sympatric migratory and stream-resident Forms. Assignment tests, based on microsatellite markers, to identify the population of origin of individuals did not suggest pronounced dispersal from the landlocked population into the down-stream population, However. it cannot be precluded that a modest degree of gene Row takes place from the landlocked population and that this may play a role in maintaining the two co-existing life-history forms among females in the down-stream population. (C) 2001 The Fisheries Society of the British Isles
Abstract: The genetic integrity of many salmonid fish populations is threatened by stocking of domesticated conspecifics. The purpose of this study was to assess the utility of microsatellite DNA markers for detecting loss of genetic diversity in hatchery strains, for estimating their genetic relationships, and for monitoring the genetic impact of stocking activity on wild populations of salmonid fishes. Brown trout from ten hatchery strains, one supportive breeding "strain," and five wild populations were screened for variation at eight loci. In most hatchery strains, genetic variation was comparable to that of wild populations, but three strains showed loss of allelic variation. In six of the hatchery strains, significant differentiation was observed between age classes. Genetic differentiation among all populations was moderate (F-ST = 0.065, p(ST) = 0.076), and only a minor part of genetic diversity was distributed between the wild and hatchery populations. We assessed whether wild populations were introgressed by stocked hatchery trout by performing assignment tests to determine population of origin and estimating maximum potential introgression rates. The results suggested that genetic introgression by hatchery trout had occurred for only two of the five populations potentially influenced by stocking. In one of these two rivers, microsatellite data obtained from a limited number of old scale samples indicated that individuals from the original population were genetically divergent from these of the present population, suggesting that extinction of the original population had taken place. The study demonstrates that microsatellite analysis provides a useful tool for distinguishing heavily introgressed populations from those unaffected by stocking. The information can be used to assist in (1) prioritizing populations for conservation and (2) the choice of wild populations to be used as sources for the reintroduction of salmonids in areas where local, indigenous gene pools have been extirpated
Abstract: Studies of genetic interactions between wild and domesticated fish are often hampered by unavailability of samples from wild populations prior to population admixture. We assessed the utility of a new Bayesian method, which can estimate individual admixture coefficients even with data missing from the populations contributing to admixture. We applied the method to analyse the genetic contribution of domesticated brown trout (Salmo trutta) in samples of anadromous trout from two stocked populations with no genetic data available before stocking. Further, we estimated population level admixture proportions by the mean of individual admixture coefficients. This method proved more informative than a multidimensional scaling analysis of individual-based genetic distances and assignment tests. The results showed almost complete absence of stocked, domesticated trout in samples of trout from the rivers. Consequently, stocking had little effect on improving fisheries. In one population, the genetic contribution by domesticated trout was small, whereas in the other population, some genetic impact was suggested. Admixture in this sample of anadromous trout despite absence of stocked domesticated trout could be because of introgression by domesticated trout adopting a resident life history
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.
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.
Abstract: Stocking with offspring of local wild fish, so-called supportive breeding, is often advocated as an alternative to stocking domesticated fish. However, it is important to ensure that supportive breeding does not result in inbreeding and loss of genetic variability. We analysed eight microsatellite loci in samples of wild and hatchery-reared brown trout (Salmo trutta) from three populations subject to supportive breeding. For calibrating statistical procedures, we included two test samples of reared offspring for which the precise number of parent fish was known and a sample from a further wild reference population. Three different statistical procedures were used to detect population bottlenecks and loss of variability: (i) a randomization test for comparing allelic diversity between samples; (ii) estimates of effective number of breeders from gametic-phase disequilibrium; and (iii) a test for assessing population bottlenecks based on detecting deviations from mutation-drift equilibrium. All three procedures were useful but they also exhibited different strengths and limitations, with the test for population bottlenecks probably being the single most useful procedure for routine monitoring. In two populations subject to supportive breeding, there were strong indications of reduced effective population sizes, and significant genetic differentiation was observed between different samples from the same population
Abstract: Levels of variation at six VNTR (variable number of tandem repeats) loci, one minisatellite and five microsatellite loci, isolated from tri- and tetranucleotide enriched DNA libraries for northern pike were generally low in two Danish populations (1-4 alleles; expected heterozygosity 0-0.57), though one highly variable microsatellite (13 alleles; expected heterozygosity 0.79) was identified. In combination with previously published microsatellites a set consisting of nine polymorphic loci appeared to be useful for discriminating populations, as determined by assignment tests. (C) 1999 The Fisheries Society of the British Isles
Abstract: Collections of old scales from salmonid fishes can be found in many fisheries institutions in Europe and North America. Such scales have been shown to be useful as a source of DNA, which can be used for analysis of microsatellites. We here describe the technical procedures in relation to extraction and PCR amplification of DNA from old scales. Further, we describe case stories of the application of old scale DNA analysis for conservation genetics with regard to: 1) Identification of native populations, 2) assessment of loss of genetic variation, 3) estimation of effective population size, 4) evaluation of anthropogenic effects on the genetic population structure/mode of migration and 5) the temporal stability of the genetic population structure. Finally, we describe the perspectives for Future genetic studies using old scale DNA. In particular, we evaluate other types of genetic markers such as mtDNA and loci subjected to selection, in association with old scale DNA, as tools for prioritising populations for conservation
Abstract: Information on genetic composition of past and present populations may be obtained by analyzing DNA from archival samples. A study is presented on the genetic population structure of extant and extinct local populations of Atlantic salmon from 1913 to 1989 using dried scales as a source of DNA. Variation at six microsatellite loci was studied. Tests for differentiation among populations and among time series within populations showed that population structure was stable over time. This was also confirmed by a neighbor-joining dendrogram which showed a clear clustering of samples from individual rivers that covered a time span of up to 76 years. These results suggest that salmon populations evolve as semi-independent units connected by modest amounts of gene flow. Additionally, a clear association between geographic and genetic distance was found. This relationship has otherwise been difficult to establish in several recent studies. The discrepancy may be due to impact of human activities on the genetic structure of present populations, whereas old samples represent populations in a more unaffected state. However, other explanations related to differences in the sampling of past and present populations may be equally valid
Abstract: The genetic relationships among morphologically and geographically divergent populations of whitefish (genus: Coregonus) from Denmark and the Baltic Sea region were studied by analysis of microsatellites and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis of mitochondrial DNA (mtDNA) segments, The endangered North Sea houting (classified as C. oxyrhynchus) differs morphologically and physiologically from other Danish whitefish (C. lavaretus). However, limited divergence of North Sea houting was observed both at the level of mtDNA and microsatellites. The implications of these results for the conservation status of North Sea houting are discussed in the light of current definitions of evolutionary significant units. Both mtDNA and microsatellite data indicated that postglacial recolonization by C. lavaretus in Denmark was less likely to have taken place from the Baltic Sea. Instead, the data suggested a recent common origin of all Danish whitefish populations, including North Sea houting, probably by recolonization via the postglacial Elbe River system. Estimates of genetic differentiation among populations based on mtDNA and microsatellites were qualitatively different. In addition, for both classes of markers analyses of genetic differentiation yielded different results, depending on whether molecular distances between alleles or haplotypes were included
Abstract: The abundance of mink, otter, and polecat may be inferred from records of their seats, and the feeding biology of the species is often studied by analysis of skeletal remains and other hard parts in faeces. However, in some situations it is difficult to distinguish between faeces from these three mustelid species. A method is described for assigning faeces to these three mustelid species, based on analysis of DNA extracted from their seats. Mustelid-specific primers were developed for PCR amplification of a part of the mitochondrial cytochrome b gene, and two restriction enzymes were found to detect species-specific sequence variation. Analysis of DNA from different faecal samples showed that the results were reproducible and that the approach provided an efficient method of species identification
Abstract: New specific primers for the mtDNA segments ND1, ND3/4 and ND5/6 designed from the rainbow trout sequence, improved PCR amplification for salmonid fishes. RFLP analysis revealed restriction site variation for all three segments in Atlantic salmon. Eleven haplotypes were detected in a screening of 30 individuals from four European populations. (C) 1998 The Fisheries society of the British Isles
Abstract: Twenty-four samples of anadromous brown trout from four river systems/geographical regions were studied by PCR-RFLP analysis of the ND-1 and ND-5/6 regions of the mitochondrial genome. A total of 14 haplotypes was observed, and these could be divided into three phylogenetic groups. Populations within river systems/regions tended to be more closely related to each other than to populations from other river systems/regions. Also, a significant correlation was observed between geographical and genetic distances between populations. These results contrast with results from other studies of mainly resident and landlocked populations, where no correspondence was observed between genetic relationships and geographical location of populations. Gene flow connecting anadromous populations is probably the reason for the observed isolation-by-distance patterns, whereas in isolated resident and landlocked trout populations drift leads to random genetic divergence of populations. Tests for nonrandom geographical distribution of phylogenetic groups of haplotypes showed that drift: and gene flow are probably the predominant factors affecting the distribution of haplotypes. There were, however, also some indications of dines in frequencies of phylogenetic groups of haplotypes
Abstract: In species exhibiting a nonrandom distribution of closely related individuals, sampling of a few families may lead to biased estimates of allele frequencies in populations. This problem was studied in two brown trout populations, based on analysis of mtDNA and microsatellites. In both samples mtDNA haplotype frequencies differed significantly between age classes, and in one sample 17 out of 18 individuals less than 1 year of age shared one particular mtDNA haplotype. Estimates of relatedness showed that these individuals most likely represented only three full-sib families. Older trout exhibiting the same haplotypes generally were not closely related
Abstract: Microsatellite analysis was applied to scale samples of Atlantic salmon collected up to 60 years ago. Samples from the 1930s, from a now endangered Danish population, were compared with recent samples (1989), to test if the present population consists of descendants from the original one. Allele frequencies had changed over time, but individuals from the two samples caught about 60 years apart clustered together when compared with the closest neighbouring population and another reference population. However, fewer alleles were detected in the recent sample from the endangered population, most likely due to a population bottleneck or sampling artefacts
Abstract: Eleven Danish brown trout hatchery strains were studied by PCR-RFLP analysis of the ND-I and ND-5/6 segments of the mitochondrial genome. For comparison, data from wild trout representing three Danish river systems also were included. Reduced variability in terms of nucleon diversity and number of haplotypes was observed in most hatchery strains. However, computer simulations showed that even with relatively large numbers of female spawners considerable loss of haplotypes could take place over time. Therefore, reduced variability in some of the strains did not necessarily indicate a critical loss of allelic Variation at nuclear loci. The genetic relationships among the strains were compared with information from hatchery managers on the origin of the strains. In one case, a strain supposed to be recently founded from wild trout appeared to be of a mixed wild and hatchery origin. Genetic differentiation among strains (Phi(ST) = 0.23) was of the same order of magnitude as that observed among wild Danish trout populations. However, minimal differentiation (Phi(ST) = 0.01) was observed among the four quantitatively most important strains, supplying 80% of all hatchery trout stocked in Denmark. (C) 1997 Elsevier Science B.V
Abstract: The genetic relationships between the only natural population of Atlantic salmon (Salmo salar L.) in Denmark and seven other European salmon populations were studied using RFLP analysis of PCR amplified mitochondrial DNA segments. Six different haplotypes were detected by restriction enzyme analyses of the NADH dehydrogenase 1 segment, employing four endonucleases. Significant genetic differentiation was observed among populations. A hierarchical analysis of the distribution of the mtDNA variability revealed that only a small part was distributed among geographical groups within the study area. No correlation was found between genetic and geographic distance among populations. The effective migration of females (Nm)(F) among rivers was estimated to be approximately one per generation
Abstract: The influence of founder effects on the genetic population structure of brown trout (Salmo trutta) was studied in a small Danish river system. Samples of trout from seven locations were analysed by allozyme electrophoresis and mitochondrial DNA restriction fragment length polymorphism analysis. For comparison, allozyme data from other Danish trout populations and mtDNA data from two hatchery strains were included. Genetic differentiation among populations was found to be small but significant. Pairwise tests for homogeneity of allele and haplotype frequencies between samples showed that significance was predominantly due to a single population. In two of the locations studied, extinction-recolonization events had taken place. In one of the populations, founding had not resulted in divergence, while the other founded population was the one that had diverged significantly from the remaining populations. Computer simulations of the influence of founder effects on mitochondrial DNA differentiation and variability showed that the observed divergence could be due either to natural founder effects or to a genetic contribution by hatchery trout. However, the allozyme results pointed towards natural founder effects as the most likely explanation
Abstract: An initial screening with 18 restriction endonucleases of brown trout mitochondrial DNA from three regions of Denmark revealed no variation in the D-loop while seven restriction endonucleases were found to detect variability in the NADH-dehydrogenase 1 and/or 5/6 regions. Thirteen different haplotypes were observed, fewer in the Lake Hald populations than in the other samples, probably a result of nonexisting gene flow due to an impassable dam, No correlation was found between geography and the genetic relationships among haplotypes. Significant genetic differentiation was observed among the three main regions. Genetic differentiation among populations was much more pronounced in the Lake Hald than in the Bornholm region. The genetic relationships among populations of the Lake Hald region suggested by mtDNA data were not in accordance with allozyme data and the known history of the populations, while estimates of genetic differentiation and gene flow inferred by the two methods were in agreement. (C) 1996 The Fisheries Society of the British Isles
Abstract: Declines in the number of anadromous brown trout in the Karup River in Denmark, due to environmental degradation, led to the stocking of large numbers of hatchery trout during the 1980s. This practice was gradually replaced by stocking with the offspring of electrofished local trout. The genetic contribution of the hatchery fish to the current population of anadromous trout in the river was estimated by restriction fragment length polymorphism analysis of mitochondrial DNA, using seven restriction endonucleases. Fish from the hatchery strain as well as from five locations in the river system, and from a further unstocked river were screened. Eight haplotypes were observed. The distribution and frequencies of the observed haplotypes revealed little genetic differentiation among stocked populations. The hatchery strain differed significantly from the stocked populations. One haplotype which was found at a high frequency in the hatchery strain was almost absent from the stocked populations. This suggests that the genetic contribution of the hatchery trout to the current population is much less than would be expected from the number of stocked fish. The possible reasons for the failure of the hatchery trout to contribute to the gene pool, and also the implications for conservation biology, are discussed
Abstract: Brown trout (Salmo trutta L.) from twelve locations in small rivers in Jutland, Denmark, were examined by allozyme electrophoresis. Seven of the locations are tributaries to the small (3.3 km2) Lake Hald. These and two other locations are assumed to have been mainly inaccessible to gene flow from outside for hundreds of years because of impassable dams. The levels of polymorphism indicated that little or no loss of genetic variation had occurred in these isolated populations compared to populations open to gene flow. In Lake Hald significant genetic differentiation among the tributary populations was detected. Intensive stocking with trout from a hatchery strain directly into the lake was shown to have had little or no effect on the genetic composition of the original populations. In contrast, transplantation of trout from one tributary to another within the lake system was successful. The geographical distribution of genetic variation indicated that the Lake Hald populations are genetically divergent from the other populations and for that reason special care concerning management practices in the lake is recommended
Abstract: This DSc thesis, which includes 23 scientific papers and a general introduction, was accepted for defence by the Faculty of Natural Sciences, University of Aarhus in 2003. The thesis describes how molecular markers have been applied for studying the genetic population structure of brown trout (Salmo trutta), Atlantic salmon (S. salar), Atlantic cod (Gadus morhua), lake whitefish and North Sea houting (Coregonus sp.) and European otter (Lutra lutra). The research targets both applied and fundamental scientific issues. This includes estimating patterns of genetic differentiation and gene flow, elucidating postglacial recolonisation processes, estimating effective population size and detecting population declines, and analysing the genetic impact of stocking domesticated fish into wild populations. A major part of the work has been based on analysing microsatellite DNA markers from contemporary and historical samples, the latter represented by up to one hundred year old archived samples of teeth and fish scales. This has allowed for analysing the genetic structure of populations on a much longer time scale than has previously been feasible, and it has provided new important tools for estimating how population declines and fish stocking activity have affected contemporary gene pools.
Notes: This pdf is the general introduction and synthesis of the thesis
