Life history shapes gene expression in salmonids.
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Animal Migration↗
Biomedical subjects
Michael M Hansen
Publications and source records attributed to Michael M Hansen.
Evidence of microsatellite hitch-hiking selection in Atlantic cod (Gadus morhua L.): implications for inferring population structure in nonmodel organisms.
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.
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Marine landscapes and population genetic structure of herring (Clupea harengus L.) in the Baltic Sea.
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.
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Genetic population structure of turbot (Scophthalmus maximus L.) supports the presence of multiple hybrid zones for marine fishes in the transition zone between the Baltic Sea and the North Sea.
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.
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Genetic detection of sex-specific dispersal in historical and contemporary populations of anadromous brown trout Salmo trutta.
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.
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Stocking impact and migration pattern in an anadromous brown trout (Salmo trutta) complex: where have all the stocked spawning sea trout gone?
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.
Animal Migration↗
Evidence of a hybrid-zone in Atlantic cod (Gadus morhua) in the Baltic and the Danish Belt Sea revealed by individual admixture analysis.
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.
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Long-term temporal changes of genetic composition in brown trout (Salmo trutta L.) populations inhabiting an unstable environment.
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.
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Estimating the long-term effects of stocking domesticated trout into wild brown trout (Salmo trutta) populations: an approach using microsatellite DNA analysis of historical and contemporary samples.
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.
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Long-term effective population sizes, temporal stability of genetic composition and potential for local adaptation in anadromous brown trout (Salmo trutta) populations.
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.
Animals↗