Genetic differentiation among populations of Caridinazebra (Decapoda: Atyidae) in tropical rainforest streams, northern Australia

1. Caridina zebra is a common atyid shrimp in some tropical rainforest streams in far north Queensland, Australia. Genetic variation at five allozyme loci was used to estimate the level of dispersal among populations of this species, within and between stream systems. Shrimps were sampled from nine streams in the Tully River catchment and two headwater streams in the adjacent Herbert River catchment in an area under consideration for extensive hydroelectric development.
2. High levels of genetic differentiation were recorded among most populations which suggests that, like other fully aquatic species, movement is limited to a very small spatial scale.
3. In the Tully catchment, populations of shrimp from streams with confluences at high altitude showed less genetic differentiation than those from streams which directly entered the lower river. Dispersal between the latter streams is clearly limited by the presence of large waterfalls and cascades.
4. Adjacent stream populations were often highly differentiated, despite their close proximity, suggesting that overland dispersal is unlikely. However, populations of shrimp in the two streams in the Herbert catchment were strikingly similar in genetic structure to those in adjacent headwater streams of the Tully. Such similarity may reflect relatively recent changes in drainage patterns.     

Allozyme diversity and population genetic structure of the caddisfly Orthopsyche fimbriata and the mayfly Acanthophlebia cruentata in New Zealand streams

1. Allozymes were used to measure genetic variation within and among regional populations of the caddisfly Orthopsyche fimbriata and the mayfly Acanthophlebia cruentata in North Island New Zealand streams.
2. High levels of genetic differentiation were recorded in populations of O. fimbriata within and among catchments separated by more than 100 km, but little or no differentiation in populations separated by around 10 km. The Auckland isthmus appears to be a major barrier to north–south gene flow, with nearly fixed allelic differences at one locus. Genotype frequencies conformed to Hardy–Weinberg equilibrium.
3.  Acanthophlebia cruentata had low levels of genetic variation; the results are unexpected given that O. fimbriata apparently has greater potential for dispersal. The limited genetic data for A. cruentata provided evidence for genetic differentiation among populations separated by around 100 km, or more, within catchments and some differentiation between catchment populations separated by only 25 km.     

Dispersal of organisms in a patchy stream environment under different settlement scenarios

1.  Previous work in streams, where many organisms disperse downstream by drifting in the water column, has suggested dispersal distances could be related to the overall proportion of the stream within dead water zones (DWZ), places such as backwaters, pools or behind large obstacles, where the water is out of the main flow and is stored temporarily. However, dispersal distances might also be influenced by the spatial organization of DWZ within a reach; this would require us to distinguish between reaches containing many small DWZ compared with those having a few large ones in order to understand fully differences in dispersal patterns among reaches differing in this regard.
2.  We constructed a spatial model of flow in stream reaches, in which we varied the density and size distribution of DWZ distributed through the reach. We defined flow conditions under which stream organisms, modelled as passive particles, would settle or continue to drift downstream. We then examined the horizontal dispersal profiles of such particles through reaches differing in arrays of DWZ.
3.  Our results support those of previous studies, but suggest that the spatial arrangement of DWZ may be just as important as the overall proportion of DWZ within a reach. On a more general note, the importance of patch configuration observed in this study reflects the growing view that a thorough understanding of population and ecosystem processes will require the explicit consideration of spatial pattern in the environment.     

Exploring patterns of population subdivision in the net-winged midge, Elporia barnardi (Diptera: Blephariceridae), in mountain streams of the south-western Cape, South Africa

1. The net-winged midges (Diptera: Blephariceridae) are a highly specialized group whose morphological characteristics and specific habitat requirements suggest a limited potential for dispersal. Levels of genetic variation were examined within streams, between streams in the same range and between mountain ranges in larval populations of Elporia barnardi in the south-western Cape of South Africa. The aim was to examine the hypothesis that population structure would reflect the poor potential for dispersal.
2. Significant deviations from Hardy–Weinberg equilibrium in 17 of the 57 individual comparisons indicate a non-random mating population. Given the swarming behaviour and life history traits, larvae sampled may reflect the product of limited matings.
3. Analysis of population substructuring revealed significant levels of differentiation among geographically proximate populations. Large differences between streams within Table Mountain, similar in magnitude to those between mountain ranges, suggest that movement of individuals out of the stream catchment is rare. Observed F _ST values are more similar to those of fully aquatic species than other lotic insects with winged adult stages.
4. Results suggest that mountain ridges provided effective physical barriers to the dispersal of E. barnardi , with the catchment representing the effective population unit.     

Macroinvertebrate diversity in headwater streams: a review

1. Headwater streams are ubiquitous in the landscape and are important sources of water, sediments and biota for downstream reaches. They are critical sites for organic matter processing and nutrient cycling, and may be vital for maintaining the 'health' of whole river networks.
2. Macroinvertebrates are an important component of biodiversity in stream ecosystems and studies of macroinvertebrate diversity in headwater streams have mostly viewed stream systems as linear reaches rather than as networks, although the latter may be more appropriate to the study of diversity patterns in headwater systems.
3. Studies of macroinvertebrate diversity in headwater streams from around the world illustrated that taxonomic richness is highly variable among continents and regions, and studies addressing longitudinal changes in taxonomic richness of macroinvertebrates generally found highest richness in mid-order streams.
4. When stream systems are viewed as networks at the landscape-scale, α-diversity may be low in individual headwater streams but high β-diversity among headwater streams within catchments and among catchments may generate high γ-diversity.
5. Differing ability and opportunity for dispersal of macroinvertebrates, great physical habitat heterogeneity in headwater streams, and a wide range in local environmental conditions may all contribute to high β-diversity among headwater streams both within and among catchments.
6. Moving beyond linear conceptual models of stream ecosystems to consider the role that spatial structure of river networks might play in determining diversity patterns at the landscape scale is a promising avenue for future research.     

Are populations of mayflies living in adjacent fish and fishless streams genetically differentiated?

1. Conspecific populations living in habitats with different risks of predation often show phenotypic variation in defensive traits. Traits of two species of mayflies (Baetidae: Baetis bicaudatus and Baetis sp. nov.) differ between populations living in fish and fishless streams in a high altitude drainage basin in western Colorado, U.S.A. We tested for genetic differentiation between mayfly populations in these two habitat types, assuming that lack of genetic differentiation would be consistent with the hypothesis that those traits are phenotypically plastic. 2. Previous work has shown that larvae of both species behave differently and undergo different developmental pathways in adjacent fish and fishless streams. These phenotypic differences in behaviour and development have been induced experimentally, suggesting that populations from fishless streams have the genetic capability to respond to fish. 3. During summer 2001 we collected Baetis larvae from several fish and fishless streams, and from fish and fishless sections of the same streams. We used allozymes and a fragment of the cytochrome oxidase subunit 1 mitochondrial gene to examine genetic variation of Baetis individuals within and among streams. 4. Results showed that genetic variation exists among populations of the same species of Baetis from different streams, but none of that variation was associated with the presence or absence of fish. These data confirm that populations of Baetis living in fish and fishless streams are not genetically distinct, and are consistent with the hypothesis that traits associated with environments of different risk are phenotypically plastic.     

Genetic and behavioural evidence for a city-wide supercolony of the invasive Argentine ant Linepithema humile (Mayr) (Hymenoptera: Formicidae) in southeastern Australia

The success of invasive ants is frequently attributed to genetic and behavioural shifts in colony structure during or after introduction. The Argentine ant ( Linepithema humile ), a global invader, differs in colony genetic structure and behaviour between native populations in South America and introduced populations in Europe, Japan, New Zealand and North America. However, little is known about its colony structure in Australia. We investigated the genetic structure and behaviour of L. humile across Melbourne, Victoria by quantifying variation at four microsatellite loci and assaying intraspecific aggression at neighbourhood (30–200 m), fine (1–3.3 km) and regional (5–82 km) spatial scales. Hierarchical analyses across these scales revealed that most genetic variation occurred among workers within nests (∼98%). However, although low genetic differentiation occurred among workers between nests at the fine and regional scales (∼2%), negligible differentiation was detected among workers from neighbouring nests. Spatial genetic autocorrelation analysis confirmed that neighbouring nests were genetically more similar to each other. Lack of aggression within and across these scales supported the view that L. humile is unicolonial and forms a large supercolony across Melbourne. Comparisons of genetic structure of L. humile among single nests sampled from Adelaide, Brisbane, Hobart and Perth with Melbourne showed no greater levels of genetic differentiation or dissimilar spatial structure, suggesting an Australia-wide supercolony.     

Population genetic structure of three freshwater mussel (Unionidae) species within a small stream system: significant variation at local spatial scales

1. Unionid mussels are highly threatened, but little is known about genetic structure in populations of these organisms. We used allozyme electrophoresis to examine partitioning of genetic variation in three locally abundant and widely distributed species of mussels from a catchment in Ohio. 2. Within‐population variation was similar to that previously reported for freshwater mussels, but genotype frequencies exhibited heterozygote deficiencies in many instances. All three species exhibited significant among‐population variation. Evidence of isolation‐by‐distance was found in Elliptio dilatata and Ptychobranchus fasciolaris, while Lampsilis siliquoidea showed no geographical pattern of among‐population variation. 3. Our results suggest that the isolating effects of genetic drift were greater in L. siliquoidea than in the other species. Differentiation of populations occurred at a much smaller spatial scale than has previously been found in freshwater mussels. Differences among species may reflect differences in the dispersal abilities of fishes that serve as hosts for the glochidia larvae of mussels. 4. Based on our results, we hypothesise that species of mussels that are common to large rivers exhibit relatively large amounts of within‐population genetic variation and little differentiation over large geographical distances. Conversely, species typical of small streams show lower within‐population genetic variation and populations will be more isolated. If this hypothesis can be supported, it may prove useful in the design of conservation strategies that maintain the genetic structure of target species.     

Fine-scale patterns of genetic variation indicate non-equilibrium gene frequency divergence in the stream lily, Helmholtzia glaberrima

1. Helmholtzia glaberrima (Philydraceae) is a rare plant, endemic to streams of the border ranges of Queensland and New South Wales, Australia.
2. We used AFLP markers to investigate genetic diversity and patterns of differentiation among 19 populations of H. glaberrima (24 for demographic analyses), and also collected data on the size, distribution and altitude of populations.
3. Based on the distribution of populations, altitude significantly influenced the spatial arrangement of H. glaberrima along stream systems, with population size and frequency greatest in upstream habitat.
4. Patterns of genetic diversity within populations were not related to population size or distribution. Altitude and genetic diversity were related, with upstream and downstream populations having higher genetic diversity than mid-stream populations. Differentiation among populations was pronounced at all spatial scales and did not conform to a hierarchical model of gene flow.
5. Both genetic diversity and differentiation data sets indicated that strong non-equilibrium conditions associated with persistent founder effects, and not landscape characteristics, have shaped patterns of genetic diversity and differentiation in H. glaberrima . Patterns of distribution indicate that populations are distributed over a discontinuous ecological gradient, which becomes marginal at lower altitudes.     

Microsatellite DNA analysis of northern pike (Esox lucius L.) populations: insights into the genetic structure and demographic history of a genetically depauperate species

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 θ_ST = 0.51; overall ρ_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 θ (a product of effective population size and mutation rate) among populations from large and small water bodies, but the relative differences in θ 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.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 84 , 91–101.     

Dynamic micro-geographic and temporal genetic diversity in vertebrates: the case of lake-spawning populations of brown trout (Salmo trutta)

Conservation of species should be based on knowledge of effective population sizes and understanding of how breeding tactics and selection of recruitment habitats lead to genetic structuring. In the stream‐spawning and genetically diverse brown trout, spawning and rearing areas may be restricted source habitats. Spatio–temporal genetic variability patterns were studied in brown trout occupying three lakes characterized by restricted stream habitat but high recruitment levels. This suggested non‐typical lake‐spawning, potentially representing additional spatio–temporal genetic variation in continuous habitats. Three years of sampling documented presence of young‐of‐the‐year cohorts in littoral lake areas with groundwater inflow, confirming lake‐spawning trout in all three lakes. Nine microsatellite markers assayed across 901 young‐of‐the‐year individuals indicated overall substantial genetic differentiation in space and time. Nested gene diversity analyses revealed highly significant (≤P = 0.002) differentiation on all hierarchical levels, represented by regional lakes (F_LT = 0.281), stream vs. lake habitat within regional lakes (F_HL = 0.045), sample site within habitats (F_SH = 0.010), and cohorts within sample sites (F_CS = 0.016). Genetic structuring was, however, different among lakes. It was more pronounced in a natural lake, which exhibited temporally stable structuring both between two lake‐spawning populations and between lake‐ and stream spawners. Hence, it is demonstrated that lake‐spawning brown trout form genetically distinct populations and may significantly contribute to genetic diversity. In another lake, differentiation was substantial between stream‐ and lake‐spawning populations but not within habitat. In the third lake, there was less apparent spatial or temporal genetic structuring. Calculation of effective population sizes suggested small spawning populations in general, both within streams and lakes, and indicates that the presence of lake‐spawning populations tended to reduce genetic drift in the total (meta‐) population of the lake.     

Small-scale patterns of genetic variation in the mayfly Bungona narilla (Ephemeroptera: Baetidae) in rainforest streams, south-east Queensland

SUMMARY 1. Genetic structure of the mayfly Bungona narilla was examined using allozymes and a section of the cytochrome oxidase I gene.
2. The study had two major aims. The first was to determine whether patterns of genetic variation in mitochondrial DNA were similar to those found previously for allozymes, i.e. that more variation was evident among pools within a single stream than among streams. The mitochondrial DNA results were similar to those reported previously for allozymes, supporting the idea that larvae within any particular pool were unrepresentative of the total population and may result from a few matings.
3. The second aim was to test the hypothesis that the variation among pools within a stream was greater after dry periods than after wet periods. This was because after wet periods, larvae would have greater opportunity for mixing because of movement among pools. This hypothesis was partly supported by the mitochondrial DNA data but not by the allozyme data, in which variation among pools was extremely low on both sampling occasions. The reasons for this difference are unclear.     

Genetic variation in Batrachospermum helminthosum (Batrachospermales, Rhodophyta) among and within stream reaches using intersimple sequence repeat molecular markers

Intersimple sequence repeat molecular markers were utilized to investigate the genetic relationship among individual gametophyte thalli of the freshwater red alga Batrachospermum helminthosum among distant stream reaches and within a stream reach. Fifteen thalli per stream reach were sampled from 11 streams throughout the known distribution in eastern North America from three locations in Ohio, and one location in Indiana, Michigan, North Carolina, Tennessee, Louisiana, Rhode Island, Massachusetts and Connecticut. The pairwise φ_ST analysis showed significant genetic differences (P<0.05) among all streams. The partitioning of genetic variation was almost equal within and among streams (45% and 55%, respectively). Genetic variation among populations did not reflect geographic distance, suggesting that long distance dispersal may be important in the distribution of this alga. Fifty‐eight individuals from Five Mile Creek, Ohio, were investigated from three distinct segments of the stream (upstream, middle and downstream) to examine small‐scale genetic variation within a stream reach. A much higher proportion of genetic variation was observed within a stream segment (79%) than among the three segments (21%). Among these stream segments within Five Mile Creek, the individuals were variously related, with genetic similarity and spatial distance uncorrelated. A similar result was obtained among individuals within other stream reaches, suggesting that genetic structure within a stream reach may be more complex than just reproduction among closely located individuals.     

Genetic structure of the stonefly, Yoraperla brevis, populations: the extent of gene flow among adjacent montane streams

1. Gene flow in populations of stream insects is expected to depend on the distance between and the connectedness of sites in stream networks, and on dispersal ability (i.e. larval drift and adult flight).
2. Yoraperla brevis (Banks) is an abundant and characteristic stonefly of smaller streams in the northern Rocky Mountains. The present authors analysed genetic structure at 27 sites in sevenz streams flowing into the Bitterroot River in western Montana, USA. Cellulose acetate electrophoresis identified five variable loci with 16 alleles.
3. Genotype frequencies conformed to Hardy–Weinberg expectations. Within-stream differentiation was low and among-stream variation ( F _st) was an order of magnitude higher.
4. UPGMA grouped sites within streams and also grouped adjacent streams. The tree produced by the Neighbour Joining Method was similar although not quite so clear cut.
5. This orderly pattern (i.e. Hardy–Weinberg proportions, homogeneity within streams and geographical structure) contrasts strongly with patterns observed in invertebrates from subtropical streams in Australia. Yoraperla brevis maintains large populations in predictable environments, has a long life-cycle with a likelihood of cohort mixing, emerges synchronously in large breeding populations and occupies streams separated by areas of high relief; the Australian situation is the opposite in most respects.
6. Further analysis of a range of species is required to determine whether the different genetic structure in Y. brevis compared to the Australian species occurs more generally in North American stream insects.     

The distribution of genetic variation in Norway spruce (Picea abies Karst.) populations in the western Alps

Aim  In order to look for a possible centre of survival for the Norway spruce ( Picea abies Karst.) in the south-western Alps, six natural populations of this area were investigated by means of genetic markers in order to assess the degree and the distribution of genetic diversity within the species.
Location  Western and South-western Alps.
Methods  Populations were genotyped using seven simple sequence repeat (SSR) markers. Basic population genetics parameters were estimated and the amount of genetic differentiation calculated.
Results  A large amount of variability was found (0.59 <  H _e < 0.67); genetic differentiation as measured by F _ST was 0.05, close to other similar studies; no isolation by distance was detected by a Mantel test. Analysis of molecular variance confirmed a high degree of variability within populations and a low degree of variability among populations. Finally, the number of populations from which those observed could have arisen was estimated by Bayesian analysis.
Main conclusions  The results presented here suggest that the present populations derive their genetic make-up from three inferred clusters. The possible existence in this area of a relict/refuge population during the last glaciation is discussed.     

Phylogeographic structure of Pinus strobiformis Engelm. across the Chihuahuan Desert filter-barrier

Aim  To explore the genetic and phylogeographic structure of a temperate forest species, Pinus strobiformis Englem., in a subtropical region in the context of climate change during the Pleistocene. It is expected that the colder conditions during glacial stages favoured range expansions of P. strobiformis , thus promoting gene flow.
Location  Mexico and the United States.
Methods  Estimates of genetic diversity and structure were obtained using chloroplast microsatellite loci of 23 populations of P. strobiformis across its entire range, seven neighbouring populations of Pinus ayacahuite Ehrenb. ex. Schtdl, and one population of Pinus flexilis James.
Results  The genetic diversity of P. strobiformis ( H _e = 0.856) was found to be high, especially in western populations, whereas eastern populations were less variable and more genetically similar to P. ayacahuite of central Mexico. We found evidence of significant phylogeographic structure ( N _ST = 0.444; P  =   0.026), high genetic structure ( R _ST = 0.270), and isolation by distance. Pairwise R _ST and samova (spatial analysis of molecular variance) results indicated an east–west partition of genetic variation, with populations within each group showing little differentiation and no isolation by distance.
Main conclusions  The phylogeographic structure of P. strobiformis across the entire range was pronounced, with two main genetic and geographic groups separated by the Chihuahuan Desert. However, within each of the two groups there was little population differentiation and no isolation by distance, suggesting genetic connectivity as a result of population expansions within these areas during glacial stages.     

Population genetics suggests effectiveness of habitat connectivity measures for the European tree frog in Switzerland

1.  Governmental authorities in many countries financially support the implementation of habitat connectivity measures to enhance the exchange of individuals among fragmented populations. The evaluation of the effectiveness of such measures is crucial for future management directions and can be accomplished by using genetic methods.
2.  We retraced the population history of the European tree frog in two Swiss river valleys (Reuss and Thur), performed comprehensive population sampling to infer the genetic structure at 11 microsatellite markers, and used first-generation migrant assignment tests to evaluate the contemporary exchange of individuals.
3.  Compared with the Thur valley, the Reuss valley has lost almost double the number of breeding sites and exhibited a more pronounced genetic grouping. However, similar numbers of contemporary migrants were detected in both valleys. In the Reuss valley, 81% of the migration events occurred within the identified genetic groups, whereas in the Thur valley migration patterns were diffuse.
4.  Our results show that the connectivity measures implemented in the Reuss valley facilitated effective tree frog migration among breeding sites within distances up to 4 km. Nevertheless, the Reuss valley exhibited high genetic differentiation, which reflected the impact of barriers to tree frog movement such as the River Reuss. By contrast in the Thur valley, a larger number of breeding sites have been preserved and high admixture indicated exchange of individuals at distances up to 16 km.
5.   Synthesis and applications . We show that genetic methods can substantiate the effectiveness of connectivity measures taken in conservation management at the landscape scale. We urge responsible authorities from both river valleys to continue implementing connectivity measures and to create a dense network of breeding sites, as spatial gaps of 8 km are rarely traversed by tree frogs.     

Genetic diversity and migration patterns of the aquatic macrophyte Potamogeton malaianus in a potamo-lacustrine system

1. Previously, the Yangtze River connected thousands of shallow lakes which together formed a potamo-lacustrine system capable of sustaining a rich variety of submerged macrophytes.
2.  Potamogeton malaianus is one of the dominant submerged macrophytes in many lakes of this area. Genetic variation and population structure of P. malaianus populations from ten lakes in the potamo-lacustrine system were assessed using inter-simple sequence repeat markers.
3. Twelve primer combinations produced a total of 166 unambiguous bands of which 117 (70.5%) were polymorphic. Potamogeton malaianus exhibited a moderate level of population genetic diversity ( P _P = 70.5%, H _E = 0.163 and I =  0.255), as compared with that of plants in the same habitat and range. The main factors responsible for this moderate value were the plant's mixed breeding system (both sexual and asexual) and the hydrological connectivity among habitats.
4.  F statistics, calculated using different approaches, consistently revealed a moderate genetic differentiation among populations, contributing about 20% of total genetic diversity. An estimate of gene flow (using F _ST) suggested that gene flow played a more important role than genetic drift in the current population genetic structure of P. malaianus ( Nm  = 1.131).
5. The genetic diversity of P. malaianus did not increase downstream. A high level of linkage–disequilibrium at the whole population level suggested that metapopulation processes may affect genetic structure. The migration pattern of P. malaianus was best explained by a two-dimensional stepping stone model, indicating that bird-mediated dispersal could greatly influence gene movements among lakes.     

Phylogeography of five Polytrichum species within Europe

Using allozymes and microsatellites we have analysed the genetic structure among European populations for several Polytrichum species to infer relevant factors, such as historical events or gene flow, that have shaped their genetic structure. As we observed low levels of genetic differentiation among populations, and no decreasing levels of genetic variation with increasing latitude within most of the examined species, no genetic evidence was obtained for a step-wise recolonization of Europe from southern refugia after the latest glacial period for P. commune , P. uliginosum , P. formosum and P. piliferum . The near absence of population substructuring within these species does indicate that extensive spore dispersal is the most important factor determining the genetic structure among European Polytrichum populations. Gene flow levels have apparently been sufficient to prevent genetic differentiation among populations caused by genetic drift, and to wipe out any genetic structure caused by the postglacial recolonization process. On the other hand, increased genetic differentiation of alpine P. formosum populations suggests that mountain ranges might restrict gene flow significantly among Polytrichum populations. In contrast to most examined Polytrichum species, P. juniperinum showed high levels of genetic differentiation and a profound genetic structure. Assuming that gene flow is not more restricted in P. juniperinum , these findings suggest that this species has recolonized Europe after the latest glacial period from two different refugia, one possibly being the British Isles.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society 2003, 78, 203–213.     

Fine-scale genetic structure of Atlantic salmon (Salmo salar) using microsatellite markers: effects of restocking and natural recolonization

1. An important goal of conservation biology is to preserve the evolutionary potential of a species by maintaining natural levels of genetic diversity. Here, we assess the population differentiation in the Atlantic salmon, Salmo salar, listed in Annex II of the European Habitats Directive, to provide valuable information for its conservation in Normandy (France).
2. Samples collected from 10 natural sites revealed that 13 of 14 microsatellite loci were polymorphic. Significant differentiation among populations was detected ( F _ST = 0.054, P  <   0.001), and all F _ST pairwise comparisons except one were significant. A genetic split was observed between populations inhabiting streams with limestone geology compared to those inhabiting streams with siliceous geology, which could reflect adaptative differences.
3. Hatchery stocks used for the restocking of two rivers were genetically distinct from native stocks.
4. Analysis of three stream habitats restored in 1995 showed that all were recolonized naturally by wild salmon from geographically close populations and no founder effects were detected. Allelic richness was similar between recolonized and wild populations.
5. From a management perspective, our study revealed that restoration of habitat is very effective to recreate new populations in rivers from which salmon have disappeared and that natural recolonization can be fast and effective in terms of genetic diversity.