Single nucleotide polymorphism discovery from expressed sequence tags in the waterflea Daphnia magna

<p>Abstract</p> <p>Background</p> <p><it>Daphnia </it>(Crustacea: Cladocera) plays a central role in standing aquatic ecosystems, has a well known ecology and is widely used in population studies and environmental risk assessments. <it>Daphnia magna </it>is, especially in Europe, intensively used to study stress responses of natural populations to pollutants, climate change, and antagonistic interactions with predators and parasites, which have all been demonstrated to induce micro-evolutionary and adaptive responses. Although its ecology and evolutionary biology is intensively studied, little is known on the functional genomics underpinning of phenotypic responses to environmental stressors. The aim of the present study was to find genes expressed in presence of environmental stressors, and target such genes for single nucleotide polymorphic (SNP) marker development.</p> <p>Results</p> <p>We developed three expressed sequence tag (EST) libraries using clonal lineages of <it>D. magna </it>exposed to ecological stressors, namely fish predation, parasite infection and pesticide exposure. We used these newly developed ESTs and other <it>Daphnia </it>ESTs retrieved from NCBI GeneBank to mine for SNP markers targeting synonymous as well as non synonymous genetic variation. We validate the developed SNPs in six natural populations of <it>D. magna </it>distributed at regional scale.</p> <p>Conclusions</p> <p>A large proportion (47%) of the produced ESTs are <it>Daphnia </it>lineage specific genes, which are potentially involved in responses to environmental stress rather than to general cellular functions and metabolic activities, or reflect the arthropod's aquatic lifestyle. The characterization of genes expressed under stress and the validation of their SNPs for population genetic study is important for identifying ecologically responsive genes in <it>D. magna</it>.</p

Guidelines for restoring connectivity around water mills: a population genetic approach to the management of riverine fish

1. While freshwater systems provide important goods and services for society, they are threatened by human activity. Fragmentation is one of the most serious ecological concerns in the riverine environment. 2. Historical and cultural values may conflict with nature restoration. Here we use the Zwalm subbasin (Scheldt basin, Belgium) as a case study for reconciling the restoration of the native fish fauna with the preservation of historical water mills (320-1000 years old). 3. We assessed the genetic structure of a barrier-sensitive species, the three-spined stickleback Gasterosteus aculeatus, to estimate the impact of fragmentation on a local to catchment scale. We show how population genetic approaches may be used to generate guidelines for restoration and management, and advance the science of river restoration. 4. Dispersal was lower in above- than in below-mill populations, and water mills provoked an average loss of almost 4% of the genetic variation. This loss accumulated to 40% over the entire system (~23 km, 13 barriers). The impact of individual mills strongly increased with upstream distance and water mill height. One mill provoked significant genetic differentiation, despite the presence of a fish passage. 5. This detailed picture of the genetic connectivity in stickleback is indicative for the basin’s depauperate fauna. Many species share the same migratory pathways and barriers to dispersal. The physical properties of the water mills are likely to have similar effects on species with a similar genetic structure to stickleback. 6. Synthesis and applications. Population genetic studies may be particularly useful during the planning of river restoration and associated ecological studies. In the case of the Zwalm subbasin, we propose a number of management actions, such as building new fish passages and translocating individuals to above-mill populations. These will counter the negative impact of the water mills on the genetic variation in aquatic fauna, whilst retaining their cultural-economical value and limiting the restoration costs. Simulations suggest that reassessment of stickleback genetic structure after a decade should reveal whether or not restoration actions have been effective.status: publishe

Divergent selection as revealed by P(ST) and QTL-based F(ST) in three-spined stickleback (Gasterosteus aculeatus) populations along a coastal-inland gradient

Three measures of divergence, estimated at nine putatively neutral microsatellite markers, 14 quantitative traits, and seven quantitative trait loci (QTL) were compared in eight populations of the three-spined stickleback (Gasterosteus aculeatus L.) living in the Scheldt river basin (Belgium). Lowland estuarine and polder populations were polymorphic for the number of lateral plates, whereas upland freshwater populations were low-plated. The number of short gill rakers and the length of dorsal and pelvic spines gradually declined along a coastal-inland gradient. Plate number, short gill rakers and spine length showed moderate to strong signals of divergent selection between lowland and upland populations in comparison between P(ST) (a phenotypic alternative for Q(ST)) and neutral F(ST). However, such comparisons rely on the unrealistic assumption that phenotypic variance equals additive genetic variance, and that nonadditive genetic effects and environmental effects can be minimized. In order to verify this assumption and to confirm the phenotypic signals of divergence, we tested for divergent selection at the underlying QTL. For plate number, strong genetic evidence for divergent selection between lowland and upland populations was obtained based on an intron marker of the Eda gene, of which the genotype was highly congruent with plate morph. Genetic evidence for divergent selection on short gill rakers was limited to some population pairs where F(ST) at only one of two QTL was detected as an outlier, although F(ST) at both loci correlated significantly with P(ST). No genetic confirmation was obtained for divergent selection on dorsal spine length, as no outlier F(ST)s were detected at dorsal spine QTL, and no significant correlations with P(ST) were observed.status: publishe

Divergent selection as revealed by P-ST and QTL-based F-ST in three-spined stickleback (Gasterosteus aculeatus) populations along a coastal-inland gradient

Three measures of divergence, estimated at nine putatively neutral microsatellite markers, 14 quantitative traits, and seven quantitative trait loci (QTL) were compared in eight populations of the three-spined stickleback (Gasterosteus aculeatus L.) living in the Scheldt river basin (Belgium). Lowland estuarine and polder populations were polymorphic for the number of lateral plates, whereas upland freshwater populations were low-plated. The number of short gill rakers and the length of dorsal and pelvic spines gradually declined along a coastal-inland gradient. Plate number, short gill rakers and spine length showed moderate to strong signals of divergent selection between lowland and upland populations in comparison between P-ST (a phenotypic alternative for Q(ST)) and neutral F-ST. However, such comparisons rely on the unrealistic assumption that phenotypic variance equals additive genetic variance, and that nonadditive genetic effects and environmental effects can be minimized. In order to verify this assumption and to confirm the phenotypic signals of divergence, we tested for divergent selection at the underlying QTL. For plate number, strong genetic evidence for divergent selection between lowland and upland populations was obtained based on an intron marker of the Eda gene, of which the genotype was highly congruent with plate morph. Genetic evidence for divergent selection on short gill rakers was limited to some population pairs where F-ST at only one of two QTL was detected as an outlier, although F-ST at both loci correlated significantly with P-ST. No genetic confirmation was obtained for divergent selection on dorsal spine length, as no outlier F(ST)s were detected at dorsal spine QTL, and no significant correlations with P-ST were observed

Modeling genetic connectivity in sticklebacks as a guideline for river restoration

Estimating genetic connectivity in disturbed riverine landscapes is of key importance for river restoration. However, few species of the disturbed riverine fauna may provide a detailed and basin-wide picture of the human impact on the population genetics of riverine organisms. Here we used the most abundant native fish, the three-spined stickleback (Gasterosteus aculeatus L.), to detect the geographical determinants of genetic connectivity in the eastern part of the Scheldt basin in Belgium. Anthropogenic structures came out as the strongest determinant of population structure, when evaluated against a geographically well-documented baseline model accounting for natural effects. These barriers not only affected genetic diversity, but they also controlled the balance between gene flow and genetic drift, and therefore may crucially disrupt the population structure of sticklebacks. Landscape models explained a high percentage of variation (allelic richness: adjusted R2 = 0.78; pairwise FST: adjusted R2 = 0.60), and likely apply to other species as well. River restoration and conservation genetics may highly benefit from riverine landscape genetics, including model building, the detection of outlier populations, and a specific test for the geographical factors controlling the balance between gene flow and genetic drift

High genetic diversity in Schistosoma mansoni in the Senegal River Basin: a population genetic analysis 20 years after the epidemic outbreak

About twenty years ago, two dams were constructed in the Senegal River Basin (SRB) in order to improve the agricultural conditions in Northern Senegal. The subsequent ecological changes stimulated the growth and spreading of Bulinus and Biomphalaria snail species, intermediate hosts of Schistosoma haematobium and S. mansoni, respectively. This resulted in a major outbreak of intestinal schistosomiasis. A recent study highlighted an increase in urinary schistosomiasis while infection intensity is decreasing for S. mansoni (Polman K, pers. comm.). This is a unique system where the origin of an epidemic outbreak is exactly known and its evolution carefully monitored, providing an opportunity to study the molecular evolution of pathogens in a relative short time frame. Demographic parameters such as the effective population size reflects the adaptive potential of a parasite, i.e. how the parasite population can cope with selection pressure of the host or the environment, while gene flow estimates illustrate the transmission dynamics between populations and localities. Here we report on the population genetic structure of S. mansoni. In March 2006 and 2007, urine and stool samples were collected along the lower and middle valley of the SRB. Eggs have been isolated and hatched. Individual miracidia were collected on Whatman FTAR indicator cards and genotyped for 9 microsatellite loci (a single multiplex). A selection of samples has also been sequenced for ITS1 rDNA and partial cox1 mtDNA. A thorough population genetic analysis revealed a high genetic diversity within populations, but low genetic differentiation between populations, suggesting extensive migration between villages

Transmission site in Mbane, Senegal.

<p>Hybrid parasites were recovered from snails (<i>Bulinus truncatus</i>) collected at this habitat.</p