Extinction hazards in experimental Daphnia magna populations: effects of genotype diversity and environmental variation

Extinction is ubiquitous in natural systems and the ultimate fate of all biological populations. However, the factors that contribute to population extinction are still poorly understood, particularly genetic diversity and composition. A laboratory experiment was conducted to examine the influences of environmental variation and genotype diversity on persistence in experimental Daphnia magna populations. Populations were initiated in two blocks with one, two, three, or six randomly selected and equally represented genotypes, fed and checked for extinction daily, and censused twice weekly over a period of 170 days. Our results show no evidence for an effect of the number of genotypes in a population on extinction hazard. Environmental variation had a strong effect on hazards in both experimental blocks, but the direction of the effect differed between blocks. In the first block, variable environments hastened extinction, while in the second block, hazards were reduced under variable food input. This occurred despite greater fluctuations in population size in variable environments in the second block of our experiment. Our results conflict with previous studies, where environmental variation consistently increased extinction risk. They are also at odds with previous studies in other systems that documented significant effects of genetic diversity on population persistence. We speculate that the lack of sexual reproduction, or the phenotypic similarity among our experimental lines, might underlie the lack of a significant effect of genotype diversity in our study.     

温度和食物浓度对大型溞Daphnia magna种群动态和两性生殖的影响

在4个温度(15、20、25、30℃)和3个食物浓度(1×104,1×105,5×105 cells ml-1)下研究了大型溞(Daphnia magna)淮河种群的动态和两性生殖,结果表明:(1)在实验初期,大型溞种群密度不断增加,达到最大值后种群密度呈现缓慢下降或趋于稳定的趋势.除15℃下最大瞬时增长率(1.36 d-1)出现在中食物浓度组外,20℃(1.51 d-1)、25℃(1.39 d-1)、30℃(0.69 d-1)下的最大瞬时增长率均出现在高食物浓度组.(2)相同温度下,食物浓度与大型溞最大种群密度间存在显著正相关(p<0.01).(3)相同食物浓度下,随温度升高,大型溞首次产幼溞时间(5～21d)和到达最大种群密度的时间(15～29d)缩短,首次抱卵时的体长(1.75～2.67 mm)减少.(4)在较低的温度和中食物浓度组下,大型溞产生了较多的休眠卵或卵鞍(15℃:(16.7±2.5) ind. 和20℃:(18.3±3.8) ind.);30℃下没有出现休眠卵或卵鞍.除15℃、中食物浓度组外,其它实验组均产生雄体.实验25d后,雄体密度与种群密度呈显著的相关性(30℃:p<0.05;15～25℃:p<0.01).(5)本研究结果暗示大型溞休眠卵的形成受温度、食物浓度和种群密度的共同影响,且较低的温度是大型溞休眠卵形成的主要诱因.     

Effects of algal food quality on sexual reproduction of Daphnia magna

The objective of our study was to investigate sexual reproduction of Daphnia magna associated with mating behaviors and hatching rates, according to different algal food sources. Since a diatom is known to contain more abundant long‐chain poly unsaturated fatty acids (PUFAs), we hypothesized that the diatom‐consuming D. magna would exhibit more successful reproduction rates. Upon the hypothesis, we designed three experiments using two algal species, a green alga (Chlorella vulgaris) and a diatom (Stephanodiscus hantzschii). From the results, we found that the mating frequency and copulation duration increased in the treatment with S. hantzschii, resulting in a significant increase of hatching rates of resting eggs. In the other two repetitive mating strategies (e.g., one female vs. multiple males, and one male vs. multiple females), we found that the hatching rates of resting eggs were greater in the S. hantzschii treatment. In addition to the mating strategy, male body size significantly increased in the diatom treatment, hence average diameter of penis was also statistically different among the treatments (greater diameter in the S. hantzschii treatment). To examine the effect of algal food quality, we estimated quantity of fatty acids in the two algal species. Our result showed that S. hantzschii had a higher proportion of long‐chain PUFAs than C. vulgaris. Furthermore, a stable isotope analysis revealed that carbon and nitrogen originated from S. hantzschii were more assimilated to D. magna. In summary, our study manifested that diatom consumption of D. magna leads to more successful sexual reproduction. We then discussed how the diatom consumption of zooplankton influences food web dynamics in a freshwater ecosystem.     

Carapace epithelia are rich in large filamentous actin bundles in Daphnia magna,Daphnia pulex,and Sida crystallina (Crustacea: Cladocera)

Cladocerans (water fleas) are planktonic crustaceans that typically have a bivalved carapace. Each valve of the carapace consists of two cuticle‐secreting epithelial layers that are separated by a hemolymphatic chamber and joined by pillar structures. Ultrastructural analyses in several species of Cladocera have shown that the carapace epithelia and pillars contain filamentous structures of unknown composition. In the present study we used a fluorescent phalloidin conjugate to show that the carapaces of three cladocerans, Daphnia magna, D. pulex, and Sida crystallina, are rich in large bundles of filamentous actin (F‐actin). In D. magna we employed confocal microscopy and orthogonal views of three‐dimensional reconstructions to show that these bundles extend radially from foci in the pillars towards the integument surfaces, and their structure is consistent with that of contractile stress fibers. Using a fluorescent lipophilic stain, DiOC₆(3), we show that the F‐actin bundles are distributed in membrane‐rich regions within the carapace epithelia, and that, in the superficial epithelium, these may be large membrane‐bound organelles. In D. magna, the F‐actin bundles are present in embryonic, juvenile instar, and adult, developmental stages, and through development the bundles become larger, contain more F‐actin, and become more widely spaced. We present an alignment of the deduced amino acid sequences of six putative D. pulex actin genes, and discuss the implications that their respective sequences have on the likelihood of their inclusion into the F‐actin bundles of the carapace. Our identification of these large F‐actin bundles within the pillars of three cladocerans provides new insight into the role these structures play in influencing carapace dynamics within this order.     

Ecological genetics of sediment browsing behaviour in a planktonic crustacean

Zooplankton can display complex habitat selection behaviours that influence the way they interact with their environments. Some species, although primarily pelagic, can exploit sediment‐borne particles as a food source or use sediments as a refuge from pelagic predation. However, this strategy may increase the exposure to other risks such as benthic predation and infection from sediment‐borne parasite transmission stages. The evolution of habitat selection behaviour in these species is thus expected to be influenced by multiple and possibly contrasting selective forces. Here, we study the browsing behaviour of the water flea Daphnia magna on bottom sediments. First, we demonstrated genetic variation for sediment browsing among D. magna genotypes from natural populations sampled across a broad geographic range. Next, we used an F2 recombinant panel to perform a QTL analysis and identified three regions in the D. magna genome contributing to variation in browsing behaviour. We also analysed the correlation between our data and previously published data on the phototactic behaviour of genotypes from the same F2 panel. Clonal means of the two behavioral traits were not correlated, suggesting that they may evolve independently. Browsing behaviour is likely to be a relevant component of habitat selection in D. magna, and its study may help to incorporate the interactions with the sediment into eco‐evolutionary models of this key freshwater species.     

Approximate Bayesian estimation of extinction rate in the Finnish Daphnia magna metapopulation

Approximate Bayesian computation (ABC) is useful for parameterizing complex models in population genetics. In this study, ABC was applied to simultaneously estimate parameter values for a model of metapopulation coalescence and test two alternatives to a strict metapopulation model in the well‐studied network of Daphnia magna populations in Finland. The models shared four free parameters: the subpopulation genetic diversity (θ_S), the rate of gene flow among patches (4Nm), the founding population size (N₀) and the metapopulation extinction rate (e) but differed in the distribution of extinction rates across habitat patches in the system. The three models had either a constant extinction rate in all populations (strict metapopulation), one population that was protected from local extinction (i.e. a persistent source), or habitat‐specific extinction rates drawn from a distribution with specified mean and variance. Our model selection analysis favoured the model including a persistent source population over the two alternative models. Of the closest 750 000 data sets in Euclidean space, 78% were simulated under the persistent source model (estimated posterior probability = 0.769). This fraction increased to more than 85% when only the closest 150 000 data sets were considered (estimated posterior probability = 0.774). Approximate Bayesian computation was then used to estimate parameter values that might produce the observed set of summary statistics. Our analysis provided posterior distributions for e that included the point estimate obtained from previous data from the Finnish D. magna metapopulation. Our results support the use of ABC and population genetic data for testing the strict metapopulation model and parameterizing complex models of demography.     

Positive selection of digestive proteases in Daphnia: A mechanism for local adaptation to cyanobacterial protease inhibitors

Due to the combined effects of global warming and eutrophication, the frequency of deleterious cyanobacterial blooms in freshwater ecosystems has increased. In line with this, local adaptation of the aquatic keystone herbivore Daphnia to cyanobacteria has received major attention. Besides microcystins, the most frequent cyanobacterial secondary metabolites in such blooms are protease inhibitors (PIs). Recently, it has been shown that a protease gene showed copy number variation between four D. magna populations that differed in tolerance to PIs. From that study, we chose two distinct populations of D. magna which had or had not coexisted with cyanobacteria in the past. By calculating F_ST values, we found that the two populations were genetically more distant in the protease loci than in neutral loci. Population genetic tests applied to the tolerant population revealed that positive selection was most probably acting on the gene loci of the digestive protease CT448 and CT802. We conclude that the selection of digestive proteases and subsequent reduction in copy number is the molecular basis of evolutionary changes leading to local adaptation to PIs.     

Daphnia females adjust sex allocation in response to current sex ratio and density

Cyclical parthenogenesis presents an interesting challenge for the study of sex allocation, as individuals’ allocation decisions involve both the choice between sexual and asexual reproduction, and the choice between sons and daughters. Male production is therefore expected to depend on ecological and evolutionary drivers of overall investment in sex, and those influencing male reproductive value during sexual periods. We manipulated experimental populations, and made repeated observations of natural populations over their growing season, to disentangle effects of population density and the timing of sex from effects of adult sex ratio on sex allocation in cyclically parthenogenetic Daphnia magna. Male production increased with population density, the major ecological driver of sexual reproduction; however, this response was dampened when the population sex ratio was more male‐biased. Thus, in line with sex ratio theory, we show that D. magna adjust offspring sex allocation in response to the current population sex ratio.     

Parasite‐mediated selection in a natural metapopulation of Daphnia magna

Parasite‐mediated selection varying across time and space in metapopulations is expected to result in host local adaptation and the maintenance of genetic diversity in disease‐related traits. However, nonadaptive processes like migration and extinction‐(re)colonization dynamics might interfere with adaptive evolution. Understanding how adaptive and nonadaptive processes interact to shape genetic variability in life‐history and disease‐related traits can provide important insights into their evolution in subdivided populations. Here we investigate signatures of spatially fluctuating, parasite‐mediated selection in a natural metapopulation of Daphnia magna. Host genotypes from infected and uninfected populations were genotyped at microsatellite markers, and phenotyped for life‐history and disease traits in common garden experiments. Combining phenotypic and genotypic data a Q_ST–F_ST‐like analysis was conducted to test for signatures of parasite mediated selection. We observed high variation within and among populations for phenotypic traits, but neither an indication of host local adaptation nor a cost of resistance. Infected populations have a higher gene diversity (Hs) than uninfected populations and Hs is strongly positively correlated with fitness. These results suggest a strong parasite effect on reducing population level inbreeding. We discuss how stochastic processes related to frequent extinction‐(re)colonization dynamics as well as host and parasite migration impede the evolution of resistance in the infected populations. We suggest that the genetic and phenotypic patterns of variation are a product of dynamic changes in the host gene pool caused by the interaction of colonization bottlenecks, inbreeding, immigration, hybrid vigor, rare host genotype advantage and parasitism. Our study highlights the effect of the parasite in ameliorating the negative fitness consequences caused by the high drift load in this metapopulation.     

The temperature‐size rule in Daphnia magna across different genetic lines and ontogenetic stages: Multiple patterns and mechanisms

Ectotherms tend to grow faster, but reach a smaller size when reared under warmer conditions. This temperature‐size rule (TSR) is a widespread phenomenon. Despite the generality of this pattern, no general explanation has been found. We therefore tested the relative importance of two proposed mechanisms for the TSR: (1) a stronger increase in development rate relative to growth rate at higher temperatures, which would cause a smaller size at maturity, and (2) resource limitation placing stronger constraints on growth in large individuals at higher temperatures, which would cause problems with attaining a large size in warm conditions. We raised Daphnia magna at eight temperatures to assess their size at maturity, asymptotic size, and size of their offspring. We used three clonal lines that differed in asymptotic size and growth rate. A resource allocation model was developed and fitted to our empirical data to explore the effect of both mechanisms for the TSR. The genetic lines of D. magna showed different temperature dependence of growth and development rates resulting in different responses for size at maturity. Also, at warm temperatures, growth was constrained in large, but not in small individuals. The resource allocation model could fit these empirical data well. Based on our empirical results and model explorations, the TSR of D. magna at maturity is best explained by a stronger increase in development rate relative to growth rate at high temperature, and the TSR at asymptotic size is best explained by a size‐dependent and temperature‐dependent constraint on growth, although resource limitation could also affect size at maturity. In conclusion, the TSR can take different forms for offspring size, size at maturity, and asymptotic size and each form can arise from its own mechanism, which could be an essential step toward finding a solution to this century‐old puzzle.     

Evidence for local adaptation in neighbouring Daphnia populations: a laboratory transplant experiment

1. We tested whether two neighbouring Daphnia galeata populations (from Lake Blankaart and Fish Pond), separated only by 5 m of land and with the occasional exchange of water were genetically differentiated in allozyme markers and life history traits. Allozyme electrophoresis revealed that the populations differed in allelic as well as in genotypic composition. 2. In a laboratory transplant experiment, in which animals of four clones of each of the populations were raised in the water of both ponds, survival in Blankaart water was high for both the Blankaart and Fish Pond clones, whereas survival in Fish Pond water was high for the Fish Pond clones, but low for the Blankaart clones. 3. Fish Pond clones produced fewer neonates than Blankaart clones when cultured in Blankaart water. High egg mortality was observed for animals that were raised in Blankaart water, and this egg mortality was higher for Fish Pond clones than for Blankaart clones. 4. Our results provide evidence for genetic differentiation between Daphnia populations inhabiting neighbouring water bodies and suggest local adaptation to environmental conditions other than direct predation.     

QTL mapping and the genetic basis of adaptation: recent developments

Quantitative trait loci (QTL) mapping has been used in a number of evolutionary studies to study the genetic basis of adaptation by mapping individual QTL that explain the differences between differentiated populations and also estimating their effects and interaction in the mapping population. This analysis can provide clues about the evolutionary history of populations and causes of the population differentiation. QTL mapping analysis methods and associated computer programs provide us tools for such an inference on the genetic basis and architecture of quantitative trait variation in a mapping population. Current methods have the capability to separate and localize multiple QTL and estimate their effects and interaction on a quantitative trait. More recent methods have been targeted to provide a comprehensive inference on the overall genetic architecture of multiple traits in a number of environments. This development is important for evolutionary studies on the genetic basis of multiple trait variation, genotype by environment interaction, host–parasite interaction, and also microarray gene expression QTL analysis.     

Patterns and dynamics of rapid local adaptation and sex in varying habitat types in rotifers

Local adaptation is an important principle in a world of environmental change and might be critical for species persistence. We tested the hypothesis that replicated populations can attain rapid local adaptation under two varying laboratory environments. Clonal subpopulations of the cyclically parthenogenetic rotifer Brachionus calyciflorus were allowed to adapt to two varying harsh and a benign environment: a high‐salt, a food‐limited environment and untreated culture medium (no salt addition, high food). In contrast to most previous studies, we re‐adjusted rotifer density to a fixed value (two individuals per ml) every 3–4 days of unrestricted population growth, instead of exchanging a fixed proportion of the culture medium. Thus our dilution regime specifically selected for high population growth during the entire experiment and it allowed us to continuously track changes in fitness (i.e., maximum population growth under the prevailing conditions) in each population. After 56 days (43 asexual and eight sexual generations) of selection, the populations in the harsh environments showed a significant increase in fitness over time relative to the beginning compared to the population in untreated culture medium. Furthermore, the high‐salt population exhibited a significantly elevated ratio of sexual offspring from the start of the experiment, which suggested that this environment either triggered higher rates of sex or that the untreated medium and the food‐limited environment suppressed sex. In a following assay of local adaptation we measured population fitness under “local” versus “foreign” conditions (populations adapted to this environment compared to those of the other environment) for both harsh habitats. We found significantly higher fitness values for the local populations (on average, a 38% higher fitness) compared to the foreign populations. Overall, local adaptation was formed rapidly and it seemed to be more pronounced in the high‐salt treatment.     

Life-strategy shift by intraspecific interaction in Daphnia magna : change in reproduction from quantity to quality

In Daphnia magna, high animal density causes a mutual intraspecific influence, called life-strategy shift by intraspecific interaction (LiSSII). We investigated mothers (F₀), living singly or in groups of four per 50 ml, and their F₁ offspring. Clutch sizes of F₀ daphnids living in groups were smaller than those of singly living ones. However, the F₁ neonates were bigger in size, had higher dry weights and contained more lipids. They were also able to survive longer starvation periods. If these F₁␣daphnids were again kept in groups of four, the effects of LiSSII on some life-history parameters were stronger. As compared to group-living F₀ daphnids, juvenile development time was prolonged from 7.5 to 10.0 days. In contrast, body size was reduced and the further reduction in offspring number was slight. The F₂␣neonates exhibited the same change towards bigger size and higher dry weight as observed in the F₁. In contrast F₁ daphnids, that were the offspring of daphnids living in groups but were kept singly were bigger and produced more offspring than single daphnids that were the offspring of daphnids kept singly. The neonates of the former were bigger in size and heavier. It is suggested that for the F₀ generation the ecological significance of the LiSSII effects is an increase in both the parent and offspring survival probability when food is limited. LiSSII acts before food conditions deteriorate seriously. Daphnids affected by LiSSII invest less of their biomass into offspring. Offspring release is well-timed and quality is better, at the expense of quantity. Under favourable environmental conditions, F₂ daphnids that are the offspring of mothers affected by LiSSII appeared well adapted to fast recolonisation when living at low density. Received: 18 December 1995 / Accepted: 21 November 1996     

Winter hardiness of Miscanthus (II): Genetic mapping for overwintering ability and adaptation traits in three interconnected Miscanthus populations

Miscanthus × giganteus (M×g) is the primary species of Miscanthus for bioenergy feedstock production. The current leading biomass cultivar, M×g ‘1993‐1780’, is insufficiently adapted in temperate regions with cold winters such as USDA hardiness zone 5 (average annual minimum temperature of ?28.9 to ?23.3°C) or lower. Three interconnected Miscanthus F₁ populations that shared a common parent were planted in a replicated field trial at Urbana, IL (hardiness zone 5b; average annual minimum temperature of ?26.1 to ?23.3°C) in spring 2011. The winter of 2013–2014 was especially cold in Urbana, with a minimum soil temperature at 10 cm of ?6.2°C and a minimum air temperature of ?25.3°C, giving us an opportunity to evaluate hardiness on established year‐3 plants. The parent in common to all three populations, M. sinensis ssp. condensatus ‘Cosmopolitan’, is native to maritime southern Japan, and in Urbana, it is winter‐damaged most years. In contrast, the three other parents, M. sacchariflorus ‘Robustus’ (MapA), M. sinensis ‘Silberturm’ (MapB), and M. sinensis ‘November Sunset’ (MapC), are typically winter hardy in Urbana. Nearly all MapA progeny plants survived and grew vigorously in spring 2014, whereas in MapB and MapC, many progeny plants did not survive the winter, and most of the survivors were severely damaged, with poor vigor. Negative correlations between overwintering ability and spring regrowth date and autumn dormancy date suggested that the genotypes most likely to survive winters were those that emerged early in spring and/or went dormant early in autumn. Using joint‐population analysis, we identified 53 quantitative trait loci (QTLs) for nine adaptation traits, including nine QTLs for overwintering ability and 11 for spring hardiness scores. Many biologically intuitive candidate genes were observed within or near the QTLs detected in this study, suggesting their validity and potential for further study.     

Food availability modulates temperature‐dependent effects on growth,reproduction, and survival in Daphnia magna

Reduced body size and accelerated life cycle due to warming are considered major ecological responses to climate change with fitness costs at the individual level. Surprisingly, we know little about how relevant ecological factors can alter these life history trade‐offs and their consequences for individual fitness. Here, we show that food modulates temperature‐dependent effects on body size in the water flea Daphnia magna and interacts with temperature to affect life history parameters. We exposed 412 individuals to a factorial manipulation of food abundance and temperature, tracked each reproductive event, and took daily measurements of body size from each individual. High temperature caused a reduction in maximum body size in both food treatments, but this effect was mediated by food abundance, such that low food conditions resulted in a reduction of 20% in maximum body size, compared with a reduction of 4% under high food conditions. High temperature resulted in an accelerated life cycle, with pronounced fitness cost at low levels of food where only a few individuals produced a clutch. These results suggest that the mechanisms affecting the trade‐off between fast growth and final body size are food‐dependent, and that the combination of low levels of food and high temperature could potentially threaten viability of ectotherms.     

Ethanol resistance in Drosophila melanogaster has increased in parallel cold‐adapted populations and shows a variable genetic architecture within and between populations

Understanding the genetic properties of adaptive trait evolution is a fundamental crux of biological inquiry that links molecular processes to biological diversity. Important uncertainties persist regarding the genetic predictability of adaptive trait change, the role of standing variation, and whether adaptation tends to result in the fixation of favored variants. Here, we use the recurrent evolution of enhanced ethanol resistance in Drosophila melanogaster during this species’ worldwide expansion as a promising system to add to our understanding of the genetics of adaptation. We find that elevated ethanol resistance has evolved at least three times in different cooler regions of the species’ modern range—not only at high latitude but also in two African high‐altitude regions. Applying a bulk segregant mapping framework, we find that the genetic architecture of ethanol resistance evolution differs substantially not only between our three resistant populations, but also between two crosses involving the same European population. We then apply population genetic scans for local adaptation within our quantitative trait locus regions, and we find potential contributions of genes with annotated roles in spindle localization, membrane composition, sterol and alcohol metabolism, and other processes. We also apply simulation‐based analyses that confirm the variable genetic basis of ethanol resistance and hint at a moderately polygenic architecture. However, these simulations indicate that larger‐scale studies will be needed to more clearly quantify the genetic architecture of adaptive evolution and to firmly connect trait evolution to specific causative loci.     

Approaches to interval mapping of QTL in a multigeneration pedigree: the example of porcine chromosome 4

Quantitative trait loci (QTLs) have been mapped in many studies of F2 populations derived from crosses between diverse lines. One approach to confirming these effects and improving the mapping resolution is genetic chromosome dissection through a backcrossing programme. Analysis by interval mapping of the data generated is likely to provide additional power and resolution compared with treating data marker by marker. However, interval mapping approaches for such a programme are not well developed, especially where the founder lines were outbred. We explore alternative approaches to analysis using, as an example, data from chromosome 4 in an intercross between wild boar and Large White pigs where QTLs have been previously identified. A least squares interval mapping procedure was used to study growth rate and carcass traits in a subsequent second backcross generation (BC2). This procedure requires the probability of inheriting a wild boar allele for each BC2 animal for locations throughout the chromosome. Two methods for obtaining these probabilities were compared: stochastic or deterministic. The two methods gave similar probabilities for inheriting wild boar alleles and, hence, gave very similar results from the QTL analysis. The deterministic approach has the advantage of being much faster to run but requires specialized software. A QTL for fatness and for growth were confirmed and, in addition, a QTL for piglet growth from weaning at 5 weeks up to 7 weeks of age and another for carcass length were detected.