Genetic Diversity,Heteroplasmy, and Recombination in Mitochondrial Genomes of Daphnia pulex,Daphnia pulicaria,and Daphnia obtusa

Genetic variants of mitochondrial DNA at the individual (heteroplasmy) and population (polymorphism) levels provide insight into their roles in multiple cellular and evolutionary processes. However, owing to the paucity of genome-wide data at the within-individual and population levels, the broad patterns of these two forms of variation remain poorly understood. Here, we analyze 1,804 complete mitochondrial genome sequences from Daphnia pulex, Daphnia pulicaria, and Daphnia obtusa. Extensive heteroplasmy is observed in D. obtusa, where the high level of intraclonal divergence must have resulted from a biparental-inheritance event, and recombination in the mitochondrial genome is apparent, although perhaps not widespread. Global samples of D. pulex reveal remarkably low mitochondrial effective population sizes, <3% of those for the nuclear genome. In addition, levels of population diversity in mitochondrial and nuclear genomes are uncorrelated across populations, suggesting an idiosyncratic evolutionary history of mitochondria in D. pulex. These population-genetic features appear to be a consequence of background selection associated with highly deleterious mutations arising in the strongly linked mitochondrial genome, which is consistent with polymorphism and divergence data suggesting a predominance of strong purifying selection. Nonetheless, the fixation of mildly deleterious mutations in the mitochondrial genome also appears to be driving positive selection on genes encoded in the nuclear genome whose products are deployed in the mitochondrion.     

Variation in ephippial buoyancy in Daphnia pulicaria

1. Freshwater zooplankton often produce diapausing eggs to survive environmental stress. The diapausing eggs of Daphnia (Crustacea, Cladocera) are encased in an ephippium that either floats at the surface or sinks to the sediment. These two types of ephippia may represent different strategies between spatial (floaters) and temporal (sinkers) dispersal of offspring. 2. We observed floating and sinking characteristics of ephippia obtained from eight lakes. We then conducted an experiment with 26 Daphnia pulicaria clones obtained from six of these lakes and observed the production of buoyant and non‐buoyant ephippia under high and low food conditions. 3. Ephippia were more often non‐buoyant than buoyant both from females caught in nature and those reared in the laboratory. The experiment revealed that each clone was able to produce both types of ephippia, but that there was considerable among‐clone variation in the percentage of non‐buoyant ephippia produced. 4. We conclude that production of non‐buoyant versus buoyant ephippia may be driven by both genetic and environmental factors.     

Seasonal analysis of Daphnia pulicaria swimming behavior

Our study documents individual swimming behavior of Daphnia pulicaria over a yearly cycle in a temperate lake. We collected D. pulicaria, a common freshwater zooplankton, from Lake Mendota on 10 dates between July 1994 and June 1995 from two depths, 2 m and 10 m. The Daphnia were rushed to the laboratory and video-taped as they swam in lake water under lake-ambient temperature and light conditions. Five-second swimming tracks of individual Daphnia were filmed and digitized using a motion analysis system. We measured average turning angle, swimming speed and sinking rate for each track. D. pulicaria swimming behavior varied over the annual cycle. We found significant differences in turning angle between depths and among months. Sinking rate and swimming speed were significantly different among months but not depths. Sinking rate and swimming speed were not significantly correlated with water temperature. Our results were contrary to Stokes' Law predictions, in that D. pulicaria had the slowest sinking speed in June, not in the winter when water temperatures were lowest and viscosity was highest. Body length was significantly correlated with all three swimming variables. We also studied swimming behavior in clonal populations of D. pulicaria in different concentrations of the alga, Chlamydomonas reinhardtii. D. pulicaria did not change swimming speed, turning angle or sinking rate over a range of food concentrations. Finally, swimming behavior in a D. pulicaria clone, tested at two temperatures in the laboratory, confirmed the results from our seasonal study; Daphnia did not sink as predicted by changes in viscosity.     

Eutrophication mediates rapid clonal evolution in Daphnia pulicaria

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Molecular Identification and Hidden Diversity of Novel Daphnia Parasites from European Lakes

Parasites play important roles in local population dynamics and genetic structure. However, due to insufficient diagnostic tools, detailed host-parasite interactions may remain concealed by hidden parasite diversity in natural systems. Microscopic examination of 19 European lake Daphnia populations revealed the presence of three groups of parasites: fungi, microsporidia, and oomycetes. For most of these parasites no genetic markers have been described so far. Based on sequence similarities of the nuclear small-subunit and internal transcribed spacer (ITS) rRNA gene regions, one fungus, four microsporidian, and nine oomycete taxa were discovered in 147 infected Daphnia (and/or three other zooplankton crustaceans). Additionally, cloning of rRNA gene regions revealed parasite sequence variation within host individuals. This was most pronounced in the ITS region of one microsporidian taxon, where the within-host sequence variation ranged from 1.7% to 5.3% polymorphic sites for parasite isolates from 14 different geographical locations. Interestingly, the parasite isolates from close locations grouped together based on sequence similarities, suggesting that there was parasite dispersal. Taken together, the data obtained in this study revealed hidden diversity of parasite communities in Daphnia lake populations. Moreover, a higher level of resolution for identifying parasite strains makes it possible to test new hypotheses with respect to parasite dispersal, transmission routes, and coinfection.During the last decade, microparasites of Daphnia species, which are small zooplankton crustaceans, have become a popular study system in ecological and evolutionary research (for a review, see reference 15). It has been shown both in the field and under controlled laboratory conditions that parasites have a substantial impact on Daphnia fitness (7, 21, 52). Parasite-induced reductions in Daphnia population density (11, 12) or even population crashes (17) might result in disruptions of aquatic food webs, as daphnids play important roles as main phytoplankton grazers and as a major food of planktivorous fish (27). Moreover, as infections are often genotype specific (6, 8), they can lead to changes in the gene pool of a Daphnia population (7, 14), sometimes significantly increasing the genetic diversity of the host population (12, 54). Thus, Daphnia parasites cause not only ecological but also evolutionary changes in aquatic systems.Conclusions regarding the importance of parasites in natural systems require powerful tools to detect and properly identify parasite taxa. Thus far, few species-specific molecular markers have been developed for Daphnia parasites (33, 38, 39, 41) and then used in experimental studies (3). In surveys of natural Daphnia populations, parasite identification has been based primarily on microscopic examination (4, 5, 29, 52), with only one exception (32). The parasites recorded in natural populations of Daphnia are thus considered members of certain taxa, or even species, without genetic confirmation. The fact that molecular markers are not used to characterize Daphnia infections makes it difficult to compare epidemic patterns across different habitats and/or various field surveys, as parasites cannot be unambiguously identified by microscopic examination alone. Even if microscopic identification is theoretically possible (for example, by examining ultrastructural morphology by electron microscopy [37]), this approach is not feasible for routine analysis. Consequently, classification of parasites that actually belong to different taxa in the same group might introduce noise into field surveys, as parasite taxa differ widely in virulence and host range (for a review, see reference 15).Most of the known Daphnia parasites that have been described were obtained from small temporary ponds and rock pools (4, 16, 43). In permanent lakes, lower parasite diversity was assumed, mainly because increased fish predation reduces the population density of potential hosts (18), whereas high host density is a crucial determinant of epidemic spread (1, 2, 45). In addition, infected Daphnia spp. are more vulnerable to fish that hunt visually due to loss of their transparent appearance (11, 13). On the other hand, it was recently shown that even if Daphnia host density was reduced by selective fish predation, the prevalence of infection did not decline, probably due to the very high rates of transmission of the parasite that was observed (11). In contrast, we expected that the highly heterogeneous biotic and abiotic conditions in permanent lakes (27) would provide a variety of niches (for a review, see reference 47), which also favor a high level of parasite diversity. Therefore, Czech canyon-shaped reservoirs were chosen as our main study systems, because in these lakes environmental gradients are particularly pronounced in both the horizontal and vertical dimensions (42). Moreover, the Daphnia communities of these reservoirs are dominated by members of the Daphnia longispina complex (35), taxa which have previously been shown to be infected by a variety of parasites (52).The results of our study revealed a high level of diversity of Daphnia parasites in permanent lakes. Fourteen different parasite taxa were detected using nuclear small-subunit (SSU) and internal transcribed spacer (ITS) rRNA gene sequence information. In addition, a high level of sequence variation was observed in the ITS region of one microsporidian taxon. Thus, molecular markers are now available which allow discrimination with high resolution among and within parasite taxa and provide tools to address more detailed questions concerning lake Daphnia-microparasite systems.     

The complex causality of geographical parthenogenesis

Asexual organisms usually have larger and more northern distributions than their sexual relatives. This phenomenon, called geographical parthenogenesis, has been controversially attributed to predispositions in certain taxa; advantages of polyploidy and/or hybrid origin; better colonizing abilities because of uniparental reproduction; introgression of apomixis into sexuals; niche differentiation of clones; or biotic interactions. This review on apomictic plants demonstrates that each of these factors alone has not been able to explain the observed distributions. Establishment of the complex regulatory system of apomixis requires taxonomic and geographical predispositions; hybridization and/or polyploidization do create diversity, but they do not necessarily result in large distributions; colonizing abilities depend on clonal diversity and are outweighed by sexuals by self-compatibility and higher potentials for speciation; niche differentiation, ploidy levels and selfing keep sympatric sexuals and apomicts separated; and the impact of biotic interactions on distributions is uncertain. In conclusion, the distributional success of apomicts has a complex causality and depends on certain circumstances and combinations of factors. The rare establishment of apomixis may help to explain the predominance of sexuality on the large scale.     

Influence of food quality on depth selection of Daphnia pulicaria

We studied the habitat choice of juvenile and adult Daphniapulicaria in thermally stratified water columns (plankton towers)with a deep water algal maximum (DCM). The DCM consisted ofeither filamentous cyanobacteria (Planktothrix agardhii), non-filamentousChlorophyceae (Scenedesmus obliquus) or a mixture of both. AdultD. pulicaria spent more time at colder temperatures in the presenceof P. agardhii than in the presence of S. obliquus, either asthe sole food source or when mixed with P. agardhii. JuvenileD. pulicaria did not show a different habitat choice in thethree food treatments. In a fourth treatment, we also determinedDaphnia distribution in the absence of food. Comparing the habitatchoice of juveniles and adults in each of the four treatments,the latter spent more time at colder temperatures when foodwas absent or when in the sole presence of P. agardhii. Additionalgrazing and stable isotopic marker experiments showed that D.pulicaria ingested and assimilated Planktothrix filaments. Theresults suggest that the differences in habitat choice betweenadult D. pulicaria in the presence of different food types wereinfluenced by food quality effects: adult Daphnia which moveto colder waters in the presence of low quality P. agardhiidecrease their metabolic rate and might thus be able to investmore resources into reproduction when environmental conditionsimprove.     

Genetic versus environmental influence on pigment variation in the ephippia of Daphnia pulicaria

1. The dormant eggs of Daphnia (Crustacea: cladocera) are encased in a protective, chitonous casing known as an ephippium. Ephippia are pigmented with melanin, and the degree of pigmentation ranges from transparent to opaque. Variation in pigmentation exists within and across populations and species, raising questions about the factors that influence the natural distribution of pigmentation. 2. We used image analysis to quantify pigmentation in ephippial casings of Daphnia pulicaria that were produced both in the field and in the laboratory. The percentage of the surface area of ephippia that is darkly pigmented ranged from 0.5 to 99.5%. The range, mean and variance of ephippial pigmentation varied across our 11 study lakes. 3. Laboratory experiments compared clonal variation (five clones/lake) and population variation (five lakes) at three temperatures (15 °C, 20 °C and 25 °C). The degree of pigment variation between clones was much greater than pigment variation between temperatures, indicating that there is a genetic component to pigmentation in the ephippia which is stronger than the effect of temperature. 4. Comparisons of pigment levels and lake characteristics were used to identify physical and biological factors associated with ephippial pigmentation. Investment in ephippial production was the strongest predictor with darker ephippia occurring more often in lakes with the highest ephippial production.     

Cryptic intercontinental colonization in water fleas Daphnia pulicaria inferred from phylogenetic analysis of mitochondrial DNA variation

The water fleas of the Daphnia pulex complex play a key role in freshwater ecosystems throughout the northern hemisphere. Despite the fact that they have been the subject of study for numerous biological disciplines, their phylogeny and species delimitation remain controversial. We used DNA sequence variation of the mitochondrial ND5 gene to reconstruct the phylogenetic relationships of D. pulicaria Forbes, a widespread member of this complex from North America and Europe. Populations from the two continents respectively split into two evolutionary lineages, Eastern Nearctic and European, which each belong to another main clade within the D. pulex complex (the pulicaria and tenebrosa groups, respectively). Unexpectedly, melanin and carotenoid pigmented D. pulicaria populations from European high-mountain lakes were not allied with the transparent populations inhabiting the same lakes and the lowland ponds and reservoirs throughout Europe, but were included with the samples from Canada and Greenland in the Eastern Nearctic lineage. Until now populations belonging to this lineage were known only from Canada and North Atlantic islands, but not from mainland Europe. Independent data from microsatellite markers supported the genetic distinctiveness of the sympatric carotenoid pigmented and transparent populations and suggested that they may have undergone transition to obligate parthenogenesis, possibly as a consequence of past introgressive hybridization. Two different taxa are therefore confused under the name D. pulicaria in Europe. The close phylogenetic relationships of European populations with those from Canada and Greenland suggest that the Nearctic lineage is of recent origin in Europe via intercontinental dispersal from the North America. It has evolved melanin and carotenoid pigmentation as adaptations against the UV light stress, which enable it to share habitat occupied by the transparent European species. The Nearctic D. pulicaria thus provides a new model for studying successful intercontinental invasion. In general, our study demonstrates that a considerable part of the diversity among widespread taxa of cladoceran crustaceans has been overlooked in morphological taxonomies.     

The genetics of obligate parthenogenesis in an aphid species and its consequences for the maintenance of alternative reproductive modes

Although loss of sex is widespread among metazoans, the genetic mechanisms underlying the transition to asexuality are poorly understood. Aphids are good models to address this issue because they frequently show reproductive-mode variation at the species level, involving cyclical parthenogens (CP) that reproduce sexually once a year and obligate parthenogens (OP) that reproduce asexually all year round. Here, we explore the genetic basis of OP in the cereal aphid Sitobion avenae by crossing several genotypes with contrasting reproductive modes and then characterising the reproductive phenotypes of F1 and F2 offspring. The analysis of phenotypic variation in F1 and F2 progenies suggests that at least two autosomal loci control OP in S. avenae. First, the transition to asexuality seems to depend on a single recessive locus, because the offspring from self-crossed cyclical parthenogenetic genotypes contain either 0 or 25% OP. Second, as we observed OP in the F1 progenies from crosses between CP and OP, and some CP in the offspring from outcrossed OP, a dominant ‘suppressor'' gene may also be involved, being inactive when in a recessive homozygous state in CP; this is the most parsimonious explanation for these results. This oligogenic inheritance of OP in S. avenae appears to be an efficient genetic system to generate new OP genotypes continually. It also allows asexuality-inducing alleles to be protected locally during harsh winters when extreme frost kills most OP, and then to spread very quickly after winter.     

Cyanobacterial protease inhibitor microviridin J causes a lethal molting disruption in Daphnia pulicaria

Laboratory experiments identified microviridin J as the source of a fatal molting disruption in Daphnia species organisms feeding on Microcystis cells. The molting disruption was presumably linked to the inhibitory effect of microviridin J on daphnid proteases, suggesting that hundreds of further cyanobacterial protease inhibitors must be considered potentially toxic to zooplankton.     

Cyanobacterial Protease Inhibitor Microviridin J Causes a Lethal Molting Disruption in Daphnia pulicaria

Laboratory experiments identified microviridin J as the source of a fatal molting disruption in Daphnia species organisms feeding on Microcystis cells. The molting disruption was presumably linked to the inhibitory effect of microviridin J on daphnid proteases, suggesting that hundreds of further cyanobacterial protease inhibitors must be considered potentially toxic to zooplankton.     

Meiosis genes in Daphnia pulex and the role of parthenogenesis in genome evolution

Background  

Thousands of parthenogenetic animal species have been described and cytogenetic manifestations of this reproductive mode are well known. However, little is understood about the molecular determinants of parthenogenesis. The Daphnia pulex genome must contain the molecular machinery for different reproductive modes: sexual (both male and female meiosis) and parthenogenetic (which is either cyclical or obligate). This feature makes D. pulex an ideal model to investigate the genetic basis of parthenogenesis and its consequences for gene and genome evolution. Here we describe the inventory of meiotic genes and their expression patterns during meiotic and parthenogenetic reproduction to help address whether parthenogenesis uses existing meiotic and mitotic machinery, or whether novel processes may be involved.     

The great escape: Daphnia pulicaria from post-Bythotrephes invasion time periods have an enhanced escape ability

Hydrobiologia - Non-native species introductions are becoming increasingly common, but long-term consequences of the introduction of non-native predators on native prey species remains poorly...     

Paleogenetic records of Daphnia pulicaria in two North American lakes reveal the impact of cultural eutrophication

Understanding the evolutionary consequences of the green revolution, particularly in wild populations, is an important frontier in contemporary biology. Because human impacts have occurred at varying magnitudes or time periods depending on the study ecosystem, evolutionary histories may vary considerably among populations. Paleogenetics in conjunction with paleolimnology enable us to associate microevolutionary dynamics with detailed information on environmental change. We used this approach to reconstruct changes in the temporal population genetic structure of the keystone zooplankton grazer, Daphnia pulicaria, using dormant eggs extracted from sediments in two Minnesota lakes (South Center, Hill). The extent of agriculture and human population density in the catchment of these lakes has differed markedly since European settlement in the late 19th century and is reflected in their environmental histories reconstructed here. The reconstructed environments of these two lakes differed strongly in terms of environmental stability and their associated patterns of Daphnia population structure. We detected long periods of stability in population structure and environmental conditions in South Center Lake that were followed by a dramatic temporal shift in population genetic structure after the onset of European settlement and industrialized agriculture in its watershed. In particular, we noted a 24.3‐fold increase in phosphorus (P) flux between pre‐European and modern sediment P accumulation rates (AR) in this lake. In contrast, no such shifts were detected in Hill Lake, where the watershed was not as impacted by European settlement and rates of change were less directional with a much smaller increase in sediment P AR (2.3‐fold). We identify direct and indirect effects of eutrophication proxies on genetic structure in these lake populations and demonstrate the power of using this approach in understanding the consequences of anthropogenic environmental change on natural populations throughout historic time periods.     

Reconstructing geographical parthenogenesis: effects of niche differentiation and reproductive mode on Holocene range expansion of an alpine plant

Asexual taxa often have larger ranges than their sexual progenitors, particularly in areas affected by Pleistocene glaciations. The reasons given for this ‘geographical parthenogenesis’ are contentious, with expansion of the ecological niche or colonisation advantages of uniparental reproduction assumed most important in case of plants. Here, we parameterized a spread model for the alpine buttercup Ranunculus kuepferi and reconstructed the joint Holocene range expansion of its sexual and apomictic cytotype across the European Alps under different simulation settings. We found that, rather than niche broadening or a higher migration rate, a shift of the apomict's niche towards colder conditions per se was crucial as it facilitated overcoming of topographical barriers, a factor likely relevant for many alpine apomicts. More generally, our simulations suggest potentially strong interacting effects of niche differentiation and reproductive modes on range formation of related sexual and asexual taxa arising from their differential sensitivity to minority cytotype disadvantage.     

Food quality of gelatinous colonial chlorophytes to the freshwater zooplankters Daphnia pulicaria and Diaptomus oregonensis

1. The capacities of the gelatinous colonial chlorophytes Pandorina morum and Sphaerocystis schroeteri to sustain survival and reproduction in the calanoid copepod Diaptomus oregonensis and the cladoceran Daphnia pulicaria were evaluated quantitatively. Control groups of animals were fed equivalent biovolumes of Cryptomonas reflexa, which is known to favour high levels of survival and reproduction. 2. On a biovolume basis, all three algae sustained equal survival of Daphnia, but Cryptomonas and Pandorina allowed longer survival of Diaptomus than did Sphaerocystis. 3. Both animals produced significantly more offspring clutch^?1 and more total offspring on Cryptomonas than on either chlorophyte. Both animals produced more total offspring on Pandorina than on Sphaerocystis. 4. The interclutch duration for Daphnia was significantly longer on Pandorina than the other algae, and the interclutch duration for Diaptomus was longer on Pandorina than on Cryptomonas. 5. Daphnia utilized the gelatinous chlorophytes more effectively than did Diaptomus.     

Contribution of cyclic parthenogenesis and colonization history to population structure in Daphnia

Cyclic parthenogenesis, the alternation of parthenogenetic and sexual reproduction, can lead to a wide scope of population structures, ranging from almost monoclonal to genetically highly diverse populations. In addition, sexual reproduction in aquatic cyclic parthenogens is associated with the production of dormant stages, which both enhance potential gene flow among populations as well as impact local evolutionary rates through the formation of dormant egg banks. Members of the cladoceran genus Daphnia are widely distributed key organisms in freshwater habitats, which mostly exhibit this reproduction mode. We assessed patterns of genetic variation within and among populations in the eurytopic and morphologically variable species Daphnia longispina , using data from both nuclear (13 microsatellite loci) and mitochondrial (partial sequencing of the 12S rRNA gene) markers from a set of populations sampled across Europe. Most populations were characterized by very high clonal diversity, reflecting an important impact of sexual reproduction and low levels of clonal selection. Among-population genetic differentiation was very high for both nuclear and mitochondrial markers, and no strong pattern of isolation by distance was observed. We also did not observe any substantial genetic differentiation among traditionally recognized morphotypes of D. longispina . Our findings of high levels of within-population genetic variation combined with high among-population genetic differentiation are in line with predictions of the monopolization hypothesis, which suggests that in species with rapid population growth and potential for local adaptation, strong priority effects due to monopolization of resources lead to reduced levels of gene flow.     

Effect of previous feeding conditions on survival in Daphnia pulicaria (Crustacea: Cladocera)

Survival of natural Daphnia populations without previous acclimatization in filtered water under laboratory conditions (starvation) was used as a parameter describing the actual competitive ability of populations in periods of food limitation. Two populations (1 and 2) of Daphnia pulicaria Forbes coming from two enclosures with a low (< 1 mgC l^–1) and a high (about 3 mgC l^–1) seston level were examined in their resistance to starvation. Juveniles of both populations survived better than adult females in the conditions without seston as well as in the control experiment, despite their much lower biomass. Animals from population 1 had lower mortality than those from population 2 in all variants of the experiment. The results confirm the hypothesis that the ability of daphnids to starve depends also on adaptation to previous feeding conditions.