Clonal diversity,clonal persistence and rapid taxon replacement in natural populations of species and hybrids of the Daphnia longispina complex

Hybridization is common among cyclical parthenogens, especially in zooplankton species assemblages of the genus Daphnia. To explore hybridization dynamics and the extent of clonal diversity in the Daphnia longispina complex, we analysed population structure in eight permanent lakes. Based on 15 microsatellite loci, three major taxonomic units emerged: two species, D. galeata and D. longispina and their F1 hybrids, supported by factorial correspondence analysis and two Bayesian methods. At the same time, the detection of backcross classes differed between methods. Mean clonal diversity was lowest in the F1 hybrids, as expected from the high rate of asexual reproduction. Within taxa, replicated genotypes were of clonal origin, but clonal lineages persisted in subsequent years in only one of three resampled lakes. In another lake, the taxon composition changed from being dominated by hybrids to complete dominance by one parental taxon. Such a year‐to‐year taxon replacement has not been reported for the D. longispina complex before. Our data on this hybrid complex illustrate that high‐resolution genotyping is essential for the understanding of ecological and evolutionary outcomes of hybridization in partially clonal taxa.     

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.     

Discrimination of hybrid classes using cross-species amplification of microsatellite loci: methodological challenges and solutions in Daphnia

Microsatellite markers are important tools in population, conservation and forensic studies and are frequently used for species delineation, the detection of hybridization and introgression. Therefore, marker sets that amplify variable DNA regions in two species are required; however, cross-species amplification is often difficult, as genotyping errors such as null alleles may occur. To estimate the level of potential misidentifications based on genotyping errors, we compared the occurrence of parental alleles in laboratory and natural Daphnia hybrids (Daphnia longispina group). We tested a set of 12 microsatellite loci with regard to their suitability for unambiguous species and hybrid class identification using F(1) hybrids bred in the laboratory. Further, a large set of 44 natural populations of D. cucullata, D. galeata and D. longispina (1715 individuals) as well as their interspecific hybrids were genotyped to validate the discriminatory power of different marker combinations. Species delineation using microsatellite multilocus genotypes produced reliable results for all three studied species using assignment tests. Daphnia galeata × cucullata hybrid detection was limited due to three loci exhibiting D. cucullata-specific null alleles, which most likely are caused by differences in primer-binding sites of parental species. Overall, discriminatory power in hybrid detection was improved when a subset of markers was identified that amplifies equally well in both species.     

Strong intraspecific variation in genetic diversity and genetic differentiation in Daphnia magna: the effects of population turnover and population size

Theory predicts that genetic diversity and genetic differentiation may strongly vary among populations of the same species depending on population turnover and local population sizes. Yet, despite the importance of these predictions for evolutionary and conservation issues, empirical studies comparing high‐turnover and low‐turnover populations of the same species are scarce. In this study, we used Daphnia magna, a freshwater crustacean, as a model organism for such a comparison. In the southern/central part of its range, D. magna inhabits medium‐sized, stable ponds, whereas in the north, it occurs in small rock pools with strong population turnover. We found that these northern populations have a significantly lower genetic diversity and higher genetic differentiation compared to the southern/central populations. Total genetic diversity across populations was only about half and average within‐population diversity only about a third of that in southern/central populations. Moreover, an average southern population contains more genetic diversity than the whole metapopulation system in the north. We based our analyses both on silent sites and microsatellites. The similarity of our results despite the contrasting mutation rates of these markers suggests that the differences are caused by contemporary rather than by historical processes. Our findings show that variation in population turnover and population size may have a major impact on the genetic diversity and differentiation of populations, and hence may lead to differences in evolutionary processes like local adaptation, hybrid vigour and breeding system evolution in different parts of a species range.     

Analysis of reticulate relationships within the Daphnia longispina species complex. Allozyme phenotype and morphology

A two-step method is proposed to get reliable associations between morphology and genotype in clonal assemblages in which more than two predominantly parthenogenetic species are thought to coexist with hybrids. In dataset 1, the genetic relationships among clones of the Daphnia longispina hybrid complex from seven prealpine lakes in southern Germany were studied based on the variation at 21 enzyme loci. The spatial arrangement in the multidimensional scaling plot revealed a reticulate pattern among three presumably parental species, D. cucullata, D. galeata and D. hyalina, and three hybrid groups, D. cucullata/galeata, D. cucullata/hyalina and D. galeata/hyalina. The Got1 locus was believed to be a discriminating factor between species and hybrids (cf. Wolf and Mort, 1986). However, this locus is more variable, and 57% of the clones would have been misidentified using it. Moreover, the morphological variation within genetically defined groups is also higher than previously assumed. In dataset 2, the revision of morphological and genetic markers greatly improved the association between morphology and genotype in newly collected animals. The spatial arrangement of clones in multidimensional scaling plots and morphological asymmetries to parents suggest both, different degrees of introgression and bidirectional hybridization. Most unexpected genotypes were found in the cxh hybrid group, suggesting that F1-hybrids are fertile. The results showed (1) that the clonal diversity was very high (2) that detailed analyses of multiple morphological and allozyme markers are necessary to resolve taxonomic relationships within clonal assemblages consisting of multiple species, hybrids and differently introgressed backcrosses, and (3) that the three original species seem to have sufficient within-species recombination and a low enough rate of backcrossing to allow taxonomic identification. It must remain undecided if the present situation is locally restricted, if it is stable or represents a transient situation which could lead to either a consolidation of the three species by gradual elimination of the hybrids, to a taxonomic breakdown, or to hybrid speciation.     

Ecological genetics of Norwegian Daphnia. II. Distribution of Daphnia longispina genotypes in relation to short-wave radiation and water colour

In the mountain range of South Norway, transparent and melanic members of the Daphnia longispina complex occur. Melanic populations inhabit clearwater lakes and ponds, while transparent populations are found in ponds with slightly humic water. Mixed populations have not been detected. The distribution patterns of the two morphs are related to ambient levels of short-wave radiation, and the light absorptive properties of the inhabited waters. The pigment present is probably melanin, which is deposited in the dorsally directed parts of the carapace, head shield and antennae. Allozyme studies indicate that these distinct morphs are only remotely related, the alpine transparent group being closer to lowland, likewise transparent, populations. A melanic population found at Svalbard is closely related to the melanic mainland populations. Clonal diversity in ponds and shallow lakes is very low, in contrast to populations of deeper lakes.Deceased.     

A major shift in Daphnia genetic structure after the first ice‐free winter in a German reservoir

1. Climate warming may cause disruption of trophic linkages in aquatic ecosystems and lead to changes in abundance and genetic structure of zooplankton populations. We monitored the community of the Daphnia galeata‐hyalina hybrid complex in the Saidenbach Reservoir (Saxony, Germany) using allozyme electrophoresis for three consecutive years (2005–07), including one (2007) following an unusually warm winter that prevented the formation of ice cover for the first time in the history of the reservoir. 2. Genetic composition during the 2007 season differed substantially from the two preceding years that experienced the usual 3‐month ice period. Three abundance peaks in June, July and October 2007 were dominated by hybrids of Daphnia galeata x hyalina, whereas in the 2005 and 2006 seasons two peaks in June and September were dominated by Daphnia hyalina genotypes. 3. The genetic composition of the pool of diapausing eggs produced in autumn and the rate of change of genotype abundance during the following spring indicate recruitment of the D. hyalina subpopulation from ex‐ephippial animals during the spring population increase. 4. The differing potential to contribute to the overwintering animal pool or to the inoculum from diapausing eggs was confirmed by results from laboratory life‐table experiments. Daphnia galeata clones survived longer and produced parthenogenetic offspring under winter conditions, whereas D. hyalina clones showed a shorter lifespan and produced resting eggs. 5. Our results indicate a profound role of recruitment strategy in the observed shift in genetic composition. Increasing winter temperatures predicted in the context of climate change may thus favour overwintering animals, leading to an increase in the contribution of these genotypes to the population. Such microevolutionary processes may dampen possible seasonal mismatches between daphnid populations and their food or predator populations.     

Intra-specific rDNA-ITS restriction site variation and an improved protocol to distinguish species and hybrids in the Daphnia longispina complex

A collaborative research effort was undertaken to evaluate the robustness of a recently developed genetic tool for species identification of members in the morphologically variable Daphnia longispina species complex. This genetic method, based on restriction fragment length polymorphism (RFLP) of the internal transcribed spacer region (ITS) of nuclear ribosomal DNA (rDNA) with restriction enzymes Mwo I and Sau96 I [Billiones et al., 2004. Hydrobiologia 526: 43–53], was applied to many different European populations. Results were compared with two or more independently obtained characters (morphology, allozymes, mitochondrial DNA (mtDNA), or cloned rDNA-ITS sequences). Individuals of most taxa were readily identified, but unexpected ITS-RFLP patterns were found in many individuals indicated by other markers to be D. galeata or one of its hybrids. Among 43 investigated D. galeata populations (902 specimen analysed by ITS-RFLP), deviant RFLP fragment patterns occurred in 26 (i.e., more than half) of the populations. The deviant patterns could be attributed to the loss of one single restriction site in the ITS2 region. This loss made the distinction of D. galeata from other species unreliable, and F1 hybrids could not be identified. Future users should be aware of this shortcoming of the Billions et al. [2004. Hydrobiologia 526: 43–53] protocol. As a solution to this problem, we present an improved genetic identification protocol based on a simple double digestion of the rDNA-ITS region with the restriction enzymes BsrB I and EagI. Sequence analyses of rDNA-ITS clones and preliminary testing indicate that the new protocol is unaffected by the rDNA variation which troubled the Mwo I/Sau96 I protocol. Further, the new protocol identifies all European species of the D. longispina complex, as well as their F1 hybrids. However, a wider screening is required to verify its general utility for all species, since yet unknown variation may occur. Guest editor: Piet Spaak Cladocera: Proceedings of the 7th International Symposium on Cladocera     

The genetic legacy of polyploid Bolivian Daphnia: the tropical Andes as a source for the North and South American D. pulicaria complex

We investigated genetic variation in asexual polyploid members of the water flea Daphnia pulex complex from a set of 12 Bolivian high-altitude lakes. We used nuclear microsatellite markers to study genetic relationships among all encountered multilocus genotypes, and combined this with a phylogenetic approach using DNA sequence data of three mitochondrial genes. Analyses of mitochondrial gene sequence divergence showed the presence of three very distinct clades that likely represent cryptic undescribed species. Our phylogenetic results suggest that the Daphnia pulicaria group, a complex of predominantly North American species that has diversified rapidly since the Pleistocene, has its origin in South America, as specific tests of topology indicated that all three South American lineages are ancestral to the North American members of this species group. A comparison between variation of nuclear and mitochondrial markers revealed that closely related polyploid nuclear genotypes sometimes belonged to very divergent mitochondrial lineages, while distantly related nuclear genotypes often belonged to the same mitochondrial lineage. This discrepancy suggests that these South American water fleas originated through reciprocal hybridization between different endemic, sexually reproducing parental lineages. It is also likely that polyploidy of the investigated lineages resulted from this hybridization. Nevertheless, no putative diploid parental lineages were found in the studied region.     

Differences in genetic structure and ecological diversity between parental forms and hybrids in a Daphnia species complex

Hybridization is a common phenomenon in Daphnia species complexes. Hybrids often dominate in Daphnia populations; therefore it is worthwhile to look for principal differences between parental and hybrid populations with respect to their genetic structure and clonal differentiation. We studied natural populations of members of the Daphnia galeata/hyalina/cucullata complex in three lakes. In one of these lakes, one parental species (D. galeata) and one hybrid (D. galeata × cucullata) were investigated more intensively. The frequency of sexual reproduction was higher in parental populations, whereas clonal diversity was higher in hybrid populations. Ecological differentiation among clonal groups was more pronounced in the D. galeata × cucullata hybrid compared to D. galeata, whereas selection intensity was weaker. These results are discussed with respect to stability of clonal groups, multiple hybridizations and selective constraints.     

Allochronic differentiation among Daphnia species, hybrids and backcrosses: the importance of sexual reproduction for population dynamics and genetic architecture

Seasonal dynamics of the abundance, sexual reproduction and genetic architecture in a Daphnia hyalina-galeata hybrid complex were studied in the large and deep Lake Constance. We found evidence for the occurrence of first and second order hybridization. Our study revealed strong differences between the parental species not only regarding their seasonal dynamics, genetic architecture and diversity, but also their sexual reproductive behaviour. The overwintering D. hyalina showed low genetic diversity, no genetic differentiation during the season, and reproduced sexually in autumn, whereas D. galeata reached higher levels of genetic diversity, reproduced sexually in early summer, and exhibited changes in genetic structure during the season, but was only present from spring to autumn. However, in both species sexual reproduction was a rare event, and daphnids, including hybrids, reproduced predominantly asexually. This allows long-term persistence of hybrids as well without continuing hybridization events. Within all variables studied, F1 and F2 hybrids showed an intermediate pattern, whereas proposed backcross hybrids were more similar to their respective parentals. These differences in phenotype as well as significant differences in pairwise Fst values between parentals suggest that gene flow seems to be relatively low in the Lake Constance hybrid system. We found evidence for unidirectional introgression by backcrossing from D. galeata to D. hyalina and found a decrease in at least one of the proposed introgressed alleles in the hyalina-backcross while the season progressed. Our findings suggest allochronic differentiation within this hybrid population and different microevolutionary trajectories of the parental species, which will be discussed in the light of the ongoing reoligotrophication process of Lake Constance.     

Convergence and divergence in a long‐term old‐field succession: the importance of spatial scale and species abundance

Whether plant communities in a given region converge towards a particular stable state during succession has long been debated, but rarely tested at a sufficiently long time scale. By analysing a 50‐year continuous study of post‐agricultural secondary succession in New Jersey, USA, we show that the extent of community convergence varies with the spatial scale and species abundance classes. At the larger field scale, abundance‐based dissimilarities among communities decreased over time, indicating convergence of dominant species, whereas incidence‐based dissimilarities showed little temporal tend, indicating no sign of convergence. In contrast, plots within each field diverged in both species composition and abundance. Abundance‐based successional rates decreased over time, whereas rare species and herbaceous plants showed little change in temporal turnover rates. Initial abandonment conditions only influenced community structure early in succession. Overall, our findings provide strong evidence for scale and abundance dependence of stochastic and deterministic processes over old‐field succession.     

Temporal environmental change, clonal physiology and the genetic structure of a Daphnia assemblage (D. galeata–hyalina hybrid species complex)

1. In a combined field and laboratory study, seasonal relationships between water temperature and oxygen content, genetic structure (composition of MultiLocus Genotypes, MLGs) of a Daphnia assemblage (D. galeata–hyalina hybrid species complex), and the physiological properties of clones of frequent MLGs were studied. In accordance with the oxygen‐limited thermal tolerance hypothesis, essential physiological variables of oxygen transport and supply were measured within the tolerable temperature range. 2. A few MLGs (types T1–T4) were frequent during early spring and late autumn at surface temperatures below 10 °C. Clones of T1–T4 showed a low tolerance towards higher temperatures (above 20 °C) and a high phenotypic plasticity under thermal acclimation in comparison to clones derived from frequent MLGs from later seasons, and stored high–medium quantities of carbohydrates at 12 and 18 °C. 3. Another MLG (T6) succeeded the MLGs T1–T4. T6 was frequent over most of the year at temperatures above 10 °C and below 20 °C. A clone derived from T6 exhibited a high tolerance towards warm temperatures and a more restricted phenotypic plasticity. It stored high–medium quantities of carbohydrates at 12, 18 and 24 °C and showed a high capacity for acclimatory adjustments based on haemoglobin expression. 4. During the summer period at temperatures ≥20 °C, the MLG T6 was found mainly near to the thermocline, where temperature and oxygen content were distinctly lower, and to a lesser extent in surface water. At the surface, another MLG (T19) was predominant during this period. A clone of this MLG showed a very high tolerance towards warm temperatures, minimal phenotypic plasticity, low carbohydrate stores and a high capacity for circulatory adjustments to improve oxygen transport at higher temperatures. 5. This study provides evidence for connections between the spatio‐temporal genetic heterogeneity of a Daphnia assemblage and the seasonal changes of water temperature and oxygen content. The data also suggest that not only the actual temperature but also the dynamics of temperature change may influence the genetic structure of Daphnia populations and assemblages.     

Among-populational genetic differentiation in the cyclical parthenogen Daphnia magna (Crustacea,Anomopoda) and its relation to geographic distance and clonal diversity

Using allozyme data based on four polymorphic enzymeloci, we present an analysis of geneticdifferentiation among eight Daphnia magnapopulations, separated by less than 100 m to more than500 km from each other. In spite of the large range ofgeographic distances, there was only a slight tendencyfor an increase in genetic differentiation withincreasing geographic distance between populations,and the relation was not significant. This was mainlydue to the fact that neighbouring populations werealready highly genetically differentiated. Our resultssuggest that in populations in which only a fewabundant clones are present after a period of strongclonal selection, among-populational geneticdifferentiation as revealed by allozyme markers isinflated as a result of stochasticity involving chanceassociations of alleles with specific abundantgenotypes. Indices quantifying genetic differentiationwere much higher among populations with a low clonaldiversity than among populations with a high clonaldiversity.     

Distance‐dependent seedling mortality and long‐term spacing dynamics in a neotropical forest community

Negative distance dependence (NDisD), or reduced recruitment near adult conspecifics, is thought to explain the astounding diversity of tropical forests. While many studies show greater mortality at near vs. far distances from adults, these studies do not seek to track changes in the peak seedling curve over time, thus limiting our ability to link NDisD to coexistence. Using census data collected over 12 years from central Panama in conjunction with spatial mark‐connection functions, we show evidence for NDisD for many species, and find that the peak seedling curve shifts away from conspecific adults over time. We find wide variation in the strength of NDisD, which was correlated with seed size and canopy position, but other life‐history traits showed no relationship with variation in NDisD mortality. Our results document shifts in peak seedling densities over time, thus providing evidence for the hypothesized spacing mechanism necessary for diversity maintenance in tropical forests.     

Crop identity and memory effects on aboveground arthropods in a long‐term crop rotation experiment

Agricultural landscapes are globally dominated by monocultures under intensive management. This is one of the main reasons for biodiversity loss and insect population decline in many regions all over the world. Agroecosystem biodiversity in these areas can be enhanced by cropping system diversification, such as crop rotations. Yet, long‐term studies on effects of crop rotations on aboveground agrobiodiversity are lacking. We set up a 10‐year long‐term crop rotation experiment in Central Germany and monitored the temporal dynamics of aboveground arthropods over a full cultivation period to investigate influence of current and preceding crop identity and cropping system diversification on activity density, species richness, and community structure. We found that species composition was strongly influenced by currently grown crop although effect on arthropods varied between species groups. Especially, winter oilseed rape strongly affects arthropod community structure. Interestingly, we were also able to show an influence of the preceding crops, indicating an ecological memory effect in the aboveground arthropod community. Our results show that crop identity of both currently and previously grown crops in crop rotations may lead to an increase in arthropod activity density and changes in species composition. Diversified crop rotations including appropriate crops can be an easily implemented tool to increase arthropod biodiversity and biomass at large spatial and temporal scales, particularly in areas dominated by a single crop (e.g., wheat, maize). Our results may help to design optimized crop rotations for large‐scale enhancement of insect biodiversity in agroecosystems.     

Holarctic phylogeography of an asexual species complex – II. Allozymic variation and clonal structure in Arctic Daphnia

Previous mitochondrial (mt)DNA sequencing and restriction fragment length polymorphism (RFLP) studies have shown that the Holarctic Daphnia pulex complex is divisible into two major groups (pulicaria and tenebrosa) that exhibit distinct phylogeographic patterns. Here we examine allozymic variation at six polymorphic enzyme loci to ascertain clonal structure and clonal distribution patterns within each group. Specimens were collected from a total of 850 populations encompassing the Arctic. A significant negative relationship (Mantel test) between similarity of regional clonal arrays and geographical distance was observed. A small fraction of clones in each group was widespread (in the order of 1000s of kilometres). However, most clones were restricted to single regions, and were often found only in a single population. These data indicate that the population genetic structure is highly fragmented in this complex, but the potential for long-distance passive dispersal exists. Further, ‘hot spots’ of high clonal richness and diversity were found in each group, which is concordant with earlier work. In addition, ≈ 20% of pulicaria group clones possess nuclear genes from tenebrosa, while approximately 10% of tenebrosa group clones harbour pulicaria nuclear genes. These data indicate nuclear introgression between the two groups, which was found to be prominent in a broad zone of secondary contact encompassing parts of northwestern Russia, northern Fennoscandia, Svalbard, and extending into the high eastern Canadian Arctic.     

Unexpected genetic differentiation between recently recolonized populations of a long‐lived and highly vagile marine mammal

Many species have been heavily exploited by man leading to local extirpations, yet few studies have attempted to unravel subsequent recolonization histories. This has led to a significant gap in our knowledge of the long‐term effects of exploitation on the amount and structure of contemporary genetic variation, with important implications for conservation. The Antarctic fur seal provides an interesting case in point, having been virtually exterminated in the nineteenth century but subsequently staged a dramatic recovery to recolonize much of its original range. Consequently, we evaluated the hypothesis that South Georgia (SG), where a few million seals currently breed, was the main source of immigrants to other locations including Livingston Island (LI), by genotyping 366 individuals from these two populations at 17 microsatellite loci and sequencing a 263 bp fragment of the mitochondrial hypervariable region 1. Contrary to expectations, we found highly significant genetic differences at both types of marker, with 51% of LI individuals carrying haplotypes that were not observed in 246 animals from SG. Moreover, the youngest of three sequentially founded colonies at LI showed greater similarity to SG at mitochondrial DNA than microsatellites, implying temporal and sex‐specific variation in recolonization. Our findings emphasize the importance of relict populations and provide insights into the mechanisms by which severely depleted populations can recover while maintaining surprisingly high levels of genetic diversity.