Search

Whole genome sequencing is instrumental for the study of genome variation in natural populations, delivering important knowledge on genomic modifications and potential targets of natural selection at the population level. Large dormant eggbanks of aquatic invertebrates such as the keystone herbivore Daphnia, a microcrustacean widespread in freshwater ecosystems, provide detailed sedimentary archives to study genomic processes over centuries. To overcome the problem of limited DNA amounts in single Daphnia dormant eggs, we developed an optimized workflow for whole genome amplification (WGA), yielding sufficient amounts of DNA for downstream whole genome sequencing of individual historical eggs, including polyploid lineages. We compare two WGA kits, applied to recently produced Daphnia magna dormant eggs from laboratory cultures, and to historical dormant eggs of Daphnia pulicaria collected from Arctic lake sediment between 10 and 300 years old. Resulting genome coverage breadth in most samples was ~70%, including those from >100-year-old isolates. Sequence read distribution was highly correlated among samples amplified with the same kit, but less correlated between kits. Despite this, a high percentage of genomic positions with single nucleotide polymorphisms in one or more samples (maximum of 74% between kits, and 97% within kits) were recovered at a depth required for genotyping. As a by-product of sequencing we obtained 100% coverage of the mitochondrial genomes even from the oldest isolates (~300 years). The mitochondrial DNA provides an additional source for evolutionary studies of these populations. We provide an optimized workflow for WGA followed by whole genome sequencing including steps to minimize exogenous DNA.

DNA can be preserved in marine and freshwater sediments both in bulk sediment and in intact, viable resting stages. Here, we assess the potential for combined use of ancient, environmental, DNA and timeseries of resurrected long-term dormant organisms, to reconstruct trophic interactions and evolutionary adaptation to changing environments. These new methods, coupled with independent evidence of biotic and abiotic forcing factors, can provide a holistic view of past ecosystems beyond that offered by standard palaeoecology, help us assess implications of ecological and molecular change for contemporary ecosystem functioning and services, and improve our ability to predict adaptation to environmental stress., Ellegaard et al. discuss the potential for using ancient environmental DNA (eDNA), combined with resurrection ecology, to analyse trophic interactions and evolutionary adaptation to changing environments. Their Review suggests that these techniques will improve our ability to predict genetic and phenotypic adaptation to environmental stress.

Whole genome sequencing is instrumental for the study of genome variation in natural populations, delivering important knowledge on genomic modifications and potential targets of natural selection at the population level. Large dormant eggbanks of aquatic invertebrates such as the keystone herbivore Daphnia, a microcrustacean widespread in freshwater ecosystems, provide detailed sedimentary archives to study genomic processes over centuries. To overcome the problem of limited DNA amounts in single Daphnia dormant eggs, we developed an optimised workflow for whole genome amplification (WGA), yielding sufficient amounts of DNA for downstream whole genome sequencing of individual historical eggs, including polyploid lineages. We compare two WGA kits, applied to recently produced Daphnia magna dormant eggs from laboratory cultures, and to historical dormant eggs of Daphnia pulicaria collected from Arctic lake sediment between 10y and 300y old. Resulting genome coverage breadth in most samples was ~70%, including those from >100y old isolates. Sequence read distribution was highly correlated among samples amplified with the same kit, but less correlated between kits. Despite this, a high percentage of genomic positions with SNPs in one or more samples (maximum of 74% between kits, and 97% within kits) were recovered at a depth required for genotyping. As a by-product of sequencing we obtained 100% coverage of the mitochondrial genomes even from the oldest isolates (~300y). The mtDNA provides an additional source for evolutionary studies of these populations. We provide an optimised workflow for WGA followed by whole genome sequencing including steps to minimise exogenous DNA.

Cultural eutrophication is one of the largest threats to aquatic ecosystems with devastating ecological and economic consequences. AlthoughDaphnia, a keystone grazer crustacean, can mitigate some negative effects of eutrophication in freshwater habitats, it is itself affected by changes in nutrient composition. Previous studies have shown evolutionary adaptation ofDaphniato environmental change, including high phosphorus levels. While phosphorus is an essential macronutrient, it negatively affectsDaphnialife history when present in excessive concentrations. Here, we map weighted gene co-expression networks to phosphorus-related phenotypic traits in centuries-old ancestralDaphniaand their modern descendants, contrasting pre- and post-eutrophication environments. We find that evolutionary fine-tuning of transcriptional responses is manifested at a basic (cellular) phenotypic level, and is strongly correlated to an evolved plasticity of gene expression. At a higher phenotypic level, this contributes to the maintenance of physiological homeostasis, and a robust preservation of somatic phosphorus concentration.

Zooplankton in temporary ponds is often collected with gear originally designed for lakes, and mostly unsuitable for sampling shallow habitats. We describe a new simple and inexpensive device for sampling zooplankton in very shallow, vegetated temporary ponds. We tested the sampling efficiency by comparing species composition and density of cyclopoid copepods, an important component of the zooplankton, by sampling with both the new bag sampler and a plastic beaker frequently employed for collections of zooplankton in small waterbodies. With the bag sampler we collected a larger number of species and higher densities of copepods due to its higher efficiency in vegetated areas and near the sediment. The beaker appeared to sample almost only the water surface. The samples collected with the bag sampler revealed a distinct distribution of copepod life cycle stages in a shallow pond, which differed between depths and microhabitats. Additional advantages of the bag sampler are its small size and weight, and the possibility of fast exchange of sample bags between sample locations, thus preventing accidental faunal exchange between sample locations. We conclude that the bag sampler is a device especially useful for sampling zooplankton of shallow ponds and wetlands rich in vegetation, for diversity studies as well as for quantitative sampling. (© 2005 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)

We examined the impact of lateral and longitudinal hydrological connectiv- ity on copepod diversity (local species richness, diapause strategies and population genetics) in ponds of a North American floodplain. Results of a General Linear Model (GLM) which included three environmental pond variables showed that species rich- ness in these ponds was significantly influenced only by pond type (permanent ponds, temporary ponds with connections to other waterbodies during floods, isolated tempo- rary ponds). Local species richness in connected temporary ponds had significantly higher scores of local richness compared to isolated temporary ponds (means 7.4 and 2.7, respectively). Such enhancement of species diversity in connected ponds appears to be facilitated by increased dispersal during floods and also pertains to the diversity of diapause strategies in the ponds studied. Species with and without diapause were present in connected temporary ponds, but absent from isolated temporary ponds, which contained only species capable of diapausing during the dry season. To explore the significance of hydrological connectivity of longitudinal dispersal between up- stream and downstream sites, we used RAPD markers in populations of a calanoid co- pepod. The increase of average heterozygosity H (0.301 to 0.477) in an upstream- downstream direction and generally low genetic distances (Nei's D < 0.05) suggested maintenance of gene flow by flood-mediated dispersal between connected ponds. Lower heterozygosity (0.289) of the population in a downstream pond protected by le- vees suggested the interruption of gene flow when dispersal by flooding is blocked.

1. The survival of cyclopoid copepods was investigated in a floodplain for 2 years where flooding occurred during the cold season. The cyclopoid community was studied in three waterbodies with distinct hydroperiods: a permanent pond connected to the flooded area during inundation, a temporary pool that is part of the flooded area and an isolated temporary pool. 2. Field studies, including data obtained from samples of water, sediment and soil, showed the overall predominance of species with a summer diapause over those with a winter diapause or without diapause. Emergence of cyclopoid copepods at the onset of flooding, examined using emergence traps and data from recently filled or still isolated temporary pools, showed that some species can survive several months of drying. 3. The ability of the diapausing fourth copepodid stages of Cyclops strenuus and C. insignis, the two cyclopoids most abundant during winter and spring flooding, to survive terrestrial conditions was tested in laboratory experiments. Both species survived for several months, but rates differed among the species. A higher percentage of C. strenuus survived for a longer period, possibly explaining why this species was relatively more abundant in more temporary habitats. 4. Both dormancy and dispersal facilitated survival of cyclopoid copepods in transient habitats connected to each other during flood periods. Dormancy was the most important survival strategy, whereas dispersal could be more important following prolonged periods without flooding.

Background Copepods outnumber every other multicellular animal group. They are critical components of the world's freshwater and marine ecosystems, sensitive indicators of local and global climate change, key ecosystem service providers, parasites and predators of economically important aquatic animals and potential vectors of waterborne disease. Copepods sustain the world fisheries that nourish and support human populations. Although genomic tools have transformed many areas of biological and biomedical research, their power to elucidate aspects of the biology, behavior and ecology of copepods has only recently begun to be exploited. Discussion The extraordinary biological and ecological diversity of the subclass Copepoda provides both unique advantages for addressing key problems in aquatic systems and formidable challenges for developing a focused genomics strategy. This article provides an overview of genomic studies of copepods and discusses strategies for using genomics tools to address key questions at levels extending from individuals to ecosystems. Genomics can, for instance, help to decipher patterns of genome evolution such as those that occur during transitions from free living to symbiotic and parasitic lifestyles and can assist in the identification of genetic mechanisms and accompanying physiological changes associated with adaptation to new or physiologically challenging environments. The adaptive significance of the diversity in genome size and unique mechanisms of genome reorganization during development could similarly be explored. Genome-wide and EST studies of parasitic copepods of salmon and large EST studies of selected free-living copepods have demonstrated the potential utility of modern genomics approaches for the study of copepods and have generated resources such as EST libraries, shotgun genome sequences, BAC libraries, genome maps and inbred lines that will be invaluable in assisting further efforts to provide genomics tools for copepods. Summary Genomics research on copepods is needed to extend our exploration and characterization of their fundamental biological traits, so that we can better understand how copepods function and interact in diverse environments. Availability of large scale genomics resources will also open doors to a wide range of systems biology type studies that view the organism as the fundamental system in which to address key questions in ecology and evolution.

The viable propagule banks of a tempo- rary stream were studied from sections with different agricultural history. Hatching of zooplankton (cope- pods, rotifers and cladocerans) was recorded in the laboratory under controlled temperature and light conditions from an agriculturally modified area with average hydroperiods of about a week per year and two semi-natural reference areas with average hyd- roperiods of more than 3 weeks per year. We found significant differences in both taxon richness and abundance of zooplankton hatching between areas, which were lower in the agriculturally modified section, compared to the reference sections. Another factor likely to have influenced hatching in our experiment was conductivity, which differed between the two reference sections and might have affected hatching at high conductivities. For restora- tion purposes, hydrological reconnection of stream segments is important to facilitate dispersal from the high diversity upstream segments to the depleted sites downstream

The magnitude of community-wide dispersal is central to metacommunity models, yet dispersal is notoriously difficult to quantify in passive and cryptic dispersers such as many freshwater invertebrates. By overcoming the problem of quantifying dispersal rates, colonization rates into new habitats can provide a useful estimate of the magnitude of effective dispersal. Here we study the influence of spatial and local processes on colonization rates into new ponds that indicate differential dispersal limitation of major zooplankton taxa, with important implications for metacommunity dynamics. We identify regional and local factors that affect zooplankton colonization rates and spatial patterns in a large-scale experimental system. Our study differs from others in the unique setup of the experimental pond area by which we were able to test spatial and environmental variables at a large spatial scale. We quantified colonization rates separately for the Copepoda, Cladocera and Rotifera from samples collected over a period of 21 months in 48 newly constructed temporary ponds of 0.18–2.95 ha distributed in a restored wetland area of 2,700 ha in Don˜ ana National Park, Southern Spain. Species richness upon initial sampling of new ponds was about one third of that in reference ponds, although the rate of detection of new species from thereon were not significantly different, probably owing to high turnover in the dynamic, temporary reference ponds. Environmental heterogeneity had no detectable effect on colonization rates in new ponds. In contrast, connectivity, space (based on latitude and longitude) and surface area were key determinants of colonization rates for copepods and cladocerans. This suggests dispersal limitation in cladocerans and copepods, but not in rotifers, possibly due to differences in propagule size and abundance.