Project

Paleo-ecogenomics in Daphnia: developing a model for studying evolutionary impacts of climate and environmental change

Goal: PALECOEVOL is a highly multidisciplinary study combining population genomics with paleoecology, and is firmly embedded in the theoretical framework of evolutionary ecology. This transformative research is based on the direct observation of evolution in the past 2000 years in the highly endangered Arctic environment. By recording population genomic parameters before and after environmental shifts, a pioneering dataset unprecedented in genomic detail will be supplied and rigorously combined with historic environmental data. The overarching goal is to study, across millennia, the genomic responses of the ecological and genomic model organism Daphnia, an aquatic keystone herbivore, to repeated shifts in temperature and related environmental parameters, and to lay the foundation for establishing a novel model system to study the effects of environmental change at the population level.

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Dagmar Frisch
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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.
Dagmar Frisch
added a research item
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.
Dagmar Frisch
added a research item
Climate and environmental condition drive biodiversity at many levels of biological organization, from populations to ecosystems. Combined with paleoecological reconstructions, palaeogenetic information on resident populations provides novel insights into evolutionary trajectories and genetic diversity driven by environmental variability. While temporal observations of changing genetic structure are often made of sexual populations, little is known about how environmental change affects the long-term fate of asexual lineages. Here, we provide information on obligately asexual, triploid Daphnia populations from three Arctic lakes in West Greenland through the past 200-300 years to test the impact of environmental change on the temporal and spatial population genetic structure. The contrasting ecological state of the lakes, specifically regarding salinity and habitat structure may explain the observed lake-specific clonal composition over time. Palaeolimnological reconstructions show considerable regional environmental fluctuations since 1,700 (the end of the Little Ice Age), but the population genetic structure in two lakes was almost unchanged with at most two clones per time period. Their local populations were strongly dominated by a single clone that has persisted for 250-300 years. We discuss possible explanations for the apparent population genetic stability: (a) persistent clones are general-purpose genotypes that thrive under broad environmental conditions, (b) clonal lineages evolved subtle genotypic differences unresolved by microsatellite markers, or (c) epigenetic modifications allow for clonal adaptation to changing environmental conditions. Our results motivate research into the mechanisms of adaptation in these populations, as well as their evolutionary fate in the light of accelerating climate change in the polar regions.
Dagmar Frisch
added a research item
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.
Dagmar Frisch
added a research item
Climate and environmental condition drive biodiversity at many levels of biological organisation, from populations to ecosystems. Combined with palaeoecological reconstructions, palaeogenetic information on resident populations provides novel insights into evolutionary trajectories and genetic diversity driven by environmental variability. While temporal observations of changing genetic structure are often made of sexual populations, little is known about how environmental change affects the long-term fate of asexual lineages. Here, we provide information on obligately asexual, triploid Daphnia populations from three Arctic lakes in West Greenland through the past 200-300 years to test the impact of a changing environment on the temporal and spatial population genetic structure. The contrasting ecological state of the lakes, specifically regarding salinity and habitat structure may explain the observed lake-specific clonal composition over time. Palaeolimnological reconstructions show considerable environmental fluctuations since 1700 (the end of the Little Ice Age), but the population genetic structure in two lakes was almost unchanged with at most two clones per time period. Their local populations were strongly dominated by a single clone that has persisted for 250-300 years. We discuss three possible explanations for the apparent population genetic stability: (1) the persistent clones are general purpose genotypes that thrive under broad environmental conditions, (2) clonal lineages evolved subtle genotypic differences that are unresolved by microsatellite markers, or (3) epigenetic modifications allow for clonal adaptation to changing environmental conditions. Our results will motivate research into the mechanisms of adaptation in these populations, as well as their evolutionary fate in the light of accelerating climate change in the polar regions
Dagmar Frisch
added an update
As a preliminary step preceding whole genome sequencing, a microsatellite analysis was performed. This study included eggs isolated from sediment cores of three lakes in the Kangerlussuaq area, across 50 - 300 years. Ten microsatellite markers were used to genotype individual eggs. The analysis revealed very low clonal diversity in all three lakes and all time periods tested, and that the population of each lake was formed by distinct genotypes that were not shared between lakes despite their geographic proximity. This microsatellite analysis also showed that the Daphnia pulex populations in the three lakes consisted of asexual, probably triploid individuals. In addition, identical microsatellite genotypes were detected across hundreds of years, despite rapid environmental change, suggesting genetic stability in the face of rapid environmental change.
 
Dagmar Frisch
added an update
This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 658714.
 
Dagmar Frisch
added a project goal
PALECOEVOL is a highly multidisciplinary study combining population genomics with paleoecology, and is firmly embedded in the theoretical framework of evolutionary ecology. This transformative research is based on the direct observation of evolution in the past 2000 years in the highly endangered Arctic environment. By recording population genomic parameters before and after environmental shifts, a pioneering dataset unprecedented in genomic detail will be supplied and rigorously combined with historic environmental data. The overarching goal is to study, across millennia, the genomic responses of the ecological and genomic model organism Daphnia, an aquatic keystone herbivore, to repeated shifts in temperature and related environmental parameters, and to lay the foundation for establishing a novel model system to study the effects of environmental change at the population level.