Biology subjects

Frisch, D.

Publications and source records attributed to Frisch, D..

6 recordsLinked to original sources

bioRxiv2024

Phenotypic divergence associated with genomic changes suggest local adaptation in obligate asexuals

Local adaptation is a key evolutionary process that generates global biodiversity and is promoted by environmental heterogeneity. Most of the existing knowledge on adaptive capacity is focused on sexual organisms, while the adaptation potential of asexually reproducing eukaryotes as well as their vulnerability to environmental change remains unclear. Cyclical parthenogens of the keystone freshwater grazer Daphnia are known to be locally adapted with genetic differentiation related to environmental conditions even between neighbouring ponds. Similar patterns have been found in obligate parthenogenetic congeners, however studies on their local adaptation potential are rare. Here, we use respiration rate and whole genome sequencing to test the local adaptation of Arctic asexual polyploid Daphnia from lakes with contrasting oxygen environments. The genomic data revealed the presence of two genetic clusters which differed significantly in respiration rates, suggesting molecular evolution as an adaptive mechanism. Functional enrichment pointed to differences in metabolic processes between the two genetic clusters. Our results, combining phenotypic and whole genome sequencing data, suggest that these clones are locally adapted to low oxygen concentrations and provide support for local adaptation by evolution in an obligate parthenogen.

evolutionary biology↗

bioRxiv2024

Single-egg Comet Assay: a protocol to quantify DNA damage in aquatic dormant stages

O_LIThe comet assay (CA) was originally developed as toxicity test and quantifies DNA integrity from the distribution of DNA across an electric field. Compromised DNA moves across electric fields faster than intact DNA strands, leaving a quantifiable signature that resembles a comet tail. The dimensions of this comet tail reflect relative DNA damage. C_LIO_LIWe optimized the CA protocol for individual dormant propagules (Single-egg Comet Assay or SE-CA) to inform downstream analyses such as DNA sequencing, of the DNA quality contained in natural genetic archives of past populations. As a model we used dormant eggs of the microcrustacean Daphnia. C_LIO_LIWe tested the SE-CA protocol on impact of processing and storage conditions for dormant eggs and used it to assess DNA damage related to aging of eggs retrieved from recently deposited to centuries-old lake sediment. The SE-CA successfully determined the degree of DNA damage in individual eggs frozen in liquid nitrogen, or at -80{degrees}C as well as damage caused by bleaching and historical egg age. C_LIO_LIIn conclusion, our protocol provides a cost-effective method of assessing DNA damage in sedimentary propagules such as dormant Daphnia eggs. More generally, the SE-CA can be applied to test DNA integrity in individual propagules prior to genome sequencing or to quantify environmental impacts on natural sedimentary biobanks. C_LI

ecology↗

bioRxiv2024

A tale of two lakes: divergent evolutionary trajectories of two Daphnia populations experiencing distinct environments

Most studies of local adaptation substitute the correlation between spatial distance and environmental heterogeneity for the temporal dynamics over which local adaptation evolves. The availability of detailed ecological and genomic information from lake sediments provides an opportunity to study local adaptation with unparalleled clarity from the temporal perspective. Inference can be further enhanced by including multiple lakes along ecological axes to further isolate the effects of ecological change in driving local adaptation. Lakes throughout the world face the impact of numerous anthropogenically induced environmental changes. Top among these is the eutrophication of freshwaters from agriculture, development and land-use change. Here we use the genetic information recorded in lake sediments of two lakes experiencing contrasting histories of land-use change to study the evolution of local adaptation in the lakes Daphnia pulicaria populations. Utilizing nextRAD derived Single Nucleotide Polymorphisms (SNPs), we studied the evolutionary trajectories of Daphnia pulicaria in both lakes. Using gene-environment correlations and Fst tests for selection we found SNPs that appear to be under selection in both lakes. Specifically, we found more outlier SNPs in the highly impacted lake using Fst-based tests for selection. Conversely, gene-environment tests revealed the reverse pattern. We discuss numerous facets of experimental design that must be considered when using resurrection ecology to study local adaptation and critically evaluate how they may have impacted the results of this investigation. Lay SummaryResurrection ecology, the resuscitation or hatching of decades or centuries old dormant eggs, seeds or cysts provides the opportunity to study evolution in action. Here, we use resurrection ecology paired with Single Nucleotide Polymorphism (SNP) genotyping to study the evolutionary responses of two populations of Daphnia pulicaria to contrasting changes in the nutrient dynamics of their respective lakes. In the lake with more drastic changes in nutrient pollution, we find a stronger shift in allele frequencies through time and at a larger number of affected genomic positions compared with the environmentally more stable lake. However, Bayesian gene-environment correlations were stronger in the more stable lake reflecting higher power to detect correlations among allele frequency change and paleo-environmental variables in this location. Our results suggest that numerous factors might impact the ability to use different methodologies to detect local adaptation over time using resurrection ecology.

evolutionary biology↗

bioRxiv2021

Refining the evolutionary time machine: an assessment of whole genome amplification using single historical Daphnia eggs

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.

genomics↗

bioRxiv2020

Centennial clonal stability of asexual Daphnia in Greenland lakes despite climate variability

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.

ecology↗

bioRxiv2019

Dissecting the transcriptomic basis of phenotypic evolution in an aquatic keystone grazer

Cultural eutrophication is one of the largest threats to aquatic ecosystems with devastating ecological and economic consequences. Although Daphnia, 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 of Daphnia to environmental change, including high phosphorus levels. While phosphorus is an essential macronutrient, it negatively affects Daphnia life history when present in excessive concentrations. Here, we map weighted gene co-expression networks to phosphorus-related phenotypic traits in centuries-old ancestral Daphnia and 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.

evolutionary biology↗