Supervising Team: Ralph Tiedemann, Guntram Weithoff, Niels Blaum, Jana Petermann (external)
Workplace: University of Potsdam
0. Brief expected profile of PhD student
We are looking for a highly motivated candidate holding a Master’s degree in molecular ecology, evolutionary biology or in a related field. The candidate should have an expertise in genetics and genomics, preferably in non-model organisms. The position further requires the willingness to organize and perform field work (bird capture & tracking, plankton sampling). A good conceptual, statistical and bioinformatics background is welcomed. Further valuable skills include knowledge on geographic information systems (GIS), scientific writing and working in a team.
1. Short Abstract
This project will look for local adaptations in strains/ clones of rotifers. It will identify candidate genes underlying these adaptations by utilizing already available transcriptomic resources. We hypothesize that the different strains/ clones available in ponds of the Uckermark constitute a reservoir of lineages adapted to different environmental conditions. They may serve as a stabilizing mechanism for biodiversity, as these lineages may immigrate into populations where they had been rare or absent before. The study will determine, whether this immigration is preferentially vertical (i.e., from the egg bank into the adult population of the same pond) or horizontal (i.e., by dispersal among ponds). The role of water birds as mobile links for horizontal dispersal will be evaluated by radio-telemetry of selected species (mallard, grey heron, coot). Further, we will investigate internal and external transport of invertebrates via waterbirds as vectors by looking for invertebrates in faeces and on feathers by a combination of microscopical analysis and DNA meta-barcoding.
2. Background and previous work
The study will be performed using a set of permanent and temporary ponds in the agricultural landscape of the Uckermark. Within this landscape, hundreds of small, natural ponds (kettle holes) are scattered in areas of different land use types and intensities, such as crop, meadows, and forests. From those, a subset of 19 ponds has been investigated during the first three years of the project for the occurrence and genetic population structure of rotifers, with a particular focus on Brachionus calyciflorus, a locally abundant rotifer. Specifically, a combination of microscopical observation and molecular barcoding (mitochondrial COI gene) has been applied to characterize the species composition in the water column (adult specimens), the sediment (resting eggs), as well as in windsocks (wind-dispersed specimens/resting eggs). Furthermore, for the focus species Brachionus calyciflorus, a set of nuclear markers (ITS, microsatellites) has been developed to characterize diversity below the species level, i.e., to identify different strains/clones. These markers have been used to characterize the spatio-temporal metapopulation structure. For this species, transcriptomic resources have been established de novo. Strains/ evolutionary lineages have been found to differ in their thermotolerance and their temperature-dependent gene expression patterns.
We hypothesize that different strains/clones of rotifers are differentially adapted to specific environmental conditions (e.g., different temperature). The strains’/ clones’ occurrence varies in space and time (among ponds and years), depending on environmental conditions. We aim to identify adaptive genetic variation (adaptive point mutations or gene expression patterns) by utilizing our existing transcriptomic resources.
We will further evaluate two hypotheses regarding immigration into current adult rotifer populations:
Vertical immigration, i.e., all clones are present as resting eggs in the sediment, only those hatch which match the current environmental conditions.
Horizontal immigration, i.e., different clones are present in different ponds depending on present environmental conditions. They disperse among ponds via wind or mobile links (water birds).
4. Outline work program
In combination with the common garden experiments of P08, we will look for spatio-temporally locally adapted strains/clones across ponds (including sediments). From these clones, we aim at identifying genes responsible for local adaptation. We will utilize already available transcriptomic resources to identify single nucleotide polymorphisms (SNPs) and gene expression patterns in candidate genes for adaptation to environmental perturbations, most notable temperature adaptation and thermotolerance.
To investigate the role of birds as mobile links for rotifer dispersal across ponds, we will track movements of selected waterbirds (mallard, grey heron, coot) among ponds. A representative number of birds will be caught and equipped with a telemetry sender, either GPS or ATLAS. Tracking will be performed in collaboration with other project scientists using the ATLAS system in the study area. Furthermore, we will collect bird feces and wash off remnants from bird feathers to look for internal or external transport of invertebrates. Specifically, we will assess invertebrate diversity in feces and attached to feathers by a combination of microscopical analysis and DNA meta-barcoding, the latter using our Next Generation Sequencing platform. By the end of the project, we aim hence to know (i) to what extent rotifer strains/clones are locally adapted, (ii) which gene variants are responsible for this adaptation, (iii) how birds as potential mobile links commute among ponds, and (iv) how important these mobile links are for dispersal of different invertebrate species.
5. Linkage to ‘BioMove’ hypotheses, objectives and concepts
Resting stages and or/adults in different ponds are hypothesized to constitute a reservoir of differentially adapted lineages, available for immigration into extant adult populations, when environmental conditions are suitable. Such an immigration of strains/clones into populations where they had been rare or absent before constitutes a stabilizing mechanism on the landscape scale. We will further evaluate the spatio-temporal dynamics of this immigration, i.e., whether it occurs mostly vertically (from the egg bank) or horizontally (from other ponds), by assessment of genetic similarity/differentiation within and among ponds.