URPP GCB: Project 5 - Ecological genomics of plastic and evolutionary responses to environmental changes (UZH)

Table of contents


PIs: Kentaro Shimizu, Bernhard Schmid, Masaki Kobayashi
PhDs: Terhi Hahl, Sofia van Moorsel



Phenotypic plasticity and evolution in biodiversity experiments – Plants selected for 10 years in the Jena biodiversity experiment (Roscher et al., Ecol. Lett. 2004) will be used to test the hypothesis of increased combining ability due to evolution or phenotypic plasticity. Model ecosystems with plants of different selection history (i.e., none, monoculture, mixtures) will be assembled to test if the predicted changes also lead to increased productivity and thus functioning at the system level. We will use 8–12 species from the Jena biodiversity experiment for the experimental and quantitative genetic/phenotypic plasticity studies. Among these species, we will select one with a small genome for genomic analysis. A good candidate is Prunella vulgaris with a genome size of 636 Mb. For this species we also have extensive experience about phenotypic variation in experimental systems (e.g. Schmid, J. Ecol. 1985). Phenotypic data and ecosystem functions will be assessed over time and be analysed using a range of statistical approaches. For the genomic work with Prunella, three libraries (insertion size: 200bp, 500bp and 800bp) will be sequenced (total ~100 times coverage of the genome) using Illumina HiSeq, and medium-quality assembly and annotation will be used for the reference genome of later analysis. Fifteen individuals x two culture conditions x two time points will be sequenced with ~6-fold coverage, and the reads will be mapped onto the reference genome. We hypothesize that monoculture and mixture genotypes can be distinguished and that genomic differences can be related to phenotypic differences in combining ability.