Identifying genes and pathways that respond differently to dietary C:P between old (~700-yr-old) and young (~10-yr-old) resurrected Daphnia pulicaria genotypes that differ in C and P physiology

How does environmental change drive phenotypic evolution? We addressed this question using Daphnia genotypes separated by ~1600-years of evolution in a Minnesota lake using methods in resurrection ecology (i.e., reviving dormant eggs from sediments) and found substantial genetic and physiological differentiation. These shifts are highly correlated with anthropogenic environmental change, specifically phosphorus (P)-driven eutrophication. Here, we explore transcriptomic changes that may underlie the observed shifts in P use physiology (see poster by Fricsh et al for a detailed explanation). We compared the transcriptomes of two ancient and two contemporary genotypes in ancient (i.e., low P; LP) and contemporary (i.e., high P; HP) conditions using an 11000-gene microarray. Ancient and contemporary genotypes differed in the number of differentially expressed genes in the HP (mean ± SD; 645 ± 112.95) and LP (1071 ± 211.63) treatments. These results indicate considerable transcriptomic variation between ancient and contemporary genotypes in both dietary treatments, with stressful (LP) conditions invoking differential expression of more genes (t= -2.51; P= 0.04). Moreover, ancient and contemporary genotypes exhibited markedly different transcriptomic responses to dietary treatments. Contemporary genotypes upregulated 84.5 ± 28.99 while ancient genotypes upregulated 413.5 ± 26.16 genes (t= 164.5; P= 0.003). Similarly, ancient (127.5 ± 101.1) and contemporary (316 ± 98.99) genotypes differed significantly in the number of genes downregulated between the HP and LP treatments (t= 125.66; P= 0.005). These results indicate substantial regulatory shifts may underlie the striking physiological differences observed. Further analyses of gene families that were differentially expressed (DE) between ancient and contemporary genotypes revealed several gene families already known to be important in mitigating stoichiometric imbalances driven by P availability. Agglomerative hierarchical cluster analyses of DE loci between ancient and contemporary genotypes indicating age-based clustering will be presented. Together, our theoretical framework based on elemental supply, and unique model system enabled a millennial-scale exploration of the environmental contribution to phenotypic evolution. 2 ~700-yr-old clones (SC1X & SC3X), 2 ~10-yr-old clones (SC4B & SC15A), two dietary treatments (C:P~120 and C:P~800) of Scenedesmus algae. Exposed for 3 days.