Priyanka Roy Chowdhury

Differential transcriptomic responses of ancient and modern Daphnia genotypes to phosphorus supply

Little is known about the role of transcriptomic changes in driving phenotypic evolution in natural populations, particularly in response to anthropogenic environmental change. Previous analyses of Daphnia genotypes separated by centuries of evolution in a lake using methods in resurrection ecology revealed striking genetic and phenotypic shifts that were highly correlated with anthropogenic environmental change, specifically phosphorus (P)‐driven nutrient enrichment (i.e. eutrophication). Here, we compared the transcriptomes of two ancient (~700‐year‐old) and two modern (~10‐year‐old) genotypes in historic (low P) and contemporary (high P) environmental conditions using microarrays. We found considerable transcriptomic variation between ‘ancient’ and ‘modern’ genotypes in both treatments, with stressful (low P) conditions eliciting differential expression (DE) of a larger number of genes. Further, more genes were DE between ‘ancient’ and ‘modern’ genotypes than within these groups. Expression patterns of individual genes differed greatly among genotypes, suggesting that different transcriptomic responses can result in similar phenotypes. While this confounded patterns between ‘ancient’ and ‘modern’ genotypes at the gene level, patterns were discernible at the functional level: annotation of DE genes revealed particular enrichment of genes involved in metabolic pathways in response to P‐treatments. Analyses of gene families suggested significant DE in pathways already known to be important in dealing with P‐limitation in Daphnia as well as in other organisms. Such observations on genotypes of a single natural population, separated by hundreds of years of evolution in contrasting environmental conditions before and during anthropogenic environmental changes, highlight the important role of transcriptional mechanisms in the evolutionary responses of populations.

Functional genomics of intraspecific variation in carbon and phosphorus kinetics in Daphnia

Understanding how the genome interacts with the environment to produce a diversity of phenotypes is a central challenge in biology. However, we know little about how traits involved in nutrient processing interact with key ecological parameters, such as the supply of mineral nutrients, particularly in animals. The framework of ecological stoichiometry uses information on the content of key elements such as carbon (C) and phosphorus (P) in individuals to predict the success of species. Nevertheless, intraspecific variation in content and the underlying mechanisms that generate such variation has been poorly explored. We studied two genotypes (G1 and G2) of Daphnia pulex that exhibit striking genotype × environment (G × E) interaction in response to shifts in dietary stoichiometry (C:P). G1 had higher fitness under C:P ∼ 100 diet, while G2 performed better in C:P ∼ 800. Dual (14) C/(33) P radiotracer assays show that G1 was more efficient in C processing, while G2 was more efficient in P use. Microarrays revealed that after 3 days of incubation, the genotypes differentially expressed ∼ 25% (7,224) of the total genes on the array under C:P ∼ 100 diet, and ∼ 30% (8,880) of genes under C:P ∼ 800. These results indicate large differences in C and P use between two coexisting genotypes. Importantly, such physiological differences can arise via differential expression of the genome due to alterations in dietary stoichiometry. Basic frameworks such as ecological stoichiometry enable integration of physiological and transcriptomic data, and represent initial steps toward understanding the interplay between fundamental ecological parameters such as nutrient supply and important evolutionary processes such as G × E interactions.

Differences in phosphorus use between ancient and extant Daphnia genotypes alters algal stoichiometry and abundance

Abstract Understanding the ecological relevance of intraspecific variation and evolutionary change in traits is a central frontier in contemporary ecology. Ecological stoichiometry uses variation in the content and kinetics of elements among species to predict key ecological functions such as nutrient recycling. Although much work has focused on interspecific variation, little is known about the ecological consequences of intraspecific variation and evolutionary change in the processing of ecologically relevant elements such as phosphorus (P). We tested whether physiological evolution can alter somatic P content of Daphnia and algal stoichiometry and abundance as predicted by stoichiometric models of consumer-driven nutrient recycling. We used genotypes of Daphnia pulicaria hatched from resting eggs in lake sediments separated by several hundreds of years of evolution in the wild. Although no significant differences were observed in somatic P content of genotypes from different sediment layers, radiotracer (33P) assays in 2 P–supply conditions (HiP and LoP) revealed considerable differences in P incorporation, particularly under HiP conditions. Further, algae co-occurring with the modern, P-inefficient Daphnia genotypes contained more 33P and exhibited faster population growth compared to counterparts co-occurring with ancient, P-efficient genotypes, with differences more prominent under HiP conditions. This study highlights the potential for intraspecific variation in P-use physiology in affecting trophic interactions via consumer-driven nutrient recycling. Melding ecological stoichiometry and resurrection ecology should elucidate the evolutionary sources and ecological consequences of such variation.

Resurrected ‘ancient’ Daphnia genotypes show reduced thermal stress tolerance compared to modern descendants

Understanding how populations adapt to rising temperatures has been a challenge in ecology. Research often evaluates multiple populations to test whether local adaptation to temperature regimes is occurring. Space-for-time substitutions are common, as temporal constraints limit our ability to observe evolutionary responses. We employed a resurrection ecology approach to understand how thermal tolerance has changed in a Daphnia pulicaria population over time. Temperatures experienced by the oldest genotypes were considerably lower than the youngest. We hypothesized clones were adapted to the thermal regimes of their respective time periods. We performed two thermal shock experiments that varied in length of heat exposure. Overall trends revealed that younger genotypes exhibited higher thermal tolerance than older genotypes; heat shock protein (hsp70) expression increased with temperature and varied among genotypes, but not across time periods. Our results indicate temperature may have been a selective factor on this population, although the observed responses may be a function of multifarious selection. Prior work found striking changes in population genetic structure, and in other traits that were strongly correlated with anthropogenic changes. Resurrection ecology approaches should help our understanding of interactive effects of anthropogenic alterations to temperature and other stressors on the evolutionary fate of natural populations.

Genotype-specific relationships among phosphorus use, growth and abundance in Daphnia pulicaria

The framework ecological stoichiometry uses elemental composition of species to make predictions about growth and competitive ability in defined elemental supply conditions. Although intraspecific differences in stoichiometry have been observed, we have yet to understand the mechanisms generating and maintaining such variation. We used variation in phosphorus (P) content within a Daphnia species to test the extent to which %P can explain variation in growth and competition. Further, we measured 33P kinetics (acquisition, assimilation, incorporation and retention) to understand the extent to which such variables improved predictions. Genotypes showed significant variation in P content, 33P kinetics and growth rate. P content alone was a poor predictor of growth rate and competitive ability. While most genotypes exhibited the typical growth penalty under P limitation, a few varied little in growth between P diets. These observations indicate that some genotypes can maintain growth under P-limited conditions by altering P use, suggesting that decomposing P content of an individual into physiological components of P kinetics will improve stoichiometric models. More generally, attention to the interplay between nutrient content and nutrient-use is required to make inferences regarding the success of genotypes in defined conditions of nutrient supply.