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

Abstract

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.