DOI: 10.5061/dryad.vdncjsxtm
title: Resurrecting the metabolome: Rapid evolution magnifies the metabolomic plasticity to predation in a natural Daphnia population

description: Populations rely on already present plastic responses (ancestral
 plasticity) and evolution (including both evolution of mean trait values,
 constitutive evolution, and evolution of plasticity) to adapt to novel
 environmental conditions. Because of the lack of evidence from natural
 populations, controversy remains regarding the interplay between ancestral
 plasticity and rapid evolution in driving responses to new stressors. We
 addressed this topic at the level of the metabolome utilizing a
 resurrected natural population of the water flea Daphnia magna that
 underwent a human-caused increase followed by a reduction in predation
 pressure within ~16 years. Predation risk induced plastic changes in the
 metabolome which were mainly related to shifts in amino acid and sugar
 metabolism, suggesting predation risk affected protein and sugar
 utilization to increase energy supply. Both the constitutive and plastic
 components of the metabolic profiles showed rapid, likely adaptive
 evolution whereby ancestral plasticity and evolution contributed nearly
 equally to the total changes of the metabolomes. The subpopulation that
 experienced the strongest fish predation pressure and showed the strongest
 phenotypic response, also showed the strongest metabolomic response to
 fish kairomones, both in terms of the number of responsive metabolites and
 in the amplitude of the multivariate metabolomic reaction norm. More
 importantly, the metabolites with higher ancestral plasticity showed
 stronger evolution of plasticity when predation pressure increased, while
 this pattern reversed when predation pressure relaxed. Our results
 therefore highlight that the evolution in response to a novel pressure in
 a natural population magnified the metabolomic plasticity to this
 stressor.
description: We tested for effects of fish kairomones, subpopulation and their
 interaction on the metabolomes in a full factorial experiment. The total
 design consisted of 6 clones × 3 subpopulations × 2 fish kairomone
 treatments × 8 replicates = 288 experimental units. The metabolome of
 <i>Daphnia </i>samples were analysed using nano-electrospray
 ionization - direct infusion mass spectrometry (nESI-DIMS) as described by
 Southam <i>et al.</i> (2017). Briefly, polar metabolites were
 first extracted from <i>D. magna</i> samples using a biphasic
 method. Then, all samples were analysed in both positive and negative
 ionisation modes using an Orbitrap Elite mass spectrometer (Thermo Fisher
 Scientific, Bremen, Germany) with a direct infusion, chip-based
 nano-electrospray ionization source (Triversa, Advion Biosciences, Ithaca,
 NY, USA). The data processing was done using the Galaxy online platform
 using the selected ion monitoring (SIM) stitching algorithm and data were
 acquired from mass to charge ratios (m/z) in the range 50–620 (Southam et
 al., 2017). After several steps (replicate filter, blank filter, sample
 filter, see details in Supporting Information), the processed data
 matrices were used for bioinformatics and statistical analyses.
description: Thre are two datasets: one for the positive ionization mode and
 one for the negative ionization mode. The file type is .raw which is
 generated from DIMS, and a specific software (not open access) is needed
 to open the file. We can confirm that these files: 1) do not contain any
 copywritten or licensed materials, 2) these files do not contain and human
 subject information or endangered species information, 3) these files are
 not corrupt. A detailed list of all the files and the meanings for each
 file was in the ReadMe file.