DOI: 10.5061/dryad.qrfj6q5h5
title: Data from: Experimental evidence of rapid heritable adaptation in the absence of initial standing genetic variation

description: The success of genetically depauperate populations in the face of
 environmental change is contrary to the expectation that high genetic
 diversity is required for rapid adaptation. Alternative pathways such as
 environmentally induced genetic modifications and non-genetic heritable
 phenotypes have been proposed mechanisms for heritable adaptation within
 an ecologically relevant timeframe. However, experimental evidence is
 currently lacking to establish if, and to what extent, these sources of
 phenotypic variation can produce a response. To test if adaptation can
 rapidly occur in the absence of initial standing genetic variation and
 recombination in small populations, we (i) exposed replicate monoclonal
 populations of the microzooplankton Brachionus calyciflorus to a
 culturing regime that selected for phenotypic variants with elevated
 population growth with either high or low phosphorus food for a period of
 55 days and (ii) examined population-level response in two fully factorial
 common garden experiments at day 15 and 35 of the exposure experiment.
 Within six generations, we observed heritable local adaptation to nutrient
 limitation. More specifically, populations with a history of exposure to
 P-limited food exhibited higher population growth rates under low P food
 conditions than populations with a high P exposure history. However, the
 capacity for such a response was found to vary among clones. Our study
 finds that although standing genetic variation is considered essential for
 rapid heritable adaptation, the rapid emergence of de
 novo genetic variation or alternative sources of phenotypic
 variation could aid in the establishment and persistence of low diversity
 populations.
description: The goal of this study was to experimentally test if adaptation
 can occur in the absence of initial standing genetic variation and
 recombination in small populations within an ecologically relevant time
 frame. To investigate this question, we conducted a two-part experiment
 using two genotypes of the microzooplankton Brachionus calyciflorus. In
 the first part of the experiment (further referred to as the ‘exposure
 experiment’), we exposed replicate monoclonal populations to a culturing
 regime selecting for phenotypic variants with elevated population growth
 rates for at least 20 generations with either high (HP) or low (LP)
 phosphorus food. LP food has a C:P content that deviates strongly from the
 requirements for growth in B. calyciflorus, and thus represents
 low-quality food in comparison to HP food (Sterner & Hessen, 1994;
 Zhou & Declerck, 2019). In the second part of the experiment, we
 performed two full factorial common garden experiments at two successive
 time points, using individuals isolated from the exposure
 experiment. Population growth rate was the response
 variable in both the exposure and common garden experiments. Population
 growth rate was calculated on a daily basis as
 (lnN<sub>t</sub>-lnN<sub>0</sub>)/t, where N0 and
 Nt represent the population size at the start and end of each 24-h period,
 and t the duration of the period in days.   
description: Exposure Experiment Metadata (Exposure_Experiment.csv)
 
 Variable Units Description Levels FoodQual   Food quality experimental population was exposed to HP: High phosphorus treatment       LP: Low phosphorus treatment Clone   Identity of the genotype of a given experimental population 128D       7B Treatment   Factor combining clone ID and the exposure food quality of an experimental population HP_128D: Clone 128 exposed to high P food resources       HP_7B: Clone 7 exposed to high P food resources       LP_128D: Clone 128 exposed to low P food resources       LP_7B: Clone 7 exposed to low P food resources Exp_Unit   Unique numerical identifier for each experimental population (1-20)   ID   Unique factor ID for each experimental population (n=20) LP-7B-1       LP-7B-2       LP-7B-3       LP-7B-4       LP-7B-5       LP-128D-1       LP-128D-2       LP-128D-3       LP-128D-4       LP-128D-5       HP-7B-1       HP-7B-2       HP-7B-3       HP-7B-4       HP-7B-5       HP-128D-1       HP-128D-2       HP-128D-3       HP-128D-4       HP-128D-5 Day day Day of the exposure experiment (0-55)   PGR day<sup>-1</sup> Population growth rate      Common Garden Experiment Metadata (Common_Garden_Experiment.csv) Variable Units Description Levels CG_EXP   Common garden experiment ID 1: First Common Garden       2: Second Common Garden Clone   Identity of the genotype of a given experimental population 128D       7B Exp_Unit   Replicate ID for each experimental population (1-20)   EH   Exposure History of experimental population LP-EH: Population provided low P food resources       HP-EH: Population provided high P food resources CG_Food   Food quality experimental population was exposed to in common garden experiment HP: High phosphorus treatment       LP: Low phosphorus treatment Day day Day of the common garden experiment   PGR day<sup>-1</sup> Population growth rate    Due to an clerical error data was not collected during common garden one for replicates 13 or 14 in the LP treatment on days 1-6, these observations are thus represented by NA. Please note that Days 1-6 were not included in the final analysis for any experimental units in the LP treatment. All code for data wrangling and statistical analysis can be found in "AwAGV_Analysis.R" contained within the folder "Lemmen_etal_2021_FE_AwSGV.zip"