This repository contains open-source code, data, and text files for the eco-evo-stoich project to evaluate the effects of nutrient stoichiometry on the eco-evolutionary feedbacks between a cyanobacterial host and its phage.
Population Dynamics (pop-dynamics)
ts-counts_raw: epi-fluorescent microscope field densities for each of ten images collected for each chemostat through 100 samplings (s1-s100). Columns 1-6 correspond to information about the image, organism, chemostat, nutrient treatment replicate, phage treatment type (phage amended [Infect] or non-phage amended [Control], and nutrient treatment type (N-limited [N] or P-Limited[P])
ts-counts: reduced microscopy data (ts-counts_raw) using the function microsope.counts. Each value represents the mean of ten images for each sampling date. Columns 1-6 correspond to information about the microbe (Synechococcus or phage), unique chemostat identifier, treatment replicate, phage treatment type (phage amended [Infect] or non-phage amended [Control], and nutrient treatment type (N-limited [N] or P-Limited[P]).
cid-means: Synechococcus and phage population counts as long form
cstat-means: Synechococcus and phage population counts as matrix with calculated standard error of the mean for each population. This file was used for the production of Figure 1 and Figure S2.
Evolutionary dynamics (evo-dynamics)
inf-mat: binary infection data (0 = infection/lack of Synechococcus growth, 1 = no infection/Synechococcus growth) collected for each Synechococcus strain (columns) and phage strain (rows) challenge. Strain information including the treatment (trt; C = Control, T = Treatment), nutrient limitation (lim; N = nitrogen-limited, P = phosphorus-limited), the unique chemostat identifier (cID; Ni = nitrogen-limited replicate, Pi = phosphorus-limited replicate), the isolation day in the timecourse (daynumber), the series time point (tm.pt), and isolate number (iso). Each strain was assigned a unique strain identifier using the series time point, cID, and isolate number. NAs correspond to challenges with conflicting results in the triplicate analysis.
inf-mat-processed: inf-mat file transformed from a matrix to long form data. This file was used for the production of all figures related to the infection data.
20150710-infmatrixNcoevo, 20150710-infmatrixPcoevo, 20150710-infmatrixNcontrols, 20150710-infmatrixPcontrols: Calculated coevolutionary dynamics between coevolving and noncoevolving strains within the chemostats. Values represent the proportion of successful infections between time group isolates within treatment and control chemostats. These data were used for the production of Figure 2.
*Supplemental
NutrGR: Reduced auto-fluorescence growth rates (GR) for triplicate cultures (biorep) following addition of nitrogen (N) or phosphorus (P; med.add) to the nutrient limiting media (media.base; NL = nitrogen-limited, PL = phosphorus-limited) used in the chemostat study.
Dr. Jay T. Lennon and Dr. Megan L. Larsen Department of Biology, Indiana University