Skip to content

LennonLab/eco-evo-stoich

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

20 Commits
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

Stoichiometry drives eco-evolutionary feedbacks

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.

Project Questions

Repository contents

data

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.

ccf-dataset-sas-abundances: modification of cid-means used for the SAS CCF analysis. Measurements are labeled sequentially with a sample number that corresponds to the chemostat time (time) and the population abundance of Synechococcus or phage in each of the replicate chemostats (N-limited Synechococcus = BNL2, BNL3, BNL5; N-limited phage = PNL2, PNL3, PNL5, P-limited Synechococcus = BPL2, BPL4, BPL5; P-limited phage = PPL2, PPL4, PPL5).

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.

biwebstats summarized results from the BiWeb analysis including the number of rows in the matrix (nrow), number of columns in the matrix (ncol), the number of interactions (n.intxn), connectance, modularity metrics (.qb and .qr), and nestedness metrics (nodf and ntc), for each chemostat replicate (cID) between the two nutrient treatments (lim: N = N-limited, P = P-limited). These data were used for the production of Figure 5.

*Supplemental

PercChange: Percent change in growth rates from triplicate cultures using the nutrient limited media (med.base: NL = N-limited, PL = P-limited) from the chemostat experiment with additional N (+N) or P (+P). This data corresponds to Figure S1.

Contributors

Dr. Jay T. Lennon and Dr. Megan L. Larsen Department of Biology, Indiana University

About

No description, website, or topics provided.

Resources

License

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published