Environment- and system-specific interactions between population and trait dynamics
Abstract
Understanding population dynamics across environmental contexts is essential to predict ecosystem stability. Functional traits influence population growth, which can in turn influence the traits and thus create feedback between population and trait dynamics. Here, by augmenting models of population and trait change with trait and population information, respectively, we demonstrate that such feedback occurred in an autotrophic but not in a heterotrophic microbial system. Furthermore, exposure to a pollutant disrupted this feedback: trait change and population growth ceased to interact in either system. Finally, when the models augmented with trait/population information were superior, the improvement was substantial, showing that density-trait feedbacks are potentially large, even though they are system- and environment-specific.
README: Ciliates and cyanobacteria: populations and traits
Data
All data is stored in the data/ folder. This contains two CSVs.
data/ciliates.csv : cilate system data with following columns :
- species : abbreviated species/genus name (string)
- strain : strain name (string)
- treat : treatment abbreviation - C control, A atrazine, T temperature, AT atrazine and temperature (string)
- day : sampling time in days (float)
- density : cell density in cells per millilitre (float)
- aspect_ratio : mean cell aspect ratio (float)
- size : mean cell surface area in square micrometres (float)
- speed : mean cell movement speed in micrometres per second (float)
- linearity : mean linearity of cell movement (float)
data/cyanobacteria.csv :
- day : sampling time in days (integer)
- strain : strain name (string)
- species : cyanobacteria clade name (string)
- treat : treatment abbreviation (string / factor)
- C : control
- A : atrazine
- T : temperature
- AT : atrazine and temperature
- repl : replicate number between 1 and 3 (integer)
- density : cell density in cells per microlitre (float)
- size : unitless mean cell size as quantified by the forward scatter of the flow cytometer (float)
- phycoerythrin : unitless mean phycoerythrin quantity as quantified by the flourescence channels of the flow cytometer (float)
- chlorophyll : unitless mean chlorophyll quantity as quantified by the flourescence channels of the flow cytometer (float)
- phycocyanin : unitless mean phycocyanin quantity as quantified by the flourescence channels of the flow cytometer (float)
Code
Code files to run analyses and generate figures associated with manuscript "Environment- and system-specific interactions between population and trait dynamics". Created figures will be saved in the figures/ folder (which does not initially exist - you will be prompted to create it when saving the plots).
- 00-data.r : load in the raw data and transform into more useful forms including performing the PCA to aggregate the traits
- 01-fit-models.r : fit the different models described in text i.e. growth ~ f(N, T), trait change ~ g(N, T)
- 02-bootstrapping.r : run the PBLR test
- 03-model-info.r : combine and summarise the test results
- 04-plots.r : create the figures