A major question in ecology is how often competing species evolve to reduce competitive interactions and facilitate coexistence. One untested route for a reduction in competitive interactions is through ontogenetic changes in the trophic niche of one or more of the interacting species. In such cases, theory predicts that two species can coexist if the weaker competitor changes its resource niche to a greater degree with increased body size than the superior competitor. We tested this prediction using stable isotopes that yield information about the trophic position (δ15N) and carbon source (δ13C) of two coexisting fish species: Trinidadian guppies (Poecilia reticulata) and killifish (Rivulus hartii). We examined fish from locations representing three natural community types: 1) where killifish and guppies live with predators; 2) where killifish and guppies live without predators; and 3) where killifish are the only fish species. We also examined killifish from communities in which we had introduced guppies, providing a temporal sequence of the community changes following the transition from a killifish only to a killifish-guppy community. We found that killifish, which are the weaker competitor, had a much larger ontogenetic niche shift in trophic position than guppies in the community where competition is most intense (killifish-guppy only). This result is consistent with theory for size-structured populations, which predicts that these results should lead to stable coexistence of the two species. Comparisons with other communities containing guppies, killifish and predators and ones where killifish live by themselves revealed that these results are caused primarily by a loss of ontogenetic niche changes in guppies, even though they are the stronger competitor. Comparisons of these natural communities with communities in which guppies were translocated into sites containing only killifish showed that the experimental communities were intermediate between the natural killifish-guppy community and the killifish-guppy-predator community, suggesting contemporary evolution in these ontogenetic trophic differences. These results provide comparative evidence for ontogenetic niche shifts in contributing to species coexistence and comparative and experimental evidence for evolutionary or plastic changes in ontogenetic niche shifts following the formation of new communities. 

The data/data.csv file contains information on the ontogenetic niche shifts of the guppies and killifish in different natural and experimental communities. The data includes the following variables:

• Location: the location where the fish sample was collected (a factor variable with three levels: "predator", "no predator", and "killifish only").
• Species: the species of fish (a factor variable with two levels: "guppy" and "killifish").
• Size: the size of the fish in millimeters.
• δ15N: the stable isotope metric for trophic position.
• δ13C: the stable isotope metric for carbon source.

The data set has 1,052 observations and 5 variables. The data set includes missing values that need to be removed or imputed before the analysis.

Overview

This repository contains the R code for analyzing data on the ontogenetic niche shifts of two coexisting fish species, Trinidadian guppies (Poecilia reticulata) and killifish (Rivulus hartii), in three different natural community types and experimental communities. The study aims to test the prediction that competing species can reduce competitive interactions and facilitate coexistence through ontogenetic changes in the trophic niche of one or more of the interacting species.

The project utilized stable isotopes (δ15N and δ13C) to examine fish from different locations representing the three natural community types, and experimental killifish and guppy communities. The results provide comparative evidence for ontogenetic niche shifts in contributing to species coexistence and comparative and experimental evidence for evolutionary or plastic changes in ontogenetic niche shifts following the formation of new communities.

The R code in Main_script.R provides a reproducible and documented analysis of the data and can be used as a template for analyzing similar data sets. The data is in CSV format, which can be opened using a wide range of software programs, including:

Microsoft Excel (proprietary)

Google Sheets (web-based)

LibreOffice Calc (open-source)

Apache OpenOffice Calc (open-source)

RStudio (open-source)

Of these programs, R together with RStudio is the recommended software for analyzing the data in the CSV file, as it provides an integrated development environment (IDE) for the R programming language and includes tools for importing, manipulating, and visualizing data. RStudio is free and open-source and can be downloaded from the RStudio website (https://www.rstudio.com/).

The R packages required for running the code in R/Main_script.R are listed in the requirements.R file. You can install the packages by running the following command in your R console:

install.packages(c("MuMIn","partR2","stringr","plyr","lme4","lmerTest","Hmisc"))