DOI: 10.5061/dryad.2959s
title: Data from: Ecological interactions and coexistence are predicted by gene expression similarity in freshwater green algae

description: Phenotypic variation controls the species interactions which determine
 whether or not species coexist. Long-standing hypotheses in ecology and
 evolution posit that phenotypic differentiation enables coexistence by
 increasing the size of niche differentiation. This hypothesis has only
 been tested using macroscopic traits to date, but niche differentiation,
 particularly of microscopic organisms, also occurs at the molecular and
 metabolic level. We examined how phenotypic variation that arises at the
 level of gene expression over evolutionary time affects phytoplankton
 species interactions and coexistence. We predicted that similarity in gene
 expression among species would decline with phylogenetic distance, and
 that reduced similarity in gene expression would weaken competition,
 increase facilitation and promote coexistence. To test this, we grew eight
 species of freshwater green algae in monocultures and bicultures for 46
 days in a laboratory microcosm experiment. We quantified the strength of
 species interactions by: (i) fitting Lotka–Volterra models to time-series
 densities and estimating interaction coefficients, and (ii) calculating
 relative densities that compare species’ steady-state densities in
 biculture to those in monoculture. We used Illumina high throughput
 sequencing to quantify the expression of 1253 families of homologous
 genes, including a set of 17 candidate genes that we hypothesized a priori
 to be involved in competition or facilitation. Synthesis. We found that
 closely related species had greater similarity in gene expression than did
 distantly related species, but as gene expression became more similar,
 species experienced weaker competition or greater facilitation, and were
 more likely to coexist. We identified gene functional categories that were
 uniquely differentially regulated in association with particular species
 interaction types. Contrary to common thinking in ecology and evolution,
 similarity in gene expression, and not differentiation, was associated
 with weaker competition, facilitation and coexistence.
description: Monoculture and
 biculture fitting: data, scripts, and output"Monoculture
 parameter estimates.xls" = file showing the parameter estimates from
 fits of the logistic growth model to each monoculture. "Biculture
 data parameter estimates.xls" = file showing the parameter estimates
 from fits of the Lotka-Volterra competition model to every biculture
 replicate, as well as estimates of relative yield and phylogenetic
 distance. Both files contain a sheet with relevant meta-data. Two folders,
 "Fitting bicultures" and "Fitting monocultures”, contain
 the data, R scripts and in the case of the bicultures, a package used for
 fitting the data to models. Parameter estimates were obtained by running
 the scripts in "Fitting bicultures.txt" or "Fitting
 monocultures.txt" in R. Starting parameter estimates for the
 optimization algorithms were estimated and entered for each monoculture or
 biculture separately.Monoculture and biculture
 fitting_data, scripts, and output.zip