DOI: 10.5061/dryad.40qt2
title: Data from: Interacting livestock and fire may both threaten and increase viability of a fire-adapted Mediterranean carnivorous plant

description: 1. Quantifying interactive effects of environmental drivers on population
 dynamics can be critical for a robust analysis of population viability.
 Fire regimes, among the most widespread disturbances driving population
 dynamics, are increasingly modified by and interact with human activities.
 However, viability of fire-adapted species is typically assessed
 overlooking disturbance interactions, potentially resulting in suboptimal
 management actions. 2. We investigated whether increasing human
 disturbances in fire-prone ecosystems may pose a threat or an opportunity
 to improve population viability, using demographic data of the
 carnivorous, post-fire recruiting plant Drosophyllum lusitanicum, endemic
 to heathlands in the southwestern Mediterranean Basin. We built integral
 projection models and simulated population dynamics under different
 combinations of two key disturbance types affecting populations: fire and
 livestock browsing and trampling. We used perturbation analyses to
 determine potential long-term consequences of maintaining fundamentally
 different disturbance types. 3. Despite most populations inhabiting
 browsed habitats, simulations showed a greater extinction risk in
 populations under high livestock pressure compared with ones under low or
 moderate pressures. Extinction risk decreased when fire return intervals
 shortened in populations under low or moderate livestock pressure;
 however, the opposite pattern emerged in heavily browsed populations,
 where short intervals between fires increased extinction. 4. Elasticity
 analyses showed that decreases in viability under frequent disturbance
 interactions (heavy browsing and frequent fire) may be explained by
 selection against seed dormancy in populations with frequent browsing and
 trampling. This may potentially cause populations to collapse when fires
 kill above-ground plants without populations being able to recover from a
 seed bank. 5. Synthesis and applications: Incorporating disturbance
 interactions can result in a different assessment of viability of a
 fire-adapted species than considering fire regimes alone. In Mediterranean
 ecosystems, fire management may be more effective when integrating
 moderate human activities. However, replacing fires by human disturbances,
 a currently widespread strategy in many fire-prone ecosystems, is not
 recommended since it may fundamentally alter population dynamics and
 selection pressures and decrease viability of fire-adapted species.
description: Overview of the R code
 provided in the manuscriptHere, we provide an
 overview of the R scripts and data files to accompany the main text,
 "Interacting livestock and fire may both threaten and increase
 viability of a fire-adapted Mediterranean carnivorous subshrub" and
 found in this depository. The .R files should be opened with an R editor
 (e.g., R Studio). The R code is fully commented.JPEpaniwSA2.docxdataDrosoDemographic transitions of Drosophyllum lusitanicum populations recorded in five annual censuses (from 2011to 2015) in eight populations differing in time-since-fire (TSF) and livestock browsing (LS) in their habitats. These data are used to quantify vital rates of above-ground individuals.dataDrosoSBSeed fates (in a binary format) inferred from two experiments. These data are used to quantify the transitions related to the seedbank.mcmcOUTIn case the reader wishes to forego the step of fitting the Bayesian models, which can be very time consuming (&gt; 24 h on 3.40 GHz processor), we provided a mcmcOUT.csv file with 600 posterior parameter values for each of the parameters estimated with Bayesian models using uninformative priors.vitalRateModelsExecutes and saves the results of a Bayesian model quantifying all vital rates using uniformed priors; illustrates basic diagnostics that can be run on the results of an MCMC run (i.e., the posterior parameter distribution) to check for model convergence and autocorrelation of the posterior samples.makeIPMDemonstrates how to construct IPMs including continuous (above-ground) and discrete (seedbank) transitions for parameter means of the Bayesian models; saves IPMs for each combination of TSF (n =5) × LS (n = 2) × site (n = 8) (Part A). The code also saves IPMs for each TSF × LS averaged over sites (Part B). Site-specific and average kernel transitions for the vital rate growth (γ in main text) are also saved. The IPMs in Part A are used to calculate the stochastic population growth rate log λs, and extinction probability, Pq(t) by t = 300 years. The IPMs in parts A and B are used to calculate elasticities of log λs to changes in mean transitions across environmental states (TSF & LS) and in the standard deviation of transitions.sLambdafixedLSRuns and plots results of simulations of log λs using IPMs constructed for mean parameter values. The simulations consider fire as a stochastic process in which transitions between TSF states are based on fire return interval. Transitions between LS are not considered.sLambdaStochLSRuns and plots results of simulations of log λs using IPMs constructed for mean parameter values. Here, the growth kernel transitions are also included alongside the full IPMs. The simulations consider both fire and livestock browsing as an integrated stochastic process in which transitions between combinations of TSF × LS states are based on fire return interval and browsing management efforts.elastVRRuns and plots results of simulations of log λs and elasticities using IPMs constructed for lower vital rate survival (σ). The simulations consider fire as a stochastic process in which transitions between TSF states are based on fire return interval. Transitions between LS are not considered.