DOI: 10.5061/dryad.b2rbnzsph
title: Apex predators can structure ecosystems through trophic cascades: linking the frugivorous behaviour and seed-dispersal patterns of mesocarnivores

description: Current global change scenarios demand knowledge on how anthropogenic
 impacts affect ecosystem functioning through changes in food web
 structure. Frugivorous mesocarnivores are a key link in trophic cascades
 because, while their abundance and behaviour are usually controlled by
 apex predators, they can provide high-quality seed-dispersal services to
 plant communities. Thus, the recent rewilding of large carnivores
 worldwide can trigger cascading effects for plants. We
 investigated the top-down effects of an apex predator (Iberian
 lynx Lynx pardinus) on seed-dispersal services mediated by two
 mesocarnivore species (red fox Vulpes vulpes and stone marten Martes
 foina) at the plant community level by comparing areas with and without
 lynx in a Mediterranean mountain range in Southern Spain. We
 collected scats of mesocarnivores (n = 1575) to assess frugivory and seed
 dispersal of 15 plant species over two consecutive fruiting seasons and
 two habitat types (open and forest). Specifically, we assessed the effect
 of lynx presence on (i) seed occurrence and fleshy-fruit biomass per scat,
 (ii) the number of scats containing seeds, and (iii) the diversity of
 dispersed seeds. The quantity and diversity of dispersed seeds drastically
 decreased under predation risk for both mesocarnivore species. Seed
 dispersal by stone martens was negatively affected by the presence of
 lynx, with a marked reduction in the number of scats with seeds (93%) and
 the diversity of dispersed seeds (46%). Foxes dispersed 68% fewer seeds in
 open habitats when coexisting with lynx, probably leading to differential
 contributions to seed-dispersal effectiveness among habitats. Our
 study reveals a novel trophic cascade from apex predators to plant
 communities. The behavioural responses of frugivorous mesocarnivores to
 predation risk and the reduction in the intensity of their faecal
 deposition pattern are probably related to their lower abundance when
 co-occurring with apex predators. While rewilding apex predators is a
 successful conservation tool, attention should be paid to cascading
 effects across food webs, particularly where frugivore megafauna are
 missing and mesocarnivores provide unique services to plant communities.
description: <strong>Collection/generation of
 data: </strong> We used an experimental design
 comparing five localities with a year-round territorial presence of
 reproductive Iberian lynx individuals and five localities without lynxes
 with similar habitat characteristics. Thus, we were able to compare the
 seed-dispersal patterns of mesocarnivores among predation-risk and
 predation-free scenarios. Since mesocarnivores can alter their habitat-use
 patterns under predation risk, we selected two different types of habitats
 in each locality: a) mature forest with a dense shrub stratum and b) open
 vegetation with scarce shrubs and isolated trees. Along 1.5 km transects
 previously selected in each habitat type, we conducted mesocarnivore scat
 sampling from October to March 2018–2019 and 2019–2020. Sampling was
 conducted at 1.5-month intervals, allowing each transect to be replicated
 four times per fruiting season, for a total of 160 visits (four replicates
 per transect × two habitats × 10 sites × two seasons). Two mammalian scat
 experts sampled the transects (~3 m in width) twice on the same day with a
 1-meter buffer on both sides of the transect. In addition, we performed
 DNA barcoding analysis on a subsample of 70 stone marten scats to confirm
 our visual identification (95% success). We estimated the seed content of
 the collected faeces to quantify the potential effect of predation risk on
 quantitative seed dispersal. Two experts visually identified the seeds
 according to morphological concordance with a reference collection (see
 González-Varo et al. 2021, for a similar approach). The number of seeds in
 each scat was quantified by counting them under a lens in a Petri dish.
 When the number of seeds exceeded 100 (n = 24) within one scat, we divided
 the seed content into four homogeneous quadrants and extrapolated the
 number of seeds in one quadrant to the entire sample through
 multiplication. The fleshy-fruit biomass per scat was estimated to
 quantify the effect of lynx on the fruit consumption behaviour of
 mesocarnivores (we assumed mesocarnivores ate the whole fruit). We used
 the number of quantified seeds per scat and the relationship between the
 average number of seeds per fruit and the average fleshy-fruit biomass
 obtained from the frubase database (Jordano 2013) for each consumed plant
 species. We then calculated two metrics of alpha seed diversity for each
 locality and fruiting season to determine the differences in the effective
 number of equally common and dominant species among predation risk
 scenarios: (1) Hill-Shannon and (2) Hill-Simpson (Chao et al. 2014,
 Roswell et al. 2021).  To account for the potential
 effects of fruit availability on fruit consumption and seed dispersal by
 mesocarnivores, we estimated the available fruit density during the
 fruiting peak. At the same time that we carried out scat sampling, we
 visually estimated the coverage percentage and the individual crop size
 inside plots of 15 × 15 m every 200 m on both sides of the transect. We
 estimated crop size using a semi-logarithmic fruit abundance index: 0 = no
 fruits, 1 = 1–10 fruits, 2 = 11–100 fruits, 3 = 101–1000 fruits, 4 =
 1001–10000, 5 &gt; 10000. Fruit estimation was performed only along
 forest habitat-type transects because, in open habitats, fleshy-fruited
 plants were rare or absent, except for <em>P. bourgaeana</em>.
 This tree most often occurred on substrates lacking other vegetation.
 Therefore, we estimated its crop size by searching for adult individuals
 in a 100 m buffer across the open habitat transects. Peak fruit density
 (no. fruits / m<sup>2</sup>) for each plant species was
 calculated for each locality and fruiting season as the average crop size
 of all sampled plots along each transect. Fruit diversity was calculated
 as the Hill–Shannon/Simpson diversity index of available fruits to
 describe seed diversity. <strong>Processing the
 data: </strong> We fitted generalised and linear
 mixed models (GLMM and LMM) using the R package lme4 v.1.1-27.1 (Bates et
 al. 2020) to evaluate the effects of Iberian lynx presence, habitat type,
 and fruit availability on fruit consumption and seed-dispersal patterns of
 mesocarnivores. We also fitted generalised linear models (GLM) to assess
 the effects of lynx presence on seed-dispersal diversity by
 mesocarnivores. We modelled red fox and stone marten data separately for
 fruit consumption and seed dispersal and analysed the following response
 variables: (1) seed occurrence per scat (Bernoulli- distributed variable:
 0 = absence, 1 = presence), (2) fleshy-fruit biomass per scat (zero not
 included), (3) number of scats with seeds (zero included), and (4) seed
 diversity. Seeds of common fig and rare plant species (grouped in
 ‘Others’) were not included in the modelling because of their low
 occurrence in carnivore diets but were included in the diversity analyses.
 We used binomial errors for seed occurrence, Gaussian errors (identity
 link) on log-transformed data for fruit biomass, Poisson errors (log link)
 for the number of scats with seeds, and gamma errors (log link) for seed
 diversity. We used lynx presence or absence (L) as a
 fixed effect. Fruit density (FD; no. fruits/m<sup>2</sup>) was
 included as a fixed effect for seed occurrence, fruit biomass, and scats
 with seeds models. Fruit diversity was previously discarded because it
 resulted in non-significant Pearson’s correlations with seed diversity to
 avoid overfitting owing to the reduced sample size (n = 20). We also added
 habitat type (H) to the number of scats with seeds as a fixed term.
 Interactions FD × L and H × L were also included in the respective models
 to account for the differential effects of these variables among the
 predation risk scenarios. Fruiting season (n = 2) was also added as a
 fixed effect for all response variables. Locality (n = 10) was added as
 the random effect in all mixed models, except for the seed diversity
 models.  Candidate models contained all the possible
 combinations with a biological sense of fixed effects and interaction
 terms explained above, compared to models without our variable of
 interest, lynx presence/absence and a null model (intercept). Due to the
 reduced sample size for seed diversity, we performed model selection by
 comparing models including only the fixed term lynx (L) with null models.
 We ranked the candidate models according to the Akaike Information
 Criterion adjusted for small sample sizes (AICc). If no other models were
 within two AICc units from the top-ranked model (∆AICc = 0), the top model
 was considered the best but if other models were within two AICc units of
 the top model (∆AICc ≤ 2.0) these were considered to be a set of models
 with similar support (Burnham and Anderson 2002). We used the MuMIn
 package v.1.43.17 (Barton 2013) for model selection. We calculated the
 marginal and conditional coefficients of determination (pseudo-R2) for the
 selected models (Nakagawa et al. 2017). We carried out post-hoc
 simple-slope pairwise comparisons to estimate the model coefficients of
 the interaction terms using the R package emmeans v.1.6.3 (Russell V. et
 al. 2021). Model residuals were inspected using the DHARMa package v.
 0.4.6 (Hartig and Lohse 2022) and a Moran’s I test indicated no spatial
 autocorrelation (p-values &gt;0.05). All analyses were conducted in R
 (version 3.6.1; R Core Team 2019).
 References: Chao, A., Chiu, C.H.,
 & Jost, L. (2014). Unifying species diversity, phylogenetic
 diversity, functional diversity, and related similarity and
 differentiation measures through hill numbers. Annual Review of Ecology,
 Evolution, and Systematics, 45(September), 297–324. 
 González-Varo, J.P., Rumeu, B., Albrecht, J., Arroyo, J.M.,
 Bueno, R.S., Burgos,T., … Traveset, A. (2021). Limited potential for bird
 migration to disperse plants to cooler latitudes. Nature, 595(7865),
 75–79. Jordano, P. (2013). Data from: Angiosperm
 fleshy fruits and seed dispersers: a comparative analysis of adaptation
 and constraints in plant-animal interactions, Dryad,
 Dataset.<br>Roswell, M., Dushoff, J., & Winfree, R. (2021).
 A conceptual guide to measuring species diversity. Oikos, 130,
 321–338. Barton, K. (2013). Package “MuMIn:
 Multi-model inference” for R. R Package Version 1.9.5, 45.
 Bates, D., Mächler, M., Bolker, B.M., & Walker, S.C.
 (2020). lme4: linear mixed-effects models. R Package Version 1.1.21.
 Retrieved from https://github.com/lme4/lme4/ Burnham,
 K.P., & Anderson, D.R. (2002). Model Selection and Multimodel
 Inference: A Practical Information-Theoretic Approach (2nd ed). In
 Ecological Modelling (Vol. 172).  Hartig, F.
 & Lohse, L. (2022). Package ‘DHARMa’. R Package Version
 0.4.6. Nakagawa, S., Johnson, P.C.D., &
 Schielzeth, H. (2017). The coefficient of determination R2 and intra-class
 correlation coefficient from generalized linear mixed-effects models
 revisited and expanded. Journal of the Royal Society Interface,
 14(134).  Russell V.L., Buerkner, P., Herve, M.,
 Love, J., & Singmann, H. (2021). Package ‘ emmeans .’ R Package
 Version 1.5.4.
description: # Apex predators can structure ecosystems through trophic cascades:
 linking the frugivorous behaviour and seed-dispersal patterns of
 mesocarnivores
 [https://doi.org/10.5061/dryad.b2rbnzsph](https://doi.org/10.5061/dryad.b2rbnzsph) Data were collected in ten localities (3x3 km) and two fruiting seasons (October-March 2018-2019 and 2019-2020) in Sierra de Andújar Natural Park; 38°14'27.71"N, 4° 4'45.03"W, Jaén, Andalucía, Spain. We used an experimental design comparing five localities with a year-round territorial presence of reproductive Iberian lynx individuals and five localities without lynxes. The dataset allowed us to compare the seed-dispersal patterns (number of scats with seeds, seed occurrence, and fleshy-fruit biomass per scat) and the diversity of dispersed seeds by mesocarnivores among predation-risk and predation-free scenarios. ## Description of the data and file structure File List: * fruits_model.csv: fleshy-fruit biomass per scat and occurrence of seeds per scat. * nscats_seeds_model.csv: number of scats with seeds dispersed by mesocarnivores per transect, locality, and fruiting season. * diversity_model.csv: diversity index (Hill-Shannon and Hill-Simpson) of seeds dispersed by mesocarnivores and diversity of available fruits per study locality and fruiting season. Relationship between files: "nscats_seeds_model.csv" is a summary with the sum of the number of scats with seeds per transect from "fruits_model.csv". ### DATA-SPECIFIC INFORMATION FOR: \[fruits\_model.csv] 1. Number of variables: 12 2. Number of cases/rows: 14175 3. Variable List: * fruiting_season: Factor (1,2) for the fruiting season * locality: Factor (n=10) for the study locality * habitat: Factor for the habitat type (open or closed) * lynx: Factor (LP, LA) for the presence/absence of the Iberian lynx * species: Factor for the mesocarnivore species (scientific name) that deposited the scat * plant_species: Factor for the plant species dispersed (scientific name). All plants refers to the sum of all plant species dispersed. All plants fruitset refers to all plant species dispersed excluding *F. carica* and other plants * fruits_oc: Factor for the occurrence of seeds in the scats (0,1) * fruit_biomass: fruit biomass (g) estimated per scat * seeds_number: number of seeds counted per scat * fruit_density: crop size (fruits/m^2) including the sum of all plant species estimated along the surveyed transects where the scat was found * UTMX: UTM coordinates (30 Huse) for the x-axis of the starting point of the transect where the scat was found * UTMY: UTM coordinates (30 Huse) for the y-axis of the starting point of the transect where the scat was found ### DATA-SPECIFIC INFORMATION FOR: \[nscats\_seeds\_model.csv] 1. Number of variables: 10 2. Number of cases/rows: 800 3. Variable List: * fruiting_season: Factor (1,2) for the fruiting season * lynx: Factor (LP, LA) for the presence/absence of the Iberian lynx * locality: Factor (n=10) for the study locality * habitat: Factor for the habitat type (open or closed) * species: Factor for the mesocarnivore species (scientific name) * plant_species: Factor for the plant species dispersed (scientific name). Other refers to less common plant species dispersed. All plants refers to the sum of all plant species dispersed. All plants fruitset refers to all plant species dispersed excluding *F. carica* and other plants * nscats: number of scats with seeds of such plant species per transect * fruit_density: crop size (fruits/m^2) including the sum of all plant species estimated along the surveyed transects * UTMX: UTM coordinates (30 Huse) for the x-axis of the starting point of the transect * UTMY: UTM coordinates (30 Huse) for the y-axis of the starting point of the transect ### DATA-SPECIFIC INFORMATION FOR: \[diversity\_model.csv] 1. Number of variables: 11 2. Number of cases/rows: 34 3. Variable List: * fruiting_season: Factor (1,2) for the fruiting season * lynx: Factor (LP, LA) for the presence/absence of the Iberian lynx * locality: Factor (n=10) for the study locality * species: Factor for the mesocarnivore species (scientific name) * richness: number of plant species dispersed by mesocarnivores * shannon: Hill-Shannon diversity index for the dispersed seeds by mesocarnivores * simpson: Hill-Simpson diversity index for the dispersed seeds by mesocarnivores * fruit_density: crop size (fruits/m^2) including the sum of all plant species estimated along the surveyed transects * fruit_diversity_shannon: Hill-Shannon diversity index for the available fleshy-fruited plant species along the surveyed transects * fruit_diversity_simpson: Hill-Simpson diversity index for the available fleshy-fruited plant species along the surveyed transects