Supporting Information: The role of diversity of interaction types and

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Supporting Information:
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The role of diversity of interaction types and space in ecological networks stability
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Miguel Lurgi, Daniel Montoya and José M. Montoya
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Appendix S1: Full description of the methods
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Spatially explicit individual-based, bio-energetic model
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Generation of species interactions networks
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Once a food web was generated using the niche model (Williams & Martinez 2000) (see
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main text), and in order to obtain a ‘hybrid’ interaction network, some links in the network,
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among those specifying interactions between basal species and species in the first trophic
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level (i.e. herbivore links) were selected to become mutualistic links according to the
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corresponding MAI ratio. The MAI ratio hence corresponds to the proportion of plant
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herbivores vs. plant mutualists in our networks. We generated networks with this
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characteristics for MAI ratios ranging from 0 to 1.0 with steps of 0.1: [0, 0.1, 0.2, 0.3 … 1],
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making up a total of 11 different MAI ratios, from communities with no mutualistic
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interactions to communities with only mutualistic links between basal resources and first
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order consumers and no herbivores. This way of choosing mutualistic links does not ensure a
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predictable proportion of mutualistic plants versus non-mutualistic (i.e., wind dispersed)
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plants. This fraction was however always equal or larger than the MAI ratio, because a given
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plant species would become mutualistic (and cease to be wind dispersed) as soon as a
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mutualistic link was assigned to it.
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Our approach to create the interaction networks ensures that mutualistic partners (both animal
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and plants) are embedded in a whole community context alongside other trophic groups such
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as omnivores and top predators. It also ensures that a trophic pyramid is maintained within
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the community, with mutualistic interactions sitting at the bottom of the pyramid between
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basal species and primary consumers (Fig. 1 in the main text). An example of the interaction
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networks generated in this way for one of the model communities is shown in Fig. S1. In
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summary, this method creates a network architecture that is consistent with food webs while
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at the same time allowing for a well-identified section composed of mutualistic interactions,
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from which network properties that are exclusive of mutualistic networks can be calculated.
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Figure S1. Example of a food web taken from one of the model communities. Nodes represent species
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and are color-coded by species type: yellow = mutualistic plants, green = non-mutualistic plants,
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blue = herbivores, purple = mutualistic animals, orange = primary predators, and red = top
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predators. Links (lines joining nodes) are trophic or mutualistic relationships amongst them. Thicker
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part of the line shows the end of the link. Links go from prey to predator species. The layout orders
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species per trophic level with higher trophic levels towards the top of the diagram.
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Individual-based spatially explicit dynamics
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All individuals in the IBM are equipped with an energy storage unit. This energy is the
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currency governing the actions performed by individuals, their lifespan, and the mean by
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which the economy of the whole artificial ecosystem is maintained.
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Thus, the basic processes that occur at the individual level are:
1. Death: Individuals possessing less than a fixed level of energy (relative to the size of
the energy storage unit) die and are removed from the system.
2. Movement: Individuals can move to one of its 8 neighbouring cells (see Fig. 2 in main
text) chosen randomly, provided that it is available.
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3. Reproduction: Individuals can reproduce using one of two strategies if they have
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enough resources (i.e., energy) to do so (see Table S1 for parameter values):
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a. Sexual reproduction occurs between two individuals of the same non-basal
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(animal) species. A reproductive event occurs if and only if two conditions are
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met: (i) the subject individual encounters another individual of its same
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species and with enough resources to reproduce within its neighbouring cells
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(see Fig. 2 in main text), and (ii) there is an empty (or containing only a plant
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individual) cell within the individual’s 4-cell radius neighbourhood. The
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offspring (new individual) created during the reproductive event is placed in
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this randomly chosen empty cell.
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b. Asexual reproduction occurs in basal species (i.e., plants). The model allows
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for two mechanisms of asexual reproduction: (1) ‘Wind dispersal’ and (2)
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Mutualistic dispersal. In the former case, as for the sexual reproduction
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scenario, a 4-cell radius neighbourhood around the plant individual defines the
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spatial extent of the dispersal event. For the reproductive event to occur, the
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plant must possess enough resources to reproduce (see Table S1 for parameter
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value), and one of the cells (randomly chosen) in the spatial neighbourhood
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mentioned above must be empty (or containing only an animal individual).
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The new individual produced during the ‘wind dispersal’ event is placed in
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that empty cell.
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In the latter case (mutualistic dispersal), dispersal is done by the animal
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partner, which means that the ‘seed’ for a new individual can travel farther
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before it settles. The spatial extent of this dispersal event will depend on (1)
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the movements of the animal disperser after it has visited a mutualistic plant
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partner, (2) its efficiency in dispersing the ‘seed’ (mutualistic efficiency), and
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(3) a cooling effect that decreases the dispersal (mutualistic) efficiency as time
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lapses (see Table S1 for parameters governing this process and their
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explanation). If, before this time lapses (when the dispersal efficiency
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becomes zero), the animal partner comes across an empty cell in the
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landscape, it ‘creates’ an offspring for the plant previously visited with a
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probability given by its mutualistic efficiency. Although plants can reproduce
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sexually, we only needed to simulate the ecological fact that plants can
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reproduce without the need of physically encountering another individual of
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the same species.
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4. Feeding: This is perhaps the most fundamental mechanism of the model. It occurs
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when two potentially interacting individuals, as defined in the interaction matrix, find
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each other in space (i.e. one is occupying the cell that it was chosen by the other when
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moving). Several outcomes are possible (see Table S1 for bioenergetic parameters
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governing each one of these outcomes):
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a. If both individuals are not primary producers, a predation event occurs, in
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which the prey dies and the predator increases its energy storage unit’s level.
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b. If one individual is a basal species and the other is a non-mutualistic primary
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consumer (i.e., herbivore), then the herbivore takes some resources from the
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plant and both continue living, with effects on the energy storage.
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c. If it is a mutualistic relation (mutualistic plant and mutualistic animal), the
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animal takes resources from the individual plant while at the same time ‘keeps
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track’ of the species it belongs to until some point in the future. If, before this
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time lapses, the animal partner comes across an empty cell in the landscape, it
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‘creates’ an offspring for the plant previously visited with a probability given
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by its mutualistic efficiency (see Table S1).
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In all feeding events an efficiency or assimilation rate of resources is applied. This
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coefficient differs between herbivore and carnivore links, since assimilation varies
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depending on whether the food is plant material or animal material (Ings et al.
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2009). Additionally, an omnivory trade-off is applied to the resources obtained by
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an omnivore individual when feeding on a basal resource (plant). This models the
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fact that omnivores are less efficient at eating plant material than herbivores. See
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Table S1 for the specification of the parameter values governing these processes.
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In addition to the aforementioned demographic processes, the model incorporates
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immigration, which is simulated by assigning to each empty cell on the grid a probability (see
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Table S1) of colonization by a new individual from a randomly chosen species from the
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original species pool (i.e., a species from the original ecological network). Each iteration or
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time step without an interaction event will reduce the energy storage of every individual due
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to metabolic losses. Because reproduction demands an energy investment, this loss of energy,
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without replenishment via feeding interactions, will make more difficult the individual’s
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reproduction and will eventually cause the extinction of that individual. With the exception of
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efficiency transfer coefficients, bio-energetic parameters are identical for all species in the
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ecosystem (see Table S1 for a full list of parameters).
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Table S1: Parameters for the model described in the text, including bio-energetic values
Parameter name
Value
Description
OCCUPIED_CELLS
0.4
MAX_RESOURCE
20
MIN_RESOURCE
3
LIVING_EXPEND
0.01
MATING_RESOURCE
0.5
MATING_ENERGY
0.2
Fraction of the grid initially occupied by individuals randomly placed on
it.
Maximum amount of resource an individual may possess at any given
time.
Death threshold: minimum amount of resource at individual may possess.
Any individual possessing less than this amount at any given iteration will
die (see text).
Fraction of resource an individual spends in living every iteration of the
model. Metabolic rate.
Fraction of MAX_RESOURCE that is required for an individual to be
able to reproduce.
Fraction of resource given to the offspring by the parent during
reproduction. Each parent gives the same fraction. The total amount
depends on how much resource the parent possesses at the time of
reproduction.
Probability that a new individual will appear in a cell of the grid each
iteration. The species this individual belongs to is randomly chosen from
the original species pool.
Fraction of resource that is autotrophically created by each individual
from the basal species every iteration. This is the only energy input to the
system.
Fraction of resource lost to herbivores by individuals belonging to a basal
species during a trophic event, i.e. a species in the first trophic level
feeding on a species in the basal level.
Fraction of resource that omnivores are effectively able to gather when
feeding on a species from the basal level (a plant).
Fraction of resource of a primary producer (basal species individual) that a
mutualistic partner obtains when an interaction of this type occurs.
Probability that a predator individual embark upon a trophic relationship
with one of its prey individuals when it encounters it.
Fraction of the resource the prey that is assimilated by the predator in a
carnivorous interaction, i.e. trophic interaction not involving individuals
from the basal species.
Fraction of the resource of the prey assimilated by the herbivore in an
herbivorous interaction.
Efficiency of an individual mutualist when dispersing a plant partner. In
other words, the probability with which a mutualistic individual will
facilitate the creation of a new individual of the last species of plant it
visited when it is positioned on an empty cell immediately after it
interacted with a mutualistic plant partner.
Cooling factor for the mutualistic efficiency of plant dispersers
(mutualists). This is the fraction of mutualistic efficiency that remains
after each iteration.
Reproduction rate of non-mutualistic plant species. Probability with which
an individual belonging to a plant species that does not possess mutualistic
partners for dispersal will create an offspring in any given iteration of the
simulation run.
IMMIGRATION
0.005
SYNTHESIS_ABILITY
0.1
HERB_FRACTION
0.7
OMNI_TRADEOFF
0.4
MUT_FRACTION
0.25
CAPTURE_PROB
0.4
EFFICIENCY_TRANSF
0.2
HERB_EFFICIENCY
0.8
MUT_EFFICIENCY
0.8
MUT_COOLING
0.9
REPROD_RATE
0.01
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Analysis of community properties and stability metrics
Community diversity
The Shannon diversity index is defined as:
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𝑆
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′
𝐻 = − ∑ 𝑝𝑖 ∙ 𝑙𝑛 𝑝𝑖
𝑖=1
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where S is the number of species and pi is the proportion of individuals of species i in the
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community. When the index is calculated within functional groups the proportion of
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individuals is taken only considering the species within the group. Shannon evenness index
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on the other hand is calculated as:
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𝐽′ =
𝐻′
𝑙𝑛 𝑆
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Community stability
The centroid of each species population was calculated as the average of the positions
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of all individuals belonging to that species in the 2D grid. It is thus a measure composed of
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two values: x and y coordinates for the average of the locations. Moran’s I and Geary’s C are
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metrics commonly used for the quantification of spatial correlation or ‘aggregation’ in
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spatially explicit data (Fortin & Dale 2005). Moran’s I for a given species is defined as:
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where N is the number of spatial units indexed by i and j, cells in the 2D grid in our simulated
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landscape; X is the variable of interest, which takes the value of 1 if an individual of the
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̅ is the
species for which the index is being calculated is present in that cell and 0 otherwise; X
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mean of X; and wij is an element of a matrix of spatial weights. In our case, the weights of
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this matrix are always 1 because all the cells in the grid are equally important for the
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calculation of the index. Geary’s C is defined as:
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where in addition to the values defined for the Moran’s I, we also have W, which is the sum
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of all wij; in our case, the number of cells in the grid. These two indices are used to quantify
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spatial aggregation at the global (Moran’s I) and at the local (Geary’s C) scales, and are
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therefore complementary ways of quantifying spatial aggregation.
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Sensitivity/Robustness analyses
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To assess the robustness of our results to differences in species richness, landscape lattice
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size, and number of generated communities, we performed a series of sensitivity analyses.
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These analyses revealed that model simulation outcomes are affected to some extent by these
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factors, but only until some identifiable threshold, after which results are qualitatively and
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quantitatively similar. We chose the values that allowed us to obtain results consistent with
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larger community sizes. Simulations were performed with lattice sizes of 50x50, 150x150,
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200x200 (the value used for the simulations reported in the manuscript), and 250x250, which
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demonstrated that for lattice sizes above 200x200 results are qualitatively and quantitatively
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similar. For smaller sizes (i.e., 50x50 and 150x150) some of the patterns observed varied
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quantitatively. Different values for the number of species in our communities were
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considered: 40, 60, 80, and 100. In this case, again, significant differences in community
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patterns were not observed between species richness values of 60 and greater. Experiments
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were performed considering 25, 50, and 100 replicates of communities for a subset of the
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MAI ratios studied. We found no statistically significant differences between results obtained
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for these three values. Because trade-offs needed to be considered between computation costs
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and size of the experiments, we chose the smaller lattice size, number of species, and number
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of replicates that better allowed us to obtain the most accurate results in order to save
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computation time.
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Similarly, we tested the robustness of our results by conducting sensitivity analyses of the
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different parameters used in the model. We have modified individually every parameter of
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the model (i.e. those described in table S1). In doing so, we have changed the original value
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reported in the table by ± 10% and used GLMs to test whether significant changes on the
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relationship between MAI ratios and network properties/stability metrics analysed exist.
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Results are summarized in tables S2 and S3 (GLMs, d.f., a significant difference is
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considered for p<0.05). In general, no significant differences were observed for any of the
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parameters modified.
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188
189
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Table S2. Sensitivity analyses for the parameter values included in the model reported in
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table S1 - 10% of their value. P-values for the GLMs are reported, indicating whether
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significant differences exist on the relationship between the MAI ratio and the network
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property analyzed. Red values indicate significant differences (p<0.05).
properties
IMMIGRATION REPROD_RATE LIVING_EXP MATING_ENERGY MATING_RESOURCE MAX_RESOURCE MIN_RESOURCE SYNTHESIS_ABILITY
L
0,620
0,069
0,243
0,572
0,636
0,466
0,641
0,117
L/S
0,623
0,071
0,240
0,569
0,638
0,468
0,637
0,117
C
0,620
0,074
0,240
0,569
0,636
0,466
0,638
0,116
GenSD
0,642
0,440
0,316
0,776
0,326
0,747
0,243
0,569
VulSD
0,165
0,721
0,119
0,349
0,893
0,898
0,311
0,412
MxSim
0,396
0,336
0,160
0,757
0,093
0,965
0,483
0,117
MeanFoodChainLength
0,797
0,607
0,278
0,666
0,027
0,532
0,105
0,599
ChnSD
0,401
0,964
0,105
0,971
0,001
0,730
0,239
0,230
ChnNo
0,772
0,312
0,620
0,552
0,127
0,762
0,160
0,606
Dynamic Complexity (<i> SC^1/2)
0,982
0,332
0,685
0,459
0,644
0,263
0,873
0,102
Clustering Coefficient
0,911
0,576
0,739
0,962
0,173
0,673
0,927
0,379
Compartmentalisation
0,289
0,982
0,687
0,389
0,724
0,468
0,315
0,296
Mean Trophic Position
0,647
0,733
0,463
0,935
0,190
0,530
0,133
0,563
Standard Deviation Trophic Position
0,926
0,740
0,412
0,960
0,075
0,369
0,090
0,697
NODF (Nestedness)
0,575
0,880
0,080
0,740
0,730
0,204
0,810
0,934
Gq (Quantitative Generality)
0,229
0,661
0,289
0,870
0,921
0,126
0,145
0,619
Vq (Quantitative Vulnerability)
0,721
0,213
0,745
0,217
0,588
0,715
0,966
0,323
H2' (Mutualistic Specialisation)
0,527
0,389
0,451
0,473
0,837
0,510
0,282
0,746
Total Community Abundance
0,806
0,567
0,860
0,846
0,279
0,014
0,886
0,701
Shannon's Diversity Index
0,974
0,806
0,547
0,984
0,077
0,082
0,803
0,832
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properties
CAPTURE_PROB HERB_EFFICIENCY
HERB_FRACTION
MUT_COOLING
L
0,178
0,489
0,039
0,653
L/S
0,179
0,490
0,039
0,650
C
0,194
0,488
0,038
0,650
GenSD
0,763
0,044
0,685
0,427
VulSD
0,739
0,537
0,298
0,490
MxSim
0,308
0,530
0,035
0,766
MeanFoodChainLength
0,888
0,358
0,917
0,383
ChnSD
0,826
0,938
0,619
0,243
ChnNo
0,933
0,192
0,330
0,423
Dynamic Complexity (<i> SC^1/2)
0,695
0,651
0,316
0,708
Clustering Coefficient
0,142
0,624
0,461
0,682
Compartmentalisation
0,534
0,978
0,794
0,325
Mean Trophic Position
0,715
0,404
0,873
0,505
Standard Deviation Trophic Position
0,755
0,706
0,937
0,501
NODF (Nestedness)
0,438
0,484
0,769
0,985
Gq (Quantitative Generality)
0,592
0,655
0,182
0,976
Vq (Quantitative Vulnerability)
0,547
0,201
0,478
0,301
H2' (Mutualistic Specialisation)
0,591
0,606
0,806
0,802
Total Community Abundance
0,929
0,836
0,294
0,964
Shannon's Diversity Index
0,584
0,456
0,448
0,994
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196
197
198
199
200
201
202
203
204
205
206
10
MUT_EFFICIENCY
0,193
0,194
0,196
0,331
0,153
0,059
0,153
0,039
0,616
0,740
0,576
0,595
0,277
0,124
0,943
0,413
0,265
0,513
0,958
0,764
MUT_FRACTION OMNI_TRADEOFF EFFICIENCY_TRANSF
0,190
0,188
0,181
0,671
0,410
0,460
0,549
0,845
0,339
0,162
0,934
0,323
0,197
0,296
0,899
0,043
0,062
0,904
0,238
0,430
0,776
0,779
0,777
0,313
0,234
0,966
0,072
0,028
0,124
0,451
0,555
0,365
0,102
0,058
0,625
0,463
0,132
0,674
0,797
0,750
0,702
0,704
0,702
0,048
0,084
0,472
0,447
0,853
0,242
0,840
0,020
0,556
0,612
0,511
0,320
0,339
0,196
0,765
0,768
0,222
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Table S3. Sensitivity analyses for the parameter values included in the model reported in
208
table S1 + 10% of their value. P-values for the GLMs are reported, indicating whether
209
significant differences exist on the relationship between the MAI ratio and the network
210
property analyzed. Red values indicate significant differences (p<0.05).
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properties
IMMIGRATION
L
0,539
L/S
0,525
C
0,507
GenSD
0,874
VulSD
0,189
MxSim
0,417
MeanFoodChainLength
0,046
ChnSD
0,081
ChnNo
0,088
Dynamic Complexity (<i> SC^1/2)
0,898
Clustering Coefficient
0,114
Compartmentalisation
0,415
Mean Trophic Position
0,152
Standard Deviation Trophic Position
0,041
NODF (Nestedness)
0,333
Gq (Quantitative Generality)
0,345
Vq (Quantitative Vulnerability)
0,838
H2' (Mutualistic Specialisation)
0,063
Total Community Abundance
0,971
Shannon's Diversity Index
0,739
212
213
REPROD_RATE
0,308
0,309
0,307
0,611
0,744
0,729
0,252
0,037
0,381
0,866
0,500
0,692
0,144
0,205
0,737
0,786
0,961
0,619
0,403
0,422
LIVING_EXP
0,344
0,341
0,341
0,328
0,696
0,198
0,527
0,833
0,592
0,639
0,061
0,032
0,245
0,338
0,374
0,035
0,711
0,429
0,687
0,816
MATING_ENERGY MATING_RESOURCE MAX_RESOURCE MIN_RESOURCE
0,219
0,220
0,226
0,963
0,890
0,568
0,952
0,894
0,968
0,311
0,819
0,794
0,874
0,929
0,251
0,825
0,822
0,182
0,862
0,441
properties
CAPTURE_PROB HERB_EFFICIENCY HERB_FRACTION MUT_COOLING
L
0,536
0,187
0,295
0,309
L/S
0,533
0,194
0,296
0,369
C
0,533
0,203
0,294
0,444
GenSD
0,850
0,033
0,639
0,982
VulSD
0,759
0,732
0,589
0,728
MxSim
0,942
0,631
0,894
0,553
MeanFoodChainLength
0,927
0,917
0,323
0,875
ChnSD
0,740
0,576
0,316
0,963
ChnNo
0,600
0,806
0,301
0,947
Dynamic Complexity (<i> SC^1/2)
0,180
0,802
0,366
0,472
Clustering Coefficient
0,922
0,681
0,741
0,528
Compartmentalisation
0,496
0,020
0,667
0,761
Mean Trophic Position
0,247
0,414
0,608
0,206
Standard Deviation Trophic Position
0,497
0,880
0,550
0,922
NODF (Nestedness)
0,321
0,310
0,918
0,175
Gq (Quantitative Generality)
0,447
0,488
0,254
0,325
Vq (Quantitative Vulnerability)
0,866
0,017
0,900
0,337
H2' (Mutualistic Specialisation)
0,915
0,865
0,448
0,752
Total Community Abundance
0,425
0,521
0,544
0,237
Shannon's Diversity Index
0,358
0,588
0,863
0,712
11
0,429
0,426
0,395
0,888
0,848
0,972
0,727
0,418
0,918
0,287
0,720
0,502
1,000
0,739
0,226
0,428
0,541
0,955
0,779
0,928
MUT_EFFICIENCY
0,953
0,924
0,919
0,601
0,158
0,235
0,433
0,375
0,693
0,609
0,142
0,162
0,787
0,625
0,501
0,948
0,261
0,817
0,816
0,706
0,008
0,008
0,008
0,863
0,333
0,516
0,258
0,931
0,032
0,293
0,221
0,475
0,182
0,123
0,795
0,112
0,412
0,247
0,447
0,657
0,065
0,070
0,076
0,587
0,722
0,853
0,736
0,807
0,973
0,267
0,555
0,227
0,844
0,727
0,658
0,007
0,367
0,943
0,414
0,859
SYNTHESIS_ABILITY
0,330
0,327
0,327
0,464
0,620
0,005
0,411
0,200
0,479
0,481
0,856
0,985
0,248
0,189
0,744
0,643
0,500
0,258
0,379
0,367
MUT_FRACTION OMNI_TRADEOFF EFFICIENCY_TRANSF
0,608
0,610
0,608
0,648
0,140
0,644
0,398
0,978
0,295
0,536
0,838
0,066
0,332
0,541
0,879
0,155
0,680
0,658
0,164
0,244
0,123
0,123
0,121
0,587
0,774
0,224
0,890
0,725
0,856
0,079
0,113
0,691
0,584
0,323
0,370
0,040
0,735
0,411
0,221
0,569
0,135
0,133
0,128
0,447
0,862
0,813
0,384
0,404
0,157
0,226
1,000
0,173
0,133
0,464
0,135
0,979
0,712
0,502
0,565
0,861
214
Appendix S2: Results
215
Community structure
216
217
Figure S2. Rank-abundance distribution plots of 10 sample networks with different MAI ratios and
218
which are representative of the set of communities studied. Lines represent a fit of the data to a
219
lognormal distribution, typically observed in empirical rank-abundance distributions (Magurran
220
2004).
12
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MAI ratio
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222
Figure S3. Moran’s I and Geary’s C (at the whole community level, calculated as the mean of each
223
index across all the species in the community), plotted against MAI ratio, in model communities.
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Points show index values for each replicate. Line and shadow represent the fit of a linear model to the
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data and the standard error of the mean respectively (p-value < 0.001 for linear models fits to each
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data set).
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13
Non−mutualistic plants ***
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Geary's C
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MAI ratio
0 .1 .2 .3 .4 .5 .6 .7 .8 .9 1
MAI ratio
230
Figure S4. Geary’s C spatial aggregation index per trophic level, plotted against MAI ratio, in model
231
communities. Points show index values for each replicate. Line and shadow represent the fit of a
232
linear model to the data and the standard error of the mean respectively. * and *** represent p-value
233
< 0.05 and 0.001 for linear models fits to each data set respectively.
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14
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References
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Fortin, M.-J. & Dale, M. (2005). Spatial analysis: A guide for ecologists. Cambridge University Press,
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Cambridge, UK.
Ings, T.C., Montoya, J.M., Bascompte, J., Blüthgen, N., Brown, L.E., Dormann, C.F., et al. (2009).
Ecological networks - beyond food webs. JAE, 78, 253–269.
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Magurran, A.E. (2004). Measuring biological diversity. Blackwell Publishing, Oxford, UK.
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Williams, R.J. & Martinez, N.D. (2000). Simple rules yield complex food webs. Nature, 404, 180–
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183.
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