DOI: 10.5061/dryad.76hdr7stt
title: Uncovering structural features that underlie coexistence in an invaded woody plant community with interaction networks at multiple life stages

description: Understanding the patterns of competitive and facilitative interactions
 within and among species in plant communities is a central goal of plant
 ecology, because these patterns determine species coexistence and
 community dynamics. Network theory provides tools that allow these
 patterns to be quantified, and can provide greater understanding of
 important community properties, including community stability, than can
 documenting pairwise species interactions. I characterized the
 interactions of multiple, co-occurring invasive and native species in an
 old field woody plant community to build plant interaction networks at two
 different life stages. With the goal of identifying structural features
 that may operate to maintain species coexistence, I characterized the
 architecture of these networks at multiple scales: the entire network, the
 substructures that compose the network, and species' roles within
 substructures. I found that species-level pairwise interactions alone did
 not provide an accurate or sufficiently detailed picture of community
 structure. Rather, using a network approach, I identified substructures
 that have the potential to promote and hinder species coexistence in
 interactions among seedlings. Characterizing the nuances of network
 substructures was illuminating, as the size of the substructures and the
 pattern of interaction intensities within substructures influence the
 expected effects on species coexistence. Including interactions at
 multiple life stages was also important; the seedling species that
 benefited most from the nested structure of facilitative interactions with
 adults occupied subordinate roles in substructures with other seedlings.
 This role reversal at different life stages is a potential factor
 promoting coexistence in the community. Last, the network framework was
 useful for comparing species' roles between native and invasive
 members of the community, and the three invasive species in this system
 had different, life-stage dependent strategies in interactions with
 co-occurring plants. Synthesis. The interplay of network architecture and
 substructures within plant communities and among plants at different life
 stages is important for understanding species coexistence. In the plant
 community characterized in this study, there were several features that
 may promote coexistence, and these features were not observable in
 interactions within a single life stage or when considering pairwise
 interactions independently.
description: The raw aboveground biomass data are provided as a .csv file. 
 These data are aboveground biomasses (in g) of target seedlings from
 seedling-seedling garden experiments and adult-seedling field
 experiments. Seeds were germinated in April 2016 after
 having implemented stratification and scarification treatments as needed.
 Seedlings were transplanted into the garden and field experiments in May
 2016. In the seedling-seedling garden experiment, all intra- and
 interspecific pairwise interactions between the seven study species were
 measured using a target-neighbour design, in which a central target plant
 was surrounded by four evenly spaced neighbouring plants in pots. Study
 species included species that are invasive in northeast North America:
 <em>Rosa multiflora</em>, <em>Elaeagnus
 umbellata</em>, <em>Berberis thunbergii</em>; and
 species that are native in the region: <em>Rubus
 occidentalis</em>, <em>Rhus typhina</em>,
 <em>Cornus racemosa</em>, and <em>Pinus
 strobus</em>. Control treatments with a central target plant and no
 neighbours were also planted. The pots were placed outdoors at the field
 site (Yale-Myers Forest, Connecticut, USA). Pots were watered to field
 capacity as needed. In the adult-seedling field experiment, seedlings of
 all target species were planted under the canopy of adult individuals of
 <em>R. multiflora</em>, <em>E. umbellata</em>,
 <em>B. thunbergii</em>, <em>R. occidentalis</em>,
 and <em>P. strobus</em>. Control treatments with no adult
 individual were also planted. Plants were harvested in September 2016, and
 harvested aboveground biomass was dried to constant mass at 60°C and
 weighed. The R code used to analyze the data is also
 included in this dataset as a .zip file. Please see the manuscript for
 more complete details regarding methods.
description: Raw aboveground biomass
 data (PlantPerformance.csv) This is a CSV datafile
 of aboveground biomasses (in g) of target seedlings from seedling-seedling
 garden experiments (Experiment column "SS") and adult-seedling
 field experiments (Experiment column "AS"). Target and neighbor
 species are abbreviated using the first letters of the genus and species
 names. Entries with "NA" in the Neighbor column are control
 treatments. This dataset is the only input that needs to be read into the
 R code files. R code used to conduct
 analyses (PlantInteractionNetworkAnalysis.zip) This zip file contains
 all R code used to conduct the analyses in this manuscript:
 
 <em>MAIN.R: </em>in this file, packages are loaded and global
 variables are set. JAGS models and functions are set using sourced files.
 Sub-files for analyses are sourced. 
 <em>functions.R:</em> all functions used in the analysis are
 defined. All analyses files are dependent on this file. 
 <em>JAGSmodels.R:</em> all JAGS models used in the analysis
 are defined and written as .jags files. Analysis file
 "strength.R" is dependent on this file. 
 <em>RII.R:</em> Relative Interaction Intensities are
 calculated for all pairwise interactions using aboveground biomass
 performance data. 
 <em>strength.R:</em> in- and out-strengths are estimated using
 JAGS models (depends on JAGSmodels.R). 
 <em>substructures.R: </em>the frequency of all three- and
 four-species substructures are calculated for competitive outcomes
 networks. Species positions and competitive assymetries are also
 calculated. 
 <em>substructures_Strict.R:</em> the same analysis as in
 "substructure.R" but with stricter criteria for competitive
 outcomes. 
 <em>nestedness.R:</em> nestedness (wNODA) of the facilitative
 and competitive interactions is calculated for the adult-seedling network
 and compared with three null models. 
 <em>connectance.R:</em> calculate interaction diversity for
 the seedling-seedling and adult-seedling network and compare with three
 null models.