DOI: 10.5061/dryad.wstqjq2sr
title: Contrasting species richness in patches of alternative foundation species suggests a framework for understanding Species of Unusual Effect

description: Questions: Structurally dominant species can be especially influential in
 plant community assembly and ecosystem function as Species of Unusual
 Effect (SUEs). For example, native bunchgrasses function as foundation
 species and ecosystem engineers in the naturally high-diversity
 groundcover of longleaf pine savannas. Other species structurally dominate
 relatively small, discrete patches across the savanna landscape, e.g., the
 fern Pteridium aquilinum and the shrub Ilex glabra. Do
 patch-level species richness and composition of assemblages of groundcover
 plants and arthropods differ among alternative locally dominant species?
 Location: We conducted our study in a restored longleaf pine savanna in
 southeastern Louisiana. Methods: We compared the groundcover plant and
 arthropod assemblages within discrete patches structurally dominated by P.
 aquilinum or I. glabra to adjacent areas physically dominated by native
 bunchgrasses. We compared local plant species richness and composition,
 stem density, aboveground dry biomass, and litter dry biomass, as well as
 arthropod species richness and composition, abundance, and dry biomass.
 Results: Species richness and stem density of non-dominant groundcover
 plants were significantly lower in patches of P. aquilinum and I. glabra
 than within bunchgrass-dominated areas. Species composition of
 non-dominant groundcover plants was more variable within I. glabra patches
 compared to bunchgrass areas. Arthropod species richness and abundance
 were also significantly lower in patches of P. aquilinum compared to
 bunchgrass areas, and species composition of arthropods differed
 significantly between P. aquilinum patches and bunchgrass areas.
 Conclusions: At the local scale of groundcover plant patches (along with
 their attendant arthropods) in a longleaf pine savanna in southeastern
 Louisiana, native bunchgrasses are associated with higher species richness
 compared to the alternative foundation species P. auilinum
 or I. glabra. Although removal experiments, community-assembly
 experiments, or reciprocal replacement experiments should be conducted to
 test the hypothesis that these species differentially influence the
 groundcover as, respectively, diversity-enhancing vs. diversity-inhibiting
 SUEs, our observations exemplify how alternative foundation species could
 add complexity to natural landscapes by differentially influencing
 characteristics of their associated local communities.
description: # Contrasting species richness in patches of alternative foundation
 species suggests a framework for understanding Species of Unusual Effect R
 Scripts and data files to perform analyses and create figures for
 ‘Alternative foundation species differentially influence diversity of
 groundcover plant and arthropod assemblages among patches in a pine
 savanna in the southeastern U.S.A. ’ This study examines the effect of
 alternative foundation species on the diversity of non-foundation
 groundcover plant species and arthropods within a longleaf pine savanna in
 southeastern Louisiana. Data files: 1. fern.diversity.csv * This file
 contains species richness, stem density, and aboveground biomass (g) of
 non-foundation groundcover plants as well as litter biomass (g) from
 inside and outside of bracken fern patches. Note: Outside of bracken fern
 patches is within bunchgrass dominated areas. 2. fern.NMDS.csv * This file
 contains a species-by-site matrix used in NMDS (nonmetric multidimensional
 scaling) for non-foundation groundcover plants inside and outside of
 bracken fern patches. Each row is a quadrat and each column is a
 non-foundation groundcover plant species. Note: Outside of bracken fern
 patches is within bunchgrass dominated areas. 3. fern.env.NMDS.csv * This
 file contains location information for each quadrat in the species-by-site
 matrix of non-foundation groundcover plants inside and outside of bracken
 fern patches used in NMDS. Each row is a quadrat and each column gives the
 plot id, quadrat type (1=In, 2=Out), and quadrat id for each quadrat.
 Note: Outside of bracken fern patches is within bunchgrass dominated
 areas. 4. fern.iNext.csv * This file contains incidence data of
 non-foundation groundcover plants inside and outside of bracken fern
 patches. Each row represents a plot, either from inside or outside of
 bracken fern patches. Note: Outside of bracken fern patches is within
 bunchgrass dominated areas. 5. gallberry.diversity.csv * This file
 contains species richness, stem density, and aboveground biomass (g) of
 non-foundation groundcover plants as well as litter biomass (g) from
 inside and outside of gallberry patches. Note: Outside of gallberry
 patches is within bunchgrass dominated areas. 6. gallberry.NMDS.csv * This
 file contains a species-by-site matrix used in NMDS (nonmetric
 multidimensional scaling) for non-foundation groundcover plants inside and
 outside of gallberry patches. Each row is a quadrat and each column is a
 non-foundation groundcover plant species. Note: Outside of gallberry
 patches is within bunchgrass dominated areas. 7. gallberry.env.NMDS.csv *
 This file contains location information for each quadrat in the
 species-by-site matrix of non-foundation groundcover plants inside and
 outside of gallberry patches used in NMDS. Each row is a quadrat and each
 column gives the plot id, quadrat type (1=In, 2=Out), and quadrat id for
 each quadrat. Note: Outside of gallberry patches is within bunchgrass
 dominated areas. 8. gallberry.iNext.csv * This file contains incidence
 data of non-foundation groundcover plants inside and outside of gallberry
 patches. Each row represents a plot, either from inside or outside of
 gallberry patches. Note: Outside of gallberry patches is within bunchgrass
 dominated areas. 9. arthropod.sweep.diversity.csv * This file contains
 species richness, abundance, and biomass (g) of arthropods collected from
 sweep samples from inside and outside of bracken fern patches. Note:
 Outside of bracken fern patches is within bunchgrass dominated areas. 10.
 arthropod.sweep.NMDS.csv * This file contains a species-by-site matrix
 used in NMDS (nonmetric multidimensional scaling) for arthropods collected
 from sweep net samples inside and outside of bracken fern patches. Each
 row is a patch and each column is an arthropod species. Note: Outside of
 bracken fern patches is within bunchgrass dominated areas. 11.
 arthropod.sweep.env.NMDS.csv * This file contains location information for
 each patch in the species-by-site matrix of sweep net collected arthropods
 inside and outside of bracken fern patches used in NMDS. Each row is a
 patch and each column gives the plot id and quadrat type (1=In, 2=Out).
 Note: Outside of bracken fern patches is within bunchgrass dominated
 areas. 12. sweep.iNext.csv * This file contains incidence data of sweep
 net collected arthropods inside and outside of bracken fern patches. Note:
 Outside of bracken fern patches is within bunchgrass dominated areas. 13\.
 species.codes.csv           -This file contains scientific names for each
 six letter plant species code used in the NMDS analyses. Analysis script:
 1.
 RScript-Alternative_foundation_species_differentially_influence_diversity_of_groundcover_plant_and_arthropod_assemblages_among_patches_in_a_pine_savanna_in_the_southeastern_usa.R * This file contains scripts to run all main analyses and reproduce figures from the paper. Please read all annotations carefully when conducting these analyses.