DOI: 10.5061/dryad.pzgmsbcn7
title: Opposing community assembly patterns for dominant and non-dominant plant species in herbaceous ecosystems globally

description: Biotic and abiotic factors interact with dominant plants —the locally most
 frequent or with the largest coverage— and non-dominant plants
 differently, partially because dominant plants modify the environment
 where non-dominant plants grow. For instance, if dominant plants compete
 strongly, they will deplete most resources, forcing non-dominant plants
 into a narrower niche space. Conversely, if dominant plants are
 constrained by the environment, they might not exhaust available resources
 but instead may ameliorate environmental stressors that usually limit
 non-dominants. Hence, the nature of interactions among non-dominant
 species could be modified by dominant species. Furthermore, these
 differences could translate into a disparity in the phylogenetic
 relatedness among dominants compared to the relatedness among
 non-dominants. By estimating phylogenetic dispersion in 78 grasslands
 across five continents, we found that dominant species were clustered
 (e.g., co-dominant grasses), suggesting dominant species are likely
 organized by environmental filtering, and that non-dominant species were
 either randomly assembled or overdispersed. Traits showed similar trends
 for those sites (&lt;50%) with sufficient trait data. Furthermore,
 several lineages scattered in the phylogeny had more non-dominant species
 than expected at random, suggesting that traits common in non-dominants
 are phylogenetically conserved and have evolved multiple times. We also
 explored environmental drivers of the dominant/non-dominant disparity. We
 found different assembly patterns for dominants and non-dominants,
 consistent with asymmetries in assembly mechanisms. Among the different
 postulated mechanisms, our results suggest two complementary hypotheses
 seldom explored: (1) Non-dominant species include lineages adapted to
 thrive in the environment generated by dominant species. (2) Even when
 dominant species reduce resources to non-dominant ones, dominant species
 could have a stronger positive effect on some non-dominants by
 ameliorating environmental stressors affecting them, than by depleting
 resources and increasing the environmental stress to those non-dominants.
 These results show that the dominant/non-dominant asymmetry has ecological
 and evolutionary consequences fundamental to understand plant communities.
description: <strong>Data source:</strong>
 Plot-level plant cover and biomass data were acquired from the
 Nutrient Network server on 2018-12-20. The 78 sites with before-treatment
 data obtained from 30 plots or more were included in this analysis. In
 each plot, data collection followed the Nutrient Network protocols (as
 described in the Nutrient Network webpage www.nutnet.org), also detailed
 in the main manuscript associated with this dataset.
 Site-level descriptors were also downloaded from the Nutrient
 Network server. This data included coordinates, elevation, management
 descriptors, and bioclimatic descriptors obtained from WorldClim
 2[1]. The phylogenetic tree was based on Qian and Jin
 (2016). We added missing species to a congeneric species present in the
 tree or to a species of the same family. We tested the impact of missing
 data and found that only 7.3% of the 2437 genus-site combinations could be
 somehow affected by having one or more species absent in the phylogeny and
 at least one other congeneric in the same site. Traits
 data were gathered from TRY, BIEN, and othre flora databases. We
 standardized the codes and completed them to have a final set usable for
 the analyses, as no single database could provide enough records for our
 analyses.
 <strong>Pre-processing:</strong><br>
 <em>Cover</em> Standardize the
 name of the taxa and filtering the table to have only year zero
 Get the mean cover per plot, per site, per taxon
 Filtering to retain only sites with 30 or more plots 
 Discard the species that have no phylogenetic information. If
 any, discard the sites with high proportion of those species
 Estimate relative cover
 <em>Biomass</em> 
 Remove sites with inconsistent biomass classes
 Remove sites without graminoid biomass reported
 Remove sites with a large mismatch between biomass by functional
 group and cover by functional group 
 <em>Phylogenies</em> 
 Fill missing species Trim the tree to match
 the list 
 <strong>References</strong> 1.
 Fick, S. E., & Hijmans, R. J. (2017). WorldClim 2: New 1-km
 spatial resolution climate surfaces for global land
 areas. <i>International Journal of
 Climatology</i>, <i>37</i>(12), 4302–4315. https://doi.org/10.1002/joc.5086 2. Qian, H., & Jin, Y. (2016). An updated megaphylogeny of plants, a tool for generating plant phylogenies and an analysis of phylogenetic community structure. <i>Journal of Plant Ecology</i>, <i>9</i>(2), 233–239. https://doi.org/10.1093/jpe/rtv047