DOI: 10.5061/dryad.rbnzs7hm4
title: Data from: Mycorrhizal symbiosis increases plant phylogenetic diversity and regulate community assembly

description: The intricate mechanisms shaping plant diversity and community composition
 are the cornerstone of ecological understanding.  Yet, the role
 of mycorrhizal symbiosis, the fundamental partnership between fungi and
 plant roots, in influencing community composition has often been
 underestimated.  Here, we use extensive species survey data from
 1,315 terrestrial ecosystem sites to elucidate the influence of
 mycorrhizal symbiosis on plant phylogenetic diversity and its implications
 for community assembly processes.  Our findings demonstrate that
 increasing mycorrhizal symbiotic potential leads to greater phylogenetic
 dispersion within plant communities. Furthermore, we unveil a distinct
 dichotomy in the assembly processes governed by mycorrhizal status.
 Mycorrhizal species predominantly influence deterministic processes,
 suggesting a role in niche-based community assembly.  Conversely,
 non-mycorrhizal species exert a stronger influence on stochastic
 processes, highlighting the importance of random events in shaping
 community structure.  These results underscore the crucial but
 often hidden role of mycorrhizal symbiosis in driving plant community
 diversity and assembly. This study provides valuable insights into the
 complex mechanisms shaping ecological communities and the way for more
 informed conservation and management practices that acknowledge the
 complex interplay between symbiosis and ecological community dynamics.
description: <strong>Filed survey and data
 collection</strong> This study utilized field
 survey data collected from 1315 sites across various grassland ecosystems
 in China.  Vegetation surveys were conducted during the peak plant growth
 season, specifically from mid-July to August in middle and high latitude
 regions, including the Qinghai-Tibetan Plateau, and from August to
 September in desert, subtropical, and tropical regions.  At each site,
 plant community data was collected using ten 1m × 1m quadrats (reduced to
 0.5m × 0.5m for meadow and alpine meadow) located randomly within a 100m ×
 100m area.   For shrubland ecosystems, five 5m × 5m quadrats were randomly
 placed within the same 100m × 100m area.  Five of the ten quadrats (or all
 five quadrats in shrublands) were randomly selected for detailed
 vegetation analysis. Within these selected quadrats, plant species
 richness (SR) and species relative abundance were recorded.  Soil samples
 were collected from each quadrat using a soil core method at a depth of 20
 cm.  Soil organic carbon content (SOC) were measured for each sample. 
 Total phosphorus (TP), total nitrogen (TN), and soil pH were interpolated
 from the Basic soil property dataset of high-resolution China Soil
 Information Grids (2010-2018). To facilitate analysis
 and interpretation, the 1315 field sites were classified into four
 distinct ecosystem types: meadow (further categorized into lowland meadows
 (LM), mountain meadows (MM), and alpine meadows (AM)), steppe (divided
 into temperate steppe (TS) and alpine steppe (AS)), shrubland (classified
 as warm shrubland (WG) and tropical shrubland (TG)), and desert (DS).
  This classification was based on plant community composition, climate,
 and prevailing environmental conditions. Mean annual
 temperature (MAT, °C), mean annual precipitation (MAP, mm), and mean
 diurnal range (mean of monthly maximum temperature - minimum temperature,
 °C) for each site were obtained from the WorldClim data layers
 (specifically, bio_1 and bio_12) at a spatial resolution of 30 seconds ×
 30 seconds (approximately 1 km × 1 km at the equator)
 (http://www.worldclim.org/). Remote sensing data,
 including Fraction of Photosynthetically Active Radiation (Fpar) were
 obtained from MOD15A2H Version 6 data product, slope and elevation data
 was extracted from the STRM 90m dataset 171 in China, based on the SRTM
 V4.1 database (https://www.resdc.cn/data.aspx?DATAID=123).  Fpar is
 defined as the fraction of incident photosynthetically active radiation,
 400-700 nanometers (nm), absorbed by the green elements of a vegetation
 canopy. <strong>Plant mycorrhizal status
 </strong><strong>and community mycorrhizal
 index</strong> To quantify the mycorrhizal status
 of each plant community, we calculated a mycorrhizal index representing
 the degree of potential mycorrhizal colonization within the community.
  The mycorrhizal status of each plant species was determined using an
 established database of mycorrhizal associations.  To minimize potential
 errors during the matching process, species were matched based on their
 genus level (Brundrett & Tedersoo 2019). The
 dominant mycorrhizal status of each community was determined based on the
 mycorrhizal status exhibiting the highest abundance within that community.
  This approach allowed us to differentiate communities based on the
 predominant mycorrhizal association of their constituent plant
 species. <strong>Construction of phylogenetic
 relationships and calculation of phylogenetic
 distances</strong> Phylogenetic relationships and
 distances between plant species were determined using the V. PhyloMaker
 package and picante package in R. V. PhyloMaker generated phylogenetic
 hypotheses for the 1235 plant species in our study by linking them to the
 'GBOTB.extended' megatree.  This megatree encompasses 74,531
 species, representing all families of extant vascular plants, and serves
 as the largest dated phylogeny for vascular plants.  Phylogenetic
 distances within each community were calculated using the picante package.
  We calculated two metrics: mean pairwise distance (MPD) and mean nearest
 taxon distance (MNTD).  To account for the relative abundance of each
 species within the community, species abundance was incorporated as a
 weighting factor in the phylogenetic distance calculations.
 To mitigate the influence of species richness on community
 phylogenetic distances, standardized effect size metrics for MPD (SESMPD)
 and MNTD (SESMNTD) were calculated.  This standardization involved
 generating a null distribution by randomly shuffling the distance matrix
 labels across all taxa 999 times.  The mean of the null distribution was
 then used to calculate the standardized effect size.  SES values less than
 0 indicate phylogenetic clustering, where species within the community are
 more closely related than expected by chance.  Conversely, SES values
 greater than 0 indicate phylogenetic overdispersion, where species are
 more distantly related than expected.
 <strong>Statistical analyses</strong>
 <strong>Comparison of plant community composition. 
 </strong>To compare plant community composition across different
 dominant mycorrhizal status, we first examined the relative abundance of
 different plant families within each of the community types.  We then
 performed non-metric multidimensional scaling (NMDS) using the metaMDS
 function in the vegan package, based on a Bray-Curtis distance matrix. 
 The stress function value was assessed to ensure model reliability. 
 Significant differences between groups were determined using Adonis, with
 significance levels denoted as follows: n.s. (not significant), *p
 &lt; 0.05, **p &lt; 0.01, and ***p &lt; 0.001.
 <strong>Assessing the influence of mycorrhizae on species
 richness and phylogenetic diversity.  </strong>To evaluate the role
 of mycorrhizae in shaping community species richness and phylogenetic
 diversity, we constructed a set of predictor variables encompassing
 climate (MAT, MAP, MDR, Fpar), geographic factors (longitude, latitude,
 elevation, slope), mycorrhizal status (MI), and soil properties (TN, TP,
 SOC, pH). Multiple regression models were developed
 using the MuMIn package in R to assess the effects of these predictors on
 species richness and phylogenetic diversity.  A full set of models
 incorporating all predictors was generated and ranked based on the Akaike
 information criterion (AIC) using maximum likelihood estimation.  Models
 with ΔAIC &lt; 2 were retained, and model averaging was employed to
 calculate parameter estimates and p-values.  The relative effect of each
 predictor was determined by calculating the ratio of its parameter
 estimate to the sum of all parameter estimates.  To further emphasize the
 importance of mycorrhizae in predicting species richness and phylogenetic
 diversity, we constructed comparative models excluding the mycorrhizal
 index while retaining all other predictors.  These reduced models were
 compared to their corresponding full models using AICc values, with lower
 AICc values indicating superior model performance.
 <strong>Quantifying the relative importance of stochastic
 and deterministic processes in community assembly.</strong>  To
 assess the influence of mycorrhizae on community assembly processes, we
 utilized normalized stochasticity ratio (NST) analysis.  NST, an extension
 of the Beta-diversity metric, quantifies the relative contribution of
 stochastic and deterministic processes in community assembly.  NST values
 range from 0 to 1, with 0.5 representing an equal contribution of both
 processes.  NST values predominantly above 0.5 indicate dominance of
 stochastic processes, while values below 0.5 suggest a greater influence
 of deterministic processes. We further investigated the
 impact of different mycorrhizal plant types on community assembly using
 phylogenetic bin-based null model analysis (iCAMP) (Ning<em> et
 al.</em> 2020).  This method, implemented using the iCAMP package in
 R, divides plant species into phylogenetic bins with significant
 phylogenetic signals and quantifies the contribution of each bin to
 deterministic (homogeneous selection (HoS), heterogeneous selection (HeS))
 and stochastic (dispersal limitation (DL), homogenizing dispersal (HD),
 and drift (DR)) processes.  We selected the 300 most abundant plant
 species (representing 91.6% of total individuals), assigned them to
 phylogenetic bins, and determined the dominant mycorrhizal status within
 each bin.  The relative contribution of each bin to different assembly
 processes was then assessed to quantify the influence of different
 mycorrhizal plant types on ecological processes.
description: # Mycorrhizal symbiosis increases plant phylogenetic diversity and
 regulate community assembly
 [https://doi.org/10.5061/dryad.rbnzs7hm4](https://doi.org/10.5061/dryad.rbnzs7hm4) This study utilizes extensive field survey data from 1,315 grassland sites across China to examine the effects of mycorrhizal colonization on community phylogenetic diversity and assembly processes. For each site, the data include site ID, grassland type, dominant mycorrhiza type of community, mean annual temperature (MAT), mean diurnal range (MDR), mean annual precipitation MAP), longitude, latitude, elevation, slope, fraction of photosynthetically active radiation (fPAR), soil pH, Soil organic carbon (SOC) content, soil total nitrogen (TN), soil total phosphorus (TP), mycorrhiza index (MI), species richness (SR), mean pairwise distance (MPD), mean nearest taxon distance (MNTD), standardized effect size metrics for MPD (SESMPD), and standardized effect size metrics for MNTD (SESMNTD). In this Dryad repository we have posted our data and code to recreate all figures. Codes includes maintext codes and supplementary codes. These are: 1\)     “Codes for figures in maintext.R”.  This script reads the data and generates all the images presented in the maintext.  At the beginning of the code, all the packages needed for the analysis are provided and the installation of the relevant packages is supplemented.  Each figure contains a separate folder, setting the unzipped file as the working path and read the data in each folder separately and run the figures. 2\)     “Codes for figures in supplementary information.R”.  This script reads the data and generates all the images presented in the supplementary.  Similarly, need to set the unzipped folder as the working path at the beginning of the code to run smoothly. Data includes all the processed data needed to make figures. 1\)     “Fig.1” This folder provides data for NMDS analysis of species similarity in communities dominated by different mycorrhizal status. 2\)     “Fig.2” This folder is to analyze the contribution of different factors to species richness and phylogenetic diversity.  For each site, the data include site ID, grassland type, dominant mycorrhiza type of community, mean annual temperature (MAT), mean diurnal range (MDR), mean annual precipitation MAP), longitude, latitude, elevation, slope, fraction of photosynthetically active radiation (fPAR), soil pH, Soil organic carbon (SOC) content, soil total nitrogen (TN), soil total phosphorus (TP), mycorrhiza index (MI), species richness (SR), mean pairwise distance (MPD), mean nearest taxon distance (MNTD), standardized effect size metrics for MPD (SESMPD), and standardized effect size metrics for MNTD (SESMNTD). 3\)     “Fig.3” This folder contains data on sampling sites (“China_Map.geojson”, “Nine-dotted line(2019).geojson”) and patterns of the standard phylogenetic diversity (SESMPD&SESMNTD) of communities across latitudinal gradients. 4\)     “Fig.4” This folder contains data on analysing the relationship between community mycorrhizal index and SESMPD and SESMNTD, as well as variance in phylogenetic diversity between communities in different ecosystem types. 5\)     “Fig.5” This folder contains the phylogenetic tree of the top 300 families with the high relative abundance (tree_top300.tre) in all the fields analysed by iCAMP, as well as the relative abundance of the different families of plants (icamp.bins.Class_top300.csv), as well as the relative influence of plants with different mycorrhizal status on community assembly processes in different ecosystem types (“Bintree_heatmap_desert.csv”, “Bintree_heatmap_meadow.csv”, “Bintree_heatmap_steppe.csv”, “Bintree_heatmap_shrubland.csv” 6\)     “Supplementary Fig.1” This folder is the data required for Supplementary Figure 1, which focuses on analysing the dominant families of communities dominated by plants of different mycorrhizal status. 7\)     “Supplementary Fig.2” This folder provides data on the pattern of the phylogenetic diversity (MPD&MNTD) of communities with latitudinal gradients. 8\)     “Supplementary Fig.3” This folder provides the data needed to perform NST analyses of the proportion of deterministic and stochastic processes in community assembly dominated by different mycorrhizal status. 9\)     “Supplementary Fig.4” This folder provides data related to community unsimilarity and community spatial distance based on Unifrac distance. Notes: Some figures are produced in R but then assemble in Adobe Illustrator.