DOI: 10.5061/dryad.cvdncjt9d
title: Multiple dimensions of phylogenetic diversity are needed to explain the complex aboveground-belowground diversity relationships

description: The complex relationship between aboveground and belowground diversity and
 whether they act as surrogates for one another remains unresolved.
 Increasing evidence suggests that investigating phylogenetic diversity
 could provide valuable insights into the interplay between plants and soil
 microbes, but the proliferation of phylogenetic diversity metrics has
 hindered comparative studies and the identification of general patterns.
 To overcome this challenge, we implemented a multi-dimensional framework
 that classifies phylogenetic diversity metrics into three dimensions:
 richness, divergence, and regularity, each of which captures different
 ecological aspects of species differences. Then we applied this framework
 to investigate the relationship between above and belowground diversity in
 a subtropical forest in Eastern China. We found that phylogenetic
 diversity of plant and soil microbes, including bacteria and fungi, were
 more strongly correlated at the richness and regularity dimension compared
 with divergence dimension. Further analyses revealed that these observed
 correlation patterns can be attributed to the influence of soil total
 phosphorus content, which is the limiting factor of plant and microbial
 phylogenetic diversity at richness and regularity dimensions. Together,
 our study demonstrated the necessity of using a multi-dimensional approach
 to advance our understanding of the complex relationships between plant
 and soil microbial biodiversity.
description: This study was conducted in a subtropical forest located in
 Ningbo City, Zhejiang Province, Eastern China in 2017, with a subtropical
 monsoon climate characterized by an average annual temperature of 16.2°C
 and an average annual precipitation of 1700 mm. Dominant tree species in
 the area include <em>Pinus massoniana</em>, <em>Schima
 superba</em>, and <em>Cunninghamia lanceolata</em>. Our
 study comprised 16 plots situated in three different locations, dominated
 by various tree species ( 40 – 60-year-old stand), including both
 unmanaged secondary forests and forests that underwent close-to-nature
 silviculture treatment. In total, we obtained 16 plots, representing a
 clear diversity gradient and different composition structure across sites.
 For each plot, five bulk-soil cores (3.8 cm in diameter, 0-10 cm depth),
 excluding litter and organic horizons, were collected using a five-point
 sampling method and placed in separate sterile plastic bags. We obtained a
 total of 80 soil samples from the 16 plots in October 2019. The plant
 composition of all plots was investigated in August 2019. Every tree stem
 with a diameter at breast height (DBH) ≥ 5 cm in the plot was sampled. We
 found 117 plant species in total across all the study plots, both
 gymnosperms and angiosperms were included.
description: This README file was generated on 2023-12-02 by Xiaorong Lu. GENERAL
 INFORMATION 1. This folder contains the data, computer code and document
 files for the article: Xiaorong Lu,Marc W.Cadotte,Pandeng Wang,Shan
 Rao,Xiaoye Shi,Siyuan Ren,Xihua Wang,Shao-peng Li(2023).Multiple
 dimensions of phylogenetic diversity are needed to explain the complex
 aboveground-belowground diversity relationships. Oikos. 1. Author
 Information Principal Investigator Name: Xiaorong Lu Institution: School
 of Ecological and Environmental Sciences, East China Normal University,
 Shanghai 200241, P.R. China Email:
 [smilelxr0904@gmail.com](mailto:smilelxr0904@gmail.com) ``` Corresponding
 Investigator Name: Shao-peng Li Institution: School of Ecological and
 Environmental Sciences, East China Normal University, Shanghai 200241,
 P.R. China Email: spli@des.ecnu.edu.cn Co-investigator 1 Name: Prof Marc
 W. Cadotte Institution: Department of Biological Sciences, University of
 Toronto Scarborough, Toronto M1C 1A4, Canada Email:
 marc.cadotte@utoronto.ca Co-investigator 2 Name: Pandeng Wang Institution:
 School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen
 518107, China Email: wangpd@mail2.sysu.edu.cn Co-investigator 3 Name: Shan
 Rao Institution: School of Ecological and Environmental Sciences, East
 China Normal University, Shanghai 200241, P.R. China
 Email:shan.rao@foxmail.com Co-investigator 4 Name: Xiaoye Shi Institution:
 School of Ecological and Environmental Sciences, East China Normal
 University, Shanghai 200241, P.R. China Email: xiaoye.shi@foxmail.com
 Co-investigator 5 Name: Siyuan Ren Institution: China Aero Geophysical
 Survey and Remote Sensing Center for Natural Resources， Beijing 100083,
 China Email: rsy9999ml@163.com Co-investigator 6 Name: Xihua Wang
 Institution: School of Ecological and Environmental Sciences, East China
 Normal University, Shanghai 200241, P.R. China Email:
 xhwang@des.ecnu.edu.cn ``` 2. Date of data collection: 2019 3. Geographic
 location of data collection: Ningbo City, Zhejiang Province, eastern China
 4. Funding sources that supported the collection of the data: National
 Natural Science Foundation of China (NSFC3222051, NSFC31971553), the
 Shanghai Rising-Star Program (20QA1402900), and the Fundamental Research
 Funds for the Central Universities. 5. Comments and requests should be
 addressed to Xiaorong Lu:
 [smilelxr0904@gmail.com](mailto:smilelxr0904@gmail.com). All material is
 free of use, but I would appreciate being told, and this dataset and the
 matching paper cited if appropriate. 6. Recommended citation for this
 dataset: Xiaorong Lu et al. (2023), Data from: Multiple dimensions of
 phylogenetic diversity are needed to explain the complex
 aboveground-belowground diversity relationships. Dryad,
 [https://doi.org/10.5061/dryad.cvdncjt9d](https://doi.org/10.5061/dryad.cvdncjt9d) DATA & FILE OVERVIEW File List: * "bacteria_OTU table.csv": The OTUs table of bacteria * "fungi_OTU table.csv": The OTUs table of fungi * "plant_community table.csv":The OTUs table of plant * "bacteria_phylogenetic tree.tre": The phylogenetic tree of bacteria * "fungi_phylogenetic tree.tre": The phylogenetic tree of fungi * "plant_phylogenetic tree.tre": The phylogenetic tree of plant * "soil.csv": The soil physicochemical factors \######################################################################### DATA-SPECIFIC INFORMATION FOR: bacteria_OTU table.csv 1. Number of variables: 28119 2. Number of cases/rows: 80 3. Variable List: plots:plot code Zotu xxx: Every Zotus of each column (e.g.,Zotu10) represents the operational taxonomic units (OTUs) at the 100% similarity threshold \######################################################################### DATA-SPECIFIC INFORMATION FOR: fungi_OTU table.csv 1. Number of variables: 8997 2. Number of cases/rows: 80 3. Variable List: plots:plot code Zotu xxx: Every Zotus of each column (e.g.,Zotu6) represents the operational taxonomic units (OTUs) at the 100% similarity threshold \######################################################################### DATA-SPECIFIC INFORMATION FOR: plant_community table.csv 1. Number of variables: 59 2. Number of cases/rows: 16 3. Variable List: plots:plot code Each column represents the scientific name of plant species \######################################################################### DATA-SPECIFIC INFORMATION FOR: bacteria_phylogenetic tree.tre This is a bacterial molecular phylogenetic tree constructed by FastTree software \######################################################################### DATA-SPECIFIC INFORMATION FOR: fungi_phylogenetic tree.tre This is a fungal molecular phylogenetic tree constructed by FastTree software \######################################################################### DATA-SPECIFIC INFORMATION FOR: plant_phylogenetic tree.tre This is a plant phylogenetic tree produced form a mega-tree (i.e. GBOTB.extended.tre) using R package V.PhyloMaker \######################################################################### DATA-SPECIFIC INFORMATION FOR: soil.csv 1. Number of variables: 6 2. Number of cases/rows: 16 3. Variable List: Plots: plot code of soil sampling\ TN: Total nitrogen (g/kg) TP: Total phosphorus (g/kg) AP: Available phosphorus (mg/kg) TOC: Soil total organic carbon (g/kg) pH: Soil pH \####################################### Rcode The file named "R_code_diversities.R" contains the R source code for all diversity indexes used in the paper (taking plants as an example). It should be processed using the R software.