DOI: 10.5061/dryad.9ghx3ffsp
title: Integrated effects of neighborhood composition and resource levels on growth of a dominant tree species in a tropical forest

description: Abiotic environments and biotic neighborhoods interact to influence plant
 growth and community assembly. However, the nature of this interaction
 depends very much on how biotic neighborhoods are measured, including
 their relatedness to focal plants. In a tropical seasonal rainforest, we
 examine the growth of a dominant canopy species in response to
 environmental factors, the densities and relatedness of conspecific and
 heterospecific neighbors, and their interactions. We find significant
 environmental effects and conspecific negative density dependence on
 growth. Furthermore, conspecific neighbor density has stronger negative
 effects on growth under high light and soil water resource levels, but
 weaker negative effects under low light and soil water resource levels. In
 addition, more closely related heterospecifics in the neighborhood have
 negative effects on growth under high soil phosphorus availability, but
 positive effects under low soil phosphorus availability. In contrast, more
 closely related conspecifics in the neighborhood have negative effects on
 growth under low soil potassium availability, but positive effects under
 high soil potassium availability. Our study emphasizes the importance of
 both intra- and inter-specific neighborhood composition and their
 interactions with resource levels for understanding tree growth. This
 enhances our understanding of the complex processes in community assembly
 and species coexistence within forest communities.
description: # Integrated effects of neighborhood composition and resource levels on
 growth of a dominant tree species in a tropical forest
 [https://doi.org/10.5061/dryad.9ghx3ffsp](https://doi.org/10.5061/dryad.9ghx3ffsp) ## Description of the data and file structure This study examined the tree growth of a dominant canopy species in response to abiotic environmental factors, conspecific and heterospecific neighbor densities, and intra-specific genetic-relatedness and inter-specific phylogenetic-relatedness, as well as their interactions, in a tropical seasonal rainforest. We found both of abiotic environments and conspecific neighbors play important roles. Furthermore, the neighborhood effects veried with resource levels, enhancing our understanding of the complex dynamics within forest communities. The data includes tables, R code, DNA sequence matrix and phylogenetic tree. ### Files and variables #### File: All variables for LMM.csv **Description:** Data for linear mixed-effects models (LMMs) analysis of focal juveniles. ##### Variables * No: individual list of focal juveniles * tag: individual ID of focal juveniles * gx: The vertical distance between the location of the focal juveniles and the Y-axis of the plot; * gy: The vertical distance between the location of the focal juveniles and the X-axis of the plot; * qua20: the 20 x 20 quadrats where the focal juvenile located; * DBH: Initial size (diameter at breast height; DBH); * DBH.2021: diameter at breast height (DBH) in 2021; * RGR: The individual relative growth rate (RGR) from 2016 to 2021; * TWI.10m: Topographic wetness index at 10 m spatial scale; * TWI.15m: Topographic wetness index at 15 m spatial scale; * TWI.20m: Topographic wetness index at 20 m spatial scale; * MCH.10m: Mean canopy height at 10 m spatial scale; * MCH.15m: Mean canopy height at 15 m spatial scale; * MCH.20m: Mean canopy height at 20 m spatial scale; * Con.10m: Conspecific neighbor density index at 10 m spatial scale; * Con.15m: Conspecific neighbor density index at 15 m spatial scale; * Con.20m: Conspecific neighbor density index at 20 m spatial scale; * Het.10m: Heterospecific neighbor density index at 10 m spatial scale; * Het.15m: Heterospecific neighbor density index at 15 m spatial scale; * Het.20m: Heterospecific neighbor density index at 20 m spatial scale; * Gen.10m: Conspecific neighbor genetic-relatedness index at 10 m spatial scale; * Gen.15m: Conspecific neighbor genetic-relatedness index at 15 m spatial scale; * Gen.20m: Conspecific neighbor genetic-relatedness index at 20 m spatial scale; * Phy.10m: Heterospecific neighbor phylogenetic-relatedness index at 10 m spatial scale; * Phy.15m: Heterospecific neighbor phylogenetic-relatedness index at 15 m spatial scale; * Phy.20m: Heterospecific neighbor phylogenetic-relatedness index at 20 m spatial scale; * Soil.TN: soil total nitrogen content; * Soil.AP: soil available phosphorus content; * Soil.AK: soil available potassium content; * Soil.PC1: The first principal component of soil properties; * Soil.PC2: The second principal component of soil properties; * Soil.PC3: The third principal component of soil properties; * sample.2016: The date of fist sampling; * sample.2021: The date of second sampling; * year: the number of years between two samplings. #### File: Models-LMM.r **Description:** R code for linear mixed-effects models (LMMs) of the focal individuals. #### File: Significant interactive effect.R **Description:** The code for significant interactive effect analysis in the linear mixed-effects models (LMMs) at 20 m spatial scale. #### File: Phylogenetic tree.nwk **Description:** The maximum likelihood tree in the study. #### File: Sequences for phylogenetic tree.nex **Description:** The DNA sequences metrix of coding sequences, which was used for phylogenegtic tree construction. #### File: Sequences ID-species latin.xlsx **Description:** The species latin and genebank ID of DNA sequences. #### File: Simple sequence repeats allele data.xlsx **Description:** The allele data used for caculating the genetic distance of between *Pometia pinnata* individuals. * Tag: Individual ID of each individual; * PR11-1,PR11-2: Co-dominant marker values of the primer PR11 of microsatellite loci; * PR22-1,PR22-2: Co-dominant marker values of the primer PR22 of microsatellite loci; * PR26-1,PR26-2: Co-dominant marker values of the primer PR26 of microsatellite loci; * PR34-1,PR34-2: Co-dominant marker values of the primer PR34 of microsatellite loci; * PR75-1,PR75-2: Co-dominant marker values of the primer PR75 of microsatellite loci; * PR80-1,PR80-2: Co-dominant marker values of the primer PR80 of microsatellite loci; * PR91-1,PR91-2: Co-dominant marker values of the primer PR91 of microsatellite loci; * PR93-1,PR93-2: Co-dominant marker values of the primer PR93 of microsatellite loci; * PR95-1,PR95-2: Co-dominant marker values of the primer PR95 of microsatellite loci; ## Code/software 1 SOFTWARE: R-4.0.2 is needed to view your data.Download and install R online([https://www.r-project.org/](https://www.r-project.org/)). 2 PACKAGES: install.packages("tidyverse") library(tidyverse) \# Fit model install.packages("lmerTest") library(lmerTest) \#calculate the R^2 for linear mixed models. install.packages("MuMIn") library(MuMIn) \#Determination of the relative importance of collinear predictors (i.e. fixed effects) to response variables install.packages("glmm.hp") library(glmm.hp) \#Create graphics install.packages(c("sjPlot", "ggplot2")) library(sjPlot) library(ggplot2) \#Arrange plots into a grid and adding labels to them library(cowplot)