DOI: 10.5061/dryad.kprr4xhbf
title: Functional genomics and co-occurrence in a diverse tropical tree genus: The roles of drought and defense related genes

description: Tropical tree communities are among the most diverse in the world. A small
 number of genera often disproportionately contribute to this diversity.
 How so many species from a single genus can co-occur represents a major
 outstanding question in biology. Niche differences are likely to play a
 major role in promoting congeneric diversity, but the mechanisms of
 interest are often not well-characterized by the set of functional traits
 generally measured by ecologists. To address this knowledge gap,
 we used a functional genomic approach to investigate the mechanisms of
 co-occurrence in the hyper-diverse genus Ficus. Our study focused on over
 800 genes related to drought and defense, providing detailed information
 on how these genes may contribute to the diversity of Ficus
 species. We find widespread and consistent evidence of the
 importance of defense gene dissimilarity in co-occurring species,
 providing genetic support for what would be expected under the
 Janzen-Connell mechanism. We also find that drought-related gene sequence
 similarity is related to Ficus co-occurrence, indicating that similar
 responses to drought promote co-occurrence. We provide the first
 detailed functional genomic evidence of how drought- and defense-related
 genes simultaneously contribute to the local co-occurrence in a
 hyper-diverse genus. Our results demonstrate the potential of community
 transcriptomics to identify the drivers of species co-occurrence in
 hyper-diverse tropical tree genera.
description: In this work, we utilized a community transcriptomics workflow to
 assess the functional similarity of co-occurring 13 <em>Ficus
 </em>species in 20-ha tropical forest dynamics plot in
 Xishuangbanna, Yunnan Province, China. We used a torus-translation test to
 quantify the habitat associations of focal <em>Ficus</em> tree
 species. Then we performed functional phylogenomic inference using the
 techniques and tools that recently published in the Yang <em>et
 al</em>. (2015), and then estimated the homologous functional gene
 trees of <em>Ficus</em> species in the community, in
 particular, the distance separating species in a gene tree represents the
 degree of their functional gene similarity. To investigate whether the
 degree of sequence similarity in drought and defense genes was related to
 the degree of pairwise species co-occurrence in the plot, we conducted a
 statistical approach that involved correlating the genetic distance
 between two species with their co-occurrence at the 20 m × 20 m scale in
 the forest dynamics plot. We used these gene trees to calculate the SES
 value for each 20 X 20 m subplot, and then compared these observed SES
 values to a null distribution to test for significant deviations from
 random co-occurrence patterns. We used a linear model to examine the
 association between the SES value and soil moisture gradient.
description: # Functional genomics and co-occurrence in a diverse tropical tree genus:
 The roles of drought- and defense-related genes
 Functional genomic
 approach to investigate the mechanisms of co-occurrence in the
 hyper-diverse genus *Ficus* in Xishuangbanna tropical forest Yunnan
 Province, China. ## Description of the data and file structure There are
 three documents and three files in this manuscript. (1) The document of
 "defense_and_drought_gene_data.zip" contains the annotated
 defense and drought gene data of focal 13 Ficus. The column name is the
 name of the 13 Ficus species. The row name is the annotated defense and
 drought gene in "defense.gene.csv" and
 "drought.gene.csv" respectively. The value means how many
 annotated genes there are in this species. (2) The document of
 "Schoener.zip" including the observed and a standardized effect
 size (S.E.S.) value of Schoener's index results of the co-occurrence
 of Ficus in the plot. Both files show the species dissimilarity of the
 focal Ficus species. We first quantified the observed co-occurrence of
 species using Schoener's index of co-occurrence, a measure of
 co-occurrence that takes into account both the presence or absence of
 species in each plot and their proportional abundances. We calculated
 observed co-occurrence values at the 20 m × 20 m scale and then compared
 them to a null distribution of 999 values. To generate the null
 distribution, we randomized the community data matrix using the
 independent swap algorithm. We then calculated a standardized effect size
 (S.E.S.) by quantifying the difference between the observed values and the
 mean of the null distribution and dividing this value by the standard
 deviation of the null distribution. Positive S.E.S. values indicate more
 than expected species co-occurrence and negative values indicate less than
 expected species co-occurrence. The values in these files do not have
 units. (3) The document "gene.data.zip" containing the results
 of the Net Relatedness Index (NRI) and Nearest Taxon Index (NTI) of
 defense, drought-related, and other genes. There are 6 files in this
 folder, which are the NRI and NTI results for defense, drought-related,
 and other genes. In each file, "qua" means the plot number.
 "hab.clus" means the habitat types, we have a total of 3 habitat
 types in this study. "ntaxa" means the number of species in that
 plot. "NRI/NTI means the Net Relatedness Index or Nearest Taxon Index
 value of this plot. The values of NRI and NTI do not have units.
 "Type" means the type of defense or drought gene. "the
 null.model" means which null model we used to calculate NRI and NTI.
 NA in these files means that there were few genes annotated in that plot
 and the NRI/NTI value could not be calculated. The plots with missing
 values were not included in the proportion results. (4) The
 "gene.proportion.csv" file contains the proportion data of
 defense, drought-related, and other genes. We selected defense,
 drought-related genes and also randomly selected 1000 homologous genes not
 related to defense or drought, and re-ran all our analyses. We used these
 gene trees to calculate the SES value for each 20 x 20 m subplot, and then
 compared these observed SES values to a null distribution to test for
 significant deviations from random co-occurrence patterns. We calculated
 the proportion of clustering and overdispersion of these 3 types of
 drought, defense, and other genes by NRI and NTI. In these data, including
 the index1, habitat, group and proportion. The index1 means the types of
 genes: drought, defense or other genes. The habitat means the two index of
 NRI and NTI. The group means the clistering or overdispersion of these
 data. The proportion means the calculated value of these kinds. The unit
 of the value in this file is percentage (%). (5) The
 "soil.3hab.csv" file is the average soil water content data in
 the Xishuangbanan Tropical Forest Dynamics plot by 20 X 20 m scale. This
 data includes the plot name, the mean soil water content, and the habitat
 type to which it belongs. The mean soil water content is the percentage of
 water mass to soil mass, so the unit is percentage (%). (6) The file
 "Ficus13.tre" is a maximum likelihood phylogenetic tree of 13
 focal species constructed from genome-wide SNPs. Sharing/Access
 information Transcriptome sequencing data are available in NCBI under
 BioProject ID: PRJNA1045068. ## Code/Software The code for figure 2,
 figure 3 and mantel test in the manuscript.