Functional genomics and co-occurrence in a diverse tropical tree genus: The roles of drought and defense related genes
Data files
Jan 04, 2024 version files 44.58 KB
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defense_and_drought_gene_data.zip
5.59 KB
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Ficus13.tre
449 B
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gene.data.zip
21.41 KB
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gene.proportion.csv
424 B
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README.md
4.52 KB
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Schoener.zip
3.65 KB
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soil.3hab.csv
8.53 KB
Abstract
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.
README: Functional genomics and co-occurrence in a diverse tropical tree genus: The roles of drought- and defense-related genes
https://doi.org/10.5061/dryad.kprr4xhbf
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.
Methods
In this work, we utilized a community transcriptomics workflow to assess the functional similarity of co-occurring 13 Ficus 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 Ficus tree species. Then we performed functional phylogenomic inference using the techniques and tools that recently published in the Yang et al. (2015), and then estimated the homologous functional gene trees of Ficus 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.