Functional genomics and co-occurrence in a diverse tropical tree genus: The roles of drought and defense related genes

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 fin..., 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..., , # 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 Ficu...