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

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.