Can functional genomic diversity provide novel insights into mechanisms of community assembly? A pilot study from an invaded alpine streambed.

Hannah E Marx,Franck Delbart,Rolland Douzet,Sébastien Lavergne,Marta Carboni,Christophe Perrier,Wilfried Thuiller,David C Tank

doi:10.1002/ece3.7973

Abstract

An important focus of community ecology, including invasion biology, is to investigate functional trait diversity patterns to disentangle the effects of environmental and biotic interactions. However, a notable limitation is that studies usually rely on a small and easy‐to‐measure set of functional traits, which might not immediately reflect ongoing ecological responses to changing abiotic or biotic conditions, including those that occur at a molecular or physiological level. We explored the potential of using the diversity of expressed genes—functional genomic diversity (FGD)—to understand ecological dynamics of a recent and ongoing alpine invasion. We quantified FGD based on transcriptomic data measured for 26 plant species occurring along adjacent invaded and pristine streambeds. We used an RNA‐seq approach to summarize the overall number of expressed transcripts and their annotations to functional categories, and contrasted this with functional trait diversity (FTD) measured from a suite of characters that have been traditionally considered in plant ecology. We found greater FGD and FTD in the invaded community, independent of differences in species richness. However, the magnitude of functional dispersion was greater from the perspective of FGD than from FTD. Comparing FGD between congeneric alien–native species pairs, we did not find many significant differences in the proportion of genes whose annotations matched functional categories. Still, native species with a greater relative abundance in the invaded community compared with the pristine tended to express a greater fraction of genes at significant levels in the invaded community, suggesting that changes in FGD may relate to shifts in community composition. Comparisons of diversity patterns from the community to the species level offer complementary insights into processes and mechanisms driving invasion dynamics. FGD has the potential to illuminate cryptic changes in ecological diversity, and we foresee promising avenues for future extensions across taxonomic levels and macro‐ecosystems.

Highlights

Species invasions have become an important study system for understanding community assembly (Pearson et al, 2018; Strauss et al, 2006) and eco-evolutionary feedbacks (Colautti et al, 2017; Strauss, 2014), due to the ubiquity, replication, and detailed records of invasions and invaded systems at different scales around the globe (Sax et al, 2007)
For native species shared between the two communities, linear regression was used to test whether changes in measures of differential expression (DE) correlated with the difference in relative abundance of each native species in the invaded community compared with the pristine community
Transcriptomes assembled from RNA-seq data have the capacity to provide a detailed perspective on functional genomic diversity (FGD) by investigating patterns of the number of distinct transcribed genes and their annotations to biologically meaningful functional (GO slim) categories, or the magnitude of differential gene expression

Summary

| INTRODUCTION

Species invasions have become an important study system for understanding community assembly (Pearson et al, 2018; Strauss et al, 2006) and eco-evolutionary feedbacks (Colautti et al, 2017; Strauss, 2014), due to the ubiquity, replication, and detailed records of invasions and invaded systems at different scales around the globe (Sax et al, 2007). We may expect phenotypic convergence between alien and native congeners if communities are assembled through a mechanism of habitat filtering (e.g., pre-adaptation to stress tolerance; Diaz et al, 1998; Keddy, 1992; Li et al, 2018) or a mechanism of self-organized similarity along a niche access that can result from the competition if niche differences are the dominant coexistence mechanism (Scheffer & van Nes, 2006). This leads to the prediction that successful aliens should be functionally similar to the native species. A relationship (positive or negative) between DE and change in relative abundance from the invaded to the pristine community would indicate that variation in FGD resulting from the presence of alien species can shape local native community structure

| MATERIALS AND METHODS

Findings

| DISCUSSION