DOI: 10.5061/dryad.v0rp5
title: Data from: Transcriptomic responses to conspecific and congeneric competition in co-occurring Trifolium

description: Species coexistence requires differential response to inter- and
 intraspecific competition, typically conceptualized as niche
 differentiation. Coexistence of close relatives therefore poses an
 interesting scenario with regards to niche differentiation since these
 species generally have many traits in common due to shared ancestry.
 Native Californian Trifolium assemblages are locally diverse and represent
 a unique system for understanding competitive interactions among close
 relatives. We conducted two similar greenhouse studies in which Trifolium
 fucatum was grown alone, with a conspecific competitor, and with a
 congeneric competitor (Trifolium macraei). In the first study, we assessed
 biomass production in T. fucatum, and in the second study we conducted an
 RNAseq analysis of T. fucatum roots to test for differentially expressed
 genes that may mediate competitive interactions and potentially
 coexistence. Compared to plants grown alone, competition (i.e. growth in
 the same pot) with a conspecific resulted in a greater reduction in
 biomass than competition with a congener, as predicted by theory. However,
 competition with a congener resulted in twice as many differentially
 expressed genes as competition with a conspecific. Annotations of
 identified genes differentiating congeneric from conspecific competition
 suggest several functions attributed to interactions with third-party
 organisms, including nodulation with rhizobial mutualists, and defence
 responses against pathogens and herbivores. In addition, salt-responsive
 genes and an iron transporter were differentially expressed in congeneric
 competition, and comparisons of sodium and iron concentrations in field
 soils where these species are found showed that T. fucatum occurs in
 higher sodium and iron microsites than T. macraei. Thus, the transcriptome
 highlighted abiotic niche axes worth pursuing in future ecological
 experiments as potential mediators of coexistence. We also found a subset
 of genes that responded similarly to both congeneric and conspecific
 competition in both direction and magnitude, indicating some conserved
 responses to competition, regardless of neighbour identity. Synthesis.
 Transcriptomic analyses represent novel tools for identifying the
 molecular mechanisms underlying interactions among species. Working
 iteratively with ecological experimentation and observation,
 transcriptomes may allow us to identify novel dimensions of the
 n-dimensional niche that determine species’ distributions and their
 ability to coexist.
description: Trifolium field
 co-occurrence datacsv file of occurrence
 values for T. fucatum and T. macraei at Bodega Bay,
 Californiafield_occurrence_data.csvTrifolium greenhouse competition datacsv file of plant growth data for Trifolium fucatum and Trifolium macraei in greenhouse competition experimentcompetition_data.csvRNAseq analysis scriptszip archive of scripts used to assemble de novo transcriptome of Trifolium fucatum and assess differential expressionTfuc-competition-rnaseq-denovo-master-8c96c40f524188a48db32adec3ae7cf58f4988b5.zip