DOI: 10.5061/dryad.bk3j9kdf9
title: Negotiating mutualism: a locus for exploitation by rhizobia has a broad effect size distribution and context-dependent effects on legume hosts

description: In mutualisms, variation at genes determining partner fitness provides the
 raw material upon which coevolutionary selection acts, setting the
 dynamics and pace of coevolution. However, we know little about variation
 in the effects of genes that underlie symbiotic fitness in natural
 mutualist populations. In some species of legumes that form root nodule
 symbioses with nitrogen-fixing rhizobial bacteria, hosts secrete
 nodule-specific cysteine-rich (NCR) peptides that cause rhizobia to
 differentiate in the nodule environment. However, rhizobia can cleave NCR
 peptides through the expression of genes like the plasmid-borne Host range
 restriction peptidase (hrrP), whose product degrades target NCR peptides.
 Although hrrP activity can confer host exploitation by depressing host
 fitness and enhancing symbiont fitness, the effects of hrrP on symbiosis
 phenotypes depend strongly on the genotypes of the interacting partners.
 However, the effects of hrrP have yet to be characterized in a natural
 population context, so its contribution to variation in wild mutualist
 populations is unknown. To understand the distribution of effects of hrrP
 in wild rhizobia, we measured mutualism phenotypes conferred by hrrP in 12
 wild Ensifer medicae strains. To evaluate context dependency of hrrP
 effects, we compared hrrP effects across two Medicago polymorpha host
 genotypes and across two experimental years for five E. medicae strains.
 We show for the first time in a natural population context that hrrP has a
 wide distribution of effect sizes for many mutualism traits, ranging from
 strongly positive to strongly negative. Furthermore, we show that hrrP
 effect size varies across both host genotype and experiment year,
 suggesting that researchers should be cautious about extrapolating the
 role of genes in natural populations from controlled laboratory studies of
 single genetic variants.
description: We genetically disrupted the <em>hrrP </em>locus in
 12 wild <em>Mesorhizobium</em> strains and inoculated the
 wildtype (hrrP+) and knockout mutant (hrrP-) strains onto a single
 genotype of <em>Medicago polymorpha</em> plants in greenhouse
 conditions. We collected data on the reproductive fitness of the wildtype
 and knockout mutant strains in nodules (2018_knockout_CFU_data.csv) and on
 plant response traits such as shoot mass and nodule count
 (2018_knockout_greenhouse_data.csv). In a second year, we used a subset of
 5 wildtype and knockout mutant strains and inoculated them onto two
 genotypes of <em>M. polymorpha</em> in greenhouse conditions.
 We measured reproductive fitness of rhizobia in nodules
 (2019_GxG_knockout_CFU_data_330plants.csv) and plant response traits
 (2019_GxG_knockout_CFU_data_330plants.csv).
description: We provide four datasets as csv files and one R code file that
 contains code for analyzing the data in these files. See the
 "README" file for metadata for each dataset. The contents of
 each file are as follows: * 2018_knockout_CFU_data.csv
 contains nodule culturing data (counts of colony forming units) from the
 2018 Knockout Experiment *
 2018_knockout_greenhouse_data.csv contains plant harvest data from the
 2018 Knockout Experiment *
 2019_GxG_knockout_CFU_data_330plants.csv contains nodule culturing data
 (counts of colony forming units) from the 2019 GxG Knockout
 Experiment *
 2019_GxG_knockout_greenhouse_data_330plants.csv contains plant harvest
 data from the 2019 GxG Knockout Experiment *
 Wendlandt_et_al_2022_JEvolBiol_code.R contains R code for importing,
 processing, and analyzing data from the above four datasets. It also
 contains code for producing figures from these data.