DOI: 10.6086/d1v68x
title: Evolution of specialization in a plant-microbial mutualism is explained by the oscillation theory of speciation

description: This is a compilation of the different sets of data that were gathered and
 analyzed to understand the evolution of plant-microbial mutualisms in a
 genus of native legumes in California (Acmispon) described in the paper:
 "Torres-Martínez L, Porter SS, Wendlandt CE, Purcell J, Ortiz-Barbosa
 GS, Rothschild J, Lampe M, Warisha F, Le T, Weisberg AJ, Chang JH, Sachs
 JL. Evolution of specialization in a plant-microbial mutualism is
 explained by the oscillation theory of speciation. Evolution. 2021 Mar 30.
 doi: 10.1111/evo.14222". Here we use a multidisciplinary approach
 were niche modeling, phylogenetic approaches and a manipulative green
 house experiment were implemented to test two specific hypothesis on the
 evolution of specialization: whether generalist interactions evolve to
 become more specialized or if partner switches evolve without any change
 in niche breadth. First, we assesed the rhizobia taxa that associate with
 Acmispon spp in nature by performing field collections of root
 nodules,bacteria isolation in cultures and subsequent sequencing to
 identify the genus of each isolate. Then, to evaluate how symbiont
 specificity has evolved within the genus we reconstructed the phylogeny of
 Acmispon using available sequence data and performed ancestral trait
 reconstruction ("SymbiontSpecificity"). Second, we collected and
 genotyped multiple maternal lines of two sister Acmispon spp
 ("RADseq"), A. strigosus and A. wrangelianus, within their
 California range and evaluated phylogenetic relationships among the
 different lines to test for phylogenetic signal on symbiosis specificity.
 Third, to gather information on symbiosis specificity of the two sister
 species to their mutualist partners ("SymbiosisTraitData") we
 performed a reciprocal inoculation experiment where rhizobial strains of
 the Bradyrhizobium genus and that associate with A. strigosus in nature
 were inoculated to multiple maternal lines of both A. strigosus and A.
 wrangelianus under controlled green house conditions. Strains of the
 Mesorhizobium genus and that associate with A. wrangelianus in nature were
 also inoculated in the same maternal lines of both host species. Multiple
 symbiosis traits were measured to asses specificity, including the
 probability of nodulation, the number of nodules formed, the investment
 into nodulation and the relative host growth. Lastly, we evaluated the
 levels of specialization of the two Acmispon host species along two
 abiotic niche axis ("Niche Modelling"), climatic and edaphic. We
 extracted climatic and soil data from occurrence records of the species
 and performed a principal component analysis to estimate the environmental
 space that the species occupy. The main outcomes of these analyses were:
 1) Most Acmispon spp exclusivery associate with one genus of rhizobia, but
 some exceptions exist and switches only occurred between Mesorhizobium and
 Bradyrhizobium and no other rhizobial genus. 2) A. strigosus and A.
 wrangelianus retain the ability to associate with ancestral rhizobial
 partner taxa, although this trend was not phylogenetically conserved
 across genotypes. Instead, genetic variation in specificity traits was
 observed within each host species. 3) A. strigosus genotypes tended to be
 more generalists than A. wrangelianus genotypes, suggesting asymetry along
 the mutualist niche. 4) Niche breadth of the climatic and edaphic axes was
 also broader in A. strigosus than A. wrangelianus. Together these
 findings, supported the oscillation mode of specialization.
description: The field collections of the rhizobial partners of
 <em>Acmispon spp</em> were performed across California at
 multiple UC Reserves over the spring of 2019 (February-March). The RADseq
 data was obtained from maternal lines grown under green house conditions.
 Library preparation was done in the laboratory of Dr. Jessica Purcel at
 the University of California, Riverside. Library sequencing was performed
 at UC Berkeley. Data analyses of RADseq reads were performed using Stacks.
 Trait data was analyzed through a series of generalized linear mixed
 models in R. For specific details about the methods implemented for each
 each data set please refer to the published manuscript in
 Evolution.
description: A general README file contains a comprehensive explanation for
 the data. For each folder you will find the associated R codes implemented
 to analyze the described datasets and a README file explaining the
 contents of each file. Specific details of the analyses can be found
 inside each R code. Missing data was coded as "NA".
 Information on how the trait measurements were done can be found
 in the associated manuscript referenced above. To obtain the sequence data
 for the host genotypes please visit the NCBI BioProjectID: PRJNA663103.
 The sequences implemented to identify the rhizobial isolates can be found
 at the NCBI, BankIt2430228: MW625102 - MW625375.