Data from: Intra-population genomics in a model mutualist: population structure and candidate symbiosis genes under selection in Medicago truncatula

Bottom-up evolutionary approaches, including geographically-explicit
population genomic analyses, have the power to reveal the mechanistic
basis of adaptation. Here we conduct a population genomic analysis in the
model legume, Medicago truncatula, in order to characterize population
genetic structure and identify symbiosis-related genes showing evidence of
spatially-variable selection. Using RAD-seq, we generated over 26,000 SNPs
from 191 accessions from within three regions of the native range in
Europe. Results from STRUCTURE analysis identify 5 distinct genetic
clusters with divisions that separate east and west regions in the
Mediterranean basin. Much of the genetic variation is maintained within
sampling sites, and there is evidence for isolation by distance. Extensive
linkage disequilibrium was identified, particularly within populations. We
conducted genetic outlier analysis with FST-based genome scans and a
bayesian modeling approach (PCAdapt). There were 70 core outlier loci
shared between these distinct methods with one clear candidate symbiosis
related gene, DMI1. This work sets that stage for functional experiments
to determine the important phenotypes that selection has acted upon and
complementary efforts in rhizobium populations.