DOI: 10.5061/dryad.717vp
title: Data from: The effects of recombination, mutation and selection on the evolution of the Rp1 resistance genes in grasses

description: Plant immune genes, or resistance genes, are involved in a co-evolutionary
 arms race with a diverse range of pathogens. In agronomically important
 grasses, such R genes have been extensively studied because of their role
 in pathogen resistance and in the breeding of resistant cultivars. In this
 study, we evaluate the importance of recombination, mutation and selection
 on the evolution of the R gene complex Rp1 of Sorghum, Triticum,
 Brachypodium, Oryza and Zea. Analyses show that recombination is
 widespread, and we detected 73 independent instances of sequence exchange,
 involving on average 1567 of 4692 nucleotides analysed (33.4%). We were
 able to date 24 interspecific recombination events and found that four
 occurred postspeciation, which suggests that genetic introgression took
 place between different grass species. Other interspecific events seemed
 to have been maintained over long evolutionary time, suggesting the
 presence of balancing selection. Significant positive selection (i.e. a
 relative excess of nonsynonymous substitutions (dN/dS&gt;1)) was
 detected in 17–95 codons (0.42–2.02%). Recombination was significantly
 associated with areas with high levels of polymorphism but not with an
 elevated dN/dS ratio. Finally, phylogenetic analyses show that
 recombination results in a general overestimation of the divergence time
 (mean = 14.3%) and an alteration of the gene tree topology if the tree is
 not calibrated. Given that the statistical power to detect recombination
 is determined by the level of polymorphism of the amplicon as well as the
 number of sequences analysed, it is likely that many studies have
 underestimated the importance of recombination relative to the mutation
 rate.
description: Maximum clade
 credibility trees using the total alignement with no priors on divergence
 times.Maximum clade
 credibility trees using the total alignment with no priors on divergence
 times. Trees were inferred using BEAST v1.62. Estimated ages of divergence
 are depicted in bold and posterior probabilities in italic. Abbreviations,
 Sb: Sorghum bicolor, Ta1 and Ta2: Triticum aestivum, Bd: Brachypodium
 distachyon.no_date_allMaximum clade credibility trees using the truncated alignment with no priors on divergence times.Maximum clade credibility trees using the truncated alignment with no priors on divergence times. Trees were inferred using BEAST v1.62. Estimated ages of divergence are depicted in bold and posterior probabilities in italic. Abbreviations, Sb: Sorghum bicolor, Ta1 and Ta2: Triticum aestivum, Bd: Brachypodium distachyon.no_date_without_blocksMaximum clade credibility trees using the total alignment as well as fossil calibrationsMaximum clade credibility trees using the total alignment as well as fossil calibrations. Trees were inferred using BEAST v1.62. Estimated ages of divergence are depicted in bold and posterior probabilities in italic. Abbreviations, Sb: Sorghum bicolor, Ta1 and Ta2: Triticum aestivum, Bd: Brachypodium distachyon.calibration_allMaximum clade credibility trees using the truncated alignment as well as fossil calibrations.Maximum clade credibility trees using the truncated alignment as well as fossil calibrations. Trees were inferred using BEAST v1.62. Estimated ages of divergence are depicted in bold and posterior probabilities in italic. Abbreviations, Sb: Sorghum bicolor, Ta1 and Ta2: Triticum aestivum, Bd: Brachypodium distachyon.calibration_without_blocksTotal alignment of Rp1 sequences from the 5 Poaceae genera used in this study.This alignment was used to construct phylogenetic trees with and without calibration points and evaluate the incidence of recombination.whole_sequences_alignment.fasTruncated alignment of Rp1 sequences from the 5 Poaceae genera used in this study.This alignment was used to construct phylogenetic trees with and without calibration points and to test for a correlation between positively-selected amino-acids and the incidence of recombination.without_blocks_alignment.fas