DOI: 10.5061/dryad.d143r
title: Data from: Correlation between sequence divergence and polymorphism reveals similar evolutionary mechanisms acting across multiple timescales in a rapidly evolving plastid genome

description: Background: Although the plastid genome is highly conserved across most
 angiosperms, multiple lineages have increased rates of structural
 rearrangement and nucleotide substitution. These lineages exhibit an
 excess of nonsynonymous substitutions (i.e., elevated dN/dS ratios) in
 similar subsets of plastid genes, suggesting that similar mechanisms may
 be leading to relaxed and/or positive selection on these genes. However,
 little is known regarding whether these mechanisms continue to shape
 sequence diversity at the intraspecific level. Results: We examined
 patterns of interspecific divergence and intraspecific polymorphism in the
 plastid genome of Campanulastrum americanum, and across plastid genes
 found a significant correlation between dN/dS and pN/pS (i.e., the
 within-species equivalent of dN/dS). A number of genes including ycf1,
 ycf2, clpP, and ribosomal protein genes exhibited high dN/dS ratios.
 McDonald-Kreitman tests detected little evidence for positive selection
 acting on these genes, likely due to the presence of substantial
 intraspecific divergence. Large-scale structural variation was also
 observed between populations. Conclusions: These results suggest that
 mechanisms leading to structural rearrangements and increased nucleotide
 substitution rates in the plastid genome are continuing to act at the
 intraspecific level. Accelerated plastid genome evolution may increase the
 likelihood of intraspecific cytonuclear genetic incompatibilities, and
 thereby contribute to the early stages of the speciation process.
 Background: Although the plastid genome is highly conserved across most
 angiosperms, multiple lineages have increased rates of structural
 rearrangement and nucleotide substitution. These lineages exhibit an
 excess of nonsynonymous substitutions (i.e., elevated dN/dS ratios) in
 similar subsets of plastid genes, suggesting that similar mechanisms may
 be leading to relaxed and/or positive selection on these genes. However,
 little is known regarding whether these mechanisms continue to shape
 sequence diversity at the intraspecific level. Results: We examined
 patterns of interspecific divergence and intraspecific polymorphism in the
 plastid genome of Campanulastrum americanum, and across plastid genes
 found a significant correlation between dN/dS and pN/pS (i.e., the
 within-species equivalent of dN/dS). A number of genes including ycf1,
 ycf2, clpP, and ribosomal protein genes exhibited high dN/dS ratios.
 McDonald-Kreitman tests detected little evidence for positive selection
 acting on these genes, likely due to the presence of substantial
 intraspecific divergence. Large-scale structural variation was also
 observed between populations. Conclusions: These results suggest that
 mechanisms leading to structural rearrangements and increased nucleotide
 substitution rates in the plastid genome are continuing to act at the
 intraspecific level. Accelerated plastid genome evolution may increase the
 likelihood of intraspecific cytonuclear genetic incompatibilities, and
 thereby contribute to the early stages of the speciation process.
description: SingleGeneAlignmentsContains four species single gene alignments used for the M-K tests in the manuscript.PAMLInputFilesContains the codeml.ctl text files and tree files used to run the PAML analyses.PAMLOutputFilesContains the output text files for the PAML analyses.PAMLAlignmentsclpP full and partial duplicationPhylip alignment of the full clpP coding sequence for Campanulastrum americanum as well as the partial duplication of the first exon.clpPAlignment.phy