10.5061/DRYAD.D143R
Barnard-Kubow, Karen B.
University of Virginia
Sloan, Daniel B.
Colorado State University
Galloway, Laura F.
University of Virginia
Data from: Correlation between sequence divergence and polymorphism
reveals similar evolutionary mechanisms acting across multiple timescales
in a rapidly evolving plastid genome
Dryad
dataset
2014
dN/dS
plastid
Campanula americana
Chloroplast
Campanulastrum americanum
2014-12-31T21:30:37Z
2014-12-31T21:30:37Z
en
https://doi.org/10.1186/s12862-014-0268-y
420344 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
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
eastern United States