Data from: Transcriptome sequencing reveals genome-wide variation in molecular evolutionary rate among ferns

Background: Transcriptomics in non-model plant systems has recently
reached a point where the examination of nuclear genome-wide patterns in
understudied groups is an achievable reality. This progress is especially
notable in evolutionary studies of ferns, for which molecular resources to
date have been derived primarily from the plastid genome. Here, we utilize
transcriptome data in the first genome-wide comparative study of molecular
evolutionary rate in ferns. We focus on the ecologically diverse family
Pteridaceae, which comprises about 10 % of fern diversity and includes the
enigmatic vittarioid ferns—an epiphytic, tropical lineage known for
dramatically reduced morphologies and radically elongated phylogenetic
branch lengths. Using expressed sequence data for 2091 loci, we perform
pairwise comparisons of molecular evolutionary rate among 12 species
spanning the three largest clades in the family and ask whether previously
documented heterogeneity in plastid substitution rates is reflected in
their nuclear genomes. We then inquire whether variation in evolutionary
rate is being shaped by genes belonging to specific functional categories
and test for differential patterns of selection. Results: We find
significant, genome-wide differences in evolutionary rate for vittarioid
ferns relative to all other lineages within the Pteridaceae, but we
recover few significant correlations between faster/slower vittarioid loci
and known functional gene categories. We demonstrate that the faster rates
characteristic of the vittarioid ferns are likely not driven by positive
selection, nor are they unique to any particular type of nucleotide
substitution. Conclusions: Our results reinforce recently reviewed
mechanisms hypothesized to shape molecular evolutionary rates in
vittarioid ferns and provide novel insight into substitution rate
variation both within and among fern nuclear genomes.