Data from: Multilocus analyses reveal little evidence for lineage wide adaptive evolution within major clades of soft pines (Pinus subgenus Strobus)

Estimates from molecular data for the fraction of new nonsynonymous
mutations that are adaptive vary strongly across plant species. Much of
this variation is due to differences in life-history strategies as they
influence the effective population size (Ne). Ample variation for these
estimates, however, remains even when comparisons are made across species
with similar values of Ne. An open question thus remains as to why the
large disparity for estimates of adaptive evolution exists among plant
species. Here, we have estimated the distribution of deleterious fitness
effects (DFE) and the fraction of adaptive nonsynonymous substitutions (α)
for 11 species of soft pines (subgenus Strobus) using DNA sequence data
from 167 orthologous nuclear gene fragments. Most newly arising
nonsynonymous mutations were inferred to be so strongly deleterious that
they would rarely become fixed. Little evidence for long-term adaptive
evolution was detected, as all 11 estimates for α were not significantly
different from zero. Nucleotide diversity at synonymous sites, moreover,
was strongly correlated with attributes of the DFE across species, thus
illustrating a strong consistency with the expectations from the Nearly
Neutral Theory of molecular evolution. Application of these patterns to
genome-wide expectations for these species, however, was difficult as the
loci chosen for analysis were a biased set of conserved loci which greatly
influenced estimates of the DFE and α. This implies that genome-wide
parameter estimates will need truly genome-wide data, so that many of
existing patterns documented previously for forest trees (e.g. little
evidence for signature of selection) may need revision.