The majority of variation in rates of molecular evolution among seed plants remains both unexplored and unexplained.
Although some attention has been given to flowering plants, reports of molecular evolutionary rates for their sister plant
clade (gymnosperms) are scarce, and to our knowledge differences in molecular evolution among seed plant clades have
never been tested in a phylogenetic framework. Angiosperms and gymnosperms differ in a number of features, of which
contrasting reproductive biology, life spans, and population sizes are the most prominent. The highly conserved morphology
of gymnosperms evidenced by similarity of extant species to fossil records and the high levels of macrosynteny at
the genomic level have led scientists to believe that gymnosperms are slow-evolving plants, although some studies have
offered contradictory results. Here, we used 31,968 nucleotide sites obtained from orthologous genes across a wide
taxonomic sampling that includes representatives of most conifers, cycads, ginkgo, and many angiosperms with a
sequenced genome. Our results suggest that angiosperms and gymnosperms differ considerably in their rates of molecular
evolution per unit time, with gymnosperm rates being, on average, seven times lower than angiosperm species.
Longer generation times and larger genome sizes are some of the factors explaining the slow rates of molecular evolution
found in gymnosperms. In contrast to their slow rates of molecular evolution, gymnosperms possess higher substitution
rate ratios than angiosperm taxa. Finally, our study suggests stronger and more efficient purifying and diversifying
selection in gymnosperm than in angiosperm species, probably in relation to larger effective population sizes.