De La Torre Amanda R, Li Zhen, Van de Peer Yves, Ingvarsson Pär K
Department of Plant Sciences, University of California-Davis, Davis, CA.
Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden.
Mol Biol Evol. 2017 Jun 1;34(6):1363-1377. doi: 10.1093/molbev/msx069.
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.
种子植物分子进化速率的大部分差异仍未得到探索和解释。虽然已经对开花植物给予了一些关注，但关于其姊妹植物类群（裸子植物）分子进化速率的报道却很少，据我们所知，种子植物类群之间分子进化的差异从未在系统发育框架中进行过测试。被子植物和裸子植物在许多特征上存在差异，其中最突出的是生殖生物学、寿命和种群大小的差异。裸子植物高度保守的形态学特征，表现为现存物种与化石记录的相似性以及基因组水平上的高度宏观同线性，这使得科学家们认为裸子植物是进化缓慢的植物，尽管一些研究给出了相互矛盾的结果。在这里，我们使用了从广泛分类取样的直系同源基因中获得的31968个核苷酸位点，该取样包括大多数针叶树、苏铁、银杏的代表以及许多具有测序基因组的被子植物。我们的结果表明，被子植物和裸子植物的单位时间分子进化速率存在显著差异，裸子植物的速率平均比被子植物低七倍。较长的世代时间和较大的基因组大小是解释裸子植物分子进化速率缓慢的一些因素。与它们缓慢的分子进化速率相反，裸子植物的替代率比被子植物类群更高。最后，我们的研究表明，裸子植物中的纯化选择和多样化选择比被子植物更强且更有效，这可能与更大的有效种群大小有关。
