Phylogeny and divergence times of gymnosperms inferred from single-copy nuclear genes.

Phylogenetic reconstruction is fundamental to study evolutionary biology and historical biogeography. However, there was not a molecular phylogeny of gymnosperms represented by extensive sampling at the genus level, and most published phylogenies of this group were constructed based on cytoplasmic DNA markers and/or the multi-copy nuclear ribosomal DNA. In this study, we use LFY and NLY, two single-copy nuclear genes that originated from an ancient gene duplication in the ancestor of seed plants, to reconstruct the phylogeny and estimate divergence times of gymnosperms based on a complete sampling of extant genera. The results indicate that the combined LFY and NLY coding sequences can resolve interfamilial relationships of gymnosperms and intergeneric relationships of most families. Moreover, the addition of intron sequences can improve the resolution in Podocarpaceae but not in cycads, although divergence times of the cycad genera are similar to or longer than those of the Podocarpaceae genera. Our study strongly supports cycads as the basal-most lineage of gymnosperms rather than sister to Ginkgoaceae, and a sister relationship between Podocarpaceae and Araucariaceae and between Cephalotaxaceae-Taxaceae and Cupressaceae. In addition, intergeneric relationships of some families that were controversial, and the relationships between Taxaceae and Cephalotaxaceae and between conifers and Gnetales are discussed based on the nuclear gene evidence. The molecular dating analysis suggests that drastic extinctions occurred in the early evolution of gymnosperms, and extant coniferous genera in the Northern Hemisphere are older than those in the Southern Hemisphere on average. This study provides an evolutionary framework for future studies on gymnosperms.

系统发育重建对于研究进化生物学和历史生物地理学至关重要。然而，此前并没有一个在属水平上广泛取样的裸子植物分子系统发育树，而且该类群大多数已发表的系统发育树是基于细胞质DNA标记和/或多拷贝核核糖体DNA构建的。在本研究中，我们利用LFY和NLY这两个源于种子植物祖先一次古老基因复制的单拷贝核基因，基于对现存属的完整取样来重建裸子植物的系统发育并估计其分化时间。结果表明，LFY和NLY编码序列的组合能够解决裸子植物的科间关系以及大多数科的属间关系。此外，内含子序列的加入能够提高罗汉松科的分辨率，但对苏铁科却没有作用，尽管苏铁属的分化时间与罗汉松科属的分化时间相近或更长。我们的研究有力地支持苏铁是裸子植物最基部的谱系，而不是银杏科的姐妹群，并且支持罗汉松科和南洋杉科之间以及三尖杉科 - 红豆杉科和柏科之间的姐妹关系。此外，基于核基因证据讨论了一些存在争议的科的属间关系，以及红豆杉科和三尖杉科之间以及针叶树和买麻藤目之间的关系。分子测年分析表明，裸子植物在早期进化过程中发生了剧烈的灭绝，并且北半球现存的针叶树属平均比南半球的更古老。本研究为未来裸子植物的研究提供了一个进化框架。