Three genome-based phylogeny of Cupressaceae s.l.: Further evidence for the evolution of gymnosperms and Southern Hemisphere biogeography

Phylogenetic information is essential to interpret the evolution of species. While DNA sequences from different genomes have been widely utilized in phylogenetic reconstruction, it is still difficult to use nuclear genes to reconstruct phylogenies of plant groups with large genomes and complex gene families, such as gymnosperms. Here, we use two single-copy nuclear genes, together with chloroplast and mitochondria] genes, to reconstruct the phylogeny of the ecologically-important conifer family Cupressaceae s.l., based on a complete sampling of its 32 genera. The different gene trees generated are highly congruent in topology, supporting the basal position of Cunninghamia and the seven-subfamily classification, and the estimated divergence times based on different datasets correspond well with each other and with the oldest fossil record. These results imply that we have obtained the species phylogeny of Cupressaceae s.l. In addition, possible origins of all three polyploid conifers were investigated, and a hybrid origin was suggested for Cupressus, Fitzroya and Sequoia. Moreover, we found that the biogeographic history of Cupressaceae s.l. is associated with the separation between Laurasia and Gondwana and the further break-up of the latter. Our study also provides new evidence for the gymnosperm phylogeny. (C) 2012 Elsevier Inc. All rights reserved.

系统发育信息对于解释物种的进化至关重要。虽然来自不同基因组的DNA序列已广泛用于系统发育重建，但对于具有大基因组和复杂基因家族的植物类群（如裸子植物），利用核基因重建系统发育仍然困难。在此，我们使用两个单拷贝核基因，连同叶绿体和线粒体基因，基于对柏科（广义）32个属的完整取样，重建在生态上具有重要意义的柏科（广义）的系统发育。所生成的不同基因树在拓扑结构上高度一致，支持杉木属的基部位置以及七个亚科的分类，并且基于不同数据集估计的分化时间相互吻合良好，且与最古老的化石记录相符。这些结果意味着我们已经获得了柏科（广义）的物种系统发育。此外，对所有三种多倍体针叶树可能的起源进行了研究，并提出柏木属、智利柏属和红杉属为杂交起源。而且，我们发现柏科（广义）的生物地理历史与劳亚大陆和冈瓦纳大陆的分离以及冈瓦纳大陆随后的进一步分裂有关。我们的研究也为裸子植物的系统发育提供了新的证据。（C）2012爱思唯尔公司。保留所有权利。