Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada.
UBC Botanical Garden & Centre for Plant Research, University of British Columbia, 6804 Marine Drive SW, Vancouver, BC, V6T 1Z4, Canada.
Cladistics. 2020 Oct;36(5):481-504. doi: 10.1111/cla.12417. Epub 2020 Jun 17.
We used a bi-organellar phylogenomic approach to address higher-order relationships in Pandanales, including the first molecular phylogenetic study of the panama-hat family, Cyclanthaceae. Our genus-level study of plastid and mitochondrial gene sets includes a comprehensive sampling of photosynthetic lineages across the order, and provides a framework for investigating clade ages, biogeographic hypotheses and organellar molecular evolution. Using multiple inference methods and both organellar genomes, we recovered mostly congruent and strongly supported relationships within and between families, including the placement of fully mycoheterotrophic Triuridaceae. Cyclanthaceae and Pandanaceae plastomes have slow substitution rates, contributing to weakly supported plastid-based relationships in Cyclanthaceae. While generally slowly evolving, mitochondrial genomes exhibit sporadic rate elevation across the order. However, we infer well-supported relationships even for slower evolving mitochondrial lineages in Cyclanthaceae. Clade age estimates across photosynthetic lineages are largely consistent with previous studies, are well correlated between the two organellar genomes (with slightly younger inferences from mitochondrial data), and support several biogeographic hypotheses. We show that rapidly evolving non-photosynthetic lineages may bias age estimates upwards at neighbouring photosynthetic nodes, even using a relaxed clock model. Finally, we uncovered new genome structural variants in photosynthetic taxa at plastid inverted repeat boundaries that show promise as interfamilial phylogenetic markers.
我们采用双细胞器系统发育方法来解决 Pandanales 目中的高级分类关系，包括对巴拿马草帽科 Cyclanthaceae 的首次分子系统发育研究。我们对质体和线粒体基因集的属级研究包括对该目中所有光合谱系的全面采样，为研究进化枝年龄、生物地理假说和细胞器分子进化提供了框架。使用多种推断方法和两个细胞器基因组，我们在科内和科间恢复了大多数一致且得到强烈支持的关系，包括完全菌根异养的 Triuridaceae 的位置。Cyclanthaceae 和 Pandanaceae 的质体基因组具有较慢的替换率，导致 Cyclanthaceae 中基于质体的关系支持较弱。虽然线粒体基因组通常进化缓慢，但在整个目中存在零星的速率升高。然而，即使在 Cyclanthaceae 中进化较慢的线粒体谱系中，我们也推断出得到很好支持的关系。在光合谱系中，进化枝年龄估计与先前的研究基本一致，在两个细胞器基因组之间具有很好的相关性（线粒体数据的推断稍年轻），并支持几个生物地理假说。我们表明，即使使用松弛时钟模型，快速进化的非光合谱系也可能使相邻光合节点的年龄估计向上偏。最后，我们在质体反向重复边界处发现了光合作用分类群中的新基因组结构变体，这些变体有望成为种间系统发育标记。
