Brassicales phylogeny inferred from 72 plastid genes: A reanalysis of the phylogenetic localization of two paleopolyploid events and origin of novel chemical defenses
Brassicales phylogeny inferred from 72 plastid genes: A reanalysis of the phylogenetic localization of two paleopolyploid events and origin of novel chemical defenses
复制标题
DOI：
10.1002/ajb2.1040
复制
发表时间：
2018-03-01
影响因子：
3
通讯作者：
Pires, J. Chris
中科院分区：
文献类型：
--
作者：
Edger, Patrick P.;Hall, Jocelyn C.;Pires, J. Chris
研究前提：以前利用分子标记进行的系统发育研究已经对油菜目之间的进化史产生了不同的见解，但许多科之间的关系仍然缺乏支持或尚未解决。最近一种利用1155个核标记的系统转录学方法对17个家族中的14个之间的关系进行了可靠的估计。在这里，我们报告了一个完整的利用叶绿体基因组估计的家族水平的系统发育。方法：我们对分布在所有17个科的物种的72个叶绿体基因的44,926个核苷酸的串联数据集进行了系统发育分析。我们的分析包括了另外三个科，Tovaraceae，Saladoraceae和Setchellanthaceae，这三个科在以前的系统转录研究中被遗漏了。KEY结果：我们的系统发育分析得到了完全解决的估计，并有力地支持了整个Brassicales的所有节点的估计。重要的是，这些发现与系统转录研究中报道的拓扑学是一致的。这种一致性表明，未来的研究可能会利用叶绿体基因组作为标记，解决油菜目中一些出了名的困难分支之间的关系。我们使用这个新的系统发育框架来验证at事件在十字花科起源附近的位置，中位数日期估计在31.8到4280万年前，并将at事件限制在两个节点中的一个节点上，中位数日期估计在8500万到9220万年前。这些事件最终导致了新的化学防御，并与随后的净多样化比率的变化有关。结论：我们预计这些发现将有助于未来在甘蓝类之间的比较进化研究，包括选择全基因组测序项目的候选对象。
PREMISE OF THE STUDY: Previous phylogenetic studies employing molecular markers have yielded various insights into the evolutionary history across Brassicales, but many relationships between families remain poorly supported or unresolved. A recent phylotranscriptomic approach utilizing 1155 nuclear markers obtained robust estimates for relationships among 14 of 17 families. Here we report a complete family-level phylogeny estimated using the plastid genome.METHODS: We conducted phylogenetic analyses on a concatenated data set comprising 44,926 bp from 72 plastid genes for species distributed across all 17 families. Our analysis includes three additional families, Tovariaceae, Salvadoraceae, and Setchellanthaceae, that were omitted in the previous phylotranscriptomic study.KEY RESULTS: Our phylogenetic analyses obtained fully resolved and strongly supported estimates for all nodes across Brassicales. Importantly, these findings are congruent with the topology reported in the phylotranscriptomic study. This consistency suggests that future studies could utilize plastid genomes as markers for resolving relationships within some notoriously difficult clades across Brassicales. We used this new phylogenetic framework to verify the placement of the At- event near the origin of Brassicaceae, with median date estimates of 31.8 to 42.8 million years ago and restrict the At- event to one of two nodes with median date estimates between 85 to 92.2 million years ago. These events ultimately gave rise to novel chemical defenses and are associated with subsequent shifts in net diversification rates.CONCLUSIONS: We anticipate that these findings will aid future comparative evolutionary studies across Brassicales, including selecting candidates for whole-genome sequencing projects.