Phylogenetic signal detection from an ancient rapid radiation: Effects of noise reduction, long- branch attraction, and model selection in crown clade Apocynaceae

Crown clade Apocynaceae comprise seven primary lineages of lianas, shrubs, and herbs with a diversity of pollen aggregation morphologies including monads, tetrads, and pollinia, making them an ideal group for investigating the evolution and function of pollen packaging. Traditional molecular systematic approaches utilizing small amounts of sequence data have failed to resolve relationships along the spine of the crown clade, a likely ancient rapid radiation. The previous best estimate of the phylogeny was a five-way polytomy, leaving ambiguous the homology of aggregated pollen in two major lineages, the Periplocoideae, which possess pollen tetrads, and the milkweeds (Secamonoideae plus Asclepiadoideae), which possess pollinia. To assess whether greatly increased character sampling would resolve these relationships, a plastome sequence data matrix was assembled for 13 Apocynaceae taxa, including nine newly generated complete plastomes, one partial new plastome, and three previously reported plastomes, collectively representing all primary crown clade lineages and outgroups. The effects of phylogenetic noise, long-branch attraction, and model selection (linked versus unlinked branch lengths among data partitions) were evaluated in a hypothesis-testing framework based on Shimodaira-Hasegawa tests. Discrimination among alternative crown clade resolutions was affected by all three factors. Exclusion of the noisiest alignment positions and topologies influenced by long-branch attraction resulted in a trichotomy along the spine of the crown clade consisting of Rhabdadenia + the Asian clade, Baisseeae + milkweeds, and Periplocoideae + the New World clade. Parsimony reconstruction on all optimal topologies after noise exclusion unambiguously supports parallel evolution of aggregated pollen in Periplocoideae (tetrads) and milkweeds (pollinia). Our phylogenomic approach has greatly advanced the resolution of one of the most perplexing radiations in Apocynaceae, providing the basis for study of convergent floral morphologies and their adaptive value.

夹竹桃科冠群（Crown clade Apocynaceae）包含藤本、灌木和草本共7个主要支系，其花粉聚集形态多样，涵盖单粒花粉（monads）、四分体花粉（tetrads）与花粉块（pollinia），是研究花粉包装演化与功能的理想类群。传统分子系统学研究方法仅采用少量序列数据，未能厘清该冠群核心支系的系统发育关系——该支系疑似经历过一次古老快速辐射演化事件。此前最优的系统发育估计结果为五歧多歧支，导致两大支系的聚集花粉同源性无法明确：一类是具四分体花粉的杠柳亚科（Periplocoideae），另一类是具花粉块的马利筋类群（鲫鱼藤亚科（Secamonoideae）+马利筋亚科（Asclepiadoideae））。为评估大幅增加性状采样能否厘清这些系统发育关系，研究团队针对13个夹竹桃科类群构建了质体基因组（plastome）序列数据矩阵，其中包含9个新测序获得的完整质体基因组、1个新测序的部分质体基因组，以及3个已发表的质体基因组，类群覆盖了冠群所有主要支系与外类群（outgroups）。研究基于岛田-长谷川检验（Shimodaira-Hasegawa tests）的假设检验框架，评估了系统发育噪音、长枝吸引（long-branch attraction）以及模型选择（数据分区间分支长度的连锁与非连锁模式）对系统发育分析的影响。结果显示，这三个因素均会影响不同冠群拓扑结构的分辨能力。剔除噪音最高的比对位点以及排除受长枝吸引影响的拓扑结构后，冠群核心支系形成三歧支：棒腺藤属（Rhabdadenia）+亚洲支系、贝赛族（Baisseeae）+马利筋类群，以及杠柳亚科+新世界支系。对噪音剔除后所有最优拓扑结构进行简约法重建（parsimony reconstruction），结果明确支持杠柳亚科的四分体花粉与马利筋类群的花粉块存在平行演化。本系统基因组学研究极大推进了夹竹桃科最棘手的辐射演化事件之一的分辨率，为后续研究趋同花部形态及其适应价值奠定了基础。