Data from: 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 taxa of Apocynaceae, 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7个主要支系，涵盖藤本、灌木与草本类群，其花粉聚集形态多样，包含单粒花粉（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。传统利用少量序列数据的分子系统学研究手段，未能解析该冠群核心支系的演化关系——这被推测为一次古老的快速辐射演化事件。此前最完善的系统发育估算结果为五歧分结，导致两个主要支系的聚集花粉同源性难以判定：一是具有四分体花粉的杠柳亚科（Periplocoideae），二是具有花粉块的马利筋类群（包含鲫鱼藤亚科（Secamonoideae）与马利筋亚科（Asclepiadoideae））。为评估大幅增加性状采样量能否解析此类演化关系，研究人员针对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个新测得的完整质体基因组、1个新测得的部分质体基因组，以及3个已发表的质体基因组，覆盖了冠群所有主要支系与外类群。本研究基于Shimodaira-Hasegawa检验（Shimodaira–Hasegawa tests）的假设检验框架，评估了系统发育噪声、长枝吸引（long-branch attraction）以及模型选择（数据分区间分支长度关联与非关联模式）对系统发育分析的影响。上述三类因素均会影响不同冠群演化关系假说的分辨能力。去除噪声最高的比对位点以及受长枝吸引干扰的拓扑结构后，冠群核心支系的演化关系被解析为三歧分结：分别为棒腺藤属（Rhabdadenia）+ 亚洲支系、拜塞族（Baisseeae）+ 马利筋类群，以及杠柳亚科（Periplocoideae）+ 新世界支系。在去除噪声后的所有最优拓扑结构上进行简约法重建，结果明确支持杠柳亚科（四分体花粉）与马利筋类群（花粉块）的聚集花粉性状为平行演化而来。本系统发育基因组学研究极大提升了夹竹桃科中最棘手的辐射演化事件之一的解析度，为后续研究趋同花部形态及其适应价值奠定了基础。