State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Palaeoenvironment, Chinese Academy of Sciences, No. 39, Beijing Eastroad, Nanjing 210008, China.
Genes (Basel). 2021 Oct 27;12(11):1705. doi: 10.3390/genes12111705.
It is still a challenge to reconstruct the deep phylogenetic relationships within spinicaudatans, and there are several different competing hypotheses regarding the interrelationships among Eocyzicidae, Cyzicidae s. s., Leptestheriidae, and Limnadiidae of the Suborder Spinicaudata. In order to explore the source of the inconsistencies, we focus on the sequence variation and the structure model of two rRNA genes based on extensive taxa sampling. The comparative sequence analysis revealed heterogeneity across species and the existence of conserved motifs in all spinicaudatan species. The level of intraspecific heterogeneity differed among species, which suggested that some species might have undergone a relaxed concerted evolution with respect to the gene. The Bayesian analyses were performed on nuclear (, ) and mitochondrial (, ) genes. Further, we investigated compositional heterogeneity between lineages and assessed the potential for phylogenetic noise compared to signal in the combined data set. Reducing the non-phylogenetic signals and application of optimal rRNA model recovered a topology congruent with inference from the transcriptome data, whereby Limnadiidae was placed as a sister group to Leptestheriidae + Eocyzicidae with high support (topology I). Tests of alternative hypotheses provided implicit support for four competing topologies, and topology I was the best.
重建螺旋尾类动物的深层系统发育关系仍然是一个挑战，对于 Eocyzicidae、Cyzicidae s. s.、Leptestheriidae 和 Limnadiidae 这几个亚目之间的相互关系，存在几种不同的竞争假说。为了探究不一致的来源，我们基于广泛的分类群采样，重点研究了两个 rRNA 基因的序列变异和结构模型。比较序列分析揭示了物种之间的异质性和所有螺旋尾类动物物种中保守基序的存在。种内异质性的水平在物种之间存在差异，这表明一些物种可能在 rRNA 基因方面经历了放松的协同进化。对核（、）和线粒体（、）基因进行了贝叶斯分析。此外，我们研究了谱系之间的组成异质性，并评估了组合数据集相对于信号的系统发育噪声的潜在影响。减少非系统发育信号并应用最佳 rRNA 模型恢复了与转录组数据推断一致的拓扑结构，其中 Limnadiidae 与 Leptestheriidae + Eocyzicidae 形成姐妹群，支持度很高（拓扑结构 I）。替代假说的检验为四个竞争拓扑结构提供了隐含支持，拓扑结构 I 是最佳的。
