Data from: From cacti to carnivores: improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales

Premise of the Study— The Caryophyllales contains ~12,500 species and is known for its cosmopolitan distribution, convergence of trait evolution, and extreme adaptations. Some relationships within the Caryophyllales, like those of many large plant clades, remain unclear and phylogenetic studies often recover alternative hypotheses. We explore the utility of broad and dense transcriptome sampling across the order for resolving evolutionary relationships in Caryophyllales.
Methods— We generated 84 transcriptomes and combined these with 224 publicly available transcriptomes to perform a phylogenomic analysis of Caryophyllales. To overcome the computational challenge of ortholog detection in such a large data set, we developed an approach for clustering gene families that allowed us to analyze >300 transcriptomes and genomes. We then inferred the species relationships using multiple methods and performed gene tree conflict analyses.
Key Results— Our phylogenetic analyses resolved many clades with strong support, but also showed significant gene-tree discordance. This discordance is a common feature of phylogenomic studies but also represents an opportunity to understand processes that have structured phylogenies. We also found taxon sampling influences species-tree inference, highlighting the importance of more focused studies with additional taxon sampling.
Conclusions— Transcriptomes are useful both for species tree inference and for uncovering evolutionary complexity within lineages. Through analyses of gene-tree conflict and multiple methods of species tree inference, we demonstrate that phylogenomic data can provide unparalleled insight into the evolutionary history of Caryophyllales. We also discuss a method for overcoming computational challenges associated with homolog clustering in large datasets.

研究背景— 石竹目（Caryophyllales）包含约12500个物种，以其全球广布性、性状演化的趋同性以及极端适应性而闻名。与诸多大型植物演化支一样，石竹目内部的部分类群亲缘关系仍未明确，相关系统发育研究常常得出不同的演化假说。本研究旨在探究对该目开展广泛且密集的转录组取样，在解析石竹目演化关系方面的应用价值。
研究方法— 本研究新生成84套转录组数据，并将其与224套公开可得的转录组数据相结合，开展石竹目的系统基因组学分析。为应对超大数据集下直系同源基因（ortholog）检测所面临的计算挑战，我们开发了一套基因家族聚类方法，得以分析超过300套转录组与基因组数据。随后我们采用多种方法推断物种演化关系，并开展了基因树冲突（gene-tree discordance）分析。
主要结果— 本研究的系统发育分析解析了多个具有高支持率的演化支，但同时也揭示了显著的基因树冲突现象。基因树冲突是系统基因组学研究的常见特征，但同时也为理解塑造系统发育树的演化过程提供了研究契机。我们还发现类群取样策略会影响物种树（species-tree）的推断结果，这凸显了增加类群取样的针对性研究的重要性。
结论— 转录组数据既可用于物种树推断，也可用于揭示演化支内部的演化复杂性。通过基因树冲突分析与多种物种树推断方法，本研究证实系统基因组学数据能够为石竹目的演化历史提供前所未有的研究视角。我们同时还讨论了一种可解决大规模数据集下同源基因（homolog）聚类相关计算难题的方法。