Data from: Phylogenomic analyses reveal extensive gene flow within the magic flowers (Achimenes)

Premise of the study: The Neotropical Gesneriaceae is a lineage known for its colorful and diverse flowers, as well as an extensive history of intra- and intergeneric hybridization, particularly among Achimenes (the magic flowers) and other members of the subtribe Gloxiniinae. Despite numerous studies seeking to elucidate the evolutionary relationships of these lineages, relatively few have sought to infer specific patterns of gene flow despite evidence of widespread hybridization.
Methods: To explore the utility of phylogenomic data for reassessing phylogenetic relationships and inferring patterns of gene flow among species of Achimenes, we sequenced 12 transcriptomes. We used a variety of methods to infer the species tree, examine gene tree discordance, and infer patterns of gene flow.
Key results: Phylogenomic analyses resolve clade relationships at the crown of the lineage with high support. In contrast to previous analyses, we recovered strong support for several new relationships despite a significant amount of gene tree discordance. We present evidence for at least two introgression events between two species pairs that share pollinators and suggest that the species status of A. admirabilis be reexamined.
Conclusions: Our study demonstrates the utility of transcriptome data for phylogenomic analyses and inferring patterns of gene flow despite gene tree discordance. Moreover, these data provide another example of prevalent interspecific gene flow among Neotropical plants that share pollinators.

研究背景：新热带区苦苣苔科（Neotropical Gesneriaceae）是一类以花色艳丽、花型多样而闻名的类群，同时其属内及属间杂交的历史极为悠久，尤其集中在长筒花属（Achimenes，俗称魔术花）以及大岩桐亚族（Gloxiniinae）的其他类群之间。尽管已有诸多研究试图阐明该类群的演化亲缘关系，但针对其广泛存在的杂交现象，解析基因流具体模式的研究仍相对匮乏。
研究方法：为探究系统基因组学（phylogenomics）数据在重新评估长筒花属（Achimenes）物种种间亲缘关系、解析基因流模式方面的应用潜力，我们对12份转录组（transcriptome）样本进行了测序。我们采用多种方法推断物种树、检测基因树冲突，并解析基因流模式。
主要结果：系统基因组学分析对该类群冠群支系的亲缘关系给出了高支持度的解析。与此前的研究结果不同，尽管存在显著的基因树冲突现象，我们仍得到了多个新的亲缘关系的强支持证据。我们发现了至少两起发生在共享传粉者的物种对之间的渐渗事件，并提出需重新评估A. admirabilis的物种地位。
研究结论：本研究证实了转录组（transcriptome）数据在系统基因组学分析以及解析存在基因树冲突情况下的基因流模式方面的应用价值。此外，这些数据还为新热带区共享传粉者的植物类群中普遍存在的种间基因流提供了又一例证。