Data from: Dated tribe-wide whole chloroplast genome phylogeny indicates recurrent hybridizations within Triticeae

Background. Triticeae, the tribe of wheat grasses, harbours the cereals barley, rye and wheat and their wild relatives. Although economically important, relationships within the tribe are still not understood. We analysed the phylogeny of chloroplast lineages among nearly all monogenomic Triticeae taxa and polyploid wheat species aiming at a deeper understanding of the tribe's evolution. We used on- and off-target reads of a target-enrichment experiment followed by Illumina sequencing.
Results. The read data was used to assemble the plastid locus ndhF for 194 individuals and the whole chloroplast genome for 183 individuals, representing 53 Triticeae species and 15 genera. We conducted Bayesian and multispecies coalescent analyses to infer relationships and estimate divergence times of the taxa. We present the most comprehensive dated Triticeae chloroplast phylogeny and review previous hypotheses in the framework of our results. Monophyly of Triticeae chloroplasts could not be confirmed, as either Bromus or Psathyrostachys captured a chloroplast from a lineage closely related to a Bromus-Triticeae ancestor. The most recent common ancestor of Triticeae occurred approximately between ten and 19 million years ago.
Conclusions. The comparison of the chloroplast phylogeny with available nuclear data in several cases revealed incongruences indicating past hybridizations. Recent events of chloroplast capture were detected as individuals grouped apart from con-specific accessions in otherwise monopyhletic groups.

背景： 小麦族（Triticeae）是禾本科小麦类草本植物的族级类群，涵盖大麦、黑麦、小麦及其野生近缘物种。尽管该类群具有重要经济价值，但其内部的系统发育关系仍未被完全阐明。本研究针对几乎所有单基因组小麦族类群及多倍体小麦物种的叶绿体（chloroplast）谱系开展系统发育分析，以期深入解析该族的演化历程。本研究采用目标富集实验产生的靶区及脱靶序列读段（reads），随后进行Illumina测序。
结果： 本研究利用该测序读段数据，为194个样本组装了质体基因座ndhF，同时为183个样本组装了完整叶绿体基因组，涵盖53个小麦族物种及15个属。我们采用贝叶斯分析及多物种溯祖分析，对类群间的系统发育关系进行推断，并估算其分化时间。本研究构建了目前最全面的带分化时间标定的小麦族叶绿体系统发育树，并基于本研究结果对既往提出的演化假说进行了梳理评述。小麦族叶绿体的单系性未能得到证实，原因在于雀麦属（Bromus）或新麦草属（Psathyrostachys）曾从与雀麦-小麦族祖先近缘的谱系中捕获了叶绿体。小麦族的最近共同祖先大约起源于1000万至1900万年前。
结论： 本研究将叶绿体系统发育树与已公开的核基因数据进行比对，在多个案例中发现了系统发育冲突，这表明该族曾发生过古代杂交事件。研究还检测到近期发生的叶绿体捕获事件，表现为部分样本被聚类至原本为单系的类群之外，与同物种种质分离开来。