Many conflicting hypotheses regarding the relationships among crops and wild species closely related to wheat (the genera Aegilops, Amblyopyrum, and Triticum) have been postulated. The contribution of hybridization to the evolution of these taxa is intensely discussed. To determine possible causes for this, and provide a phylogeny of the diploid taxa based on genome-wide sequence information, independent data were obtained from genotyping-by-sequencing and a target-enrichment experiment that returned 244 low-copy nuclear loci. The data were analyzed using Bayesian, likelihood and coalescent-based methods. D statistics were used to test if incomplete lineage sorting alone or together with hybridization is the source for incongruent gene trees. Here we present the phylogeny of all diploid species of the wheat wild relatives. We hypothesize that most of the wheat-group species were shaped by a primordial homoploid hybrid speciation event involving the ancestral Triticum and Am. muticum lineages to form all other species except Ae. speltoides. This hybridization event was followed by multiple introgressions affecting all taxa except Triticum. Mostly progenitors of the extant species were involved in these processes, while recent interspecific gene flow seems insignificant. The composite nature of many genomes of wheat-group taxa results in complicated patterns of diploid contributions when these lineages are involved in polyploid formation, which is, for example, the case for tetraploid and hexaploid wheats. Our analysis provides phylogenetic relationships and a testable hypothesis for the genome compositions in the basic evolutionary units within the wheat group of Triticeae.

中文翻译：

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全基因组序列信息揭示了二倍体小麦野生亲缘种之间的经常性杂交。

关于与小麦密切相关的农作物与野生物种之间的关系（埃吉洛普属，弱视菌属和小麦属）的关系，存在许多相互矛盾的假设。强烈讨论了杂交对这些分类单元的进化的贡献。为了确定可能的原因，并基于全基因组序列信息提供二倍体分类的系统发育，从测序的基因分型和靶标富集实验中获得了独立数据，该实验返回了244个低拷贝核基因座。使用贝叶斯，似然和基于聚结的方法对数据进行了分析。D统计量用于测试单独的不完整的谱系分类或与杂交一起的不完整谱系是否是来源。在这里，我们介绍了小麦野生近缘种所有二倍体物种的系统发育。我们假设大多数小麦类物种是由涉及祖先小麦和Am的原始同倍体杂种形成事件形成的。muticum谱系，以形成除Ae外的所有其他物种。speltoides。此杂交事件之后，多次渗入影响除小麦外的所有分类群。大多数现存物种的祖细胞参与了这些过程，而最近的种间基因流动似乎无关紧要。当这些谱系参与多倍体形成时，小麦类群的许多基因组的合成性质会导致复杂的二倍体模式，例如，四倍体和六倍体小麦就是这种情况。