Phylogeny of a Genomically Diverse Group of Elymus (Poaceae) Allopolyploids Reveals Multiple Levels of Reticulation

The grass tribe Triticeae (=Hordeeae) comprises only about 300 species, but it is well known for the economically important crop plants wheat, barley, and rye. The group is also recognized as a fascinating example of evolutionary complexity, with a history shaped by numerous events of auto- and allopolyploidy and apparent introgression involving diploids and polyploids. The genus Elymus comprises a heterogeneous collection of allopolyploid genome combinations, all of which include at least one set of homoeologs, designated St, derived from Pseudoroegneria. The current analysis includes a geographically and genomically diverse collection of 21 tetraploid Elymus species, and a single hexaploid species. Diploid and polyploid relationships were estimated using four molecular data sets, including one that combines two regions of the chloroplast genome, and three from unlinked nuclear genes: phosphoenolpyruvate carboxylase, β-amylase, and granule-bound starch synthase I. Four gene trees were generated using maximum likelihood, and the phylogenetic placement of the polyploid sequences reveals extensive reticulation beyond allopolyploidy alone. The trees were interpreted with reference to numerous phenomena known to complicate allopolyploid phylogenies, and introgression was identified as a major factor in their history. The work illustrates the interpretation of complicated phylogenetic results through the sequential consideration of numerous possible explanations, and the results highlight the value of careful inspection of multiple independent molecular phylogenetic estimates, with particular focus on the differences among them.

禾本科的小麦族（Triticeae，亦称Hordeeae）仅包含约300个物种，却因涵盖小麦、大麦、黑麦这类具有重大经济价值的作物而享誉学界。该类群同时也是演化复杂性的经典研究范例，其演化历史历经多次同源多倍化（autopolyploidy）、异源多倍化（allopolyploidy）事件，以及涉及二倍体与多倍体的显著遗传渐渗（introgression）过程。披碱草属（Elymus）包含一组由异源多倍体基因组组合构成的异质性类群，所有类群均至少携带一套源自伪鹅观草属（Pseudoroegneria）、被命名为St的同祖同源染色体组（homoeologs）。本研究分析涵盖了21个四倍体披碱草物种与1个六倍体披碱草物种，这些类群在地理分布与基因组组成上均具有多样性。本研究通过四组分子数据集解析二倍体与多倍体间的演化关系：其中一组联合了叶绿体基因组的两个区域，另外三组分别来自三个非连锁核基因——磷酸烯醇式丙酮酸羧化酶（phosphoenolpyruvate carboxylase）、β-淀粉酶（β-amylase）与颗粒结合淀粉合成酶I（granule-bound starch synthase I）。研究采用最大似然法（maximum likelihood）构建了四棵基因树，多倍体序列的系统发育定位结果表明，该类群的演化不仅涉及异源多倍化，还存在广泛的网状进化现象。研究结合多种已知会使异源多倍体系统发育分析复杂化的演化现象对基因树进行解读，最终确认遗传渐渗是该类群演化历史中的关键影响因素。本研究通过依次考量多种潜在解释路径，阐明了复杂系统发育结果的解读方法；同时研究结果也凸显了对多组独立分子系统发育分析结果进行细致检视、并重点关注其差异的重要价值。