Phylogenetics and Morphological Diversity of the Grass Subfamily Pooideae (Poaceae)

在草科（禾本科）中，大约有10,000种，十二个亚科中两个最大的亚科之一是禾本科，大约有3300种。这个亚科包括温带和北方地区的大部分草。在许多其他物种中，它包括小麦、大麦、黑麦，以及它们的亲戚，在其系统发育和基因组关系方面一直是深入研究的重点。杂交和多倍体的常见现象已经在这个群体中得到了充分的记录，部分原因是这个物种在这个组合中的经济重要性。该亚科的大多数物种（约2200种）属于另一个类群，该类群由以前分配给三个不同部落的物种组成（Aveneae， Poeae和Hainardieae）。这一类群，即APH复合体，包括许多具有经济重要性的物种，如燕麦、提莫西草、弯草、羊茅和蓝草。康奈尔大学的Jerrold Davis教授获得的初步数据表明，在APH复合体中先前确认的三个主要部落在系统发育上是混合的。这表明，传统上用来区分这些群体的性状已经平行出现了好几次，或者同一群体中来自不同谱系的物种之间的杂交产生了新的（可能是多倍体的）群体，这些群体结合了各种亲本的特征，就像在相关的小麦科中经常发生的那样。与小麦科相比，APH类群要大得多，却鲜为人知。本研究的主要目标是建立Pooideae亚科的系统发育假说，并特别关注APH复合体。为了实现这一目标，将生成三个数据集，并分别和组合分析。这三个字符集是质体基因组中的一组连锁基因（ndhF、ndhH和rbcL），一个核编码基因（GBSSI），以及一个结构字符集，包括小穗结构和叶片解剖等特征。这些数据集之间不一致的实例将被检查，以确定特征平行和逆转的证据，以及谱系间杂交。ndhF和ndhH的一个有趣的特性是它们位于质体基因组短单拷贝（SSC）区域的两端附近，靠近该区域与侧倒重复（IR）区域的边界。在一些草中，ndhH的5‘端延伸到IR区，因此在基因组中被复制，而在另一些草中，ndhF的3’端延伸到IR区，因此被复制。除了工作的系统发育目标外，这些属性的分布，重复部分的大小以及这些区域之间基因交换的动态也是研究的主题。这项工作的一个更广泛的影响将是培养本科生，他们将从事目标群体的分子和结构特征的研究。此外，还将建立一个网站，描述该亚科的关键结构和解剖特征，并提供分类群描述、数据矩阵、树、图像和分类群，突出显示有问题的分类群。APH类群包括许多具有经济重要性的物种，然而，如上所述，类群内的系统关系尚不清楚。这一组的物种，以及整个Pooideae亚科的物种，在许多领域都引起了研究者的极大兴趣，包括遗传学、生态学、农学、牧场管理等，一个描述这一组草的网站，描述了分类群的特征和它们之间的关系，将引起许多科学家和其他人的兴趣，并将激发更多的研究。因此，在拟议的工作过程中产生的信息将迅速传播给学生、专业人员和其他人员。

Within the grass family (Poaceae), which includes about 10,000 species, one of the two largest of the twelve subfamilies is the Pooideae, with about 3300 species. This subfamily includes most of the grasses of temperate and boreal regions. Among many other species, it includes wheat, barley, rye, and their relatives of the tribe Triticeae, which has been the focus of intensive study, in terms of its phylogenetic and genomic relationships. The common occurrence of hybridization and polyploidy have been thoroughly documented in this group, in part because of the economic importance of the species in this assemblage. Most species of the subfamily (about 2200) fall within another group, which consists of species formerly assigned to three different tribes (Aveneae, Poeae, and Hainardieae). This group, the APH complex, includes many species of economic importance such as oats, timothy, bentgrass, the fescues, and the bluegrasses. Preliminary data acquired by Prof. Jerrold Davis at Cornell University indicate that the three major tribes previously recognized within the APH complex are intermixed phylogenetically. This suggests that the characters traditionally used to distinguish these groups have arisen in parallel several times or that hybridization among species from different lineages within the group has generated new (possibly polyploid) groups that combine the features of the various parents, as has occurred so frequently in the related Triticeae. In comparison to the Triticeae, the APH group is much larger, and much more poorly known. The main goal of the proposed work is to generate a phylogenetic hypothesis for subfamily Pooideae, with specific attention to the APH complex. To accomplish this, three data sets will be generated and analyzed separately and in combination. The three character sets are a set of linked genes in the plastid genome (ndhF, ndhH, and rbcL), a nuclear-encoded gene (GBSSI), and a structural character set that includes features such as spikelet structure and leaf anatomy. Instances of incongruence among these data sets will be examined to identify evidence of character parallelisms and reversals, and inter-lineage hybridization. One interesting quality of ndhF and ndhH is that they lie near opposite ends of the short single-copy (SSC) region of the plastid genome, near the boundaries of this region with the flanking inverted repeat (IR) regions. In some grasses the 5' end of ndhH extends into the IR region, and thus is duplicated in the genome, while in others the 3' end of ndhF extends into the IR region, and thus is duplicated. In addition to the phylogenetic goals of the work, the distribution of these attributes, the sizes of the duplicated portions, and the dynamics of gene exchange between these regions are topics of research.One of the broader impacts of the proposed work will be the training of undergraduate students, who will be engaged in study of molecular and structural characters of the target group. Also, a website will be developed that will depict the critical structural and anatomical features of the subfamily, and will provide taxon descriptions, data matrices, trees, images, and a classification of the group, with problematic taxa highlighted. The APH group includes numerous species of economic importance, yet, as indicated above, systematic relationships within the group are poorly understood. The species of this group, and of subfamily Pooideae as a whole, are of great interest to investigators in a variety of areas, including genetics, ecology, agronomy, range management, etc., and a website that describes the grasses of this group, and that depicts characteristics of the taxa and relationships among them, will be of interest to many scientists and other persons, and will stimulate additional investigation. Thus, the information generated during the course of the proposed work will be disseminated rapidly to students, professionals, and other persons.