Untangling evolutionary dynamic and speciation of allotetraploid StH-genomic Elymus species by population phylogenetics

杂交和多倍体的起源一直被认为是植物多样化和物种形成的重要原因。杂交的基因流动在物种形成中起着重要作用。更好地了解多倍体的形成过程和每个多倍体物种的基因流动的后果是研究进化的广泛兴趣。麦草属与小麦、大麦和黑麦属于同一类群。这一属的禾本科植物已经适应了各种气候和栖息地，使它们成为谷物和饲料育种的宝贵遗传资源，也是进化、分类学和物种形成研究的优秀群体。所有的小麦草都由至少两组不同的染色体组成，其中大多数品种都有StY和StH染色体组合。有StH组合的物种约有50种。其中St基因组来自于原属Pseudoroegneria， H基因组来自于野生大麦。根据形态学特征，将石草属5种植物分为7个类群。由于环境和发育阶段都可能影响形态特征，因此具有相似形态的物种可能在遗传上并不接近。例如，3个欧亚和8个北美羊草分类群的DNA分析并不完全支持形态分类。考虑到遗传因素和环境因素对形态性状的影响，我们假设具有相似形态的羊草属物种之间并不一定具有遗传相关性。大多数多倍体的起源和系统发育尚不清楚，基于每个物种的几个个体和多组单拷贝或低拷贝核位点的StH多倍体系统发育研究仍然缺乏。因此，我们将使用单拷贝核基因和叶绿体DNA序列来分析羊草，每个物种有4-5个加入，以及它们的祖先物种。将分析序列数据以确定这些物种之间的关系；将遗传关系与基于形态学提出的StH种的区段界限进行比较，以检验具有相似形态的物种之间是否存在遗传亲缘关系。了解不完全生殖隔离的物种形成动力学是进化生物学的挑战之一。大多数异源四倍体羊草物种可以杂交，形成部分或完全可育的杂种，这导致了不同物种之间的基因流动。基因流动可以阻止杂交物种形成所必需的遗传分化，但会导致基因从一个物种持续流入另一个物种，从而打破先前建立的物种界限。基因流动的程度及其在羊草中创造多样性和物种形成中的作用尚未得到研究。我们将使用群体遗传学的方法来研究羊草种间的渐渗程度及其在物种形成中的作用。为此，我们将利用AFLP、微卫星和DNA序列对20个犬、纤维、变异、阿拉斯加四种犬的纯种群和15个混合种群进行分析。种群遗传方法将用于分析“混合”种群中的标记模式，并将其与“纯”种群进行比较，以确定重叠区域和单独区域之间基因流动的可能性。这些研究将为基因渗入和杂交物种形成的基因组和进化结果提供新的见解，并指导保护决策。由于羊草属中有许多农业上有用的物种，它们也将具有农艺学意义。更好地了解过去杂交事件的动态性质也将有助于准确分类和生物多样性管理。

Hybridization and polyploidy origin have long been recognized as important causes of plant diversification and speciation. Gene flow through hybridization plays important roles in speciation. A better understanding of polyploidy formation processes and the consequences of gene flow in each polyploid species is of widespread interest for studying evolution. Wheatgrass genus Elymus is within the same group as wheat, barley and rye. Grasses within this genus have adapted to various climates and habitats, making them valuable genetic resources for cereal and forage breeding as well as an excellent group for research in evolution, taxonomy, and speciation. All wheatgrasses are made up of at least two different sets of chromosomes with most species having the StY and StH chromosome combination. There are about 50 species with StH combination. The St genome comes from ancestor species in genus Pseudoroegneria and H from wild barley. Based on morphological traits, the StH species in the genus Elymus were classified into seven sections. Since both environment and the stage of development could affect morphological traits, species with similar morphology may not be close genetically. For example, DNA analysis of three Eurasian and eight North American Elymus taxa did not fully support the morphological classification. Given that both genetic factors and environment could affect morphological traits, we hypothesized that the species in Elymus with similar morphology are not necessarily genetically related to each other. The origin and phylogeny of most polyploids remains unclear, a phylogenetic study of StH polyploids based on several individuals per species and multiple sets of single- or low copy nuclear locus is still lacking. Thus, we will use single copy nuclear gene and chloroplast DNA sequences to analyze Elymus species, each with 4-5 accessions along with their ancestor species. Sequence data will be analyzed to determine relationships among these species; the genetic relationships will be compared with the circumscription of the sections proposed for StH species based on morphology to test whether species with similar morphology are genetically related to each other. Understanding the dynamics of speciation with incomplete reproductive isolation is one of the challenges in evolutionary biology. Most allotetraploid Elymus species can hybridize and form partially or fully fertile hybrids, which causes gene flow between different species. Gene flow can prevent genetic differentiation necessary for hybrid speciation, but will result in continuous gene flow from one species into the other that will break the previously established species boundaries. The extent of gene flow and its role in creating diversity and speciation in Elymus has not been examined. We will use a population genetic approach to investigate the extent of introgression among Elymus species and its role in speciation. To fulfill this, AFLP, microsatellites and DNA sequence will be used to analyze 20 pure populations from E. caninus, E. fibrosus, E. mutabilis and E. alaskanus, and 15 mixed populations of these species. Population genetic approach will be used to analyze the pattern of markers in “mixed” populations, and compare them to the “pure” populations to determine how likely gene flow between overlap zones and separate zones is. These studies will provide new insight into the genomic and evolutionary consequences of introgression and hybridization speciation and guide conservation decisions. They will also have agronomic relevance because of the many agriculturally useful species in Elymus. A better understanding of the dynamic nature of past hybridization events will also lend insight into accurate classification and biodiversity management.