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

长期以来，杂交和多倍体起源一直被认为是植物多样化和物种形成的重要原因。通过杂交的基因流动在物种形成中起着重要的作用。更好地了解多倍体的形成过程和每个多倍体物种中基因流动的后果对于研究进化具有广泛的兴趣。冰草属披碱草与小麦、大麦和黑麦同属一类。该属中的牧草适应了不同的气候和生境，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类群。所有的冰草都是由至少两组不同的染色体组成的，大多数物种都有S染色体和S染色体的组合。与Sth组合的物种约有50种。ST基因组来自假鹅观草属的祖先种，H来自野生大麦。根据形态特征，将披碱草属植物划分为7个组。由于环境和发育阶段都会影响形态特征，因此形态相似的物种在遗传上可能不是很接近。例如，对3个欧亚和8个北美披碱草分类群的DNA分析并不完全支持形态分类。鉴于遗传因素和环境因素都可以影响形态特征，我们假设披碱草属中形态相似的物种不一定在遗传上彼此相关。大多数多倍体的起源和系统发育尚不清楚，基于每个物种几个个体和多组单拷贝或低拷贝核基因座的Sth多倍体的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序列来分析披碱草属物种，每个物种包括4-5个种质及其祖先种。将分析序列数据以确定这些物种之间的关系；遗传关系将与根据形态为Sth物种建议的区段范围进行比较，以测试具有相似形态的物种是否在遗传上彼此相关。在不完全生殖隔离的情况下理解物种形成的动力学是进化生物学中的挑战之一。大多数异源四倍体披碱草物种可以杂交，形成部分或完全可育的杂交种，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需的遗传分化，但将导致从一个物种到另一个物种的持续基因流动，这将打破先前建立的物种边界。在披碱草属植物中，基因流动的程度及其在创造多样性和物种形成中的作用尚未得到检验。我们将使用种群遗传学方法来研究披碱草属物种间的渐渗程度及其在物种形成中的作用。为了实现这一目标，我们将利用AFLP、微卫星和DNA测序技术，对20个犬种、纤维种、碱蓬种和阿拉斯加种的纯种群及其15个混合种群进行分析。种群遗传学方法将被用来分析“混合”种群中的标记模式，并将它们与“纯”种群进行比较，以确定重叠区和分隔区之间的基因流动的可能性。这些研究将为渗入和杂交物种形成的基因组和进化后果提供新的见解，并指导保护决策。它们还将具有农学相关性，因为披碱草属植物中有许多农业上有用的物种。更好地了解过去杂交事件的动态性质也将有助于深入了解准确的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.