Evolutionary genomic approaches to understand the origin and maintenance biodiversity in forest and agricultural landscapes

大多数植物物种被认为是由过去的杂交事件产生的，现在的杂交可能对生物多样性的维持产生积极或消极的影响。尽管杂交现象广泛存在，但其在生物多样性起源和维持中的作用仍存在争议。对选定植物类群中过去和现在的杂交模式的详细了解对于深入了解生物多样性的起源和维持是必不可少的。系统发育分析为推断过去的杂交和网状进化提供了一种手段，而利用基因型数据对选定的植物群体进行亲本分析对于推断当前的杂交水平是非常宝贵的。因此，至关重要的是要有一个生态和形态多样化的森林树木群体的健全的系统发育作为一个框架，形态学，生物地理，生态和遗传数据可以叠加在其上，以阐明进化模式和网状进化。森林乔木属杨树是树木生物学研究的新兴模式生物，其地理分布广泛，杂交广泛，适应多种生境，作为主要木材来源具有许多工业应用和经济重要性，以及广泛的遗传、基因组和生化工具的可用性，为研究杂交在生物多样性进化中的作用提供了理想的系统。我们将i)基于几乎完整的叶绿体和核基因组的DNA序列重建杨树的健全系统发育树(s), ii)开发物种诊断分子标记来鉴定杂交后代的亲本，iii)确定选择的杨树物种在自然杂交带的杂交和渗入水平。本研究将利用高通量基因组学技术的最新进展，生成几乎完整的核和叶绿体基因组序列，重建系统发育树，并利用高通量基因分型技术，对全基因组单核苷酸多态性进行基因分型，以前所未有的分辨率确定种间杂交的亲代。所得到的系统发育树将用于a)检验杨树的进化假设和网状进化，b)作为杨树属分类群系统分类的框架。由此产生的关于杂交的渗入和亲本的水平和方向性的知识将有价值：1)理解杂交带的遗传结构和进化动力学，以及b)开发模型来预测本地和潜在入侵的非本地物种之间杂交的遗传后果。此外，所得到的物种诊断分子标记将作为基因组定位和亲本鉴定的工具，用于杨树育种计划，以应对气候条件变化下森林、纸浆和生物燃料工业对木材和能源需求的挑战。

Majority of plant species are considered to have derived from past hybridization events and the present hybridization may have positive or negative influence on the maintenance of biodiversity. Despite widespread occurrence of hybridization, its role in the origin and maintenance of biodiversity remains controversial. A detailed understanding of the past and present hybridization patterns in selected groups of plants is essential for gaining insights into the origin and maintenance of biodiversity. Phylogenetic analyses provide a means to infer past hybridization and reticulate evolution, and parentage analyses of selected plant populations using genotypic data are invaluable to infer the present hybridization levels. Therefore, it is crucial to have a robust phylogeny of an ecologically and morphologically diverse group of forest trees as a framework onto which morphological, biogeographical, ecological and genetic data can be super-imposed to elucidate evolutionary patterns and reticulate evolution. The forest tree genus Populus, the emerging model organism of tree biology research, with its wide geographic distribution, extensive hybridization, adaptability to a variety of habitats, many industrial applications and economic importance as a major source of wood, and the availability of extensive genetic, genomic and biochemical tools provides an ideal system to investigate the role of hybridization in evolution of biodiversity. We will i) reconstruct robust phylogenetic tree(s) of the genus Populus based on DNA sequences of nearly complete chloroplast and nuclear genomes, ii) develop species diagnostic molecular markers to identify the parentage of hybrids, and iii) determine the levels of hybridization and introgression in natural hybrid zones of selected Populus species. This research will capitalize on recent advances in high throughput genomics techniques to generate nearly complete sequences of the nuclear and chloroplast genomes to reconstruct phylogenetic trees, and high throughput genotyping technologies to genotype genome-wide single nucleotide polymorphism to determine the parentage of inter-specific hybrids at an unprecedented level of resolution. The resulting phylogenetic tree(s) will be used a) to test evolutionary hypotheses and reticulate evolution in poplars, and b) as a framework for systematic classification of taxa within the genus Populus. The resulting knowledge of the levels and directionality of introgression and parentage of hybrids will be valuable for a) understanding the genetic architecture and evolutionary dynamics of hybrid zones, and b) developing models to predict genetic consequences of hybridization between native and potentially invasive, non-native species. In addition, resulting species diagnostic molecular markers will serve as a tool for genome mapping and parentage identification in poplar breeding programs geared to address challenges in meeting wood and energy demands of the forest, paper pulp and biofuel industries under changing climatic conditions.