It has long been recognized that hybridization and polyploidy are prominent processes in plant evolution. Although classically recognized as significant in speciation and adaptation, recognition of the importance of interspecific gene flow has dramatically increased during the genomics era, concomitant with an unending flood of empirical examples, with or without genome doubling. Interspecific gene flow is thus increasingly thought to lead to evolutionary innovation and diversification, via adaptive introgression, homoploid hybrid speciation and allopolyploid speciation. Less well understood, however, are the suite of genetic and genomic mechanisms set in motion by the merger of differentiated genomes, and the temporal scale over which recombinational complexity mediated by gene flow might be expressed and exposed to natural selection. We focus on these issues here, considering the types of molecular genetic and genomic processes that might be set in motion by the saltational event of genome merger between two diverged species, either with or without genome doubling, and how these various processes can contribute to novel phenotypes. Genetic mechanisms include the infusion of new alleles and the genesis of novel structural variation including translocations and inversions, homoeologous exchanges, transposable element mobilization and novel insertional effects, presence-absence variation and copy number variation. Polyploidy generates massive transcriptomic and regulatory alteration, presumably set in motion by disrupted stoichiometries of regulatory factors, small RNAs and other genome interactions that cascade from single-gene expression change up through entire networks of transformed regulatory modules. We highlight both these novel combinatorial possibilities and the range of temporal scales over which such complexity might be generated, and thus exposed to natural selection and drift.

早就认识到杂交和多倍体是植物进化中的重要过程。尽管传统上公认物种形成和适应具有重要意义，但在基因组学时代，对种间基因流重要性的认识已大大增加，伴随着无休止的经验例子泛滥，无论有无基因组加倍。因此，越来越多地认为种间基因流通过适应性渗入，同倍体杂种形成和异源多倍体形成导致进化创新和多样化。然而，鲜为人知的是，分化基因组的合并推动了一系列遗传和基因组机制的启动，以及时间尺度，在此尺度上，由基因流介导的重组复杂性可能被表达并暴露于自然选择。我们在这里集中讨论这些问题，考虑可能有两个遗传物种（无论有无基因组加倍）之间的基因组合并的盐化事件推动的分子遗传和基因组过程的类型，以及这些不同的过程如何促成新的表型。遗传机制包括新等位基因的注入和新的结构变异的发生，包括易位和倒位，同源交换，可转座因子动员和新的插入效应，存在缺失变异和拷贝数变异。多倍体会产生大量的转录组和调控改变，大概是由于调控因子的化学计量比被破坏而引起的，从单基因表达中级联的小RNA和其他基因组相互作用在整个转化的调节模块网络中发生变化。我们着重介绍了这些新颖的组合可能性以及可能产生这种复杂性并因此暴露于自然选择和漂移的时间尺度范围。