Reticulation, caused by hybridization and allopolyploidization, is considered an important and frequent phenomenon in the evolution of numerous plant lineages. Although both processes represent important driving forces of evolution, they are mostly ignored in phylogenetic studies involving a large number of species. Indeed only a scattering of methods exists to recover a comprehensive reticulated evolutionary history for a broad taxon sampling. Among these methods, comparisons of topologies obtained from plastid markers with those from a few nuclear sequences are favored, even though they restrict in-depth studies of hybridization and polyploidization. The genus Rosa encompasses c. 150 species widely distributed throughout the northern hemisphere and represents a challenging taxonomic group in which hybridization and polyploidization are prominent. Our main objective was to develop a general framework that would take patterns of reticulation into account in the study of the phylogenetic relationships among Rosa species. Using amplicon sequencing, we targeted allele variation in the nuclear genome as well as haploid sequences in the chloroplast genome. We successfully recovered robust plastid and nuclear phylogenies and performed in-depth tests for several scenarios of hybridization using a maximum pseudo-likelihood approach on taxon subsets. Our diploid-first approach followed by hybrid and polyploid grafting resolved most of the evolutionary relationships among Rosa subgenera, sections, and selected species. Based on these results, we provide new directions for a future revision of the infrageneric classification in Rosa. The stepwise strategy proposed here can be used to reconstruct the phylogenetic relationships of other challenging taxonomic groups with large numbers of hybrid and polyploid taxa. [Amplicon sequencing; interspecific hybridization; polyploid detection; reticulate evolution.]

中文翻译：

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用系统基因组学揭示网状进化过程的模式：蔷薇属的杂交和多倍体

由杂交和异源多倍体化引起的网状化被认为是众多植物谱系进化中重要且常见的现象。尽管这两个过程都代表了进化的重要驱动力，但在涉及大量物种的系统发育研究中，它们大多被忽略。实际上，只有少数几种方法可以为广泛的分类单元采样恢复全面的网状进化历史。在这些方法中，比较喜欢从质体标记获得的拓扑结构与来自少数核序列的拓扑结构进行比较，尽管它们限制了对杂交和多倍体化的深入研究。蔷薇属包括c。150 种广泛分布于整个北半球，代表了一个具有挑战性的分类群，其中杂交和多倍化是突出的。我们的主要目标是开发一个总体框架，在研究蔷薇物种之间的系统发育关系时将网状模式考虑在内。使用扩增子测序，我们针对核基因组中的等位基因变异以及叶绿体基因组中的单倍体序列。我们成功地恢复了稳健的质体和核系统发育，并使用分类单元子集的最大伪似然方法对几种杂交场景进行了深入测试。我们的二倍体优先方法，然后是杂交和多倍体嫁接，解决了罗莎亚属、部分和选定物种之间的大部分进化关系。基于这些结果，我们为未来修订 Rosa 的亚属分类提供了新的方向。这里提出的逐步策略可用于重建具有大量杂种和多倍体分类群的其他具有挑战性的分类群的系统发育关系。[扩增子测序；种间杂交；多倍体检测；网状进化。]