Vargas Oscar M, Ortiz Edgardo M, Simpson Beryl B
Integrative Biology and Plant Resources Center, The University of Texas at Austin, Austin, TX, 78712, USA.
Department of Ecology and Evolutionary Biology, University of Michigan, 830 N. University Ave, Ann Arbor, MI, 48109, USA.
New Phytol. 2017 Jun;214(4):1736-1750. doi: 10.1111/nph.14530. Epub 2017 Mar 23.
High-throughput sequencing is helping biologists to overcome the difficulties of inferring the phylogenies of recently diverged taxa. The present study analyzes the phylogenetic signal of genomic regions with different inheritance patterns using genome skimming and ddRAD-seq in a species-rich Andean genus (Diplostephium) and its allies. We analyzed the complete nuclear ribosomal cistron, the complete chloroplast genome, a partial mitochondrial genome, and a nuclear-ddRAD matrix separately with phylogenetic methods. We applied several approaches to understand the causes of incongruence among datasets, including simulations and the detection of introgression using the D-statistic (ABBA-BABA test). We found significant incongruence among the nuclear, chloroplast, and mitochondrial phylogenies. The strong signal of hybridization found by simulations and the D-statistic among genera and inside the main clades of Diplostephium indicate reticulate evolution as a main cause of phylogenetic incongruence. Our results add evidence for a major role of reticulate evolution in events of rapid diversification. Hybridization and introgression confound chloroplast and mitochondrial phylogenies in relation to the species tree as a result of the uniparental inheritance of these genomic regions. Practical implications regarding the prevalence of hybridization are discussed in relation to the phylogenetic method.
高通量测序正在帮助生物学家克服推断近期分化类群系统发育的困难。本研究使用基因组浅层测序和简化基因组测序（ddRAD-seq），分析了一个物种丰富的安第斯属（双柱千里光属）及其近缘属中具有不同遗传模式的基因组区域的系统发育信号。我们分别用系统发育方法分析了完整的核核糖体顺反子、完整的叶绿体基因组、部分线粒体基因组和一个核ddRAD矩阵。我们应用了几种方法来理解数据集之间不一致的原因，包括模拟以及使用D统计量（ABBA-BABA检验）检测基因渐渗。我们发现核、叶绿体和线粒体系统发育之间存在显著不一致。通过模拟和D统计量在双柱千里光属的属间以及主要分支内部发现的强烈杂交信号表明，网状进化是系统发育不一致的主要原因。我们的结果为网状进化在快速多样化事件中的主要作用提供了证据。由于这些基因组区域的单亲遗传，杂交和基因渐渗使叶绿体和线粒体系统发育与物种树产生混淆。文中还结合系统发育方法讨论了关于杂交普遍性的实际意义。
