Hawaiian plant radiations often result in lineages with exceptionally high species richness and extreme morphological and ecological differentiation. However, they typically display low levels of genetic variation, hindering the use of classic DNA markers to resolve their evolutionary histories. Here we utilize a phylogenomic approach to generate the first generally well-resolved phylogenetic hypothesis for the evolution of the Hawaiian Bidens (Asteraceae) adaptive radiation, including refined initial colonization and divergence time estimates. We sequenced the chloroplast genome (plastome) and nuclear ribosomal complex for 18 of the 19 endemic species of Hawaiian Bidens and 4 outgroup species. Phylogenomic analyses based on the concatenated dataset (plastome and nuclear) resulted in identical Bayesian and Maximum Likelihood trees with high statistical support at most nodes. Estimates from dating analyses were similar across datasets, with the crown group emerging ~1.76-1.82 Mya. Biogeographic analyses based on the nuclear and concatenated datasets indicated that colonization within the Hawaiian Islands generally followed the progression rule with 67-80% of colonization events from older to younger islands, while only 53% of events followed the progression rule in the plastome analysis. We find strong evidence for nuclear-plastome conflict indicating a potentially important role for hybridization in the evolution of the group. However, incomplete lineage sorting cannot be ruled out due to the small number of independent loci analyzed. This study contributes new insights into species relationships and the biogeographic history of the explosive Hawaiian Bidens adaptive radiation.

中文翻译：

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通过系统基因组学揭示夏威夷拜登（菊科）适应性辐射的进化历史

夏威夷植物辐射通常会产生具有极高物种丰富度和极端形态和生态分化的谱系。然而，它们通常表现出低水平的遗传变异，阻碍了使用经典 DNA 标记来解析它们的进化历史。在这里，我们利用系统发育方法为夏威夷拜登（菊科）适应性辐射的进化生成第一个普遍解决的系统发育假设，包括精确的初始定植和发散时间估计。我们对夏威夷拜登斯的 19 种地方性物种和 4 种外群物种中的 18 种的叶绿体基因组（质体）和核糖体复合物进行了测序。基于级联数据集（塑性体和核）的系统发育分析产生了相同的贝叶斯树和最大似然树，在大多数节点上具有高统计支持。跨数据集的约会分析估计值相似，冠组出现~1.76-1.82 Mya。基于核和级联数据集的生物地理学分析表明，夏威夷群岛内的定殖通常遵循进展规则，67-80% 的定殖事件从较老的岛屿到较年轻的岛屿，而在塑性体分析中，只有 53% 的事件遵循进展规则。我们发现核-塑性体冲突的有力证据表明杂交在群体进化中可能发挥重要作用。然而，由于分析的独立位点数量较少，不能排除不完整的谱系排序。