Cytonuclear discordance, commonly detected in phylogenetic studies, is often attributed to hybridization and/or incomplete lineage sorting (ILS). New sequencing technologies and analytical approaches can provide new insights into the relative importance of these processes. Hybridization has previously been reported in the Australian endemic plant genus Adenanthos (Proteaceae). Like many Australian genera, Adenanthos is of relatively ancient origin, and provides an opportunity to examine long-term evolutionary consequences of gene flow between lineages. Using a hybrid capture approach, we assembled densely sampled low-copy nuclear and plastid DNA sequences for Adenanthos, inferred its evolutionary history, and used a Bayesian posterior predictive approach and coalescent simulations to assess relative contributions of hybridization and ILS to cytonuclear discordance. Our analyses indicate that strong incongruence detected between our plastid and nuclear phylogenies is not only the result of ILS, but also results from extensive ancient introgression as well as recent chloroplast capture and introgression between extant Adenanthos species. The deep reticulation was also detected from long-persisting chloroplast haplotypes shared between evolutionarily distant species. These haplotypes may have persisted for over 12 Ma in localized populations across southwest Western Australia, indicating that the region is not only an important area for old endemic lineages and accumulation of species, but is also characterized by persistence of high genetic diversity. Deep introgression in Adenanthos coincided with the rapid radiation of the genus during the Miocene, a time when many Australian temperate plant groups radiated in response to large-scale climatic change. This study suggests that ancient introgression may play an important role in the evolution of the Australian flora more broadly.

中文翻译：

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网状进化、古代叶绿体单倍型和澳大利亚植物 Adenanthos（Proteaceae）的快速辐射

通常在系统发育研究中检测到的细胞核不一致通常归因于杂交和/或不完全谱系分选 (ILS)。新的测序技术和分析方法可以为这些过程的相对重要性提供新的见解。杂交先前已在澳大利亚特有植物属 Adenanthos (Proteaceae) 中报道过。与许多澳大利亚属一样，Adenanthos 起源相对古老，为研究谱系之间基因流动的长期进化后果提供了机会。使用混合捕获方法，我们为 Adenanthos 组装了密集采样的低拷贝核和质体 DNA 序列，推断其进化历史，并使用贝叶斯后验预测方法和聚结模拟来评估杂交和 ILS 对细胞核不一致的相对贡献。我们的分析表明，在我们的质体和核系统发育之间检测到的强烈不一致不仅是 ILS 的结果，也是广泛的古代渗入以及最近叶绿体捕获和现存 Adenanthos 物种之间渗入的结果。从进化遥远的物种之间共享的长期存在的叶绿体单倍型中也检测到深网状结构。这些单倍型可能在西澳大利亚西南部的局部种群中持续了超过 12 Ma，表明该地区不仅是古老的地方性谱系和物种积累的重要地区，但也具有高度遗传多样性的持久性。Adenanthos 的深度渗入恰逢中新世期间该属的快速辐射，当时许多澳大利亚温带植物群响应大规模气候变化而辐射。这项研究表明，古代基因渗入可能在更广泛的澳大利亚植物群进化中发挥重要作用。