Multiple nuclear genes stabilize the phylogenetic backbone of the genus <i>Quercus</i>

Phylogenetic relationships among 108 oak species (genus <i>Quercus</i> L.) were inferred using DNA sequences of six nuclear genes selected from the existing genomic resources of the genus. Previous phylogenetic reconstructions based on traditional molecular markers are inconclusive at the deeper nodes. Overall, weak phylogenetic signals were obtained for each individual gene analysis, but stronger signals were obtained when gene sequences were concatenated. Our data support the recognition of six major intrageneric groups Cyclobalanopsis, Cerris, Ilex, Quercus, Lobatae and Protobalanus. Our analyses provide resolution at deeper nodes but with moderate support and a more robust infrageneric classification within the two major clades, the ‘Old World Oaks’ (Cyclobalanopsis, Cerris, Ilex) and ‘New World Oaks’ (Quercus, Lobatae, Protobalanus). However, depending on outgroup choice, our analysis yielded two alternative placements of the Cyclobalanopsis clade within the genus <i>Quercus</i>. When <i>Castanea</i> Mill. was chosen as outgroup, our data suggested that the genus <i>Quercus</i> comprised two clades corresponding to two subgenera as traditionally recognized by Camus: subgenus <i>Euquercus</i> Hickel and Camus and subgenus <i>Cyclobalanopsis</i> Øersted (Schneider). However, when <i>Notholithocarpus</i> Manos, Cannon and S. Oh was chosen as an outgroup subgenus <i>Cyclobalanopsis</i> clustered with Cerris and Ilex groups to form the Old World clade. To assess the placement of the root, we complemented our dataset with published data of ITS and CRC sequences. Based on the concatenated eight gene sequences, the most likely root position is at the split between the ‘Old World Oaks’ and the ‘New World Oaks’, which is one of the alternative positions suggested by our six gene analysis. Using a dating approach, we inferred an Eocene age for the primary divergences in <i>Quercus</i> and a root age of about 50–55 Ma, which agrees with palaeobotanical evidence. Finally, irrespective of the outgroup choice, our data boost the topology within the New World clade, where (Protobalanus + Quercus) is a sister clade of Lobatae. Inferred divergence ages within this clade and the Cerris–Ilex clade are generally younger than could be expected from the fossil record, indicating that morphological differentiation pre-dates genetic isolation in this clade.本研究利用从栎属（*Quercus* L.）已有基因组资源中筛选得到的6个核基因的DNA序列，解析了108个栎属物种间的系统发育关系。此前基于传统分子标记的系统发育重建在深层节点处结论不明。总体而言，单个基因分析得到的系统发育信号较弱，但将基因序列串联后则可获得更强的信号。我们的数据支持识别栎属内6个主要的属内类群：青冈亚属（Cyclobalanopsis）、Cerris组、Ilex类群、栎属（*Quercus*）、Lobatae组以及Protobalanus组。本研究的分析在深层节点上实现了分辨率，但支持度中等，且在两大演化支——"旧世界栎类"（Cyclobalanopsis、Cerris、Ilex）和"新世界栎类"（*Quercus*、Lobatae、Protobalanus）——内部建立了更为稳健的属内分类系统。 然而，根据外类群（outgroup）的选择不同，本分析得出了Cyclobalanopsis演化支在栎属内的两种不同定位。当以栗属（*Castanea* Mill.）作为外类群时，我们的数据表明栎属包含两个演化支，分别对应Camus传统定义的两个亚属：真栎亚属（*Euquercus* Hickel & Camus）和青冈亚属（*Cyclobalanopsis* Øersted (Schneider)）。而当以假石柯属（*Notholithocarpus* Manos, Cannon & S. Oh）作为外类群时，青冈亚属与Cerris组、Ilex类群聚为旧世界演化支。 为了确定树根（root placement）的位置，我们将已发表的内部转录间隔区（ITS）与CRC序列数据补充至本数据集。基于串联的8个基因序列，最可能的树根位置处于"旧世界栎类"与"新世界栎类"的分化节点，这与我们基于6个基因分析得到的其中一种备选定位一致。 利用分子定年方法，我们推断栎属的主要分化发生在始新世（Eocene），树根的定年约为5000万至5500万年前（Ma），这与古植物学证据相符。 最后，无论外类群如何选择，我们的数据均强化了新世界演化支内的拓扑结构：即（Protobalanus + *Quercus*）为Lobatae的姊妹演化支。该演化支与Cerris–Ilex演化支内推断的分化年龄普遍低于化石记录的预期值，这表明该类群的形态分化早于遗传隔离。

搜集汇总

背景与挑战

背景概述

该数据集包含108种栎树物种的6个核基因序列数据，用于构建栎属系统发育关系。研究支持栎属分为6个主要组群，并揭示了旧世界与新世界栎树两大分支的结构，同时通过测年分析推断栎属主要分化发生在始新世时期。