Multiple nuclear genes stabilize the phylogenetic backbone of the genus Quercus

Phylogenetic relationships among 108 oak species (genus Quercus 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 Quercus. When Castanea Mill. was chosen as outgroup, our data suggested that the genus Quercus comprised two clades corresponding to two subgenera as traditionally recognized by Camus: subgenus Euquercus Hickel and Camus and subgenus Cyclobalanopsis Øersted (Schneider). However, when Notholithocarpus Manos, Cannon and S. Oh was chosen as an outgroup subgenus Cyclobalanopsis 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 Quercus 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.）现有基因组资源中筛选得到的6个核基因的DNA序列，对108个栎属物种的系统发育关系进行了推断。此前基于传统分子标记的系统发育重建在深层节点处分辨率不足、结论存疑。总体而言，单个基因分析得到的系统发育信号较弱，但将基因序列拼接后可获得更强的系统发育信号。本研究数据支持识别出6个主要的属内类群：青冈亚属（Cyclobalanopsis）、栗叶栎组（Cerris）、冬青栎组（Ilex）、栎亚属（Quercus）、尖叶栎组（Lobatae）和原栎组（Protobalanus）。我们的分析在深层节点处实现了一定分辨率，但支持度中等；同时在‘旧世界栎’（青冈亚属、栗叶栎组、冬青栎组）和‘新世界栎’（栎亚属、尖叶栎组、原栎组）两个主要演化支内，得到了更为稳健的属内分类框架。不过，基于外类群的选择差异，本分析得到了青冈亚属演化支在栎属内两种不同的系统发育位置。当以栗属（Castanea Mill.）作为外类群时，数据显示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)）。但当以假石柯属（Notholithocarpus Manos, Cannon & S. Oh）作为外类群时，青冈亚属与栗叶栎组、冬青栎组聚为一支，形成旧世界栎演化支。为确定树根位置，我们补充了已发表的内部转录间隔区（ITS）和CRC序列数据以完善本数据集。基于拼接后的8个基因序列，最可能的树根位置位于‘旧世界栎’与‘新世界栎’的分化节点处，这与本研究6个基因分析得到的其中一种备选位置一致。通过分子定年方法，我们推断栎属的主要分化发生在始新世，树根的分化时间约为5000万至5500万年前，这与古植物学证据相符。最终，无论选择何种外类群，本研究数据均强化了新世界演化支内的拓扑结构：即（原栎组 + 栎亚属）为尖叶栎组的姊妹演化支。该演化支以及栗叶栎组-冬青栎组的分化时间普遍较化石记录预期更年轻，表明该类群的形态分化早于遗传隔离。