Multiple nuclear genes stabilize the phylogenetic backbone of the genus Quercus
Multiple nuclear genes stabilize the phylogenetic backbone of the genus Quercus
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DOI：
10.1080/14772000.2014.941037
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发表时间：
2014-10-02
影响因子：
1.9
通讯作者：
Kremer, Antoine
中科院分区：
文献类型：
--
作者：
Hubert, Francois;Grimm, Guido W.;Kremer, Antoine
108种栎属植物的系统发育关系从该属现有的基因组资源中选择6个核基因的DNA序列进行推断。以前基于传统分子标记的系统发育重建在更深的节点上是不确定的。总的来说，弱的系统发育信号，获得每个单独的基因分析，但更强的信号时，获得基因序列连接。我们的数据支持对六个主要属内类群青冈属、鱼藤属、冬青属、栎属、瓣叶属和原藤壶属的认识。我们的分析提供了更深的节点，但适度的支持和更强大的亚属分类在两个主要的分支，旧世界橡树（青冈属，鱼藤属，冬青属）和新世界橡树（栎属，Lobalus，Protobalanus）的决议。然而，根据外群的选择，我们的分析产生了两个替代位置的青冈属栎属内的分支。当栗木。作为外群，我们的数据表明，栎属由两个分支组成，分别对应于加缪（Camus）所认为的两个亚属：Euquercus Hickel和Camus亚属和青冈（Cyclobalanopsis Oersted（Schneider）亚属。然而，当Notholithocarpus Manos、Cannon和S. Oh被选为外群青冈属亚属，与鱼藤属和冬青属聚簇形成旧大陆分支。为了评估根的位置，我们用ITS和CRC序列的已发表数据补充了我们的数据集。基于连接的八个基因序列，最可能的根位置是在旧世界橡树和新世界橡树之间的分裂，这是我们的六个基因分析建议的替代位置之一。利用测年方法，我们推断栎属的原始分歧的始新世年龄和根的年龄约为50-55 Ma，这与古植物学证据相一致。最后，不管外类群的选择，我们的数据提升了新世界分支内的拓扑结构，其中（原藤壶+栎属）是Lobalus的姐妹分支。推断分歧年龄在这个分支和Cerris-Ilex分支一般比可以预期的化石记录，表明形态分化早于遗传隔离在这个分支。
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 Oersted (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.