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

<div><p>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.</p>