Species relationships and divergence times in beeches: new insights from the inclusion of 53 young and old fossils in a birth–death clock model

The fossilizedbirth-death (FBD) model can make use of information contained in multiple fossilsrepresenting the same clade, and we here apply this model to infer divergence times in beeches (genus Fagus), using 53 fossilsand nuclear sequences for all nine species. We also apply FBD dating to the fern clade Osmundaceae, with about 12 living species and 36 fossils. Fagus nuclear sequences cannot be aligned with those of other Fagaceae, and we therefore use Bayes factorsto choose among alternative root positions. The crown groupof Fagus is dated to 53 (62-43) Ma;divergence of the sole American species to 44 (51-39) Ma and divergence between CentralEuropean F. sylvatica and Eastern Mediterranean F. orientalis to 8.7 (20-1.8) Ma, unexpectedly old. The FBD model can accommodate fossilsas sampled ancestors or as extinct or unobserved lineages;however, this makes its raw output, which shows all fossilson short or long branches, problematic to interpret. We use hand-drawn depictions and a bipartition network to illustrate the uncertain placements of fossils. Inferred speciation and extinction rates imply approximately 5x higher evolutionary turnover in Fagus than in Osmundaceae, fitting a hypothesized low turnover in plants adapted to low-nutrient conditions. This article is part of the themed issue 'Dating species divergences using rocks and clocks'.