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

Abstract

The fossilized birth-death (FBD) model can make use of information contained in multiple fossils representing the same clade, and we here apply this model to infer divergence times in beeches (genus Fagus), using 53 fossils and 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 factors to choose among alternative root positions. The crown group of Fagus is dated to 53 (62-43) Ma; divergence of the sole American species to 44 (51-39) Ma and divergence between Central European F. sylvatica and Eastern Mediterranean F. orientalis to 8.7 (20-1.8) Ma, unexpectedly old. The FBD model can accommodate fossils as sampled ancestors or as extinct or unobserved lineages; however, this makes its raw output, which shows all fossils on 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 5× 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'.

Keywords: Osmundaceae; beeches; evolutionary turnover rate; fossil record; fossilized birth–death model; molecular-clock calibration.

Figure 1.

Maximum-likelihood (ML) phylogram from nuclear ITS and LFY-i2 sequences from representatives of all species of Fagus with the alternate roots (see Material and methods). Bayes factor comparison favoured the rooting A. Numbers at branches indicate non-parametric bootstrap support under ML optimization. Characteristic leaves are shown for each species (photos: T. Denk).

Figure 2.

A chronogram for Fagus inferred with fossilized birth death (FBD) dating and 53 fossil taxa obtained with the randomly drawn ages from within each fossil's stratigraphic age interval (electronic supplementary material, table S3). The right-most grey bars at nodes show the highest posterior density (HPD) intervals obtained with the youngest stratigraphic ages, the left-most grey bars, the HPDs obtained with the oldest stratigraphic ages and the middle grey bars, the HPDs obtained with random fossil ages. The coloured bars and dotted lines represent the chronological distribution of the respective fossil based on the palaeobotanical studies cites in electronic supplementary material, table S3 and take into account the divergence times inferred under the FBD model; the raw BEAST2 output is shown in electronic supplementary material, figure S2. Plioc., Pliocene; Qu., Quaternary (Pleistocene, Holocene).