A Review of the Effect of Relaxed Clock Method, Long Branches, Genes, and Calibrations in the Estimation of Angiosperm Age

Abstract


 The timing of angiosperm origin and diversification is crucial to understand the evolution of terrestrial ecosystems as we know them today. The fossil record and relaxed molecular clocks provide substantially different estimates of the time in which angiosperms started to diversify into lineages that originated living species. The role of different methodological and systematic factors on ages estimated with relaxed clocks across land plants, with a focus on angiosperms, are here reviewed. Different relaxed clocks and molecular data provided similar age estimates for nodes across land plants. Breaking the long branch subtending angiosperms typically did not result in substantially younger age estimates for angiosperms. Including or excluding fossil-derived calibrations on internal nodes had a pronounced effect on ages across the tree, and among examined factors, calibrations were the most influential in resulting ages. However, interactions between calibrations and genes were detected as different genes converged on similar ages when the same set of calibrations was applied. Estimated angiosperm ages were much older than angiosperm earliest fossils. Although a missing fossil history cannot be ruled out, this explanation alone is insufficient considering the gradually increasing abundance, diversity and geographical distribution of angiosperms in the fossil record; the ordered progression of their morphological and functional diversification; and the agreement in the sequence of appearance of lineages in the stratigraphic record and in molecular phylogenies. It is hypothesized that model misspecification may play a role in the observed molecular clock/fossil discrepancy.