Format: ORAL

Andrew B. Leslie1, Stephen A. Smith2, Jeremy M. Beaulieu3

1 Earth and Planetary Science, Stanford University, Stanford, USA 2 Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, USA 3 Biological Sciences, University of Arkansas, Fayetteville, USA

Conifers are the most species-rich extant gymnosperms and have the longest and best-documented fossil history of any seed plant group, making them an excellent study system for investigating plant macroevolution. An accurate time-calibrated phylogeny is important for understanding their evolutionary history, and a number of studies have developed dated molecular trees for major conifer clades or the group as a whole. Except for the possible placement of Gnetales within conifers, backbone relationships among and within conifer families are generally stable across these studies, but inferred divergence ages vary widely depending on the dating method and calibration fossils used. Our previous work in this area used a Bayesian node dating approach and generated conifer divergence age estimates that appeared both too old for many deep nodes and too young for many shallow nodes, given paleobotanical intuition as well as more recent discoveries from Southern Hemisphere fossil assemblages. Angiosperm studies have shown that rate heterogeneity among clades can bias even sophisticated molecular dating analyses, particularly for deep nodes, and this phenomenon may be important in conifers given their long branch lengths and deep divergence ages. Here we develop an updated time-calibrated molecular phylogeny of conifers (as well as other gymnosperms) using a new node-dating approach that incorporates a hidden Markov model (HMM) in estimating divergence ages. This method allows different evolutionary rate classes to be assigned to different clades, which has been shown in simulation studies to improve divergence age estimates, particularly for deep nodes. We also suggest that node dating continues to be important for fossil plants, where important characters are often found in fragmentary remains like pollen grains that do not lend themselves to total evidence analyses.