title: Reassessing the temporal evolution of orchids with new fossils and a Bayesian relaxed clock, with implications for the diversification of the rare South American genus Hoffmannseggella (Orchidaceae: Epidendroideae).
abstract: BACKGROUND
  The temporal origin and diversification of orchids (family Orchidaceae) has been subject to intense debate in the last decade. The description of the first reliable fossil in 2007 enabled a direct calibration of the orchid phylogeny, but little attention has been paid to the potential influence of dating methodology in obtaining reliable age estimates. Moreover, two new orchid fossils described in 2009 have not yet been incorporated in a molecular dating analysis. Here we compare the ages of major orchid clades estimated under two widely used methods, a Bayesian relaxed clock implemented in BEAST and Penalized Likelihood implemented in r8s. We then perform a new family-level analysis by integrating all 3 available fossils and using BEAST. To evaluate how the newly estimated ages may influence the evolutionary interpretation of a species-level phylogeny, we assess divergence times for the South American genus Hoffmannseggella (subfam. Epidendroideae), for which we present an almost complete phylogeny (40 out of 41 species sampled).
  
  
  RESULTS
  Our results provide additional support that all extant orchids shared a most recent common ancestor in the Late Cretaceous (approximately 77 million years ago, Ma). However, we estimate the crown age of the five orchid subfamilies to be generally (approximately1-8 Ma) younger than previously calculated under the Penalized Likelihood algorithm and using a single internal fossil calibration. The crown age of Hoffmannseggella is estimated here at approximately 11 Ma, some 3 Ma more recently than estimated under Penalized Likelihood.
  
  
  CONCLUSIONS
  Contrary to recent suggestions that orchid diversification began in a period of global warming, our results place the onset of diversification of the largest orchid subfamilies (Orchidoideae and Epidendroideae) in a period of global cooling subsequent to the Early Eocene Climatic Optimum. The diversification of Hoffmannseggella appears even more correlated to late Tertiary climatic fluctuations than previously suggested. With the incorporation of new fossils in the orchid phylogeny and the use of a method that is arguably more adequate given the present data, our results represent the most up-to-date estimate of divergence times in orchids.
authors.affiliation: Gothenburg Botanical Garden, Carl Skottsbergs gata 22A, 413 19 Göteborg, Sweden.
authors.forename: A Lovisa S
authors.initials: AL
authors.lastname: Gustafsson
authors.forename: Christiano F
authors.initials: CF
authors.lastname: Verola
authors.forename: Alexandre
authors.initials: A
authors.lastname: Antonelli
mesh_terms: D001499:Bayes Theorem; D018744:DNA, Plant / Q000235:genetics; D021903:DNA, Ribosomal Spacer / Q000235:genetics; D019143:Evolution, Molecular; D005580:Fossils; D016013:Likelihood Functions; D029595:Orchidaceae / Q000145:classification* / Q000235:genetics; D010802:Phylogeny; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D013020:South America
chemical_list: D018744:DNA, Plant; D021903:DNA, Ribosomal Spacer