@article {38, 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)}, journal = {BMC Evolutionary Biology}, volume = {10}, number = {1}, year = {2010}, pages = {177}, 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 (~77 million years ago, Ma). However, we estimate the crown age of the five orchid subfamilies to be generally younger (~1-8 Ma) than previously calculated under the Penalized Likelihood algorithm and using a single internal fossil calibration. The crown age of Hoffmannseggella is estimated at ~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.}, isbn = {1471-2148}, url = {http://www.biomedcentral.com/1471-2148/10/177}, author = {Gustafsson, A.L.S. and Verola, C.F. and Antonelli, Alexandre} } @article {39, title = {Climate cooling promoted the expansion and radiation of a threatened group of South American orchids (Epidendroideae: Laeliinae)}, journal = {Biological Journal of the Linnean Society}, volume = {100}, number = {3}, year = {2010}, note = {10.1111/j.1095-8312.2010.01438.x}, pages = {597-607}, abstract = {The Brazilian Cerrado is the most species-rich tropical savanna in the world. Within this biome, the Campos Rupestres ({\textquoteright}rocky savannas{\textquoteright}) constitute a poorly studied and highly threatened ecosystem. To better understand how plants characteristic of this vegetation have evolved and come to occupy the now widely-separated patches of rocky formations in eastern Brazil, we reconstruct the biogeographical history of the rare orchid genus Hoffmannseggella. We apply parsimony and Bayesian methods to infer the phylogenetic relationships among 40 out of the 41 described species. Absolute divergence times are calculated under penalized likelihood and compared with estimates from a Bayesian relaxed clock. Ancestral ranges are inferred for all nodes of the phylogeny using Fitch optimization and statistical dispersal vicariance analysis. In all analyses, phylogenetic uncertainty is taken into account by the independent analysis of a large tree sample. The results obtained indicate that Hoffmannseggella underwent rapid radiation around the Middle/Late Miocene (approximately 11201314{\textdagger}Mya). The region corresponding today to southern Minas Gerais acted as a main source area for several independent range expansions north- and eastwards via episodic corridors. These results provide independent evidence that climate cooling following the Middle Miocene Climatic Optimum (approximately 15{\textdagger}Mya) led to important vegetational shifts in eastern Brazil, causing an increase in the dominance of open versus closed habitats. Polyploidy following secondary contact of previously isolated populations may have been responsible for the formation of many species, as demonstrated by the high ploidy levels reported in the genus.{\textdagger}{\textdagger}{\textcopyright} 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 100, 5972013607.}, isbn = {1095-8312}, url = {http://dx.doi.org/10.1111/j.1095-8312.2010.01438.x}, author = {Antonelli, Alexandre and Verola, C.F. and Parisod, C. and Gustafsson, A.L.S.} }