02732nas a2200157   4500008004100000020001400041245013100055210006900186300000700255490000600262520220300268100002802471700001802499700001602517856004102533       2011                        eng d  a1741-700700aOrigin and global diversification patterns of tropical rain forests: inferences from a complete genus-level phylogeny of palms0 aOrigin and global diversification patterns of tropical rain fore  a440 v93 aBACKGROUND:Understanding how biodiversity is shaped through time is a fundamental question in biology. Even though tropical rain forests (TRF) represent the most diverse terrestrial biomes on the planet, the timing, location and mechanisms of their diversification remain poorly understood. Molecular phylogenies are valuable tools for exploring these issues, but to date most studies have focused only on recent time scales, which minimizes their explanatory potential. In order to provide a long term view of TRF diversification, we constructed the first complete genus-level dated phylogeny of a largely TRF-restricted plant family with a known history dating back to the Cretaceous. Palms (Arecaceae/Palmae) are one of the most characteristic and ecologically important components of TRF worldwide, and represent a model group for the investigation of TRF evolution.RESULTS:We provide evidence that diversification of extant lineages of palms started during the mid-Cretaceous about 100 million years ago. Ancestral biome and area reconstructions for the whole family strongly support the hypothesis that palms diversified in a TRF-like environment at northern latitudes. Finally, our results suggest that palms conform to a constant diversification model (the 'museum' model or Yule process), at least until the Neogene, with no evidence for any change in diversification rates even through the Cretaceous/Paleogene mass extinction event.CONCLUSIONS:Because palms are restricted to TRF and assuming biome conservatism over time, our results suggest the presence of a TRF-like biome in the mid-Cretaceous of Laurasia, consistent with controversial fossil evidence of the earliest TRF. Throughout its history, the TRF biome is thought to have been highly dynamic and to have fluctuated greatly in extent, but it has persisted even during climatically unfavourable periods. This may have allowed old lineages to survive and contribute to the steady accumulation of diversity over time. In contrast to other plant studies, our results suggest that ancient and steady evolutionary processes dating back to the mid-Cretaceous can contribute, at least in part, to present day species richness in TRF.1 aCouvreur, Thomas, L. P.1 aForest, Felix1 aBaker, W.J.  uhttps://palms.myspecies.info/node/2203197nas a2200229   4500008004100000245012700041210006900168260001800237300001200255490000700267520245100274100002302725700002402748700003002772700002002802700002102822700001802843700002502861700002102886700002002907856004002927       2009                        eng d00aComplete generic-level phylogenetic analyses of palms (Arecaceae) with comparisons of supertree and supermatrix approaches0 aComplete genericlevel phylogenetic analyses of palms Arecaceae w  cApril 1, 2009  a240-2560 v583 aSupertree and supermatrix methods have great potential in the quest to build the tree of life and yet they remain controversial, with most workers opting for one approach or the other, but rarely both. Here, we employed both methods to construct phylogenetic trees of all genera of palms (Arecaceae/Palmae), an iconic angiosperm family of great economic importance. We assembled a supermatrix consisting of 16 partitions, comprising DNA sequence data, plastid restriction fragment length polymorphism data, and morphological data for all genera, from which a highly resolved and well-supported phylogenetic tree was built despite abundant missing data. To construct supertrees, we used variants of matrix representation with parsimony (MRP) analysis based on input trees generated directly from subsamples of the supermatrix. All supertrees were highly resolved. Standard MRP with bootstrap-weighted matrix elements performed most effectively in this case, generating trees with the greatest congruence with the supermatrix tree and fewest clades unsupported by any input tree. Nonindependence due to input trees based on combinations of data partitions was an acceptable trade-off for improvements in supertree performance. Irreversible MRP and the use of strictly independent input trees only provided no obvious benefits. Contrary to previous claims, we found that unsupported clades are not infrequent under some MRP implementations, with up to 13% of clades lacking support from any input tree in some irreversible MRP supertrees. To build a formal synthesis, we assessed the cross-corroboration between supermatrix trees and the variant supertrees using semistrict consensus, enumerating shared clades and compatible clades. The semistrict consensus of the supermatrix tree and the most congruent supertree contained 160 clades (of a maximum of 204), 137 of which were present in both trees. The relationships recovered by these trees strongly support the current phylogenetic classification of palms. We evaluate 2 composite supertree support measures (rQS and V) and conclude that it is more informative to report numbers of input trees that support or conflict with a given supertree clade. This study demonstrates that supertree and supermatrix methods can provide effective, explicit, and complimentary mechanisms for synthesizing disjointed phylogenetic evidence while emphasizing the need for further refinement of supertree methods.1 aBaker, William, J.1 aSavolainen, Vincent1 aAsmussen-Lange, Conny, B.1 aChase, Mark, W.1 aDransfield, John1 aForest, Felix1 aHarley, Madeline, M.1 aUhl, Natalie, W.1 aWilkinson, Mark  uhttps://palms.myspecies.info/node/9