TreeBASE Search-Trees for study 15658

@ARTICLE{TreeBASE2Ref23084, author = {Sidonie Bellot and Susanne S Renner}, title = {Exploring New Dating Approaches for Parasites: The Worldwide Apodanthaceae (Cucurbitales) as an Example.}, year = {2014}, keywords = {Local clocks, molecular clocks, parasitic plants, random local clocks, substitution rates, uncorrelated lognormal clock, Bayes factors, model selection}, doi = {}, url = {http://}, pmid = {}, journal = {Molecular Phylogenetics and Evolution}, volume = {}, number = {}, pages = {}, abstract = {Gene trees of holoparasitic plants usually show distinctly longer branch lengths than seen in photosynthetic closest relatives. Such substitution rate jumps have made it difficult to infer the absolute divergence times of parasites. An additional problem is that parasite clades often lack a fossil record. Using nuclear and mitochondrial DNA sequences of Apodanthaceae, a worldwide family of endoparasites living inside Fabaceae and Salicaceae, we compared several new dating approaches: (i) an uncorrelated lognormal (UCLN) model calibrated with outgroup fossils, (ii) ages of host lineages as a maximal age in an UCLN model, (iii) user-assigned local clocks (LC), and (iv) outgroup-fossil-calibrated random local clocks (RLC) with varying prior probabilities on the number of rate changes (RLCu model, RLCp model). The resulting dated phylogenies include all 10 species of the family, three in Australia, one in Iran, one in Africa, and the remainder in the Americas. All clock models infer a drastic rate jump between nonparasitic outgroups and Apodanthaceae, but since they distribute the rate heterogeneity differently, they result in much-different age estimates. Because the UCLN model is biased against autocorrelation in small datasets and because Bayes factors favor the RLCu model over the RLCp model, we prefer the former, which places the Apodanthaceae stem age at ca. 77 my ago, the divergence between Apodanthes and Pilostyles at 36 my ago, and the crown age of the Australian clade at 8 my ago. In our study system, host-age calibrations did not yield well-constrained results, but random local clocks provided a valuable alternative to the exclusive reliance on UCLN clocks.} }