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      Calibrated chronograms, fossils, outgroup relationships, and root priors: re-examining the historical biogeography of Geraniales : Re-examining historical biogeography of Geraniales

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      Biological Journal of the Linnean Society
      Wiley-Blackwell

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          Universal primers for amplification of three non-coding regions of chloroplast DNA.

          Six primers for the amplification of three non-coding regions of chloroplast DNA via the polymerase chain reaction (PCR) have been designed. In order to find out whether these primers were universal, we used them in an attempt to amplify DNA from various plant species. The primers worked for most species tested including algae, bryophytes, pteridophytes, gymnosperms and angiosperms. The fact that they amplify chloroplast DNA non-coding regions over a wide taxonomic range means that these primers may be used to study the population biology (in supplying markers) and evolution (inter- and probably intraspecific phylogenies) of plants.
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            Estimating Absolute Rates of Molecular Evolution and Divergence Times: A Penalized Likelihood Approach

            Rates of molecular evolution vary widely between lineages, but quantification of how rates change has proven difficult. Recently proposed estimation procedures have mainly adopted highly parametric approaches that model rate evolution explicitly. In this study, a semiparametric smoothing method is developed using penalized likelihood. A saturated model in which every lineage has a separate rate is combined with a roughness penalty that discourages rates from varying too much across a phylogeny. A data-driven cross-validation criterion is then used to determine an optimal level of smoothing. This criterion is based on an estimate of the average prediction error associated with pruning lineages from the tree. The methods are applied to three data sets of six genes across a sample of land plants. Optimally smoothed estimates of absolute rates entailed 2- to 10-fold variation across lineages.
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              Paleontological evidence to date the tree of life.

              The role of fossils in dating the tree of life has been misunderstood. Fossils can provide good "minimum" age estimates for branches in the tree, but "maximum" constraints on those ages are poorer. Current debates about which are the "best" fossil dates for calibration move to consideration of the most appropriate constraints on the ages of tree nodes. Because fossil-based dates are constraints, and because molecular evolution is not perfectly clock-like, analysts should use more rather than fewer dates, but there has to be a balance between many genes and few dates versus many dates and few genes. We provide "hard" minimum and "soft" maximum age constraints for 30 divergences among key genome model organisms; these should contribute to better understanding of the dating of the animal tree of life.
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                Author and article information

                Journal
                Biological Journal of the Linnean Society
                Biol J Linn Soc Lond
                Wiley-Blackwell
                00244066
                September 2014
                September 2014
                : 113
                : 1
                : 29-49
                Article
                10.1111/bij.12297
                8d69fd95-b9a3-4524-b186-83b52f163c56
                © 2014

                http://doi.wiley.com/10.1002/tdm_license_1

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