Relaxed phylogenetics and dating with confidence drummond


06-May-2016 19:26

We attached a prior probability to each fossil-based minimum age, and explored the effects of relying on the first appearance of tricolpate pollen grains as a lower bound for the age of eudicots.Many of our divergence-time estimates for major clades coincide well with both the known fossil record and with previous estimates.In addition, the microfossil pollen record of Acacia is relatively rich and provides a good age constraint for the entire Acacia clade.By using multiple reliable fossil constraints, we applied a combination of primary calibration points to produce a comprehensive study of divergence dates in Acacia s.s. Previous dating studies included very limited samples of the diversity of Australian Acacia and experienced difficulties in identifying appropriate age calibrations for the lineage, leading to considerable variation in their results.

relaxed phylogenetics and dating with confidence drummond-88

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clade and for related lineages across the Mimosoideae subfamily.

Although the methods used here do help to correct for lineage-specific heterogeneity in rates of molecular evolution (associated, for example, with evolutionary shifts in life history), we remain concerned that some such effects (e.g., the early radiation of herbaceous clades within angiosperms) may still be biasing our inferences.

Our understanding of the history of life depends critically on knowledge of the ages of major clades.

In analyses of large multigene datasets, it is often appropriate to use multiple relaxed-clock models to accommodate differing patterns of rate variation among genes.

We present Clocksta R, a method for selecting the number of relaxed clocks for multigene datasets.

The notion of the existence of a so-called "molecular clock" was first attributed to Émile Zuckerkandl and Linus Pauling who, in 1962, noticed that the number of amino acid differences in hemoglobin between different lineages changes roughly linearly with time, as estimated from fossil evidence.



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