Relaxed phylogenetics and dating

We examined whether: i) strict clock models are generally more appropriate in shallow phylogenies where rate variation is expected to be low, ii) the likelihood ratio test of the clock (LRT) reliably informs which model is appropriate for dating divergence times.Strict and relaxed models were used to analyse sequences simulated under different levels of rate variation.

The timing of land plant evolution is fundamental to the interpretation of earth history and macroevolution throughout the Phanerozoic.

Age estimates bear directly on our interpretation of the tempo and mode of morphological and molecular evolution of plants themselves, but also on our interpretation of the evolution of many other groups.

For example, the age of origin of the angiosperms has variously been related to the evolution of other plant lineages (e.g., ferns) (1) and biomes (e.g., tropical forests) (2), as well as to the major insect clades and their feeding habits (3–7), and even to the evolution of fungi (8, 9) and dinosaurs (10).

Nevertheless, we argue that our older estimates should be taken into account in studying the causes and consequences of the angiosperm radiation in relation to other major events, including the diversification of holometabolous insects.

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.

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The new method approaches the problem of rate variation among lineages by proposing a series of local molecular clocks, each extending over a subregion of the full phylogeny.

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