Relaxed phylogenetics and dating

Over half of all analyses implemented one or more fossil dates as constraints, followed by geological events and secondary calibrations (15% each).

Vertebrate taxa were subjects in nearly half of all studies, while invertebrates and plants together accounted for 43%, followed by viruses, protists and fungi (3% each). doi: 10.1016/20 Pubmed Abstract | Pubmed Full Text | Cross Ref Full Text Hamilton, P.

Molecular-based divergence dating methods, or molecular clocks, are the primary neontological tool for estimating the temporal origins of clades.

While the appropriate use of vertebrate fossils as external clock calibrations has stimulated heated discussions in the paleontological community, less attention has been given to the quality and implementation of other calibration types.

Current patterns in calibration practices were disproportionate to the number of discussions on their proper use, particularly regarding plants and secondarily derived dates, which are both relatively neglected in methodological evaluations. doi: 10.1111/j.1469-7998.2009.00622.x Cross Ref Full Text Goswami, A. A dating success story: genomes and fossils converge on placental mammal origins. doi: 10.1186/2041-9139-3-18 Pubmed Abstract | Pubmed Full Text | Cross Ref Full Text Graur, D., and Martin, W. Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision.

Based on our survey, we provide a comprehensive overview of the latest approaches in clock calibration, and outline strengths and weaknesses associated with each.

As with fossils, the degree of uncertainty surrounding correspondence between the geological event and date of divergence may be expressed probabilistically. Data sets containing sequences isolated at different times, i.e., heterochronous data, are calibrated by assigning known sample ages to terminal nodes in the phylogeny.

These dates are now integrated into a wide array of biological investigations, including studies of ancient dispersal mechanisms, adaptive radiations and species interactions.

This imbalance of dialogue between researchers using alternative (non-fossil-based) calibrations and those focusing on paleontological material is not only detrimental to researchers wishing to reliably date their clades of interest, but also to the results of many studies relying on divergence estimates as a backbone for independent analyses of, among other things, diversification dynamics, biogeography, rates of phenotypic evolution, and character correlation. doi: 10.1093/aob/mcp192 Pubmed Abstract | Pubmed Full Text | Cross Ref Full Text Francisco Ornelas, J., Sosa, V., Soltis, D.

The purpose of the present study is therefore to review current patterns in calibration types employed within the major taxonomic groups (e.g., vertebrates, invertebrates, plants, fungi, bacteria) and compare this to the number of publications discussing their appropriate use.

In lieu of appropriate fossils, many workers instead rely on geological events, substitution rates, known sampling dates, or secondarily and even tertiarily derived node ages to calibrate the molecular clock.

While each of these calibration types has its strengths and weaknesses, the attention they have garnered in the scientific community seems small compared to the large number of commentaries, reviews and databases dedicated to the use of fossil calibrations (see Parham et al., 2012 and references therein).

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