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phyloseminar -- a free online seminar about phylogenetics
Last update1 hour 53 min ago
October 16, 2013
The fossil record offers a rich source of macroevolutionary data. Fossils can reveal transitional forms that could not be predicted from extant taxa alone, reveal unexpected biogeographic patterns, and provide temporal information crucial for inferring rates of evolution and correlations between evolution and abiotic events. At the same time, including fossil taxa in phylogenetic analyses presents many challenges. Currently, there are a wide variety of methods for including fossil data in phylogenetic analyses ranging from indirect use of fossil ages to inform divergence dates to simultaneous analyses of fossil and extant taxa under various optimality criteria and with varying levels of constraints. One important consideration remains that fossils typically provide only morphological data, which can lead to problems related to missing data and potential violation of common assumptions for model-based phylogeny inference methods designed primarily for molecular sequence data. Morphological character data are typically harvested from from fossils taxa not at random, but with an intentional bias towards parsimony-informative characters (with apomorphies omitted from matrices). Combined with issues related to sparse codings in large combined matrices, care must be taken to avoid spurious inferences.
Tracy Heath: The Fossilized Birth-Death Process: A Coherent Model of Fossil Calibration for Divergence Time Estimation
Accurate estimates of absolute node ages are critical for addressing a wide range of questions in evolutionary biology. Because molecular sequence data are not informative on absolute time, external data–most commonly fossil age estimates–are required to calibrate estimates of species divergence times. For Bayesian divergence-time methods, the common practice for calibration using fossil information involves placing arbitrarily-chosen and parameterized parametric distributions on internal nodes, often disregarding most of the information in the fossil record. The `fossilized birth-death' (FBD) process is a model for calibrating divergence-time estimates in a Bayesian framework, explicitly acknowledging that extant species and fossils are observations from the same macroevolutionary process. Under this model, absolute node age estimates are calibrated by a single diversification model and arbitrary calibration densities are not necessary. Moreover, the FBD model allows for inclusion of all available fossils. We performed analyses of simulated data and show that node-age estimation under the FBD model results in accurate estimates of species divergence times with realistic measures of statistical uncertainty, overcoming major limitations of standard divergence time estimation methods.
The Barcode of Life
The Genealogical World of Phylogenetic Networks
BMC Evolutionary Biology
Molecular Biology and Evolution