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Divergence time estimation

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Three extant genera of freshwater thalassiosiroid diatoms from Middle Eocene sediments in northern Canada. Late Eocene nonmarine diatoms from the Beaver Divide area, Fremont County, Wyoming, (Book, 1968) [The University of Texas Libraries] A Molecular Genetic Timescale for the Diversification of Autotrophic Stramenopiles (Ochrophyta): Substantive Underestimation of Putative Fossil Ages. Introduction The photosynthetic stramenopiles (Ochrophyta) [1] constitute a highly diverse clade within Heterokonta, a clade that also includes a number of heterotrophic lineages such as plant molds and aquatic pseudofungi [e.g. 2], [3].

A Molecular Genetic Timescale for the Diversification of Autotrophic Stramenopiles (Ochrophyta): Substantive Underestimation of Putative Fossil Ages

The majority of published molecular phylogenetic analyses have indicated that the photosynthetic and non-photosynthetic stramenopiles form a monophyletic taxon [2], [3], [4], [5], [6], [7], [8]. Heterokonts are typically characterized by the presence of a flagellum with tripartite tubular hairs (stramenopiles) and a smooth flagellum (i.e. lacking mastigonemes), although these are secondarily reduced or lost in some lineages [8]. The closest living relative of the heterokont eukaryotes has traditionally remained unclear. However, in a number of recent studies, Rhizaria has been identified with high support values as the sister-lineage ([5], [6]; however, see [7], [9] for different inferred relationships).

Materials and Methods Figure 1. Table 1. 70 Ma nonmarine diatoms from northern Mexico. Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo Method. + Author Affiliations An improved Bayesian method is presented for estimating phylogenetic trees using DNA sequence data.

Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo Method.

The birth-death process with species sampling is used to specify the prior distribution of phylogenies and ancestral speciation times, and the posterior probabilities of phylogenies are used to estimate the maximum posterior probability (MAP) tree. Monte Carlo integration is used to integrate over the ancestral speciation times for particular trees. A Markov Chain Monte Carlo method is used to generate the set of trees with the highest posterior probabilities. Methods are described for an empirical Bayesian analysis, in which estimates of the speciation and extinction rates are used in calculating the posterior probabilities, and a hierarchical Bayesian analysis, in which these parameters are removed from the model by an additional integration.

Bayesian Estimation of Species Divergence Times Under a Molecular Clock Using Multiple Fossil Calibrations with Soft Bounds. + Author Affiliations E-mail: bhrannala@ucdavis.edu.

Bayesian Estimation of Species Divergence Times Under a Molecular Clock Using Multiple Fossil Calibrations with Soft Bounds

Accepted September 13, 2005. We implement a Bayesian Markov chain Monte Carlo algorithm for estimating species divergence times that uses heterogeneous data from multiple gene loci and accommodates multiple fossil calibration nodes. A birth-death process with species sampling is used to specify a prior for divergence times, which allows easy assessment of the effects of that prior on posterior time estimates.

We propose a new approach for specifying calibration points on the phylogeny, which allows the use of arbitrary and flexible statistical distributions to describe uncertainties in fossil dates. . © The Author 2005. Giraffe_Pipe_Fossils. SSU RNA timescale for diatom evolution. Representation of Fossil Calibrations on Bayesian Estimation of Species Divergence Times. + Author Affiliations *Correspondence to be sent to: Department of Biology, Galton Laboratory, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK; E-mail: z.yang@ucl.ac.uk.

Representation of Fossil Calibrations on Bayesian Estimation of Species Divergence Times

Received January 14, 2009. Revision received March 30, 2009. Accepted October 9, 2009. Abstract Bayesian inference provides a powerful framework for integrating different sources of information (in particular, molecules and fossils) to derive estimates of species divergence times. The molecular clock (rate constancy among lineages) (Zuckerkandl and Pauling 1965) provides a powerful way for dating species divergences. Most early molecular dating studies assumed that fossil calibrations provide known ages of nodes with certainty (Graur and Martin 2004). The Bayesian method provides a natural framework for integrating different sources of information, including information about divergence times based on the fossil record. Differences Between MCMCTREE and MULTIDIVTIME (4)Thus, Case 2. Bayesian Dating of Shallow Phylogenies with a Relaxed Clock. Divergence times in foraminifera.

1. Introduction 2. Material and methods 3. Results 4. Acknowledgments. A time-calibrated phylogeny of Pinnularia.