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).

70 Ma nonmarine diatoms from northern Mexico. + Author Affiliations Abstract Carbonaceous cherts of the Tarahumara Formation, exposed near Huepac, Sonora, Mexico, contain abundant diatom frustules occurring as benthic filamentous colonies.

70 Ma nonmarine diatoms from northern Mexico

Stratigraphic and paleontological observations indicate that Tarahumara sediments accumulated in a nonmarine setting; radiometric ages on encompassing volcanic rocks delimit their depositional age to ca. 70 Ma. Tarahumara fossils therefore extend the paleontological record of nonmarine diatoms from middle Eocene to Late Cretaceous. 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. 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.

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. Bayesian Dating of Shallow Phylogenies with a Relaxed Clock. Divergence times in foraminifera. A time-calibrated phylogeny of Pinnularia.