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. Citation: Brown JW, Sorhannus U (2010) A Molecular Genetic Timescale for the Diversification of Autotrophic Stramenopiles (Ochrophyta): Substantive Underestimation of Putative Fossil Ages.
PLoS ONE 5(9): e12759. Editor: M. Thomas P. Gilbert, Natural History Museum of Denmark, Denmark Received: July 1, 2010; Accepted: August 20, 2010; Published: September 16, 2010 Copyright: © 2010 Brown, Sorhannus. Funding: JWB is funded through a Rackham Predoctoral Fellowship from the University of Michigan. Competing interests: The authors have declared that no competing interests exist. 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]. Materials and Methods Taxon sampling and nucleotide alignment The software package DAMBE v4.5.55 [34] was utilized to manage the nucleotide data. Phylogenetic tree reconstruction. 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.
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.
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. A molecular phylogenetic dating study, using the PATHd8 program, was conducted to infer the time frame within which the diatoms originated and diversified.
A Proterozoic to Early Paleozoic origin was rejected while an Early Triassic (i.e. 250 Ma) to Early Jurassic (i.e. 183 Ma) evolution of the group was supported. However, when considering the inconsistencies in the divergence dates, caused by the somewhat contradictory fixages, the diatoms may have evolved between the late Permian (i.e. 267 Ma) and the Middle Jurassic (i.e. 162 Ma). According to the chronogram of the original PATHd8 analysis, modern “centric diatoms” already existed in the Early Jurassic, “araphid pennates” should be discovered in Lower Cretaceous sediments and the “raphid pennates” are expected to be present in Upper Cretaceous deposits. 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.
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).
Bayesian Dating of Shallow Phylogenies with a Relaxed Clock. Divergence times in foraminifera. Abstract Accurate and precise estimation of divergence times during the Neo-Proterozoic is necessary to understand the speciation dynamic of early Eukaryotes.
However such deep divergences are difficult to date, as the molecular clock is seriously violated. Recent improvements in Bayesian molecular dating techniques allow the relaxation of the molecular clock hypothesis as well as incorporation of multiple and flexible fossil calibrations. Divergence times can then be estimated even when the evolutionary rate varies among lineages and even when the fossil calibrations involve substantial uncertainties. In this paper, we used a Bayesian method to estimate divergence times in Foraminifera, a group of unicellular eukaryotes, known for their excellent fossil record but also for the high evolutionary rates of their genomes. Highlights Keywords Foraminifera. A time-calibrated phylogeny of Pinnularia.