Systematics, Taxonomy, Phylogeny and Evolution Systematics The systematic classification of organisms, the science of systematic classification and the.

Slides:



Advertisements
Similar presentations
The History of Classification Out of this concept was developed the "scale of nature" idea that suggested living things were arranged on a scale of perfection,
Advertisements

Alberts, Bray, Hopkins, Johnson Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings Professor: Dr. Barjis Room: P313 Phone: (718)
Microbial Taxonomy and the Evolution of Diversity 1 19 Copyright © McGraw-Hill Global Education Holdings, LLC. Permission required for reproduction or.
Phylogeny Systematics Cladistics
Chapter 17 Table of Contents Section 1 Biodiversity
THE EVOLUTIONARY HISTORY OF BIODIVERSITY
MICROBIAL TAXONOMY Phenotypic Analysis Genotypic Analysis.
Phylogenetic Trees Understand the history and diversity of life. Systematics. –Study of biological diversity in evolutionary context. –Phylogeny is evolutionary.
Phylogeny and Systematics
Plant Molecular Systematics (Phylogenetics). Systematics classifies species based on similarity of traits and possible mechanisms of evolution, a change.
PHYLOGENY AND SYSTEMATICS
Chapter 26 – Phylogeny & the Tree of Life
Lecture 2 Overview of Microbial Diversity Prokaryotic and Eukaryotic Cells Taxonomy and Nomenclature (Text Chapters: 2; 11)
Bioinformatics and Phylogenetic Analysis
CHAPTER 25 TRACING PHYLOGENY. I. PHYLOGENY AND SYSTEMATICS A.TAXONOMY EMPLOYS A HIERARCHICAL SYSTEM OF CLASSIFICATION  SYSTEMATICS, THE STUDY OF BIOLOGICAL.
Topic : Phylogenetic Reconstruction I. Systematics = Science of biological diversity. Systematics uses taxonomy to reflect phylogeny (evolutionary history).
Summer 2008 Workshop in Biology and Multimedia for High School Teachers.
AN INTRODUCTION TO TAXONOMY: THE BACTERIA
Phylogeny & The Tree of Life. Phylogeny  The evolutionary history of a species or group of species.
Phylogeny and the Tree of Life
The diversity of genomes and the tree of life
Systematics The study of biological diversity in an evolutionary context.
THE PROKARYOTES. Systematics of Prokaryotes Focus on animals and plants –History limited to 20% of evolutionary time How to classify prokaryotes? Limited.
Microbial taxonomy and phylogeny
March 3 rd, 2010  Warm Up Open to ch. 17 to follow along with lecture  Today Review Ch. 17 Lab  Homework Study for Ch. 17 exam on Friday.
Taxonomy & Classification Taxonomy- science of identifying and classifying organisms; all about the naming Classification- systematic grouping and naming.
Systematics the study of the diversity of organisms and their evolutionary relationships Taxonomy – the science of naming, describing, and classifying.
The Evolutionary History of Biodiversity
Prokaryote Taxonomy & Diversity Classification, Nomenclature & Identification Phenetic Classification Molecular Phylogeny Approach Classification (hierarchical.
Phylogenetics Chapter 26. Slide 2 of 17 Ontogeny recapitulates Phylogeny  Ontogeny – development from embryo to adult  Phylogeny – evolutionary history.
Chapter 26: Phylogeny and the Tree of Life Objectives 1.Identify how phylogenies show evolutionary relationships. 2.Phylogenies are inferred based homologies.
Updated: January 2015 By Jerald D. Hendrix. A. Classification Systems B. Levels of Classification C. Definition of “Species” D. Nomenclature E. Useful.
Prokaryote Taxonomy & Diversity
© 2012 Pearson Education, Inc. Lecture by Edward J. Zalisko PowerPoint Lectures for Campbell Biology: Concepts & Connections, Seventh Edition Reece, Taylor,
3- RIBOSOMAL RNA GENE RECONSTRUCITON  Phenetics Vs. Cladistics  Homology/Homoplasy/Orthology/Paralogy  Evolution Vs. Phylogeny  The relevance of the.
Classical Taxonomy & Molecular Phylogeny [ ] SPI 5 Apply evidence from the fossil record, comparative anatomy, amino acid sequences, and DNA structure.
Christian Rinke Microbial Genomics DOE, Joint Genome Institute Introduction to ARB (From A User's Perspective)
Warm-Up 1.Contrast adaptive radiation vs. convergent evolution? Give an example of each. 2.What is the correct sequence from the most comprehensive to.
Taxonomy of Cellular Life Taxonomy: classification (hierarchical grouping based on characteristics); nomenclature (naming); identification (define characteristics.
Identification and Classification of Prokaryotes
Chapter 26 Phylogeny and the Tree of Life
PHYLOGENY AND THE TREE OF LIFE Chapter 26 Sections 1-3 and 6.
Calculating branch lengths from distances. ABC A B C----- a b c.
Diversity of Living Things 1.1: Biodiversity. Biodiversity Number and variety of species and ecosystems on Earth By the end of 2010, 1.7 million species.
Bioinformatics for Human Biologists Rasmus Wernersson, Associate Professor Center for Biological Sequence Analysis, DTU [ -
Agenda Microevolution Test Reflection
ORGANIZING BIODIVERSITY. A SPECIES How do we define a species? A reproductive population that occupies a specific niche (plays a role) in nature Individuals.
Major characteristics used in taxonomy
Chapter 26 Phylogeny and Systematics. Tree of Life Phylogeny – evolutionary history of a species or group - draw information from fossil record - organisms.
Chapter 18 Phylogeny and the Tree of Life. Phylogeny u Phylon = tribe, geny = genesis or origin u The evolutionary history of a species or a group of.
NEW CHAPTER TOPIC: TAXONOMY.
Ch 23: Understanding Diversity: Systematics. phylogeny systematics taxonomy taxon.
General Microbiology (Micr300)
Phylogeny and the Tree of Life
Bioinformatics Overview
Introduction to Bioinformatics Resources for DNA Barcoding
Classification of Living Things
Chapter 17 Table of Contents Section 1 Biodiversity
Microbial Taxonomy and the Evolution of Diversity
Phylogeny and the Tree of Life
Chapter 17 Table of Contents Section 1 Biodiversity
Domains & Dogma.
Ch. 4 Taxonomy and Phylogeny of Animals
Chapter 25 Phylogeny and the Tree of Life
Chapter 17 Table of Contents Section 1 Biodiversity
Explore Evolution: Instrument for Analysis
CC1: Introduction to microbiology and microbial diversity
Classification of Organisms
Unit Genomic sequencing
Domains & Dogma.
Presentation transcript:

Systematics, Taxonomy, Phylogeny and Evolution Systematics The systematic classification of organisms, the science of systematic classification and the methods of classification Taxonomy Naming and classifying organisms in an ordered system indicating natural relationships Carl Linnaeus (1707 – 1778) Linnaeus set about classifying living organisms into natural groups and arranged them in a hierarchical system

.., Phylogeny and Evolution Phylogeny The sequence of events involved in the evolutionary development of a species or taxonomic group Evolution The process through which a population of organisms accumulates genetic changes enabling them to adapt to their environment or ecological niche Charles Lyell (1797 – 1875) geologic change is the steady accumulation of minute changes over enormously long spans of time Charles Darwin (1809 – 1882) Evolution – descent with modification Ernst Haeckel (1834 – 1919) First used the term phylogeny and constructed a tree

A tree from Darwin’s notebook An early tree of life from Haeckel Probably Haeckel’s most famous tree

Cytochrome c Sanger sequencing – protein sequencing!!! Cytochrome c, as a short protein – approx. 100 aa, was relatively easy to sequence Dayhoff “Atlas of protein sequence and structure” The first database of sequence data and development of computer (punch cards!) alignment and calculation of evolutionary distance

Woese C, Fox G (1977). Phylogenetic structure of the prokaryotic domain: the primary kingdoms Proc Natl Acad Sci USA 74 (11): 5088–90Phylogenetic structure of the prokaryotic domain: the primary kingdoms Proc Natl Acad Sci USA 74 (11): 5088– S RNA cataloguing

Woese C, Kandler O, Wheelis M (1990).Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 87: 4576–9Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 87: 4576–9

Conserved primer sites on 16S rRNA E. coli 16S 2° structure E. coli 30S ribosomal subunit E. coli 16S 3D structure Tung et al., 2002

93 single sided pages Fitch WM and Margoliash E (1967) Construction of phylogenetic trees There are approximately 126,551,501,141 bases in 135,440,924 sequence records in the traditional Genbank sections Aug 9, 2011 :: 1,921,179 16S rRNAs Genbank Date Bases Sequences Apr ,813,411,760171,744,486 WGS Bases Sequences 621,015,432,437143,446,790 RDP II March 7, 2014 :: 2,929,433 16S rRNAs

16S phylogenetics of Mycobacterium tuberculosis related species Retrieve the 16S sequence for the type strain of Mycobacterium tuberculosis from Genbank from RDP II - Choose related species using Blast and SeqMatch in RDP II Generate a tree to identify the group of species identified as the MTBC

Bergey’s Manual. The Mycobacteriaceae. Magee and Ward (2013) The mol% G+C of the DNA is: not determined. Type strain: ATCC GenBank accession number (16S rDNA): BX Euzeby List of Prokayotic names with standing in Nomenclature Mycobacterium tuberculosis (Zopf 1883) Lehmann and Neumann 1896, species. (Type species of the genus.) Type strain: (see also StrainInfo.net) strain H37Rv = ATCC Sequence accession no. (16S rRNA gene) for the type strain: X58890.StrainInfo.net) strain H37Rv = ATCC Sequence accession no. (16S rRNA gene) for the type strain: X58890.

Could limit to Mycobacterium? May not know how similar related sequences are – may need to experiment May not know how many relevant sequences

BLAST computes a pairwise alignment between a query and the database sequences searched. It does not explicitly compute an alignment between the different database sequences (i.e., does not perform a multiple alignment). For purposes of this sequence tree presentation an implicit alignment between the database sequences is constructed, based upon the alignment of those (database) sequences to the query. It may often occur that two database sequences align to different parts of the query, so that they barely overlap each other or do not overlap at all. In that case it is not possible to calculate a distance between these two sequences and only the higher scoring sequence is included in the tree.

Download SeaView 4.0

Seaview 4.0

Cytochrome c

>gi| |gb|CP |: Mycobacterium tuberculosis CCDC5180, complete genome

Summary Read

References C R Woese and G E Fox (1977) Phylogenetic structure of the prokaryotic domain: the primary kingdoms Proc Natl Acad Sci U S A. 74: 5088– Dayhoff, MO, Schwartz, RM and Orcutt, BC (1978) A model of evolutionary change in proteins. Atlas of protein sequence and structure Wiedenbeck J and Cohan FM (2011) Origins of bacterial diversity through horizontal genetic transfer and adaptation to new ecological niches. FEMS Microbiol Rev 35, 957–976 Tung CS, Joseph S and Sanbonnatsu KY (2002) All-atom homology model of the Escherichia coli 30S ribosomal subunit. Nature Structural Biology 9, Gouy M., Guindon S. and Gascuel O. (2010) SeaView version 4 : a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Molecular Biology and Evolution 27: Fitch WM and Margoliash E (1967) Construction of phylogenetic trees. Science 155:

Baba M, Dargat LL, Goodman M and Czelusniak J (1981) Evolution of Cytochrome C Investigated by the Maximum Parsimony Method. J Mol Evol 17: Ambler RP and Daniel M (1991) Rattlesnake cytochrome c: A re-appraisal of the reported amino acid sequence. Biochem. J. 274, Schmidt TR, Wildman DE, Uddin M, Opazo JC, Goodman M and Grossman LI (2005) Rapid electrostatic evolution at the binding site for cytochrome c on cytochrome c oxidase in anthropoid primates. PNAS 102, 6379–6384 Sandra L. Baldauf (2003) Phylogeny for the faint of heart: a tutorial. TRENDS in Genetics 19,