Systematics, Taxonomy, Phylogeny and Evolution

SystematicsThe systematic classification of

organisms, the science of systematic classification

and themethods of classification

TaxonomyNaming and classifying organisms in anordered system indicating natural

relationshipsCarl Linnaeus (1707 – 1778)

Linnaeus set about classifying living organisms into

natural groups and arranged them in a hierarchical

system

.. , Phylogeny and EvolutionPhylogeny

The sequence of events involved in the evolutionary

development of a species or taxonomic groupEvolution

The process through which a population of organisms

accumulates genetic changes enabling them to adapt

to their environment or ecological nicheCharles Lyell (1797 – 1875)

geologic change is the steady accumulation of minute changes over enormously long spans of timeCharles Darwin (1809 – 1882)

Evolution – descent with modificationErnst 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 sequenceDayhoff “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): 5088–90http://www.ncbi.nlm.nih.gov/pmc/articles/PMC432104/?page=1

16S 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: 4576–9http://www.ncbi.nlm.nih.gov/pmc/articles/PMC432104/?tool=pmcentrez

Conserved primer sites on 16S rRNA

E. coli 16S 2° structure E. coli 30S ribosomal subunit E. coli 16S 3D structureTung 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

GenbankDate Bases SequencesApr 2014 159,813,411,760 171,744,486 WGS Bases Sequences

621,015,432,437143,446,790RDP IIMarch 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 Genbankfrom RDP II - http://rdp.cme.msu.edu/

Choose related species using Blast and SeqMatch in RDP IIGenerate 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 27294.GenBank accession number (16S rDNA): BX248338.

Euzeby List of Prokayotic names with standing in NomenclatureMycobacterium tuberculosis (Zopf 1883) Lehmann and Neumann 1896, species. (Type species of the genus.) Type strain: (see also StrainInfo.net) strain H37Rv = ATCC 27294. 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 4.0http://pbil.univ-lyon1.fr/software/seaview.html

Seaview 4.0

Cytochrome c

>gi|585539546|gb|CP002885.1|:1470068-1471603 Mycobacterium tuberculosis CCDC5180, complete genome

SummaryRead

ReferencesC R Woese and G E Fox (1977) Phylogenetic structure of the prokaryotic domain: the primary kingdoms Proc Natl Acad Sci U S A. 74: 5088–5090http://www.ncbi.nlm.nih.gov/pmc/articles/PMC432104/?page=1 Dayhoff, MO, Schwartz, RM and Orcutt, BC (1978) A model of evolutionary change in proteins. Atlas of protein sequence and structurehttp://www.bio-recipes.com/Dayhoff/dayhoff1978.pdf Wiedenbeck J and Cohan FM (2011) Origins of bacterial diversity through horizontal genetic transfer and adaptation to new ecological niches. FEMS Microbiol Rev 35, 957–976Tung CS, Joseph S and Sanbonnatsu KY (2002) All-atom homology model of the Escherichia coli 30S ribosomal subunit. Nature Structural Biology 9, 750-755Gouy 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 27:221-224http://mbe.oxfordjournals.org/cgi/content/abstract/27/2/221 Fitch WM and Margoliash E (1967) Construction of phylogenetic trees. Science 155:279 284.http://hughm.cs.ukzn.ac.za/~murrellh/bio/lit/fitch_phylogeny_construction.pdf

Baba M, Dargat LL, Goodman M and Czelusniak J (1981) Evolution of Cytochrome C Investigated by the Maximum Parsimony Method. J Mol Evol 17:197---213Ambler RP and Daniel M (1991) Rattlesnake cytochrome c: A re-appraisal of the reported amino acid sequence. Biochem. J. 274, 825-831Schmidt 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, 6379–6384Sandra L. Baldauf (2003) Phylogeny for the faint of heart: a tutorial. TRENDS in Genetics 19, 345-351