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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
relationships
Carl Linnaeus (1707 – 1778)Linnaeus set about classifying living organisms
intonatural groups and arranged them in a
hierarchicalsystem
.. , 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 niche
Charles 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 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): 5088–90http://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