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
Probably
Haeckel’s most
famous tree
An early tree
of life from
Haeckel
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
16S RNA cataloguing
Woese C, Fox G (1977). Phylogenetic structure of the prokaryotic domain:
the primary kingdoms Proc Natl Acad Sci USA 74 (11): 5088–90
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC432104/?page=1
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: 4576–9
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC432104/?tool=pmcentrez
Conserved primer sites on 16S rRNA
Tung et al., 2002
E. coli 16S 2° structure E. coli 30S ribosomal subunit
E. coli 16S 3D structure
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
93 single sided pages
Fitch WM and Margoliash E (1967)
Construction of phylogenetic trees
Date
Bases
Sequences
Apr 2014 159,813,411,760 171,744,486
WGS
Bases
Sequences
621,015,432,437 143,446,790
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 - http://rdp.cme.msu.edu/
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 27294.
GenBank accession number (16S rDNA): BX248338.
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 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 4.0
http://pbil.univ-lyon1.fr/software/seaview.html
Seaview 4.0
Cytochrome c
>gi|585539546|gb|CP002885.1|:1470068-1471603 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: 5088–5090
http://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 structure
http://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, 957–976
Tung CS, Joseph S and Sanbonnatsu KY (2002) All-atom homology model of
the Escherichia coli 30S ribosomal subunit. Nature Structural Biology 9, 750755
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 27:221-224
http://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---213
Ambler RP and Daniel M (1991) Rattlesnake cytochrome c: A re-appraisal
of the reported amino acid sequence. Biochem. J. 274, 825-831
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, 345-351