2. 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

4. .. , 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

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

7. 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

9. 16S RNA cataloguing Woese C, Fox G (1977). Phylogenetic structure of the prokaryotic domain: the primary kingdoms Proc Natl Acad Sci USA74 (11): 5088–90 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC432104/?page=1

10. 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

11. 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

12. 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 2014 159,813,411,760171,744,486 WGS Bases Sequences 621,015,432,437143,446,790 RDP II March 7, 2014 :: 2,929,433 16S rRNAs 93 single sided pages Fitch WM and Margoliash E (1967) Construction of phylogenetic trees

13. 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

16. 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 Mycobacteriumtuberculosis (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.

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

18. 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.

19. Download SeaView 4.0http://pbil.univ-lyon1.fr/software/seaview.html

20. Seaview 4.0

21. Cytochrome c

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

25. Summary Read

26. References C R Woese and G E Fox (1977) Phylogenetic structure of the prokaryoticdomain: the primarykingdomsProc NatlAcadSci 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, 750-755 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

27. Baba M, Dargat LL, Goodman M and Czelusniak J (1981) Evolution of Cytochrome C Investigated by the Maximum Parsimony Method. J MolEvol17:197---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