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,