why taxonomy?why taxonomy? how to determine & classify a ... · taxonomy content why...

34
Taxonomy Content Taxonomy Content Why Taxonomy? Why Taxonomy? How to determine & classify a species Domains versus Kingdoms Domains versus Kingdoms Phylogeny and evolution

Upload: hoangnguyet

Post on 17-Aug-2019

266 views

Category:

Documents


0 download

TRANSCRIPT

Page 1: Why Taxonomy?Why Taxonomy? How to determine & classify a ... · Taxonomy Content Why Taxonomy?Why Taxonomy? How to determine & classify a species Domains versus KingdomsDomains versus

TaxonomyContent

TaxonomyContent

Why Taxonomy?Why Taxonomy?

How to determine & classify a species

Domains versus KingdomsDomains versus Kingdoms

Phylogeny and evolution

Page 2: Why Taxonomy?Why Taxonomy? How to determine & classify a ... · Taxonomy Content Why Taxonomy?Why Taxonomy? How to determine & classify a species Domains versus KingdomsDomains versus

Wh T ?Why Taxonomy?• Classification – Arrangement in groups or taxa g g p

(taxon = group)

• Nomenclature – Assigning names to taxa

• Identification – Determination of taxon to which an• Identification – Determination of taxon to which an

isolate belongs

(Most practical part of taxonomy)

Making sense of Nature

Page 3: Why Taxonomy?Why Taxonomy? How to determine & classify a ... · Taxonomy Content Why Taxonomy?Why Taxonomy? How to determine & classify a species Domains versus KingdomsDomains versus

Classification

Comparison of species based on:

• Natural – anatomical characteristics• Phenetic – phenotypic characteristics• Genotypic – genetic characteristics• Genotypic – genetic characteristics• Phylogenetic – evolutionary links

Page 4: Why Taxonomy?Why Taxonomy? How to determine & classify a ... · Taxonomy Content Why Taxonomy?Why Taxonomy? How to determine & classify a species Domains versus KingdomsDomains versus

Polyphasic TaxonomyPolyphasic Taxonomy

• used to determine the genus and species of a newly discovered procaryote

• incorporates information from genetic, h t i d h l ti l iphenotypic and phylogenetic analysis

genus – well defined group of one or more species that is clearly separate from other generathat is clearly separate from other genera

Page 5: Why Taxonomy?Why Taxonomy? How to determine & classify a ... · Taxonomy Content Why Taxonomy?Why Taxonomy? How to determine & classify a species Domains versus KingdomsDomains versus

Defining procaryotic species & strains

• Definition species:– collection of strains that share many stable properties and

differ significantly from other groups of strains

• Alternative definition:ll ti f i th t h th i– collection of organisms that share the same sequences in

their core housekeeping genes

• Strain:descended from a single pure microbial culture- descended from a single, pure microbial culture

- Type strain: usually one of first strains of a species studied

Page 6: Why Taxonomy?Why Taxonomy? How to determine & classify a ... · Taxonomy Content Why Taxonomy?Why Taxonomy? How to determine & classify a species Domains versus KingdomsDomains versus

Fig. 19.7 Hierarchical arrangement in Taxonomy.g. 9.7 e c c ge e o o y.

Binomial System of Nomenclature(Carl von Linné)

Page 7: Why Taxonomy?Why Taxonomy? How to determine & classify a ... · Taxonomy Content Why Taxonomy?Why Taxonomy? How to determine & classify a species Domains versus KingdomsDomains versus

Numerical TaxonomyNumerical Taxonomy• To create phenetic classification systemsTo create phenetic classification systems• multistep process

– code information about properties of organismscode information about properties of organisms• e.g., 1 = has trait; 0 = doesn’t have trait

– use computer to compare organisms on 50 characters

– determine association coefficientt t i il it t i– construct similarity matrix

– identify phenons and construct dendograms

Page 8: Why Taxonomy?Why Taxonomy? How to determine & classify a ... · Taxonomy Content Why Taxonomy?Why Taxonomy? How to determine & classify a species Domains versus KingdomsDomains versus

Association coefficients

• Simple matchingSimple matching coefficient (SSM)

• Jaccard coefficient– ignores characters g

that both lack

Page 9: Why Taxonomy?Why Taxonomy? How to determine & classify a ... · Taxonomy Content Why Taxonomy?Why Taxonomy? How to determine & classify a species Domains versus KingdomsDomains versus

• dendogram – treelike diagram used to display resultsdendogram treelike diagram used to display results

• phenon – group of organisms with great similarity– phenons with 80% similarity = bacterial species– phenons with 80% similarity = bacterial species

similaritymatrix

rearranged andjoined to show l t

dendogrammatrix clusters

Figure 19.6

Page 10: Why Taxonomy?Why Taxonomy? How to determine & classify a ... · Taxonomy Content Why Taxonomy?Why Taxonomy? How to determine & classify a species Domains versus KingdomsDomains versus

Techniques for Determining Microbial Taxonomy and Phylogeny

• Classical Characteristics• Classical CharacteristicsMorphological

EcologicalPh i l i lPhysiologicalBiochemical

Genetic

Page 11: Why Taxonomy?Why Taxonomy? How to determine & classify a ... · Taxonomy Content Why Taxonomy?Why Taxonomy? How to determine & classify a species Domains versus KingdomsDomains versus
Page 12: Why Taxonomy?Why Taxonomy? How to determine & classify a ... · Taxonomy Content Why Taxonomy?Why Taxonomy? How to determine & classify a species Domains versus KingdomsDomains versus

The largest bacterium: 600 μm by 80 μmThe largest bacterium: 600 μm by 80 μm

Page 13: Why Taxonomy?Why Taxonomy? How to determine & classify a ... · Taxonomy Content Why Taxonomy?Why Taxonomy? How to determine & classify a species Domains versus KingdomsDomains versus
Page 14: Why Taxonomy?Why Taxonomy? How to determine & classify a ... · Taxonomy Content Why Taxonomy?Why Taxonomy? How to determine & classify a species Domains versus KingdomsDomains versus

Ecological CharacteristicsEcological Characteristics

life-cycle patternslife-cycle patternssymbiotic relationshipsability to cause disease

habitat preferenceshabitat preferencesgrowth requirements

Page 15: Why Taxonomy?Why Taxonomy? How to determine & classify a ... · Taxonomy Content Why Taxonomy?Why Taxonomy? How to determine & classify a species Domains versus KingdomsDomains versus
Page 16: Why Taxonomy?Why Taxonomy? How to determine & classify a ... · Taxonomy Content Why Taxonomy?Why Taxonomy? How to determine & classify a species Domains versus KingdomsDomains versus

API 20E system for several physiological testsAPI 20E system for several physiological tests

Figure 35.6

Page 17: Why Taxonomy?Why Taxonomy? How to determine & classify a ... · Taxonomy Content Why Taxonomy?Why Taxonomy? How to determine & classify a species Domains versus KingdomsDomains versus

Figure 35.5a. Classic dichotomous keys for clinically important genera.

Page 18: Why Taxonomy?Why Taxonomy? How to determine & classify a ... · Taxonomy Content Why Taxonomy?Why Taxonomy? How to determine & classify a species Domains versus KingdomsDomains versus

Molecular CharacteristicsMolecular Characteristics

Comparison of proteinsNucleic acid base compositionNucleic acid base composition

Nucleic acid hybridizationyNucleic acid sequencing

Page 19: Why Taxonomy?Why Taxonomy? How to determine & classify a ... · Taxonomy Content Why Taxonomy?Why Taxonomy? How to determine & classify a species Domains versus KingdomsDomains versus

N l i id b itiNucleic acid base composition

G + C content

- Mol% G + C = (G + C/G + C + A + T)100( )

Often determined from melting temperature (T )- Often determined from melting temperature (Tm)

- Variation within a genus usually < 10%

Page 20: Why Taxonomy?Why Taxonomy? How to determine & classify a ... · Taxonomy Content Why Taxonomy?Why Taxonomy? How to determine & classify a species Domains versus KingdomsDomains versus

as temperature slowlyincreases, hydrogen bondsb k d t d

DNA issinglebreak, and strands

begin to separate

singlestranded

Figure 19.8 DNA melting curve.

Page 21: Why Taxonomy?Why Taxonomy? How to determine & classify a ... · Taxonomy Content Why Taxonomy?Why Taxonomy? How to determine & classify a species Domains versus KingdomsDomains versus
Page 22: Why Taxonomy?Why Taxonomy? How to determine & classify a ... · Taxonomy Content Why Taxonomy?Why Taxonomy? How to determine & classify a species Domains versus KingdomsDomains versus

Nucleic acid hybridizationNucleic acid hybridization

f h l• measure of sequence homology• common procedure:

bind nonradioacti e DNA– bind nonradioactive DNAto nitrocellulose filterincubate filter with radioactive– incubate filter with radioactivesingle-stranded DNA

– measure amount of radioactivemeasure amount of radioactiveDNA attached to filter

Figure 19.9

Page 23: Why Taxonomy?Why Taxonomy? How to determine & classify a ... · Taxonomy Content Why Taxonomy?Why Taxonomy? How to determine & classify a species Domains versus KingdomsDomains versus

Nucleic acid sequencingNucleic acid sequencing

• most powerful and direct method for comparing genomesp g g

• sequences of 16S & 18S rRNA (SSU rRNAs) are used most often in phylogenetic studiesare used most often in phylogenetic studies

• complete chromosomes can now be sequenced and compared(BIOINFORMATICS !)(BIOINFORMATICS !)

Page 24: Why Taxonomy?Why Taxonomy? How to determine & classify a ... · Taxonomy Content Why Taxonomy?Why Taxonomy? How to determine & classify a species Domains versus KingdomsDomains versus

Genetic AnalysisGenetic Analysis

• study of chromosomal gene exchange by transformation and conjugationtransformation and conjugation– these processes rarely cross genera

• plasmids can help to solve confusion in theplasmids can help to solve confusion in the analysis of phenotypic traits

Page 25: Why Taxonomy?Why Taxonomy? How to determine & classify a ... · Taxonomy Content Why Taxonomy?Why Taxonomy? How to determine & classify a species Domains versus KingdomsDomains versus

Fig. 19.11 Overview Genomic fingerprinting technique.

Page 26: Why Taxonomy?Why Taxonomy? How to determine & classify a ... · Taxonomy Content Why Taxonomy?Why Taxonomy? How to determine & classify a species Domains versus KingdomsDomains versus

Relative Taxonomic Resolution of Various Molecular Techniques

Figure 19.12

Page 27: Why Taxonomy?Why Taxonomy? How to determine & classify a ... · Taxonomy Content Why Taxonomy?Why Taxonomy? How to determine & classify a species Domains versus KingdomsDomains versus

The Major Divisions of LifeThe Major Divisions of Life

• Currently held: 3 domains of life:–BacteriaBacteria–Archaea–Eucarya

• Scientists do not all agree aboutScientists do not all agree aboutthis way of the “Tree of Life”

Page 28: Why Taxonomy?Why Taxonomy? How to determine & classify a ... · Taxonomy Content Why Taxonomy?Why Taxonomy? How to determine & classify a species Domains versus KingdomsDomains versus

The suggestedKingdomsKingdoms

Page 29: Why Taxonomy?Why Taxonomy? How to determine & classify a ... · Taxonomy Content Why Taxonomy?Why Taxonomy? How to determine & classify a species Domains versus KingdomsDomains versus

Figure 19.14 Variations in Design of “Tree of Life”.

Page 30: Why Taxonomy?Why Taxonomy? How to determine & classify a ... · Taxonomy Content Why Taxonomy?Why Taxonomy? How to determine & classify a species Domains versus KingdomsDomains versus

Figure 19.3 Universal Phylogenetic Tree.

Page 31: Why Taxonomy?Why Taxonomy? How to determine & classify a ... · Taxonomy Content Why Taxonomy?Why Taxonomy? How to determine & classify a species Domains versus KingdomsDomains versus

Comparative Analysis of 16S rRNA sequences

• Oligonucleotide signature sequences– short conserved sequences specific for a phylogenetically

defined group of organisms

• Organisms relatedness = association coefficient (Sab)

th hi h th S l th l l l t d th– the higher the Sab value, the more closely related the organisms

Page 32: Why Taxonomy?Why Taxonomy? How to determine & classify a ... · Taxonomy Content Why Taxonomy?Why Taxonomy? How to determine & classify a species Domains versus KingdomsDomains versus

Small Ribosomal Subunit rRNA

Fig. 19.10

Frequently used to create trees showing broad relationships

Page 33: Why Taxonomy?Why Taxonomy? How to determine & classify a ... · Taxonomy Content Why Taxonomy?Why Taxonomy? How to determine & classify a species Domains versus KingdomsDomains versus
Page 34: Why Taxonomy?Why Taxonomy? How to determine & classify a ... · Taxonomy Content Why Taxonomy?Why Taxonomy? How to determine & classify a species Domains versus KingdomsDomains versus

Universal PhylogeneticUniversal Phylogenetic Tree with Lateral Gene

TransferTransfer