Taxonomy

Question 1

Polyphasic

Answer 1

Phenotypic, phylogenetic and genotypic features

Question 2

Binomial

Answer 2

Genus and species

Question 3

Phenotypic

Answer 3

Traits we can see

Question 4

How similar does an organism have to be genetically to be classified as the same species?

Answer 4

70% related
<3% ssu rRNA
<5c melting GC pair temperature

Question 5

Melting temperature tells us…

Answer 5

GC content

Question 6

Why 16S ssu rRNA?

Answer 6

Large gene with 9 variable regions, well-conserved across species

Question 7

DNA Hybridization

Answer 7

Add organism genome to reference genome, the same places will hybridise.
More hybridisation means more similar

Question 8

Three categories for DNA hybridization

Answer 8

o 0 – 25: Different genera
o <25 >75: same genus different species
o 75 – 100: same species

Question 9

Biochemical phenotypic analysis

Answer 9

Examine fatty acids

Question 10

Phenetic Classification

Answer 10

Based on traits we can see, not necessarily weighted

Question 11

Eukaryotes utilise ____ rRNA

Answer 11

18S

Question 12

FAME

Answer 12

Fatty Acid Methyl Ester

microbes grown under identical conditions as fatty acid composition fluctuates in response to environmental factors

Question 13

Ecological Analysis

Answer 13

Based on ability to colonise a specific environment

Question 14

Morphological analysis

Answer 14

Based on structural analysis

Question 15

Physiological and metabolic

Answer 15

Microbial activity

Question 16

Phylogenetic Tree

Answer 16

Graphic display of relationships

Question 17

OTU

Answer 17

Operational Taxonomic Units

Question 18

Sequenced organisms are on

Answer 18

Branch tips

Question 19

Branching in phylogenetic trees

Answer 19

Shows divergence between organisms

Question 20

Unrooted tree

Answer 20

Takes different organisms and compares them. Direct distance shows relativity.

Question 21

Rooted tree

Answer 21

Use similar, related organisms. Horizontal distance determines relativity. Shows evolutionary progression and node represents common ancestor

Question 22

Nodes

Answer 22

Points of divergence between organisms

Question 23

Trees established via this technique

Answer 23

Gene sequencing

Question 24

Cladistic

Answer 24

Character based, start with assumptions about evolution

Question 25

UPGMA

Answer 25

unweighted pair group method using arithmetic averages

Question 26

UPGMA assumes evolutionary rates are..

Answer 26

Equal

Question 27

When won’t UPGMA work?

Answer 27

When evolutionary rates are not equal

Question 28

UPGMA starts with..

Answer 28

Unrooted tree, push out groups

Question 29

Bootstrapping

Answer 29

For accuracy, count mismatches and divide by 10. Randomise the columns and repeat. Reassemble a tree based on this sequence and gives you a bootstrap value. If you have the same tree ~70% of the time its valid.

Question 30

Microbial Classification

Answer 30

DNA-DNA hybridization at least 70%
melting temp (GC Content) within 5C
3% divergence in RNA sequence

Question 31

Horizontal Gene Transfer

Answer 31

• Movement of genes to other organisms
• Can take DNA from environment
• Can cause divergence

Question 32

Anagenesis

Answer 32

Slow drift over successive generations

Question 33

Bergey’s manual

Answer 33

Described organisms, studied and grown. Contain about 5000

Question 34

Classification Order

Answer 34

Domain > Phylum > Class > Order > Family > Genus > Species