Lecture 2: Taxonomy and Biodiversity

Question 1

What is taxonomy

Answer 1

A method of classifying organisms based on ancestry

Question 2

What is classical taxonomy and how did it classify organisms

Answer 2

An old method of classifying organisms based on phenotype

Question 3

What is molecular taxonomy and how does it classify organisms

Answer 3

A modern approach to classifying organisms base on genotype

Question 4

What are the 3 main parts of taxonomy

Answer 4

1. Classification (arrangement of organisms based on similarity)
2. Nomenclature (naming organisms)
3. Identification (determining whether an organism belong to the group which it is classified and named)

Question 5

What is microbial diversity

Answer 5

The NUMBER and ABUNDANCE of species/kinds of organisms in a community

Question 6

How did classical taxonomy ‘correctly’ classify/identify organisms

Answer 6

Scoring of characteristics/phenotypes as 1 (trait positive) or 0 (trait negative).
Therefore, the more similarities between organisms, the more related they are

Question 7

What are Analytical Process Index (“API”) Strips

Answer 7

test strips with various wells containing different conditions for bacterial suspension (inferring bacterial properties).

Question 8

What are pros and cons of API strips

Answer 8

+ Quick and easy
+ can be designed for specific bacteria; disease diagnosis
+ doesn’t require much training
- not as detailed as molecular analysis

Question 9

What is a dendrogram? Whys is it different to a phytogenic tree?

Answer 9

Dendrograms illustrate the degree of relation between organisms by grouping particular traits. Unlike a phytogenic tree, the branches of dendrograms do not insinuate and genetic ‘distance’ from each other

Question 10

How does molecular taxonomy use genomes?

Answer 10

In current times, due to limitations in sequencing technology, whole genomes aren’t often sequenced and instead smaller conserved regions are, such as rRNA genes

Question 11

What are the differences between prokaryote and eukaryotes ribosomes

Answer 11

Euk vs prok

60s+40s=80s 50s+30s=70s

Question 12

What is 16s rRNA and what is its significance?

Answer 12

It is a component of the prokaryotic 30s (small) subunit. It is present in every cell and it ~1550bps long with 1-25 copies of this gene in cells.

Some sections are highly conserved (structural elements) others are more variable

Question 13

What is an example of 2 variable regions within the 16s gene? what is their significance?

Answer 13

V3; 341F/529R and V4; 515F/806R (3rd and 4th variable regions).
nF/nR =forward and reverse primers at that nucleotide.

The 5’ and 3’ ends of these two regions are highly conserved, whereas the central regions are variable

Question 14

How can the 16s infer genomic relation?

Answer 14

Based on the number of similar or different bases down lineages within the 16s gene, level or diversion/relation can be inferred between organisms.

percentage of relation can then be calculated

Question 15

What is the problem with relying on a single gene to infer whole genome/specie relations?

Answer 15

Variations in other genes may be far higher/lower than the 16s region, meaning organisms may realistically be more/less related tan the 16s region suggests

Question 16

What do phylogenetic trees do?

Answer 16

Align homologous sequences and look at the frequency of differences between them to generate a tree

Question 17

what are the two methods of generating phylogenetic trees?

Answer 17

Maximum parsimony and maximal likelihood

Question 18

What is maximal parsimony?

Answer 18

Looks to generate a phylogenetic tree with the fewest possible branches. seeks to limit the amount of homoplasy (i.e., convergent-, parallel evolution, evolutionary reversals)

Keep it simple

Con = more than one tree may produce results consistent with the data

Question 19

What is maximal likelihood?

Answer 19

Based on statistical calculations. For each possible tree, the program calculates the likelihood (probability) that such tree would produce observed data

pro: produces just one tree

Question 20

What are the two main methods of studying diversity

Answer 20

Operational Taxonomic Unit (OTU) and Metagenomics

Question 21

What is operational taxonomic unit?

Answer 21

Used to classify groups of closely related individuals.

Clusters sequences (e.g., 16s rRNA) based on their similarity, a threshold of 97% or higher is often required to create an OTU. Organisms of 98.65% or more similarity may (or may not) be of the same species.
 OTUs = clusters of organisms of varied levels of similarity

CAN THEN BE USED TO WORK OUT DIVERSITY WITHIN A POPULATION

Con; charts don’t state n-size, just abundance

Question 22

What is metagenomics and how is it used here

Answer 22

study of a collection or genetic material. mapping the genomes/genes according to their abundance in a population