molecular systematics

Question 1

How does molecular systematics work?

Answer 1

Makes use of proteins in drawing systematic and biogeographic conclusions, including:
- Nuclear DNA
- Mitochondrial DNA
- Ribosomal nucleic acids

Question 2

The basic premise…

Answer 2

The basic assumption is that hereditary information is carried by molecules of DNA (deoxyribonucleic acid)…

Question 3

Why use molecules?

Answer 3

1. Recognition of cryptic species
2. Recognition of large, unresolved groups
3. Resolving phylogenies at higher levels.

Question 4

Nature of molecular characters

Answer 4

• Actual structure of compounds (e.g., chemical composition of toxic skin secretions/nucleotide sequences of DNA fragments)
• Comparative estimates of relative similarity of compounds (e.g., immunological assays)

Question 5

3 advantages of the molecular methods

Answer 5

1. Permits inferences on probable time of splitting of phyletic lineages
2. Permits inferences on geography of splitting events
3. Phylogenies produce important insights into taxonomy, including:
   - Evolution of characters
   - Long-term patterns and dynamics of adaptation and divergence
   - (Drawbacks: some molecules may evolve at different times in different taxa)

Question 6

Electrophoresis

molecular techniques

Answer 6

appropriate (simplicity of use/inexpensive) for relationships of individuals within and among populations

Question 7

DNA sequencing

Molecular technique

Answer 7

examination of higher-level relationships (which represent older divergences and speciation)

Question 8

molecular phylogeny

Answer 8

study of evolutionary relationships among organisms using techniques of molecular biology

Question 9

molecular marker

Answer 9

A segment of DNA found at a specific site in the genome.
Has properties that enable it to be uniquely recognized using molecular tools such as gel electrophoresis.
Examples: Isozyme loci, microsatellite loci, RFLP, mtDNA and other relevant markers

Question 10

4 examples of molecular marker

Answer 10

• Isozyme loci
• microsatellite loci
• RFLP
• mtDNA
• other relevant markers

Question 11

8 techniques in molecular systematics

Answer 11

1. Allozyme/isozyme analyses
2. Flow cytometry
3. Mitochondrial (mtDNA)
4. RAPD
5. Microsatellite
6. Minisatellite/DNA sequence
7. AFLP
8. RFLP of mt-DNA

Question 12

2 methods of DNA sequencing

Answer 12

1. Chemical degradation method
2. Chain termination method (preferred, as longer sequences can be obtained)

Question 13

1) Random Amplified Polymorphic DNAs (RAPD)

Answer 13

• Detects sequence changes within the annealing sites of PCR primers, resulting in the presence or absence of amplification products from a particular locus.
• Dominant inheritance
• Useful for screening differnces among individuals, populations, and species
• Advantages: i) PCR – lots of product ii) visible on gel without probe
• Disadvantages:
• i) hard to standardize ii) results vary depending on reaction conditions