Molecular Ecology 2025-2026 Fie Thijs
Molecular Ecology 2025-2026 – Exam questions
Chapter 1 – Molecular genetics and markers in ecology
What reagents are necessary to perform PCR?
1. 2 primers (forward and reverse)
2. template dna
3. dntp (deoxyribonucleotides)
4. PCR buffer
5. MgCl2 = cofactor of polymerase
6. polymerase (example: taq polymerase)
What can you tell about Sanger sequencing?
• Developed mid 1970’s
• Dideoxy chain termination method
• 4 reactions (1 for each base – A,T,C,G)
o Generates a set of fragments
o Appears in gel electrophoresis as bands in 4 lanes (1 lane for each base)
• Automated sequencers = bases recognized by dye-terminator
o Each base has its own colour
o Single capillary filled with a polymere
mtDNA: how many basepairs does it contain? What about genes? What % codes for proteins?
• Bp = 16 000 (humans) or 16 500 (fishes)
• Genes (also control region present)
o 13 protein coding genes
o 2 rRNA genes
o 22 tRNA genes
• % coding for proteins = 93%
Explain the genetic code in eukaryotes
• 65 possible codons (61 without stop and start codons)
• 61 sense codons for 21 AA = multiple codons for the same AA
• 3 stopcodons = UGA, UAG, UAA
• 1 start codon = AUG = methionine
• In some nuclear genes = CUG and UUG also start codons
• Mitochondrial gene codons are slightly different = UGA translates to tryptophane instead of stop
What type of mutations are there?
1. nucleotide substitution
2. insertion/deletion
3. gene conversion
4. recombination
1
, Molecular Ecology 2025-2026 Fie Thijs
What is the structure of the human genome
I. mitochondrial genome
1. non-coding dna = control region
2. coding dna
a. 13 protein coding genes
b. 2 rRNA genes
c. 22 tRNA genes
II. nuclear genome
1. genes
A. coding dna = 30 000 – 40 000 genes
B. non-coding dna
a. pseudogenes
b. introns
c. gene fragments
2. dna outside genes
A. single or low copy
B. low to high repetitive
a. LINE
b. SINE
c. satellite dna
Explain the pathway from gene to protein
1. dna
2. transcription to pre-mRNA
3. removal of introns
4. mRNA
5. translation to proteins via codons (using tRNA)
and ribosomes (made with rRNA)
6. folding into protein structure
Building blocks of dna = string of nucleotides:
1. phosphate groups
2. sugar (deoxyribose)
3. bases (4 in total)
-> sugars connected through phosphate bridges
-> nucleotides connected through hydrogen bonds
2
, Molecular Ecology 2025-2026 Fie Thijs
Chapter 2 – DNA Barcoding & Molecular systematics
Are the Pterois and Dendrochirus valid genera on their own?
• Pterois miles and P. volitans = distinct species inside Pterois clade
• Pterois and Dendrochirus = no evidence that these are distinct genera
• Historically: genera defined based on physical traits -> imperfect and incorrect method
• Dendrochirus = not monophyletic but paraphyletic -> species split across different branches
• Molecular phylogenetic analysis reclassifies Dendrochirus + certain Pterois = genus Pteropterus
Explain the phylogenetic tree of the lionfish
2 major clades:
1. Pterois
= contains sibling species P.volitans
and P.miles
2. Dendrochirus-Pteropterus
= mix of species of both genera
Geological events (vicariance):
= speciation of P.volitants and P. miles coincide with geological events in SE Asia (3.9-7.0 mya)
• formation of the Pacific Ring of Fire and lowered sea levels = caused land bridges
• restrict exchange of larvae between Indian & Pacific Oceans
• lowered sea levels due to ice ages in Pliocene and Pleistocene
• all barriers to gene flow!
3
Molecular Ecology 2025-2026 – Exam questions
Chapter 1 – Molecular genetics and markers in ecology
What reagents are necessary to perform PCR?
1. 2 primers (forward and reverse)
2. template dna
3. dntp (deoxyribonucleotides)
4. PCR buffer
5. MgCl2 = cofactor of polymerase
6. polymerase (example: taq polymerase)
What can you tell about Sanger sequencing?
• Developed mid 1970’s
• Dideoxy chain termination method
• 4 reactions (1 for each base – A,T,C,G)
o Generates a set of fragments
o Appears in gel electrophoresis as bands in 4 lanes (1 lane for each base)
• Automated sequencers = bases recognized by dye-terminator
o Each base has its own colour
o Single capillary filled with a polymere
mtDNA: how many basepairs does it contain? What about genes? What % codes for proteins?
• Bp = 16 000 (humans) or 16 500 (fishes)
• Genes (also control region present)
o 13 protein coding genes
o 2 rRNA genes
o 22 tRNA genes
• % coding for proteins = 93%
Explain the genetic code in eukaryotes
• 65 possible codons (61 without stop and start codons)
• 61 sense codons for 21 AA = multiple codons for the same AA
• 3 stopcodons = UGA, UAG, UAA
• 1 start codon = AUG = methionine
• In some nuclear genes = CUG and UUG also start codons
• Mitochondrial gene codons are slightly different = UGA translates to tryptophane instead of stop
What type of mutations are there?
1. nucleotide substitution
2. insertion/deletion
3. gene conversion
4. recombination
1
, Molecular Ecology 2025-2026 Fie Thijs
What is the structure of the human genome
I. mitochondrial genome
1. non-coding dna = control region
2. coding dna
a. 13 protein coding genes
b. 2 rRNA genes
c. 22 tRNA genes
II. nuclear genome
1. genes
A. coding dna = 30 000 – 40 000 genes
B. non-coding dna
a. pseudogenes
b. introns
c. gene fragments
2. dna outside genes
A. single or low copy
B. low to high repetitive
a. LINE
b. SINE
c. satellite dna
Explain the pathway from gene to protein
1. dna
2. transcription to pre-mRNA
3. removal of introns
4. mRNA
5. translation to proteins via codons (using tRNA)
and ribosomes (made with rRNA)
6. folding into protein structure
Building blocks of dna = string of nucleotides:
1. phosphate groups
2. sugar (deoxyribose)
3. bases (4 in total)
-> sugars connected through phosphate bridges
-> nucleotides connected through hydrogen bonds
2
, Molecular Ecology 2025-2026 Fie Thijs
Chapter 2 – DNA Barcoding & Molecular systematics
Are the Pterois and Dendrochirus valid genera on their own?
• Pterois miles and P. volitans = distinct species inside Pterois clade
• Pterois and Dendrochirus = no evidence that these are distinct genera
• Historically: genera defined based on physical traits -> imperfect and incorrect method
• Dendrochirus = not monophyletic but paraphyletic -> species split across different branches
• Molecular phylogenetic analysis reclassifies Dendrochirus + certain Pterois = genus Pteropterus
Explain the phylogenetic tree of the lionfish
2 major clades:
1. Pterois
= contains sibling species P.volitans
and P.miles
2. Dendrochirus-Pteropterus
= mix of species of both genera
Geological events (vicariance):
= speciation of P.volitants and P. miles coincide with geological events in SE Asia (3.9-7.0 mya)
• formation of the Pacific Ring of Fire and lowered sea levels = caused land bridges
• restrict exchange of larvae between Indian & Pacific Oceans
• lowered sea levels due to ice ages in Pliocene and Pleistocene
• all barriers to gene flow!
3
