L10 - Molecular Ecology

Question 1

what is molecular ecology

Answer 1

The use of molecular genetic tools to study ecological questions, including assessing genetic diversity and differentiation within and among populations or species

Question 2

what are the primary markers used in molecular ecology

Answer 2

Allozymes, microsatellites, mitochondrial DNA, nuclear sequences, single nucleotide polymorphism, and whole genomes

Question 3

what are the advantages of using mitochondrial DNA (mtDNA) in molecular ecology

Answer 3

• Maternally inherited, so it traces maternal lineage
• No recombination allows direct sequencing of haplotypes
• High mutation rate provides more variation
• Multiple copies make it easy to amplify

Question 4

what are the disadvantages of using mtDNA

Answer 4

• Genetic introgression between closely related species.
• Copies can move to the nuclear genome and form pseudogenes (numts).

Question 5

what is the difference between genotype and haplotype

Answer 5

Genotype: Full genetic composition of an individual or genomic region

Haplotype: A set of linked genetic information along a chromosome

Question 6

what are common methods for sampling genomic DNA from natural populations

Answer 6

• Tissue samples (e.g., toe clipping, ear clips, wing punches).
• Non-invasive methods (e.g., buccal swabs, hair traps, faecal swabs).
• Museum samples.

Question 7

what is the polymerase chain reaction process (PCR)

Answer 7

Denaturation: DNA strands are separated by heating.

Annealing: Primers attach to the template DNA.

Extension: Taq polymerase synthesizes a new DNA strand

Question 8

why are molecular tools crucial for biodiversity conservation

Answer 8

They help uncover cryptic diversity and reveal unknown species, especially in poorly studied taxa and regions like the tropics

Question 9

What is DNA barcoding, and how does it work?

Answer 9

DNA barcoding uses a short DNA sequence (e.g., cytochrome c oxidase 1 in animals) to distinguish species by comparing sequences to a reference database like BOLD

Question 10

What are the limitations of DNA barcoding?

Answer 10

• Overlap between inter- and intraspecific genetic variation.
• Mitochondrial introgression.
• Variable mutation rates.
• High divergence in bottleneck populations.

Question 11

What is phylogeography?

Answer 11

The study of principles and processes governing the geographic distribution of genealogical lineages within and among species

Question 12

How did glacial cycles affect species distributions in Europe?

Answer 12

• Species retreated to refugia (e.g., Iberia, Italy, Balkans).
• Post-glacial recolonization routes often originated from these refugia.
• Greater genetic diversity exists in southern regions

Question 13

What are hybrid or suture zones?

Answer 13

Areas where genetic lineages from different refugia come together, often as a result of post-glacial recolonization

Question 14

How did glacial cycles impact tropical regions?

Answer 14

• Tropical forests contracted and fragmented.
• Increased grasslands and savannahs.
• Montane regions retained high species diversity

Question 15

what is the rainforest refugia hypothesis

Answer 15

Proposed by Haffer (1969), it suggests Pleistocene glacial periods fragmented rainforests into refugia, leading to genetic divergence and speciation

Question 16

Is the Rainforest Refugia Hypothesis applicable globally?

Answer 16

It has been largely rejected for Amazonia but is applicable to Africa and Southeast Asia

Question 17

What environmental changes occurred during Pleistocene glacial periods in SE Asia?

Answer 17

• Low sea levels and precipitation.
• Increased aridity.
• Tropical forests replaced by grasslands and savannahs.

Question 18

What phylogeographic insights have been gained from the Okapi in central Africa?

Answer 18

MtDNA variation shows genetically distinct lineages consistent with repeated Plio-Pleistocene forest refugia

Question 19

Why is DNA barcoding particularly useful for poorly studied taxa?

Answer 19

It requires minimal tissue and helps identify species in groups like insects and cryptic taxa with limited existing research

Question 20

What is an example of phylogeographic patterns in the Pyrenees and Alps?

Answer 20

Grasshoppers expanded from Balkan refugia but did not cross the Pyrenees or Alps, while hedgehogs successfully recolonized across these barriers.