bioz476: dna barcoding

What is DNA barcoding?

Using DNA sequences to determine the species of an organism.

What is the morphological species concept?

Identifying species based on physical appearance and characteristics.

Why does the morphological species concept not always work?

Different species may look similar, while members of the same species may look different because of sex or age.

What is the biological species concept?

A species is a group of organisms that can interbreed and produce fertile offspring.

What is one limitation of the biological species concept?

Different species can sometimes produce hybrids, including fertile hybrids.

What is phylogeny?

Evolutionary history.

What does a phylogenetic tree show?

Evolutionary relationships among organisms or sequences.

What is a DNA polymorphism?

Variation in DNA sequences among individuals or species.

What does SNP stand for?

Single-nucleotide polymorphism.

What is an insertion-deletion mutation?

The insertion or deletion of one or more nucleotides in a DNA sequence.

What does it mean when a mutation becomes fixed?

All individuals in a population or lineage have that mutation.

What does interspecies mean?

Between different species.

What does intraspecies mean?

Within the same species.

What two variation patterns make a gene useful as a DNA barcode?

High interspecies variation and low intraspecies variation.

Why is high interspecies variation useful in DNA barcoding?

Different species have distinguishable DNA sequences.

Why is low intraspecies variation useful in DNA barcoding?

Individuals of the same species have relatively similar DNA sequences.

What does COI stand for?

Cytochrome c oxidase I.

Which primer does the lecture say the class uses for insect DNA barcoding PCR?

Bio-Rad COI insect primer.

What does the COI insect primer target?

A region of the cytochrome c oxidase I (COI) gene.

What organism should students bring for the DNA barcoding experiment?

An insect or spider.

How should a sample be kept before lab day?

Use a fresh, unprocessed sample and store it in the freezer to preserve DNA.

Why should you grind the sample thoroughly?

To break up the tissue so DNA can be extracted.

Why is using the exact tissue amount important?

Too much tissue can overload the extraction system; too little may not provide enough tissue.

What is especially important to track during DNA extraction and purification?

Keep track of which fraction contains the DNA so you do not discard it.

What is the purpose of PCR in DNA barcoding?

To amplify the selected DNA region for subsequent analysis.

What is the purpose of checking the PCR product on a gel?

To determine whether a DNA product was amplified and assess its approximate size.

How does a slower gel run affect bands, according to the lecture?

It can produce tighter, clearer bands.

What may happen when a gel is run too quickly?

Bands may spread or smear.

What primer is used for sequencing in the lecture experiment?

M13 primer.

What is BLAST used for?

To align and compare a DNA sequence against sequences in a reference database.

What can happen if your species is not present in the barcode reference library?

You may not obtain an exact species identification from the database.

What is the general DNA barcoding workflow?

Collect sample → extract DNA → amplify barcode by PCR → check PCR product → sequence DNA → compare with reference sequences.

What is an example of a medical application of DNA sequence analysis mentioned in the lecture?

Personalized medicine, including assessment of disease risk or drug response.

How can DNA barcoding help detect mislabeled products?

Compare a product sample’s DNA sequence with reference sequences to investigate whether the species matches its label.

Why does DNA barcoding not always establish a species identity conclusively?

An incomplete reference library or sequences that are too similar between species can limit identification.