Lecture 12

Question 1

Distinguish between molecular genetics and genomics.

Answer 1

MG - involves study of DNA sequences encoding SPECIFIC genes to understand function

Genomics - study of DNA sequences of ALL the organism’s genes –> called the genome

Question 2

How can you investigate variation?

Answer 2

1. compare specific situation (case control, e.g.)
2. look across distribution of a phenotype
3. look at evolutionary relationships

Question 3

How do you conduct genomic analysis of many individuals?

Answer 3

• collect samples / record phenotypes
• create ‘libraries’ and sequence
• investigate 1 locus / gene or entire genome
• identify SNPs and other genetic variation

Question 4

What do you need when sequencing genomes?

Answer 4

a sufficient sample size to determine relationships which may involve significant sequencing

Question 5

Why might it be important to associate genotypes with measurable phenotypes?

Answer 5

medical research

evolutionary biology (understanding adaptation)

agriculture (traits of economic value)

Genome-wide association studies (GWAS) provide powerful approaches for identification of genetic traits. However, accurate phenotypical information is essential.

Question 6

What is linkage disequilibrium?

Answer 6

when a mutation is linked to multiple neighbouring sites

new mutation arises, with an adaptive advantage –> the mutation might be lost by CHANCE (drift) OR “sweep” through a population

Question 7

What is selective sweep?

Answer 7

rapid increase in the frequency of a favourable allele before recombination disrupts the region of DNA

we can look at the peaks on a graph to identify when selection occurred

a process by which a new advantageous mutation eliminates or reduces variation in linked neutral sites as it increases in frequency in the population

Rapid selection at a locus that can be identified through the presence of large haplotypes.

Question 8

Is lactase persistence an example of natural selection? Explain the findings of Tishkoff et al (2007)

Answer 8

1. Phenotyped individuals (simple blood test to assess lactase activity)
2. Genotyped (sequence DNA or genotype - variety of methods)

This allowed to ask - is there positive selection at the lactase gene?

FOUND: Homozygous genotypes flanking lactase persistence polymorphisms (C/G base variant - C for persistence, G non persistence in Africa)

T/C for europe/asia

Question 9

Selective sweeps support . . .

Answer 9

strong directional (positive) selection of the locus. Positive selection removes variation.

Question 10

What is phyolgenetics?

Answer 10

the study of evolutionary relationships among biological organisms based on:
- similarities and differences in DNA
- knowledge of ‘molecular clocks’ (rate that mutations occur)
- phenotypes: behaviour, anatomy
- fossil record can be used for calibration

Question 11

What is phylogeography?

Answer 11

looks at evolutionary histories, but considers geographic distributions through fossil records and other evidence and interprets this at a landscape level

Question 12

Covid-19

Answer 12

• small genome; nucleic acid is RNA
• replicate via asexual reproduction
• replication is not accurate as in other life forms so mutation arises more rapidly

Question 13

What are some features of mitochondrial genome?

Answer 13

• inherited maternally and represent clonal lineages
• mutations occcur
• haploid genome (haplocytes)

Question 14

How were Indigenous Australians’ migration into the continent investigated?

Answer 14

Mitogenome: from hair samples collected from early European settlement

Locational information: obtained at the time of hair sample collection

Temporal information: molecular clocks (mutation rates) calibrated w archaeological data