Jordans Notes 15

Question 1

What is different about the procedure of SNP
analysis for genotyping vs trait association studies?

Answer 1

Trait association studies don’t usually use restriction digest and instead look at
entire genomes as huge amounts of SNPs are needed

Question 2

What is the DNA attached to in illumina sequencing
during PCR and sequencing?

Answer 2

a flow cell

Question 3

What software is used with the capillary machine
to analyse microsatellites

Answer 3

GeneScan

Question 4

What machine is a PCR run on?

Answer 4

A thermocycler

Question 5

How to run a BLAST (3 steps)

Answer 5

1. export consensus sequence as .fasta file
2. Upload to NCBI’s nucleotide BLAST
3. Look at the E value (or % identity)

Question 6

What is different about phylogenetic classification
and Linnaean Classification?

Answer 6

Phylogenetic classification is objective

Question 7

What is the size standard used for microsatellite
analysis?

Answer 7

LIZ size standard (orange fluorescent tag)

Question 8

What counts as a SNP?

Answer 8

Where a base pair substitution has occurred in more than 1% of individuals in a population
Otherwise it is just considered a mutation if it’s rarer

Question 9

How is evolution measured?

Answer 9

a change in proportion of heritable traits (allele frequency) in a population over generations

Question 10

natural selection impact on genetic variation

Answer 10

increases genetic variation between populations
decreases genetic variation within a population

Leads to speciation between populations!

Question 11

What is important about mutation in evolutionary
terms?

Answer 11

The only process that can create new alleles

the ultimate source of genetic variation
only if it occurs during gamete formation!

Question 12

What is different between genetic drift and natural
selection?

Answer 12

Genetic drift is a random fluctuation in allele frequencies
not the cause of environmental pressures selecting advantageous heritable traits

Question 13

What increases the effect of genetic drift?

Answer 13

small populations → often due to bottlenecks or founder effects

Question 14

Gene flow that would decrease the chance of
speciation

Answer 14

High gene flow can maintain allele frequency similarities between populations

Question 15

What does PCR bridge amplification generate?

Answer 15

Clusters of the same strand

Question 16

What are already bound to the flow cell before the
template is added?

Answer 16

oligonucleotides complimentary to the adapters ligated to each end of the template fragments

Question 17

What 5 ingredients go into sanger sequencing?

Answer 17

dNTPs (regular nucleotide building blocks)
Primer
Template (PCR product)
Thermostable DNA polymerase (and cofactor chemicals)
ddNTPs (chain terminators)

Question 18

What is a terminal node in a phylogenetic tree

Answer 18

present day species (descendants)

Question 19

What are the pros and cons of MinIon?

Answer 19

Question 20

What is a tree building method for looking at
divergence

Answer 20

Neighbour-Joining