Jordans Notes 15 Flashcards
What is different about the procedure of SNP
analysis for genotyping vs trait association studies?
Trait association studies don’t usually use restriction digest and instead look at
entire genomes as huge amounts of SNPs are needed
What is the DNA attached to in illumina sequencing
during PCR and sequencing?
a flow cell
What software is used with the capillary machine
to analyse microsatellites
GeneScan
What machine is a PCR run on?
A thermocycler
How to run a BLAST (3 steps)
- export consensus sequence as .fasta file
- Upload to NCBI’s nucleotide BLAST
- Look at the E value (or % identity)
What is different about phylogenetic classification
and Linnaean Classification?
Phylogenetic classification is objective
What is the size standard used for microsatellite
analysis?
LIZ size standard (orange fluorescent tag)
What counts as a SNP?
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
How is evolution measured?
a change in proportion of heritable traits (allele frequency) in a population over generations
natural selection impact on genetic variation
increases genetic variation between populations
decreases genetic variation within a population
Leads to speciation between populations!
What is important about mutation in evolutionary
terms?
The only process that can create new alleles
the ultimate source of genetic variation
only if it occurs during gamete formation!
What is different between genetic drift and natural
selection?
Genetic drift is a random fluctuation in allele frequencies
not the cause of environmental pressures selecting advantageous heritable traits
What increases the effect of genetic drift?
small populations → often due to bottlenecks or founder effects
Gene flow that would decrease the chance of
speciation
High gene flow can maintain allele frequency similarities between populations
What does PCR bridge amplification generate?
Clusters of the same strand
What are already bound to the flow cell before the
template is added?
oligonucleotides complimentary to the adapters ligated to each end of the template fragments
What 5 ingredients go into sanger sequencing?
dNTPs (regular nucleotide building blocks)
Primer
Template (PCR product)
Thermostable DNA polymerase (and cofactor chemicals)
ddNTPs (chain terminators)
What is a terminal node in a phylogenetic tree
present day species (descendants)
What are the pros and cons of MinIon?
What is a tree building method for looking at
divergence
Neighbour-Joining
