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Flashcards in Molecular markers Deck (56)
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What are the three hierarchical levels in molecular markers

Molecular phenotype - Allozymes and isozymes

Transcription of DNA into RNA - RNA, micro-RNAs

DNA, the genetic code
- Nuclear DNA and DNA found in organelles (mtDNA, chloroplast DNA)


What are the 4 main types of marker

DNA sequence variation
Microsatellites (or SSR, Simple sequence repeats)
SNP (or Single nucleotide polymorphism)
RAD markers (or Restriction site associated DNA markers)


What needs to be considered when choosing a marker

Cost of development and screening
Have primers / protocols been developed?
Density of marker loci
Level of polymorphism
Mutation rate
Dominant or co-dominant
Accuracy and bias


What is a linkage map

A map of the genes on a chromosome based on linkage analysis. It does not show the physical distances between genes but rather their relative positions, as determined by how often two gene loci are inherited together. The closer two genes are (the more tightly they are linked), the more often they will be inherited together


What is genetic distance and how is it measured

= recombination frequencies (measured in centiMorgan, cM)


What is a linkage group

linkage group is a group of markers that are all significantly linked (recombination ratio: r<0.5)


What does PCR stand for

polymerase chain reaction


What does PCR allow you to do

allows you to sequence a single part of the genome


What are the advantages to PCR

Specificity - Primers (short DNA fragments) containing sequences complementary to the target region
Amplification allows minute quantity of DNA to be examined
Allows us to study population genetics from a mndellianvprspective


Why are micro-satellites useful in conservation

You can look at the recent population history (100-1000 gens) because the mutation rate is so high


Pros and cons of microsatellites high polymerism

It provides high resolution for near past, but low resolution for distant past. (homoplasy)


Which methods avoids microsatellites resolution of the distant past

SNPs have a lower mutation rate so you can look deeper into coalescence and further back in the past


Which marker is becoming more popular and why

RAD markers as it still gives lots of variation without needing to make a proper genome assembly


What is a general problem with markers

trying to detemine if it is a heterozygous or homozygous individual (solution - use a codominant marker to see both forms)


What does co dominant mean

It means neither allele can mask the expression of the other allele. e.g homo is with red of white but the hetero is pink


Example of population genetics before molecular markers

genetics relied on studying phenotypic changes in drosophilia, looking at eye shape/colour to understand how alleles segregated and genotypes were selected


Which species was used to create a complete linkage map



`what is a centrimorgan

a unit of genetic length


What is used more commonly than centimorgans

now we can measure physical distance - Kb


When does linkage disequilibrium occur

when some genes work very well together, linkage blocks of low recombination can form, even is those genes are far from each other on the chromosome


Where are linkage blocks common

in heterodimers such as the MHC


What can be cause linkage disequilibrium

selection and bottlenecks


how can linkage disequilibrium be caused by a bottleneck

after a bottleneck , a few genotypes survive with a particular combination of alleles.
recombination takes time to decouple those alleles
so straight after the bottleneck you will keep seeing the same combination of alleles (haplotype)
eventually those genes will dis-aggregate
so it is linkage disequilibrium by chance


How can population sub-structuring lead to misinterpreting linkage disequilibrium

if you don't have gene flow between populations you might get combination of alleles recurring by chance
the pops have differentiated, not undergoing linkage disequilibrium


What is a limitation of using microsatellities,

F statistics are not very powerful, esp. Fst
since you get so much polymorphism, you have high heterozygosity which means the Fst will will be incredibly low as the homozygotes will be low.
The value isn't meaningful (F = fixation)


When should microsatilites be used

paternity analysis
in zoos to create pedigrees
good for population geentic studis into microevolution (migration, inbreeding, pop structure), but not when there is lots of diversity, the Fst doesn't work well


What if the mutation rate of snps

Base substitution mutation rate equals ~10−8 per base pair per generation
mutation rate is low


do snps undergo selection?

Many SNPs are silent and are under no (or negligible) selection


disadvantages of microsatellites

Relatively few loci (generally N = 6 to 30)
Very high heterozygosity for Fst based stats
High mutation rate causes size homoplasy
Expensive and labour intensive screening
Out-of-fashion and likely to be replaced by next generation type of markers, e.g. SNPs


How common are snps