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Conservation Genetics > Molecular markers > Flashcards

Molecular markers Flashcards

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1
Q

What are the three hierarchical levels in molecular markers

A

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)

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2
Q

What are the 4 main types of marker

A

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

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3
Q

What needs to be considered when choosing a marker

A 
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
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4
Q

What is a linkage map

A

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

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5
Q

What is genetic distance and how is it measured

A

= recombination frequencies (measured in centiMorgan, cM)

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6
Q

What is a linkage group

A

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

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7
Q

What does PCR stand for

A

polymerase chain reaction

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8
Q

What does PCR allow you to do

A

allows you to sequence a single part of the genome

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9
Q

What are the advantages to PCR

A

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

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10
Q

Why are micro-satellites useful in conservation

A

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

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11
Q

Pros and cons of microsatellites high polymerism

A

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

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12
Q

Which methods avoids microsatellites resolution of the distant past

A

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

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13
Q

Which marker is becoming more popular and why

A

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

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14
Q

What is a general problem with markers

A

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

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15
Q

What does co dominant mean

A

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

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16
Q

Example of population genetics before molecular markers

A

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

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17
Q

Which species was used to create a complete linkage map

A

guppies

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18
Q

`what is a centrimorgan

A

a unit of genetic length

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19
Q

What is used more commonly than centimorgans

A

now we can measure physical distance - Kb

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20
Q

When does linkage disequilibrium occur

A

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

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21
Q

Where are linkage blocks common

A

in heterodimers such as the MHC

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22
Q

What can be cause linkage disequilibrium

A

selection and bottlenecks

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23
Q

how can linkage disequilibrium be caused by a bottleneck

A

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

24
Q

How can population sub-structuring lead to misinterpreting linkage disequilibrium

A

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

25
Q

What is a limitation of using microsatellities,

A

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)

26
Q

When should microsatilites be used

A

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

27
Q

What if the mutation rate of snps

A

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

28
Q

do snps undergo selection?

A

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

29
Q

disadvantages of microsatellites

A

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

30
Q

How common are snps

A

very

31
Q

3 ways snps associated with complex diseases are identified

A

Candidate Gene Association Studies(CGAS)
Genome-Wide Association Studies (GWAS)
Pedigree studies

32
Q

advantages to snps

A

many useable loci to provide complete genome coverage
Bi-allelic marker ideal for Fst based analyses
Rapid screening using Next Generation Sequencing technologies e.g. Illumina
Can be used on both coding and non-coding dna so it can look at functional variants and neutral variation

33
Q

Why does snps work well with Fst

A

unlike other methods, small sample size does not lead to overestimation of genetic differentiation You can have small sample sizes with snps as so many loci can be used

34
Q

How do snps form and how does this show relatedness

A

snps are a copying error that can be passed on.

the more closely related, the more snps you’ll share

35
Q

what does RAD stand for

A

Restriction site Associated DNA

36
Q

what is the process of rad sequencing

A

Cut a genome with one or more restriction enzymes
Ligate the first adapter to the overhangs
Randomly shear the DNA into small fragments
Ligate with the second adapter
PCR amplify fragments that contain both adapters
Sequence the resulting fragments using an Illumina Sequencing System
This will give you data on SNPs and restriction sites

37
Q

what is an advantage of RAD

A

you can start looking at the whole genome and see how particular areas of the genome are behaving (e.g. diff parts will respond to inbreeding differently)

38
Q

What is RAD

A

randomly shearing DNA, amplifying and sequencing small parts of it and comparing SNPs

39
Q

When should you use RAD

A

Excellent for population genetics, paternity, disease association etc cus it covers the entire genome, and produces many markers andhigh density linkage maps

40
Q

disadvantage to RAD

A

still expensive with relatively few papers published

41
Q

what is targeted sequencing (Mybaits)

A

rather than looking at a single organism, eg plants, you can create baits which pull out DNA exactly matching the RNA sequence so you can capture the pathogens also inside the plant

42
Q

how do you calculate Fis

A

1-Ho/Hs

43
Q

What does Fis measure

A

measures the ratio of the observed and expected heterozygosity, and is used to measure inbreeding.

44
Q

how to calculate Fst

A

1 – Hs/Ht

45
Q

What does Fst measure

A

measures genetic drift and subpopulation divergence

46
Q

what is the symbol for nucleotide diversity

A

pi or π

47
Q

What does pi show

A

expresses the proportion of polymorphic sites within a genome.

48
Q

what does dN/dS measure

A

measures natural selection

49
Q

If the ratio dN/dS is low, what does that mean

A

The gene is undergoing purifying selection; only synonymous mutations are tolereated

50
Q

If the ratio dN/dS is high, what does that mean

A

the gene is undergoing positive selection; selection favours changes in amino acids

51
Q

what unit is used to measure recombination

A

Rho or ρ/μ

52
Q

What does a high Rho mean

A

A high value means a high level of recombination compared to the mutation rate.

53
Q

What is Theta

A

It is the the drift-mutation parameter (4Ne𝛍).

54
Q

What does Tajima’ D capture

A

it capture demographic effects and measures selection and population size expansion/contraction

55
Q

Why must you not look at Tajima’s D alone

A

you can see alleles in intermediate frequencies which suggest balancing selection, but actually there was a bottleneck and the population is expanding and there is no selection

56
Q

What does a high Tajima’s D mean

A

A high value means a lack of rare alleles, e.g. due to positive selection or a recent population size contraction.

Conservation Genetics (6 decks)

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