BIOL204 Cons Gen Session 2

Question 1

What do we need to know to inform conservation strategies?

Answer 1

1. Genetic Diversity Present
2. Gene Flow between populations
3. Effective Population size
4. Extent of any inbreeding

Question 2

What are microsatellites

Also referred to as ‘VNTRs’ (variable number of tandem repeats) or ‘SSRs‘ (simple sequence repeats)

Answer 2

Genetic markers, tandem repeats of short
repeat motifs.

Used for population and individual
level questions

Question 3

How many repeats do microsatellites use?

Answer 3

10s

Question 4

What are AFLP’s?

Amplified Fragment Length
Polymorphisms

Answer 4

Randomly scattered small
sections of DNA targeted by short primers

Used for population and individual
level questions

Question 5

How many repeats do AFLP’s use?

Answer 5

100’s

Question 6

What is sequencing?

Answer 6

DNA sequences of a 
particular part (locus/loci) of the genome 

Used for species/sub-species and
beyond depending on the
locus being sequenced.

Question 7

How many repeats does sequencing use?

Answer 7

1’s (compares single sections)

Question 8

What are SNP’s

Answer 8

Single Nucleotide Polymorphisms (often verbally ‘snips’)

DNA sequences of a
particular part (locus/loci) of the genome
Single base pair differences
randomly scattered throughout the genome

Question 9

How many sites do SNP’s use?

Answer 9

1000’s

Question 10

What were the original genetic markers used (Proteins)

Answer 10

Allozymes & minisatellites

Question 11

What is genetic variation within a population?

Answer 11

When there is more than one allele present in a population at a given locus = a polymorphic locus.

Question 12

What is a fixed/monomorphic loci?

Answer 12

When a loci has no alternative allele and members of the population are homozygous.
i.e. the allele to keep your heart pumping will have no variants

Question 13

How can new alleles occur?

Answer 13

breeding with migrants & Mutation

Question 14

What is Allele frequency?

How do we calculate it?

Answer 14

the relative proportion of an allele in a population.
sum each allele & divide by how many alleles overall to sum all frequencies to 1. (basically find the % of each allele in the pop).
note: the frequency of alleles in 1 pop can be compared with others to see if there is gene flow.
see pp 2 slide 14

Question 15

What is Genotypic frequency?

How do we calculate it?

Answer 15

the relative proportion of any particular genotype in the population.
the two alleles in an organism = 1 genotype e.g. W^a W^b = 2 alleles but 1 genotype. Find the frequency of each possible genotype in a population (similar to allelic frequency).

Question 16

What is average heterozygosity (H) ?

Answer 16

Used to measure genetic diversity. The sum of the proportions of heterozygotes at all loci divided by total number of loci sampled.

e.g. If the proportions of individuals heterozygous at 5 loci measured within in a population are 0.2(20% of individuals heterozygous), 0.4, 0.1, 0, and 0, then:

OBSERVED H (Ho)=(0.2+0.4+0.1+0+0)/5 = 0.15

more alleles = more genetic diversity

Question 17

What is allelic diversity or allelic richness?

Answer 17

the average number of alleles per locus.
So if you have 10 different loci in an individual within a population sample and the number of different alleles at each locus is: 10, 5, 2, 4, 19, 8, 9, 1, 12, and 6,
allelic diversity = 76/10 = 7.6

Question 18

What does the term ‘percentage of polymorphic loci’ mean?

Answer 18

no. of loci that are polymorphic over all loci sampled. This measure loses a lot of detail.

Question 19

What is Nucleotide diversity (pi) ?

Answer 19

the proportion of differences between sequences, expressed as a function of the length of the DNA sequence compared

Question 20

What is haplotype diversity, h ?

Answer 20

mtDNA sequence data and this refers to the number and frequency of different haplotypes in the sample.
Haplotype: the combination of alleles at loci that are found on a single chromosome or mtDNA molecule

Question 21

What is mtDNA?

Answer 21

mitochondrial DNA

Question 22

If metrics such as allelelic diversity and heterozygosity across a number of independent genetic makers is high, what would we initially conclude?

Answer 22

That it is a genetically diverse population

Question 23

What are some disadvantages of low genetic diversity?

Answer 23

low survivorship
poor sperm quality
greater susceptibility to disease

Question 24

What is the difference between adaptive markers and neutral markers?

Answer 24

Neutral markers mean that the gene variants detected do not have any direct effect on fitness. Adaptive markers are loci that effect an organisms ability to survive, good for resistance to natural selection. Neutral markers will not be affected by selection. (Kirk, 2011)
differences between populations will arise as a result of mutation and drift (and extent of gene flow)

Question 25

What is The Hardy-Weinberg Model? and what does it tell us?

Answer 25

The ‘null model’ for expectations of population genetic diversity through time.
The expected genotypes of future generations.

Question 26

What is the Hardy-Weinberg equation?

Answer 26

p^2 + 2pq + q^2 = 1

Question 27

What are the 6 assumptions of the Hardy-Weinberg Model?

Answer 27

Mendelian segregation occurs (whole model rests upon this, not used in asexual reproduction
Random mating (‘panmixia’)
No mutation
Large population (no drift)
No selection
No migration

Question 28

What is (Ho)?

Answer 28

Obseverd heterozygosity

Question 29

What is (He)?

Answer 29

Expected Heterozygosity

Question 30

What is the current favoured method of measuring genetic diversity? what is up and coming?

Answer 30

1) currently microsatellites

2) SNPs

Question 31

What is a locus (plural = Loci)?

Answer 31

different sites on chromosomes which may or may not be coding genes.

Question 32

what is an allele?

Answer 32

any one sequence variant at any one Locus:
An individual with the genotype AA has two alleles at one locus that are the same (A) and is thus described as being homozygous at that locus. Diploid.

Another individual with a genotype AB has two alleles at one locus that are different (A and B) and is thus described as being heterozygous at that locus.

Question 33

When studying genetic variation within populations, do organisms share different genes? or different alleles?

Answer 33

Members of the same species WILL ALL SHARE THE SAME GENES. What they will not all share is the same VARIANTS of those genes (i.e. ALLELES).
Gene flow is the exchange on alleles not genes!

Question 34

if you are sampling Locus ‘W’ in 10 diploid individuals, how many alleles are there?

Answer 34

20

Question 35

Case study about genetic diversity in Ursus americanus ?

Answer 35

Got samples (allozymes require tissue samples), reported extremely low heterozygosity from this study. Got worried. 
2nd study 10 years later used microsatellite genetic markers showed much higher heterozygosity. (Paetkau & Strobek, 1994) 
We don’t generally use allozymes anymore, not much variation. Microsatellites a lot higher variability and is a better method.

Question 36

At a single locus there are 2 alleles, A and a.
there are the following numbers of each genotype:
16 x AA, 26 x Aa and 10 x aa (n=52)
1) what are the allele frequencies?
2) Using p^2 + 2pq + q^2=1, predict the frequency of genotypes in the next pop
3) as there are 52, what will their genotypes expected to be in next gen

Answer 36

1) The frequency of allele A (=p) is therefore 32(AA)+26 = 58/104 (Diploid!)= 0.56
The frequency of allele a (=q) is therefore 26(aa)+20 = 46/104 = 0.44
2) p^2 = 0.31 (AA) 2pq = 0.5 (Aa) q^2 = 0.19(aa)
3) 0.3152 = 16.12AA , 0.552 = 26Aa, 0.19*52 = 9.88aa

Question 37

Chi squared equation for the HW model

Answer 37

X2=sum of(observed-expected)^2/expected
if p>0.05 then observed conforms to expected
slide 33