BIOL204 Cons Gen Session 2 Flashcards
What do we need to know to inform conservation strategies?
- Genetic Diversity Present
- Gene Flow between populations
- Effective Population size
- Extent of any inbreeding
What are microsatellites
Also referred to as ‘VNTRs’ (variable number of tandem repeats) or ‘SSRs‘ (simple sequence repeats)
Genetic markers, tandem repeats of short
repeat motifs.
Used for population and individual
level questions
How many repeats do microsatellites use?
10s
What are AFLP’s?
Amplified Fragment Length
Polymorphisms
Randomly scattered small
sections of DNA targeted by short primers
Used for population and individual
level questions
How many repeats do AFLP’s use?
100’s
What is sequencing?
DNA sequences of a particular part (locus/loci) of the genome
Used for species/sub-species and
beyond depending on the
locus being sequenced.
How many repeats does sequencing use?
1’s (compares single sections)
What are SNP’s
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
How many sites do SNP’s use?
1000’s
What were the original genetic markers used (Proteins)
Allozymes & minisatellites
What is genetic variation within a population?
When there is more than one allele present in a population at a given locus = a polymorphic locus.
What is a fixed/monomorphic loci?
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
How can new alleles occur?
breeding with migrants & Mutation
What is Allele frequency?
How do we calculate it?
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
What is Genotypic frequency?
How do we calculate it?
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).
What is average heterozygosity (H) ?
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
What is allelic diversity or allelic richness?
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
What does the term ‘percentage of polymorphic loci’ mean?
no. of loci that are polymorphic over all loci sampled. This measure loses a lot of detail.
What is Nucleotide diversity (pi) ?
the proportion of differences between sequences, expressed as a function of the length of the DNA sequence compared
What is haplotype diversity, h ?
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
What is mtDNA?
mitochondrial DNA
If metrics such as allelelic diversity and heterozygosity across a number of independent genetic makers is high, what would we initially conclude?
That it is a genetically diverse population
What are some disadvantages of low genetic diversity?
low survivorship
poor sperm quality
greater susceptibility to disease
What is the difference between adaptive markers and neutral markers?
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)
What is The Hardy-Weinberg Model? and what does it tell us?
The ‘null model’ for expectations of population genetic diversity through time.
The expected genotypes of future generations.
What is the Hardy-Weinberg equation?
p^2 + 2pq + q^2 = 1
What are the 6 assumptions of the Hardy-Weinberg Model?
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
What is (Ho)?
Obseverd heterozygosity
What is (He)?
Expected Heterozygosity
What is the current favoured method of measuring genetic diversity? what is up and coming?
1) currently microsatellites
2) SNPs
What is a locus (plural = Loci)?
different sites on chromosomes which may or may not be coding genes.
what is an allele?
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.
When studying genetic variation within populations, do organisms share different genes? or different alleles?
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!
if you are sampling Locus ‘W’ in 10 diploid individuals, how many alleles are there?
20
Case study about genetic diversity in Ursus americanus ?
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.
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
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
Chi squared equation for the HW model
X2=sum of(observed-expected)^2/expected
if p>0.05 then observed conforms to expected
slide 33
