| Why is loss of genetic diversity a problem? | Natural selection theorem - rate of evolutionary change in a population is proportional to the amount of genetic diversity available. Genetic diversity equates to evolutionary potential for response to environmental change.
High genetic variation within individuals or populations is positively related to fitness. Global pool of genetic diversity represents all the information for all biological processes on the planet “primary level of biodiversity”. |
| Why is loss of genetic diversity a problem? (pt2) | Loss of genetic diversity will decrease the ability of organisms to respond to environmental changes, and likely discard information potentially useful to humans. Conservation genetics is motivated by the
need to reduce current rates of extinction and to preserve biodiversity. |
| Why conserve biodiversity? | Food and drink, Medicines, Industrial resources, Ecosystem services, Ecotourism |
| What is genetic diversity? | Interspecific - diversity hotspots. Intraspecific (within a species): between populations, within a population, within an individual. Genetic diversity is originally generated by mutations in DNA sequence. Genetic diversity within a population may increase via migration/dispersal of gametes. Outbreeding: higher within population variation, Interbreeding: higher between population variation |
| Why measure genetic diversity? | Document losses of genetic variation. Document evolutionary changes. Document genetic differentiation of populations. Predict changes in the genetic composition of populations |
| How to measure genetic diversity? | Polymorphism (P): proportion of loci that are polymorphic i.e. loci with >1 allele
Heterozygosity (H): proportion of loci that are heterozygous in an average individual
Allelic diversity (A): mean number of alleles per locus (depends on the marker type) |
| Hardy-Weinberg Key assumptions | If large population, mating random, no mutation, migration. Allele frequencies in a population will remain at equilibrium over time. Also assumes Mendelian segregation of alleles, equal fertility of parent genotypes, equal survival of genotypes, equal fertilising capacity of gametes, random union of gametes. |
| Rare alleles and recessive traits | Most mutations are recessive as it is easier to disrupt the function of a gene than to create a new gain-of-function. They are normally also relatively rare in a population. Thus, for a recessive human disease gene, a heterozygote won’t experience any negative selection pressure. Only the homozygote form will be selected against, but because they are rare, the frequency of the double mutant will be very low. Thus, the mutant allele is maintained in a population by carriers – providing the population is large-enough. |
| Five agents of evolutionary change | 1. Mutation 2. Gene flow 3. Non-random Mating 4. Genetic drift 5. Selection |
| New Mutations | At the moment of formation a new mutation will be heterozygous. Mutation occurs in an exon: Silent mutation, conservative change, non-conservative change. Mutation occurs in the promoter: Can change where/when the
protein is expressed |
| Use of Hardy-Weinberg | Can calculate expected heterozygosity – evolutionary potential depends on genetic diversity. Can see loss of genetic diversity over time by comparing heterozygosities over time. Estimate the frequency of recessive alleles in a large population. Estimate the frequency of carriers in a population. Deviations from H-W allow us to detect inbreeding, genetic drift, migration, selection and loss of diversity |
| Microsatellite markers = Simple Sequence Repeats (SSR) | Repeats of 2-5 nucleotide sequences – powerful tool for population genetics.
High mutation rate gives high levels of genetic diversity – up to 20 alleles per microsatellite.
Usually neutral (not normally in coding sequences) – not under direct selection.
Coding region SSRs often trinucleotide repeats, corresponding to codon repeats. |
| Detection of microsatellite allele length using PCR | Need specific primers for each locus, but these can work across closely related species.
They are not multiplexed to a high degree, i.e. can only assay a small number of loci in one PCR reaction
– low throughput markers. |
| Different fragment lengths can be separated by: | 1. Gel electrophoresis
2. Use of fluorescently tagged primers and analysis on a capillary DNA sequencer
3. Or simply identify them from next gen sequence data |
| Single nucleotide polymosphisms (SNPs) | A site in a DNA sequence that is variable for at least 2 nucleotides (alleles) - the site becomes the locus.
Most are bi-allelic. In non-coding regions.
Human genome on average 1 major SNP (present in >5% population) every 300 to 1000 bp.
Non-synonymous substitutions will change protein sequence - functional variation – possible selection pressure |
| Genome-wide SNP detection methods include: | Whole genome sequencing – detailed bioinformatics.
Transcriptome sequencing – polymorphisms in genes.
Genotyping by sequencing (GBS) – high multiplexing.
SNP chips - genotyping arrays – simple data analysis. |
| Genotype by Sequencing - GBS | Robust, simple Genotyping-by-Sequencing (GBS).
Approach for high diversity species.
No knowledge of genome sequence required.
Relatively low cost due to high degree of multiplexing. |
| How is genetic diversity lost? | Decreasing population size usually results in loss of genetic diversity.
Population fragmentation stops flow of genetic material between populations - lack of dispersal.
Loss of diversity in domestic species due to agricultural policy, consumer demand and the consequences of breeding strategies. |
| Why small population size leads to loss of genetic diversity? | More vulnerable to genetic effects: genetic drift, inbreeding, population bottlenecks, Less likely to be able to maintain diversity through gene flow. Evolutionary consequences: Chance dominates, little effect of selection
= replicate small populations varying outcomes. “Sitting duck” – vulnerable to not being able to adapt |
| Effective population size, Ne | To a geneticist, populations are smaller than they seem (Ne is less than N).
Ne is the size of an idealised population that would lose genetic diversity at the same rate as the population being considered.
Genetic diversity is lost as Ne declines, not just N. |
| Genetic drift | Each generation derived from a sample of parental gametes.
Allele frequencies fluctuate/drift from one generation to another.
Effect more pronounced in smaller populations. |
| Genetic drift has major impacts on evolution of small populations | Allele frequencies change over generations.
Diversification of allele frequencies.
between fragmented populations.
Loss of genetic diversity = fixation.
Can overpower natural selection.
Some alleles go extinct or become fixed. |
| Fixation | Genetic drift ultimately causes loss of diversity through fixation, all but one allele is lost. Prob of losing an allele = (1-p)^(2N). Therefore rare alleles more likely to be lost. Alleles more likely to be lost in small pops |
| Population bottlenecks | Sharp reduction in pop size (short or long term).
Reduces genetic diversity (even if population recovers).
Time spent as small population also reduces genetic diversity. |
| Inbreeding | Leads to increased homozygosity (reduction in heterozygosity).
Inbreeding depression (reduced reproductive fitness).
Increased risk of extinction.
Unavoidable in small, closed populations. |
| Inbreeding coefficient | F = 1 - Ho/He. Probability that an individual inherits two copies of the same allele from a common ancestor on both sides of the pedigree. |
| Mechanisms to promote outbreeding | Timing of stigma and style reception differ. Timing of stigma and style reception differ. Foreign pollen out-competes self pollen. |
| Gene flow | Way to increase diversity. Fragmented populations and declining populations reduces gene flow. Decreased ability to maintain genetic diversity |
| Using genetics to map genes controlling traits: Four general approaches: | Pedigree analysis. Directly use next-generation sequencing of affected individuals
Mapping in bi-parental segregating populations. Genome-wide association mapping (GWAS) |
| Key points about genetic mapping | Recombination during meiosis (haploid gamete formation) is responsible for separating alleles (segregation) – creates new combinations of alleles in the offspring. The closer two loci are together on the genome (linkage) the more likely a pair of their alleles are to be co-inherited (co-segregate). The greater the number of recombinations sampled the greater the power to map loci. |
| In humans we will look at three approaches | Pedigree analysis. GWAS. Exome sequencing of affected individuals for rare mutations. |
| Autosomal dominant inheritance | Males/females equally affected.
Affected individuals tend to be heterozygotes, rarely homozygous.
50% chance of heterozygous parent passing mutant allele on.
Affected individuals in each generation.
Unaffected individuals do not have affected offspring. |
| Autosomal recessive inheritance | Males and females equally affected.
Individuals with one mutant allele are carriers.
50% chance of passing mutation to the next generation.
Affected children born to unaffected parents.
With two carrier parents, 25% offspring are affected, 50% are carriers, 25% are unaffected.
The disease tends to skip generations |
| X-linked recessive inheritance | Males affected more than females.
Affected males always pass affected X chromosome to daughters (obligate carriers) but never to sons.
None of the offspring of affected males are affected (unless the female parent is a carrier too - rare).
Half of sons born to carrier daughters will be affected. |
| X-linked dominant inheritance (rare) | Males and females are equally affected.
Affected males always pass affected X chromosome to daughters but never to sons.
Affected females have a 50% chance of passing it on to offspring. |
| Y-linked inheritance | No diagram needed as only males are affected.
Dominance/recessiveness is not relevant as there is only one Y allele.
Maleness is determined by the SRY gene (testes determining factor).
Apparently no non-sex-related traits are linked to the Y chromosome. |
| Biochemical basis of recessive and dominant | Recessive mutations: Loss-of-function mutations, therefore, as there are two alleles, the WT allele is usually sufficient to provide enough WT protein. Dominant mutations: Gain-of-function mutations, the WT allele is still performing its activity, but the mutant allele causes an additional unfavourable action. Semi-dominant mutations: Allele or gene dosage effect, one WT allele doesn’t provide enough active protein on its own to fully perform the required function |
| Penetrance of a mutation | The percentage of individuals with an allele who possess a disease/trait. Most single gene diseases discussed above have high penetrance – 100%. Environment also influences risk. Risk - not 100% penetrant - if you have a risk allele it doesn’t mean you will get the disease. Alleles have a high frequency in the population. The overall risk is heritable but not in a Mendelian manner. |
| Human Genetic Analysis | Families Linkage Studies: Simple inheritance, Single gene with major effect, Variant allele rare in population, Alleles in causative gene co-segregate with the trait, Mendelian ratios not observed due to small sample sizes.
Populations Association Studies: Complex Inheritance, Multiple genes with small contributions and environmental contexts, Variant allele(s) common in the population, Looking for alleles enriched in the case group. |
| How do we map a disease locus? | Recombination occurs between homologous chromosomes during meiosis. Produces gametes with new combinations of parental alleles. Independent assortment of different chromosomes – 50:50 chance of which
of the pair of parental chromosomes are inherited. Look for co-segregation of the disease with genetic markers. The more individuals sampled the more recombinations separate unlinked genetic markers from the disease locus |
| Recombination explained | Linkage - loci on different chromosomes will segregate independently. Loci close together on the same chromosome will tend to segregate together at meiosis. Recombination frequency (Rf) correlated with
distance between loci. |
| Genetically map with respect to markers | Is successful when: 1) High penetrance of the mutation 2) Unambiguous disease diagnosis 3) Reproducible between studies. Results in: small chromosome region defined. |
| Overview of linkage analysis | Use pedigrees. How is the gene inherited. Acquire DNA. Increase map power by combining fam data. Do statistical analysis. |
| Statistical test for evidence of linkage - LOD scores | Firstly, measure the recombination frequency for each marker and the trait. Calculate LOD score = Log10 of the odds: Tests whether the linkage seen is significant, evaluates probability of the test data if the two loci are linked vs probability of observing same data purely by chance. Combine information from multiple pedigrees. |
| Alternative strategy for rare mutations | Family members have large regions of sequence in common which limits precision of mapping. Rare mutations won’t be present in established SNP array assays. Exome sequencing of unrelated affected individuals ~5% sequencing cf whole genome. Screen sequences for nonsynonymous mutations (polymorphisms) in genes
that are only present in the affected individuals. Gives precise identification of causative alleles |
