Genetics Flashcards
What is genetic drift?
random changes in allele frequency over time in finite populations. This is a dispersive force that leads to a loss in variation- inversely proportional to population size. Dictates survival probability of new mutations.
What is natural selection?
The differential survival and reproduction of phenotypes so that genotypes (as reflected by phenotype) have different fitness. Highest fitness= most offspring. Strong force in big population, in small population genetic drift is a greater force.
Why is genetic diversity important?
- Evolution opportunity- the rate of evolutionary change is proportional to the amount of genetic diversity available
- Heterozygosity and fitness positively correlated- don’t always understand why. Maybe related to impacts of developmental stability or inbreeding eg correlation between oxygen consumption of American oyster and heterozygosity (low oxygen consumption means more metabolic efficiency)
What is a molecular marker
A molecular marker is a molecule contained within a sample taken from an organism (biological markers) or other matter. It can be used to reveal certain characteristics about the respective source. DNA, for example, is a molecular marker containing information about genetic disorders, genealogy and the evolutionary history of life.
Why should there be a relationship between fitness and molecular markers ?
- Direct effect hypothesis- fitness correlation as a result of overdominance at the scored loci itself. Potentially important for allozyme studies
- The local effect hypothesis- fitness correlation as a result of the loci being investigated being closely linked to functional loci associated with fitness. Requires non-random associations of alleles at different loci in gametes (linkage disequilibrium) which are expected in recently bottlenecked or expanded populations.
- General effect hypothesis- fitness correlation reflecting a general genome effect. A result of the effects of homozygosity at loci distributed across the genome.
What is the effect of a bottleneck on diversity?
- Sampling effect- likely rare alleles will be lost from the population. Alternatively, they may become fixed if they survive the bottleneck. This distortion of allele frequency is often used as a signature for a bottleneck event.
- Reduction in heterozygous individuals- recessive deleterious alleles increase because likelihood combining alleles that are identical by decent increases and will go more quickly to fixation
- Distortion of allele frequency through chance selection of alleles
What is the coalescent theory
The model looks backward in time, merging alleles into a single ancestral copy according to a random process in coalescence events. In the simplest case, coalescent theory assumes no recombination, no natural selection, and no gene flow or population structure, meaning that each variant is equally likely to have been passed from one generation to the next.
We track the genealogy back in time, every population has a 1/2 Ne chance of coalescence.
How do you create skyline plots?
Dependent on coalescent methodology and
- estimating genealogy from sequence data
- estimating population history based on genealogy
Can compare known past events to help predict future impact
How individuals are related to each other I think
Talk about the Guam Rail
After the introduction of the brown tree snake. 21 guam rail were taken into captivity. They were then released onto a snake free island. in nearby Cocos and Rota.
How can you estimate kinship?
Proportion of shared alleles is used to estimate kinship. Genetic estimation of relatedness is approxiamate and dependent on the number of genetic loci used and level of polymorphism. More markers–> better resolution.
How do you avoid inbreeding (Maximise Avoidance of Inbreeding MAI)
- Equalise family size- single family with large brood would displace other lineages genetically
- Equalise sex ratios
- Equalise population size in different generations
can initiate circular mating pattern–> delays inbreeding as long as possible. Typically used in populations when no previous information is known about kinship. This scheme makes no allowance for problems such as mortality of offspring, incompatibility of breeding pairs, reduced fertility etc
Talk about the Californian condor
Chondrodystrophy (a lethal form of dwarfism)- recessive autosomal allele at about 9% probably due to the founder effect. Ralls et al (2000) determined that elimination of the allele by selection would require preventing over 50% of 146 birds from breeding and the impact on diversity would be too great
Talk about fruit flies and captive breeding?
Gilligan and Frankham (2003)- Flies with noticeable genetic marker (white eyes) were raised under benign conditions. After some generations captive flies reared with wild type and a ‘competitive index’ was computed as a ratio of wild type to hybrid form
After 87 generations, the fitness of flies in the captive envrionment increased by a factor of 3.33. the effect started to level off after 30 generations
What causes outbreeding depression?
- Co-adaptation- when local populations evolve a genome that is internally balanced with respect to reproductive fitness eg owl monkey, local populations have differing chromosomal structures. CB failed until members of the same population were mated
- local adaptation - local pops adapt to local environment. Ibex became extinct in tatra mountains through overhunting. Successful translocations were from austria which had a similar environment. But later translocations from Turkey were not so successful. They were used to a warmer climate, so hybrids rutted early in autumn NOT winter (as native tatra pop did). Kids were born in Feb which is the coldest month of the year. Extinction
Give an example of a population that has suffered long term effects of a bottleneck
Cheetah. Believed to have a bottleneck at the end of the last ice age.
O’Brien et al. (1983) reported increased fluctuating asymmetry of skeletal measurement.
Also found physiological correlates:
1, diminished sperm count
2. elevated frequency of morphological abnormalities in sperm development (about 70%)
3. Low fecundity in CB attempts
4. CB pop not self sustaining
5. Relatively high (50%) incidence of juvenile mortality even between unrelated individuals
6. Increased population vulnerability to infectious disease, notably feline infectious peritonitis.
Additive gene
Genes make independent contributions, combined genetic variance reflects the average among loci
variation in quantitative traits may be lost following bottle neck
Non-additive
Dominance. Genes that are preferentially expressed
could increase variation (and fluctuating asymmetry) following bottleneck
Polygenic
More than one gene involved
could increase variation (and fluctuating asymmetry) following bottleneck
Epistasis
Genes controlling the expression of other genes
What is the 50:500 rule
Ne= 50 should be enough to avoid short term inbreeding depression
Ne=500 required to avoid long term erosion of genetic variation in quantitative traits with high heritability –> MVP from genetics POV
What were Lande’s main points about genetics and conservation biology
- conservation is a crisis discipline- important decisions have to be made quickly
- Ne=500 (MVP) has led to management plans that neglect other factors that may require larger pop sizes for population persistence
- He notes critical demographic factors such as the Allee effect (small pop experiencing low viability and reproduction for ‘non-genetic’ reason), demographic stochasticity, edge effects and local extinctions
- suggests gradual inbreeding or reduction in population size may result in relatively little inbreeding depression because selection will purge the population of deleterious recessive alleles when a homozygous individual is produced.
- demographic factors may be of more immediate importance than population genetics in determining the MVP of wild populations
Tell me about northern spotted owls
2500 pairs left. Require old-growth forest habitat. 1984 management plan was based on preserving at least 500 pairs (Ne/Nc) to maintain genetic diversity. Models based on stochastic demography and habitat occupancy suggested extinction under this plan - habitat too sparse
Can inbreeding impact the probability a pop will go extinct?
Experimental studies- inbreeding explained 26% of the variation in extinction risk overall
Frankham 2005
Are species driven to extinction before genetic factors can impact (the Lande effect)?
Most species are not driven to extinction before genetic impacts effect them (Spielman et al. 2004)
Do small populations lose evolutionary potential?
Hard to show. Should be related to the diversity of phenotypes but Reed and Frankham (2003) did a meta-analysis and found the correlation between molecular diversity and life history traits was low and non-significant.
However, Santos et al (2002) compared experimental founder population size for Drosophila and found strong correlation with adaptive potential
What is ESU?
Evolutionary Significant Units- unit of conspecific biodiversity. Distant populations show reciprocal monophyly for mtDNA and a significant level of divergence at nuclear DNA loci
Aim to preserve these units because variation within species’ populations make up the total adaptive variation of the species as a whole.
What is MU?
Management Units- populations that show significant differentiation at either nuclear or mtDNA loci, regardless of phylogenetic distinctiveness
Why is mtDNA expected to show greater phylogenetic structure?
It evolves quickly and has a smaller effective population size than nuclear genes (reflecting the haploid and matrilineal transmission of this genome).
How can we tell if a population has a subdivision?
Decreased population size –> decreased heterozygosity (loss of variation) within local population therefore decrease heterozygosity relative to the expected heterozygosity under random mating if the whole population was a single breeding unit (panmictic)
Why do populations become separation in allopatry
Geographic barrier.
Genetic drift and differential selection (for local adaptation)
Note: few genetic migrants are needed to render the 2 populations as essentially panmictic
Populations can also differentiate when next to each other i or in same geographic range ii
i parapatry
iii sympatry
Can occur when conspecific populations within the same or proximate ranges adapt to different habitat or resource requirements and when these differences also isolate a population with respect to mate choice
Why is the coalescent useful in assessing differentiation between pops?
You can see the directional gene flow,
can obtain quantitative estimates of rate of gene flow among pops
can calculate how divergent they are and identify any asymmetries in the pattern of migration (eg in source/sink- where local depletion of one pop has been compensated for by immigration from neighbouring pop)
Where may a conservation manager choose to maximise diversity?
Where diversity is known to correlate to fitness such as immune system genes
What is a solution if a wild population is extremely genetically depauperate?
introduction of conspecific populations are attempting to introduce genetic diversity–> potential issue is outbreeding depression
