Evolution Midterm 2

Biol 355 Uvic, Midterm 2 (2025)

What is random genetic drift?

the fluctuation in allele frequencies due to random sampling

What is this type of plot called

A Manhattan plot

Why is genetic drift especially key in small populations?

Because fluctuations can result in a loss of alleles (going to fixation)

What does this figure depict?

Genetic drift, causing the populations to diverge from one another

What does this figure depict?

The chance for a completely neutral new mutation to become fixed in small populations

what does this figure depict?

The fixation of a slightly deleterious mutation in a small population

What is the Wright-Fischer model of genetic drift?

Based on the probability of a binomial distribution

What conditions can create a genetic bottleneck?

Reduction of a population to a small number of individuals, this can be because of…

• Population crashes

• Establishment of a population from a few founders

What is an example of a genetic bottleneck?

Northern elephant seal

• thought to have been extinct in the 1800s

• today’s population descended from approximately 20-40 individuals

• Resulting in a huge reduction in heterozygosity and a decrease in fitness

• Due to the presence of a premature stop codon in 5 male fertility genes (deleterious mutation)

What classic experiment demonstrated genetic drift?

A 1956 experiment by Peter Buri on genetic frequency in a small population of mutant drosophila

• Followed 2 alleles in 107 populations started from only 16 flies in every generation

What does this figure represent?

The difference between Peter Buri’s experiment and the theoretical Wright Fisher model

• the model maintains heterozygosity to a higher degree, this is because it assumes that all individuals are involved in reproduction

Define effective population size

The effective population size (Ne) refers to the number of individuals in a population which are contributing gametes to the next generation (smaller than N)

What are the effects of genetic drift on genetic diversity?

Population size has a high effect on genetic variation

1. Smaller population size results in higher genetic drift, lower heterozygosity and higher homozygosity

2. Smaller population size increases the chance that a completely neutral new mutation will become fixed

3. Smaller populations have an increases the chance that a deleterious mutation will become fixed

4. Larger populations are much more likely to have advantageous mutations go to fixation

Define the term ‘inbreeding depression’

A reduction in fitness due to the bringing together of recessive deleterious mutations, making them homozygous and exposing them to natural selection

Does genetic drift or natural selection have a larger effect on allele frequency?

Depends on the strength of each process

• s= natural selection

• 1/Ne= genetic drift

If s»1/Ne then natural selection will have the prevailing effect

What is the longest run predator-prey experiment? What does it demonstrate?

Study of the fluctuations in population of the Isle Royale wolves (whose population was founded in the late 1940s) and the moose

• population overrun with genetic defects due to inbreeding depression

• studied the effects of a single individual wolf in recovering the population by facilitating gene flow

Define gene flow

The movement of an individual or gametes between populations

What are the potential effects of gene flow?

• can change the genetic structure of a population

• can counteract divergence among populations (greater homogeneity of populations)

How are gene flow and genetic structure measured?

Using F statistics

What is the F statistic (Fst)?

A tool used to measure the reduction of heterozygosity at different scales

• tells us how much gene flow, populations structure and differentiation there is in an allele

• values 0→1

What does it mean if your Fst is very small or very large?

Very small:

• there has been movement and exchange

• no population structure= gene flow

Very large:

• there has been little or no movement or exchange

• alleles have been fixed in different populations

• population structure= very little gene flow

What do genes with Fst outlier values mean?

They are strong indicators of positive selection/adaptation

What was revealed when investigating the effects of artificial selection on the dog genome?

A significant Fst deviation in shar-peis. Hylauronic synthase (HAS2) expression is elevated, associated with skin repair and stretch

What does a high degree of sequence conservation mean?

It indicates that a gene is essential and that there is high purifying selection on any deviations

What type of polymorphism occurs most frequently?

synonymous>non-synonymous

What do the variables dn + ds describe?

The variation within a species

What do the variables Ka + Ks describe?

The variation between species in their non-synonymous (amino acid) and synonymous (substitution) divergence

How do human and yeast ubiquitin proteins relate?

They are almost identical

Define systematic humanization

The replacement of an organism’s genes (for example in yeast) with human ones, reveals an extremely high degree of conservation

What genes have relatively low non-synonymous variation?

Essential genes such as those involved in transcription, translation and metabolic processes

What genes have relatively high non-synonymous variation?

Those involved in adaptation towards changing environmental conditions or against natural enemies

What are some of the fastest evolving genes in the fly genome?

Antiviral genes, have lots of non-synonymous mutations (high Ka/Ks)

Define adaptive radiation

The diversification of some lineages into many species in a short amount of time (cichlids)

What is the biological species concept?

Species are groups of interbreeding or potentially interbreeding individuals that are reproductively isolated from other such groups

Why are hybridization and introgression important in the evolution of species?

Because they act as sources of diversity and adaptation (ex. EPAS1 in Tibet)

What are the steps to speciation?

1. Development of a polymorphism

2. Reduction in gene flow

3. Complete or near-complete reproductive isolation

4. Accumulation of differences and isolating barriers independent of initial isolation

Define Allopatric speciation

Most common form of speciation, caused by complete geographic isolation, no gene flow

Define Sympatric/ecological speciation

Speciation which occurs without geographic isolation while populations are still exchanging genes

What are the major types of isolating barriers?

1. Premating (no mating)

2. Postmating (no fertilization)

3. Postzygotic (produce unfit offspring)

Give an example of a premating isolating barrier

Southern Cappuccino Seedeater

• 10 species which occur in overlapping ranges

• Differ in male plumage and song

• Only genetic differences occur in 3 genes associated with pigment

• Males act most aggressively towards individuals with the same plumage and song

Give an example of a postmating isolating barrier

Japanese Carabid Beetles

• Differences in male reproductive organs

• very high mortality in cases of interspecific matings and damage of reproductive organs

Give an example of a postzygotic isolating barrier

Heliconius Butterflies

• hybrids are predated upon at higher rates than their parental lines

• hybrid warning patterns aren’t recognized

What is the Bateson-Dobshansky-Muller model of hybrid incompatibility?

It states that incompatibilities will accumulate over time

• those that arise later may not be related to initial processes of speciation

Give an example of duplicate genes causing incompatibilities

Arabidopsis Thaliana

• hybrid offspring between two strains (At1g71920 and At5g10330) are unviable

• due to a premature stop codon in one and a large deletion in the other

• this is the kind of incompatibility that could result in speciation

Define parthenogenesis

Asexual reproduction

What is an example of a species which reproduces parthenogenetically but requires sperm to trigger development

Amazon mollies/ ‘sperm parasites’

Why are parthenogenetic lineages not persistent?

They are short lived due to accumulation of deleterious mutations

• parthenogenesis has evolved 39 times in scaled reptiles

What are the benefits of asexual reproduction

1. Faster growth rate

2. Reproductive assurance (don’t rely on finding a mate)

3. Don’t need to invest in expensive sexual reproductive traits

4. Avoid STD and other mating risks

5. Perseverance of successful genotypes

What is the two-fold cost of sex

Also referred to as the cost of males

• if females produce 50% males then half her resources go into offspring unable to bear offspring themselves

• an asexual individual will double in frequency every generation

What are the benefits of recombination?

• brings beneficial mutations together

• breaks associations with deleterious mutations

Define clonal interference

Competition between asexual lineages with different beneficial mutations

What is the red queen hypothesis

that because everything around you evolves so quickly you are forced to evolve simply in order to keep pace

What is the example of the New Zealand mud snail?

• Snails are a mix of obligate sexual and obligate parthenogenetic individuals

• Researchers found sexual snails to be more abundant when parasitism is high because asexual snails were more likely to be infected

Define linkage disequilibrium

The non-random association of alleles at different loci

What are potential causes of linkage disequilibrium?

• reduced recombination due to physical linkages (most common)

• inbreeding

• natural selection

What is genetic hitchhiking?

when selection favours an allele at one locus nearby linked loci may also increase in frequency

Define selective sweep

A process by which a new advantageous mutation eliminates or reduces variation in linked neutral sites as it increases in frequency in the population

What is the example of genetic hitchhiking in Drosophila?

• transposable element jumped into CHKov1 gene

• the new variant has spread rapidly and neighbouring nucleotides have come alongside

• has stronger resistance to organophosphate pesticides and viruses

What is the ‘Ruby in the rubbish’ metaphor?

When beneficial mutation are stuck in linkage with deleterious ones

What is stated in Muller’s ratchet?

deleterious mutations will accumulate in small asexual populations

(classes of individuals with the least deleterious mutations could be lost by chance and never recovered)

Which mutations can become fixed in asexual lineages but never in sexual ones?

Deleterious

What human alleles do not undergo recombination?

Mitochondrial genomes, centromeres, telomeres and Y chromosomes

What is the PAR

• pseudoautosomal region a small region of the X and Y chromosomes pair and recombine

Give an example of parthenogenesis in a eukaryote caused by bacterial infection

Encorsia hispida, an important wasp in the biocontrol of whitefly pests, parthenogenetic due to bacterial infection

• female wasps fed antibiotics can produce sons

What are cases of combinations of sexual and asexual reproduction

1. Cyclical parthenogenesis (aphids)

2. Selfing (nematodes)

3. Anisogamy (fusion of 2 different gametes)

4. Dioecious (separate male and female sexes)

5. Androdioecy or gynodioecy (a mix of individuals that produce 1 or both types of gametes)

6. Protogynous or protandrous (female→male or male→female)

What is the cause of sexual selection?

Competition for mates among individuals of the same sex

What traits are selected for in individuals with small gametes? What about for in individuals with large gametes?

• small gametes- increase mating opportunities

• large gametes- increase in the number of eggs produced

What is Bateman’s principle?

Males have greater variance in reproductive success than females

What are the two major modes of sexual selection?

• male-male competition

• female mate choice

What are 4 types of male-male competition in sexual selection?

1. scramble traits

2. contest and display

3. sperm competition

4. infanticide

What kind of selection is horn size in dung beetles

Disruptive

How is the hornlessness phenotype determined in dung beetles?

Environmentally determined

What are examples of female mate choice?

• peacock

• stalk-eyed flies

• sage grouse mating displays

Why are individuals chosen by females?

direct benefits

• mates may offer food or other resources

indirect benefits

• good genes

Give an example for mate choice for indirect benefits/good genes?

Three spined stickleback and cestode parasites

• offspring of brighter males are more resistant to parasites

Give an example of sexual selection in plants

The swift evolution of pollen and pistil traits in Mercurialis annuas in 3 generation under conditions of high or low density

How would you perform experimental evolution to remove or reduce sexual selection?

Monogamy

What does this figure depict?

The reduced female survivorship in Drosophila from mating between members of the monogamous treatment and the control treatment due to sexual selection for antagonistic or competitive traits

When is conflict between the sexes greatest?

When there is multiple matings and coevolution (polygamy»monogamy)

What are the phenotypes of antagonistic coevolution in riffle bugs?

Males with wider legs and spines (more successful in mating)

Females with thoracic hook (resist mating)

What does it mean for Ka«Ks? Ka=Ks? Ka»Ks?

Ka«Ks - purifying selection on the amino acid (gene is highly conserved)

Ka=Ks - gene is evolving close to neutral (natural selection doesn’t see the change)

Ka»Ks - positive selection (adaptation)

What are the fastest evolving human genes?

Reproductive proteins- for example the human fertilization protein zonadhesin whose exons (coding) evolve faster than their introns (non-coding)

Give 3 examples for coevolution between species

1. antagonism - host and parasite

2. competition

3. mutualism - host and beneficial endosymbiotic microbes

Give an example of coevolution between individuals within a species

sexual selection - riffle bugs

Give 3 examples of coevolution between different genes/ parts of the genome

1. organelles

2. selfish genetic element and the rest of the genome

3. genes that interact with each other

Define specific and diffuse coevolution

Specific- a 1:1 evolution between pairs of interacting organisms

Diffuse- reciprocal change among groups

Where does the key tension lie for parasites or pathogens?

Key tension between transmission and the effects on the host (you shouldn’t kill your host)

Describe the evolution of virulence in the myxoma virus

1. Infecting Australian rabbits it began with the release of a highly virulent virus

2. Followed by the evolution of a reduced/ intermediate virus

3. Evolution of host resistance

4. Current evolution of acute virulence through a novel disease phenotype, an immune collapse syndrome similar to septic shock