Topic 2: Evolution and Genetics

The classification system of Linnaeus (1707-1778)

based on morphology classification

Lamarckism

Single celled organisms can become more complex over time - it’s all about effort - eg. a giraffe can keep stretching and stretching and longer necks are passed on

• no evidence

The Fossil Record (Nicolaus Steno 1638-86)

Discovered fossils from ancient sharks which were found far from oceans near mountains

• first evidence and idea that the Earth can change over time

Mary Anning (1799-1847) - extinction introduction

She found fossils of organisms that were extinct - it was controversial

Darwin (1809-82)

He collected many specimens to shape his theories on evolution

• Galapagos finches all being the same genus but so much diversity

Evolution

Evolution is the cumulative change in the genetic composition of a population or species over time.

Darwin’s 3 major propositions: 1

diversity has to exist. - there is some variation

Darwin’s 3 major propositions: 2

changes over time in how structures are applied and used

Darwin’s 3 major propositions: 3

3. Natural selection: differences in the phenotypes of individuals cause some of them to survive and reproduce more effectively than others and therefore outcompete them.

Natural selection

Individuals with phenotypes most suited to the environment (fittest) are more likely to produce offspring. Natural Selection is a ‘driver’ of evolution and acts on heritable variation within a population

Speciation: galapagos islands

Humans can drive evolution as well

Artificial selection for different vegetables

Adaptation

An adaptation is an inherited aspect of an individual that allows it to outcompete other members of the same population that lack the trait (or that have a different version of the trait).

Adaptations are traits that have evolved through the mechanism of natural selection.

Macroevolution

Macroevolution explains evolutionary changes among large taxonomic groups above the species level.

Macroevolution includes the origin, diversification and extinction of species over long periods of time.

• eg. dinosaurs

Monophyletic group

Polyphyletic group

Paraphyletic group

Node, branch, taxon

branch is usually a species

Definitions of alleles, genotypes and phenotypes

Mutation

ultimate source of genetic variation

Mendel (1822-1884) and Franklin, Wilkins, Crick and Watson (DNA)

Trying to investigate genetics

The cycle of evolution

DNA encoding and replication

Replication is not always accurate

• DNA polymerase adds to the 3’ end of the new strand

• It should add the complementary nucleotide

• Occasionally there is a misincorporation error

Causes of mutations

Mutations can occur at diff scales and have diff impacts

Germline mutation

This is what we’re most interested in as they can be transferred to next generation

Somatic mutations

Mutation occurs without respect to phenotypes

Genetic drift

involves random changes in allele frequencies

• Alleles become more or less common simply by chance

• There is always an element of randomness in determining which alleles are passed on by the parental population

The effect of population size on genetic drift

Genetic bottlenecks

Genetic bottlenecks are caused by events that reduces the size and genetic diversity of a population significantly

Founder effects

are caused by a small number of individuals founding a new population. Random differences in allele frequencies occur when a small colony splits from a large population.

What is a population?

A group of individuals that share genetic information.

In sexual organisms, a population is a group of individuals that have the potential to exchange genetic information over a small number of generations.

What is a gene pool?

A gene pool is the sum of genetic information (the genetic composition) that is carried in the population.

Microevolution versus Macroevolution

Macroevolution: Evolution among species spanning long periods of time.

• It is revealed through:

  • Changes in the fossil record

  • Transitions across the phylogeny of life

Microevolution: Evolution within species that can be observed directly acting upon natural populations.

T

he microevolutionary process can be influenced by the ‘agents of change’.

Adaptive mutations occur

The match between phenotype and function can be exquisite

Adaptation refers to a trait:

Advantageous mutations contribute to a trait that is adaptive

Natural selection is a process:

It can act on advantageous mutations and deleterious mutations

When a variant ‘fixes’ within a species there is more ‘divergence’ between species

Sexual mating systems influencing evolution of populations

Plant populations can also have non-random mating

• Many plants (like the model plant Arabidopsis thaliana) tend to “self” rather than “outbreed”.

• Some plant species have flowering time polymorphisms (i.e. some plants that are similar might flower at different times of the year to prevent cross pollination and gene flow)

Assortative mating

increases the frequency of homozygous genotypes and allele frequencies may remain very similar unless genetic drift causes fixation of one allele over time

Disassortative mating

maintains genetic diveristy and allele frequencies may remain very similar but heterozygotes will have higher than expected frequencies

Assortative mating can shift the gene pool

hummingbirds pollinate the pink ones and moths pollinate the red ones

• differences in genotypes

Gene flow

Migration, gamete dispersal and hybridization

For gene flow to occur, individuals must be able to disperse, interbreed and produce viable offspring

What does the impact of gene flow on the gene pool depend on?

i. The genetic difference between populations

ii. The level of migration, movement or hybridisation (m)

in this case, no impact on allele frequencies bc frequencies as the same

Different population allele frequencies (migrants vs residents)

Here gene flow is increasing the frequency of A alleles in the resident population. The greater the gene flow the faster the change in frequency

How we calculate how allele frequency might change in one generation

What this means is that the new allele frequency after one generation will change from 0.4 to 0.41

Particular combinations of traits might be beneficial

Many traits are determined by the action of multiple genes

e.g. multiple genes contribute to the difference in anthocyanin amount

Inheritance of multiple genes

During meiosis, the chromatids can cross over and undergo recombination

• Recombination creates new combinations of alleles at different genes

• New combinations may be adaptive

• Recombination frequencies vary between genes

The two fold cost of sex

Evolution should favour asexual reproduction

• Asexual lineages multiply faster than sexual lineages

• No ‘search’ costs associated with finding a mate

• No risk of sexually transmitted infections

Benefits of Sexual Reproduction

• Combining beneficial alleles

• Generation of novel genotypes

• ‘Faster’ evolution

• Clearance of deleterious mutations

Allele definition

Genotype

Phenotype

Punnet squares

The genotypic ratios and phenotypic ratios that we can get from punnet squares can be useful to predict successful genotypes from crosses

Mendelian frequencies applying to a pedigree

If there is a absence of selection, due to chance via genetic drift the b and B alleles can overun each other - just depends on chance

Hardy-Weinberg Theorem - Basis of notation

How to figure out the probability of a homozygous genotype

How to figure out the probability of a heterozygous phenotype

The final Hardy-Weinberg Equation

Using the probabilities of genotypes, how do we calculate the allele frequencies in a population of 1000 mice?

How to calculate expected genotype frequencies from known allele frequencies

The Hardy-Weinberg theorem shows allele frequencies will not change from one generation to the next.

How to infer frequencies of 3 genotypes from one genotype frequency (using plot)

Under Hardy-Weinberg equilibrium (HWE), allele frequencies do not change over time…What are the assumptions?

The assumptions of the Hardy Weinberg Equilibrium are that the ‘agents of evolutionary change’ are not acting!

1. No gene flow from other populations

2. No mutation

3. No drift

4. No non-random mating

5. No selection

6. Recombination not relevant

1. No Gene flow

No new phenotypes migrating into populations

2. No mutations

We don’t have new mutations introducing different phenotypes/genotypes

3. Assuming infinite population size

Genetic drift changes allele frequency (more quickly in smaller populations). So the larger the population, the more constant the allele frequency.

4. Mating is random

We cannot have assortative mating where brown mice mate with brown mice - instead it must be random

5. Equal fitness (no selection)

Everyone is equally fit to survive and reproduce

o.66 + 0.12 (half of 0.24)

What happens when we violate assumptions of Hardy-Weinberg?

The genotype will differ from expected.

How to use Hardy-Weinberg equation to calculate expected genotype frequencies (null hypothesis)

How to find the expected number of mice using genotype frequencies and population

To check if observed frequencies match expected frequencies

We also need to see if that X2 value is significant or not

degrees of freedom is usually 1 bc number of alleles is usually 2

Chi-squared test identify loci that deviations from Hardy-Weinberg expectations can reveal microevolutionary change

IF observed genotype frequencies are significantly different to expected genotype frequencies…

• Migration may be occurring

• Mutation may have an unexpected impact

• Population sizes may be small

• Mating may not be random

• Selection may be operating

The null hypothesis of the Hardy-Weinberg Theorem

 The Hardy-Weinberg principle has a null hypothesis: genotype frequencies will not change over generational time. Drift, selection and gene flow can all have large effects.

Selection on genotypes

balancing selection

Balancing selection

maintains allele diversity in populations

Balancing selection: Negative Frequency dependent selection

Basically the more rare a phenotype becomes, the more selective advantage it has

• the less frequent it becomes, the higher reproductive success = fitness

Fitness

Fitness : success of an organism at surviving and reproducing

Relative fitness (w)

describes the success of a genotype. Relative fitness standardised by the success of other genotypes in the population and ranges from 0 to 1.0

Balancing selection: heterozygote advantage

Relative to other genotypes, the heterozygote is the fittest genotype

• is able to fight off malaria best

Selection on phenotypes types

Stabilising, directional and disruptive selection

Stabilising selection

bringing everything closer to the mean

Directional selection

Disruptive selection

can be evident with associative mating

What are the genes and alleles are causing these adaptations (reductionist approach - looking at cellular level)

Monkey flower pollination: Pink flowers make it easy for bees to pollinate and red are pollinated by birds.

Monkey Flower pollination cross example

They crossed the red and pink flowers which produced an F1 hybrid darker pink flower and then tracked the number of bumblebee visits.

Yup was caused by a partial duplication on another chromosome and the RNA would hairpin loop on itself and bind to a protein that expressed the carotenoids needed to turn a flower red. If this carotenoid was not expressed, the flower would be darker pink.

Industrial melanism of the peppered moth

He found that there was an increase in the number of the darker moths. He then took 488 light and 496 dark moths and released them in an unpolluted forrest. He recaptured them and found that twice as many were light (light had better survival) but in another forrest with pollution, when recaptured, twice the number of dark moths survived.

Dark mutation is large insertion caused by a transposable element hopping into the first intron

Genetic changes in Drosophila over time

Transposable elements increasing expression of protein that detoxifies and gets rid of DTT (repellent)

Speciation

the evolutionary process by which new species arise through reproductive isolation. Speciation causes one evolutionary lineage to split into two or more lineages.

Allopatric speciation

ancestral population is divided by a physical barrier

• no gene flow bw drosophila on different islands

Sympatric speciation

ancestral population is divided without geographic barriers

• monkey flower species are in the same geographic location but birds pollinate some and bees pollinate the others - leads to reproductive isolation without geographic barrier

Two explanations of the genetics of speciation

New alleles can become fixed

Chromosomal rearrangements

Speciation: New alleles can become fixed

Original genotype may be as shown and then speciation happens and after divergence mutations may arise and new alleles are introduced, introducing new genotypes.

• Eventually if the lineages were to connect - the offspring would be infertile

Chromosomal rearrangements

In one lineage, fusion of blue and green chromosomes have fused and in the other, another two may have fused or not

Reproductive barriers preventing gene flow to enable speciation types

Prezygotic isolation

Postzygotic isolation

Prezygotic isolation

• geographical isolation - allopatric speciation, when meet again, too different to reproduce

• mechanical: hummingbird vs bird - prevents cross pollination bw varieties

• behavioural isolation - different mating calling signals

• mating time differences - different times of the day

• ecological differences -

Postzygotic isolation

There are some zones where multiple species of frogs may cross over at their region boundaries - zygotes can form but they won’t develop/ not viable

Prezygotic isolation example

When both frog species live in same environment, there is more of a difference in mating calls in order to not confuse species

• prezygotic isolation maintains species boundaries in sympatry

Genetic distance

reproductive isolation increases with genetic divergence

• usually we would expect A and C to be more reproductively isolated but with A and B are sympatric there must be a stronger barriers to prevent hybridisation