Evolution and Genetics

Genes

Sections of DNA that code for a specific trait/protein.

Trait

Physical feature that is encoded by a protein.

Alleles

Different variations of genes.

Genotype

Sets of genes responsible for a particular trait (bb).

Phenotype

Trait that is being expressed (black).

Genetic variation

Different combinations of alleles within each organism of the given species that makes them genetically unique.

Gene pool

All the alleles within a population of a given species.

Allele frequencies

The quantity of a specific allele for a given trait.

Mutations

Changes in a sequence of DNA which lead to genetic variation within a population of a given species.

What can affect allele frequencies?

Environmental influences- predation, natural disasters, change in environmental conditions

New alleles- gene flow, and mutations

When does mutations occur?

• Mutations happen randomly during cell division.

• Can be caused by mutagens like radiation - exposure to X-rays and UV radiation, chemicals-tobacco, air pollution, and infectious agents - viruses and bacteria.

Where can mutations occur?

Mutations can occur within a single gene, several genes, or affect an entire chromosome in two different cell types:

somatic mutations - occur in a single body cell and cannot be inherited

germline mutations - occur in gametes and can be passed onto offsprings

Point mutations

Affect a single gene sequence by changing, adding, or removing a single nucleotide within the gene or RNA sequence.

Substitution

A type of point mutation that includes

• silent mutations

  • when a nucleotide is substituted for another nucleotide but leads to the same amino acid being encoded for due to the degenerate/redundancy nature of the genetic code, where multiple codons can code for the same amino acid.

• missense mutations

  • when a nucleotide is substituted for another and leads to another amino acid to be encoded for. The polypeptide chain may be affected depending on how the substituted amino acid alters the structure and function.

  • If the amino acid has the same chemical properties the final protein may still function.

• nonsense mutation

  • when a nucleotide is substituted for another and encodes for a STOP codon.

  • The amino acids after the STOP codon is not continued and renders the final protein non-functional, depending on how far along the STOP codon appears.

Frameshift mutation

If one or two or two nucleotides are added or deleted from a nucleotide sequence.

These types of point mutations have drastic effects on the polypeptide structure, hence, protein function.

Two types of frameshift mutation

-        Insertions

If one or two nucleotides are inserted into the DNA sequence, then all the remaining nucleotides within that gene are pushed forwards downstream.

This changes all the amino acid sequences past the point of the mutation.

-        Deletions

If one or two nucleotides are deleted from the DNA sequence, then all the remaining nucleotides within that gene are brought back upstream.

This changes all the amino acid sequences past the point of the mutation.

Four main types of block mutations                                                   

Deletion, Duplication, Inversion, Chromosomal translocations and insertions, reciprocal translocation

   Deletion

Often fatal as they may lead to genes being deleted or disrupted.                                              

-        Duplication

Often lead to increased gene expression due to multiple copies of the genes being duplicate.

These mutations may be harmful or beneficial depending on which genes are involved.

-        Inversion

Occur when a section of chromosome breaks off, rotates, then re-joins to the same chromosome.

These mutations still allow the genes to be expressed, however, if the inversion occurs part way through a gene, it can lead to several genes being disrupted, which may be harmful.

-        Chromosomal translocations and insertions

Involve segments of one chromosome breaking off and inserting/attaching to another non-homologous chromosome.

If this happens during meiosis, this may lead to a loss of genes.
These mutations often interrupt normal gene functioning and are often the cause of some types of cancers.

-        Reciprocal translocation

Where two non-homologous chromosomes exchange segments of chromosomes between them.

Chromosome abnormalities

• Entire chromosomes where individuals may inherit one more or one less chromosome.

• Identified with a karyotype. C

• Occur during meiosis (sperm and egg).

Two types of chromosomal abnormalities

Aneuploidy

-        Chromosome variation due to a loss or a gain of one or more chromosomes.

This results in gametes having either more or less than the usual number of chromosomes for its species.

Most often occurs during meiosis due to non-disjunction, where chromosomes fail to segregate during metaphase 1 or 2.

Trisomy (2n + 1)        Monosomy (2n - 1)

This often leads to miscarriage during pregnancy, however some aneuploid conditions do survive. i.e. Trisomy 21, Down syndrome

Polyploidy – plants

-        Organisms that have one or more complete extra sets of chromosomes.

If a diploid gamate fuses with a normal haploid gamate, the resulting individual is triploid (3n)

If two diploid gametes fuse, a tetraploid (4n) individuals will be produced. Half gametes contain two copies of each chromosome (diploid) and the rest has none. In human’s polyploidy doesn’t survive. But common for plants and animals. Advantageous as increased size and greater hardiness however, reduced fertility

Selection pressures

Environmental factors that influence allele frequency within a population.

-        Competition between species for food and territories

-        Predator-prey relationships

-        Competition within species for food, water, territories, or nesting places

-        Sexual selection: that is, selection of traits that successfully attract mates.

-        Environmental conditions that favour the survival of a specific phenotype

-        Climatic conditions (heat, cold, drought etc)

-        Ability to camouflage.

Define Natural selection and steps.

Describes how environmental selective pressures influence allele frequencies within a given population, leading to the survival of individuals with traits suited to their environment.

1)     Individuals within a population show variation of a trait [from the context], some caused by mutations.

2)     Individuals that have traits more suited to their environment (or selective pressure) make them more likely to reproduce and pass on their alleles to the next generation.

3)     Therefore, these traits (alleles) increase in frequency in the gene pool.

Variation in sexually reproducing organisms

Occurs through random mating, independent assortment of chromosomes, random fusing of gametes, mutations, and environmental selection pressures.

How does gene pool change

-        Gene pool can change as individuals move between populations.

-        New alleles can enter when individuals immigrate from another population.

-        Alleles can be lost when individuals emigrate from a population.

-        Migration results in gene flow, gene flow between populations tend to make gene pools reasonably similar.

-        Gene pools can become isolated if gene flow does not occur between populations.

Genetic drift

Describes random fluctuation in the number of allele variations in a population over time by chance events, such as bottleneck effects and founder effects.

Bottleneck effect

Occurs when a catastrophic event or adverse conditions drastically reduce the size of a population, leading to loss of genetic diversity.

Founder effect

Loss of genetic variation when a new population is established by a small number of individuals, resulting in less genetic diversity and different selection pressures.

• The new founding environment may be different from those experienced by the original population (different selection pressures) which drive changes in allele frequencies.

Describe how genetic drift affects the genetic composition of small populations.

1- Define genetic drift.

2 - Genetic drift events decreases the population size.

3 - This leads to higher chances of inbreeding which decreases the genetic diversity and would have genetic diseases.

4 - When there is a change in selection pressure, individuals within the population are unlikely to survive as they would not have an advantageous trait.

Extinction

When a species no longer exists or has the capacity to breed offspring.

Evolution

The change in the characteristics of a species over several generations which relies on the process of natural selection.

Theory of evolution - All species are somehow related and gradually change over time.

Species

Group of organisms that share a genetic lineage and are able to interbreed to create fertile offspring.

Different species are separated from each other by reproductive barriers, which are either:

-        Geographical (e.g. a mountain range separating two populations)

-        Reproductive isolation (barriers that do not allow for reproduction between the two populations)

Reproductive isolation of one species from another can be categorised into two types of mechanisms:

-        before reproduction (prezygotic)

For a species to diverge from a common ancestor and drive evolution, reproductive isolation must occur and it happens before fertilisation occurs between gametes as it keeps different species from sexually reproducing.

If individuals cannot reproduce, they are considered to be different species and diverge on the tree of life. 

-        after reproduction (postzygotic)

prevent the zygote from developing into a fertile adult

There are several types of prezygotic isolation: 7

-        Geographical isolation – separated by physical or geographical barrier.

-        Habitat isolation – individuals occupy different niches within ecosystem.

-        Temporal isolation – different breeding seasons or active during different times of the day/year

-        Behavioural isolation – different mating calls or reproductive behaviours

-        Mechanical isolation – incompatible reproductive organs

-        Gamete isolation – inability for gametes to fuse to form zygote.

-        Sexual selection - is an innate bias mates have towards members of the opposite sex based on their appearance, physical, good health or behavioural strengths.

Animals often compete with members of the same sex for the right to mate, which ensures that quality attributes (favourable alleles) are passed down to their offspring and become more predominant within the species gene pool.                                                                   

Hybrid 

Offspring resulting from the sexual union of two different species.

There are several types of postzygotic isolation:

-        Hybrid in viability- successful fertilisation but zygote does not survive.

-        Hybrid viability – zygote survives but offspring does not fully develop and survive to adulthood.

-        Hybrid sterility – hybrid survives but cannot form viable gametes and produce offspring.

-        Hybrid breakdown – if offspring eventuate, decline in fertility is likely through successive generations is likely.

Speciation

Formation of new species in the course of evolution.

The biological fields that collectively study evolution include (but not limited to):

-        Genetics

-        Evolutionary developmental biology

-        Ecology

-        Systematics (phylogenetics and biogeography) and

-        Palaeontology

Allopatric speciation, Steps

Occurs when gene flow is interrupted by a geographical barrier, leading to the isolation of populations and eventual speciation.

1)     Allopatric speciation occurs when an ancestral population becomes geographically isolated into two or more separate populations, often due to physical barriers such as mountains, rivers, or oceans.

2)     This prevents gene flow between the isolated populations.

3)     As each population experiences different selection pressures, it drives changes in the allele frequencies of the two separated populations.

4)     Overtime, genetic differences accumulate in each population becoming different species, as they are unable to interbreed even if the geographic barrier is removed.

Sympatric speciation

Occurs when two species evolve from an ancestral population while inhabiting the same geographical area.

1) Sympatric speciation occurs within an ancestral population in the same geographical area. ( As there are reproductive barriers such as differences in sexual selection, breeding time, habitat, activity time and temporal reproductive isolation. )

2) This prevents gene flow between these two populations within the same environment.

3) As each population experiences different selection pressures, it drives changes in the allele frequencies of the separated population.

4) Over time, genetic differences accumulate in each population, becoming different species, as they are unable to interbreed even though they share the same geographic area.

How does two species evolve from an ancestral population if they live in the same area?             

Some members of the population must become reproductively isolated from the others so that sexual reproduction can no longer occurs between the groups (no gene flow).                                                                                              

How could you become reproductively isolated from others when the ancestral population isn’t separated from a geographical barrier?                                             

different sexual selection (mating calls etc)

different breeding time

different habitat in the same area

different activity time (refer to prezygotic isolating mechanisms), temporal reproductive isolation.

Selective breeding

The process by which humans manipulate the gene pool of a specific population of species by selecting individuals with desired traits to breed into following generations.

Artificial selection

The process of breeding out undesired traits from a population by selecting individuals with desired traits, opposite to natural selection.

Advantages of selective breeding

1) Higher yield of goods. 2) Healthier products. 3) Survival in unsuitable conditions. 4) More nutrients provided. 5) New variations of species.

Higher yield of goods - increase the amount of milk, meat, eggs, or fruits that are produced by the animal or plant.

Healthier products - certain diseases or traits that would normally be harmful or take the lives of many animals and crops can be eradicated. Survive unsuitable conditions – crops can be tailored to grow on land or soil that they would normally not be able to

More nutrients provided - plants and animals can be bred to have more nutritional value.

New variations of species - new breeds of species can be developed and can be beneficial to people as well as the animals in the wild

Disadvantages of selective breeding

1) Reduces allele frequency. 2) Reduces biodiversity. 3) Inbreeding risks. 4) Time consuming. 

Disadvantages:

Reduces allele frequency – the frequency of allele varieties are drastically reduced with selective breeding, making the species less resistant to environmental changes, threatening the survival of the species

Biodiversity is reduced – selective breeding can replace wild varieties, reducing biodiversity which can put global food security at risk, especially in the face of climate change.

Inbreeding risks – inbreeding with close family members creates higher risk of mutations which can lead to an increase in genetic abnormalities, especially if the conditions are recessive traits.

Time consuming – it takes time to know if a trait has been passed down over many generations, and may require the process to start again if the process has been unsuccessful.

Selective breeding process:  

1) Recognising the individuals with the desired trait within a population.        

  2) Deliberately breed these individuals with each other.                                      

   3) Select the offspring that show the desired characteristics. Repeat this process over many generations until a new variety is produced with the desired traits

Palaeontology

The scientific study of past life, it includes the study of fossils to determine an organisms' evolution and interactions with each other and their environments.

Fossil

Any preserved remains, impression, or trace of any prior living thing from the past (geological time)

Examples include bones, shells, exoskeletons, imprints of animals/microbes, objects preserved in amber, hair, petrified wood, oil, coal, and DNA remnants.

Fossil record

The totality of all fossils ever discovered.

Fossilisation process, Why is fossilisation rare?

Fossilisation is quite rare after death as most organism rapidly decay or their remains are preyed upon by scavengers.

An organism dying on land is less likely to be fossilised than those that live in aquatic environments due to open exposure

 

-        Death of the organism

-        A quick burial by sediment (sand, silt, ice or mud) or becoming trapped in resin or other substance, will assist in the organism leaving behind a fossilised structure. E.g sediment, frozen in ice, trapped in tree sap, peat bog or tar pit or caught in volcanic ash. 

-        Decomposition is prevented and lies undisturbed – conditions such as extreme cold, dehydration, high acidity or the absence of oxygen (all prevent bacteria)

-        The fossil is uncovered due to erosion, land development or scientific investigation.

Relative dating

The science of determining the estimated age of a fossil based on they stratigraphic layers they are found within.

When determining the age of strata, generally the lowest stratum is the oldest and the upper strata are younger, this is called superposition.

Layer of strata are continually being eroded away and the earths tectonic plates are continually moving, which can alter the original strata sequence.

 Use Index fossils

Fossils used to define and identify geologic periods.

They must have a short age range and a wide geographic distribution

They must also be from a strata/sites for which an absolute age has been determined.

Used to determine the relative age of other fossils found in similar layers.

Fossil succession

One collection of fossil will be replaced with another as you go from the lowest to the highest strata.

Transition fossils

Fossils have features from both the older ancestral life form and the younger descendant.

Provide evidence for evolution and document important changes between groups of organisms over time.

Absolute dating

Provides a numerical age or range but does not provide an exact age.

Three types of absolute dating techniques include:                                  

Radiometric dating, Thermoluminescence, Electron spin resonance.

Half-life

The time in which half of a sample of a radioactive isotope decays into its daughter isotope.

Radiometric dating

• Radiometric dating uses a suitable radioactive isotope to date the fossil.

• Calculate the percentage of the parent isotope that has decayed by using its half life.

• The age of the fossil is then determined.

Isotopes are unstable and emit radiation. These radioactive isotopes decay over time, giving off neutrons and/or protons and become more stable daughter atoms (e.g. carbon-14 decays to nitrogen-14).

Thermoluminescence dating

Measures accumulated radiation in crystalline materials to determine age, emitting light signal proportional to absorbed radiation.

• As a crystalline material is heated during thermoluminescence measurements, the material emits a weak light signal that is proportional to the amount of radiation absorbed by the material. The older the object, the more radiation it has absorbed, therefore the more light it emits

• Used to date objects that were once heated (pottery, cooking tools) up to 500,000 years old.

Electron spin resonance (ESR)

A dating method for calcium carbonate in various materials, measuring trapped energy to determine age up to 300,000 years.

Used to date calcium carbonate in limestone, coral, fossil teeth, molluscs and egg shells.

As objects are buried, they absorb natural radiation from the soil causing some of the electrons in the minerals to move to a higher energy state.

The greater the trapped energy, the older the material was last exposed to heat and light (fire or sunlight)

ESR can be used to date samples from the last 300 000 years.

ESR does not destroy samples, like thermoluminescence can.

Structural morphology

Studies the form and structure of organisms and their specific features.

Comparative structural morphology

Evidence of evolution as it compares structures to show relationships between species, including homologous, analogous, and vestigial structures.

Homologous structures Example

Anatomical structures passed down through evolution from a common ancestor, having similar structures with different functions due to mutations.

Analogous structures Example

Anatomical structures found in unrelated species with different structures but similar functions due to similar environments.

Vestigial structures Example

Structures retained during evolution but lost ancestral function. Examples include hind limbs of snake and whale. The reduced eyes of certain blind cave fish and salamanders.

Tail bone of humans. Pelvic bones in whales and dolphins.

Divergent evolution

Build-up of genetic differences between closely related populations within a species, eventually leading to speciation.

-        Allopatric speciation

Organisms that diverge from a common ancestor will exhibit homologous structures which may adapt different functions over time.

Adaptive radiation

Form of divergent evolution in which organisms diversify rapidly from an ancestral species into a wide variety of new species

This occurs when there is a change in the environment that makes new resources available, creates new selection pressures, and opens the window to new environmental niches. This typically occurs when a mass extinction event occurs.

Examples include:

Darwin’s finches (have beaks adapted to different food types)

Convergent evolution

Unrelated species evolve through natural selection independently in similar environments and exposed to similar selection pressures.

Share analogous structures that have similar functions to survive in their environments, therefore have converged to become alike.

Extinction

Pattern of evolution where there is a permanent loss of a species from the planet.

Extinction of a species can result from:

-        Competition between species

-        Predation

-        Environmental change (global warming/cooling, volcanic eruption, loss of sea/land, disease and human impact)

Mass Extinction

These are large-scale extinctions that wipe out large quantities of many species in a relatively short period of time.

 

Scientists have narrowed down several of the most likely causes of mass extinction:

-        Flood basalt events (volcano eruptions)

-        Asteroid collisions

-        Sea level rise and fall

-        Global warming/cooling

-        Methane eruptions and oxygen deprived oceans

Following mass extinction, there are:

-        New ecological niches to inhabit

-        Sudden availability of new resources

-        Reduced competition or predation

This leads to periods of rapid divergent evolution through natural selection and speciation and new species are formed that take advantage of the new environments created.

Causes of extinction have come about through(humans):

-        Land clearing (urbanisation and deforestation)

-        Habitat loss

-        Fire regimes

-        Introduction of pests and foreign species

-        Hunting

Comparative embryology

Compares embryos of different species to show evolutionary relationships and similarities in development.

Molecular homology

Shows relatedness between species using molecular sequences, indicating evolutionary relationships.

Name two techniques to show the relatedness between species.

DNA and amino acid sequences - by comparing genetic material.

Mitochondrial DNA (mtDNA) - Used as molecular clocks to determine evolutionary timelines and relatedness between species.

Determining relatedness using molecules

According to evolutionary theory, all living organisms once shared a common ancestor, therefore, the closer they are related in the evolutionary timeline, the closer their chromosomes, DNA sequences and proteins would be.

Changes in DNA sequences come about through mutations after populations are separated and exposed to different selection pressures.

Over time, these changes become more extreme as mutation number increases, eventually leading to speciation.

Relatedness can be determined by looking at the number of changes that have occurred over time.

DNA Sequences

Analyzed to compare nucleotide differences between species.

DNA sequences for specific genes can be analysed to compare the difference in nucleotides of the same gene between different species.

If there a few differences between the sequence of nucleotides, these species are closely related, compared to a species that has more differences.

The more changes that are present indicates more time since the contrasting species shared a common ancestor.

Conserved Gene

A gene unchanged throughout evolution with important functions.

Chromosome Banding Patterns

Similar patterns suggest close relationship and recent diversion.

Amino Acid Sequences, Disadvantage

Differ due to mutations, leading to differences in amino acids, altering protein function.

When there is silient mutations, no change would be recognised when comparing the amino acids (or phenotype) but there may have been a change in the DNA sequence.

mtDNA Molecular Clocks

Uses mutation rate to estimate species divergence time by comparing the number of changes that have occurred at a particular gene locus.

The molecular clock ‘ticks’ at different rates for different proteins, especially if they are highly conserved.

mtDNA

All mitochondria found in human cells has come from the maternal line.

-        The very high number of relatively small mtDNA molecules makes it comparatively easy to extract and manipulate for sequencing.

-        It also means that, compared with nuclear DNA, there is a better chance of recovering an intact mitochondrial genome than a nuclear genome from fossil specimens.

-        Mutations can occur in mtDNA, similar to that of nuclear DNA but does not contain the same repair enzymes when a mutation occurs compared to nuclear DNA.

-        The lack of repair mechanisms in mtDNA makes it more susceptible to accumulating mutations over time, leading to a higher overall rate of mutation in mtDNA, therefore:

mtDNA is used to compare closely related species.

nuclear DNA is used to compare more distant related species.

Process of Phylogenetic tree

1 - close related species share a recent common ancestor and is represented by the species diverging

2 - The age in which they diverged from a common ancestor can be demonstrated by looking at the scale.

3- Distantly related species share a more distant common ancestor and branch off earlier.

Branching diagram that shows the evolutionary relationships between various biological species.