what is Evolution

Question 1

Natural selection and evolution are not the same thing

Answer 1

• Fisher began his famous book The Genetical Theory of Natural Selection (1930) with the sentence “Natural Selection is not Evolution.”
• 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
• Evolution is the cumulative change in a population or species over time.

Question 2

The Galapagos Islands

Answer 2

-Valuable environment for studying and understanding natural selection and evolution
-• Galapagos : a series of many islands
• Age from ~0.5 to ~3 million years old
• A wide range of habitats

Question 3

Macroevolution : the concept

Answer 3

Major evolutionary changes among large taxonomic groups( at or above the species level) over long periods of time.

Question 4

Microevolution : The concept

Answer 4

Microevolution studies the evolutionary ‘agents of change’ that shape the genome within a population

Question 5

The Hardy-Weinberg Theorem

Answer 5

• Under certain conditions , allele frequencies will not change from one generation
to the next. They remain in equilibrium and dominant alleles can’t over run recessives.
p2 + 2pq + q2 = 1.0

Question 6

The Hardy-Weinberg theorem

Allele frequencies remain in equilibrium (do not change) if five unrealistic conditions are met

Answer 6

• No migration
• No mutation
• Equal fitness
• The population size is infinite
• Mating is random

Question 7

chi-squared test

Answer 7

x2=Sum(O-E)/E and the compare at d.f(n-1_

Question 8

What does a population mean from an evolutionary perspective?

Answer 8

• A population is a group of organisms that interact and share genetic information
• Interact Same place and time
• Share Genetic Information Interbreed and produce viable offspring
• A population can vary in size, distribution and structure and influence evolutionary processes

Question 9

Why is it useful to define populations?

Answer 9

• Spread of disease
• Track resistance (e.g. insecticide)
• Risk of inbreeding
• Financial – bioprospecting
• Pest control – e.g. Fox, feral cats
• Conservation – monarch butterflies

Question 10

gene pool

Answer 10

The gene pool refers to all the genetic variation that exists among all the individuals of a population

Question 11

effective population

Answer 11

The number of individuals that contribute

offspring to the next generation

Question 12

population size, distribution and structure and influence evolutionary processes

Answer 12

– Mutation (more individuals, more chance of mutation)
– Natural Selection (smaller populations fix alleles that are under selection faster)
– Genetic Drift (smaller populations are more likely to fix alleles via random chance)
- Gene Flow can influence the flow of genetic information between populations
• Distribution - The area a population inhabits and density of the individuals
– mating Random vs. Non-random
• Mating can affect population structure and influence the effective population size (Ne)

Question 13

Germ-line versus somatic mutation

Answer 13

Germline Mutation
• Affects gametes (eggs, sperm)
• Mutation transmitted via sexual reproduction
• Mutations in the germline create new variation (alleles) and can be heritable
Somatic Mutation
• Affects all the Daughter cells of a single cell.
• Not heritable (but can be passed down in plants for example, through vegetative reproduction)

Question 14

Mutations alter DNA and can introduce variation to a population

Answer 14

-Induced DNA mutation via chemicals and radiation
-Spontaneous DNA mutation via replication errors
• Mutations can arise in all parts of the genome
• When mutations occur in a gene or their regulatory regions they may impact on an
organism phenotype

Question 15

Mutations can impact gene expression and function

Answer 15

Mutations in regulatory regions of genes may affect expression
• Have no change in expression
• Increase/decrease abundance
• Presence or absence in tissues or cells
Mutations in coding regions of genes may affect (protein) function
• Be functionally the same
• Large or small functional difference

Question 16

Mutations can occur at different scales within the genome have differing impacts.

Answer 16

Smaller Changes: More common but often less genetic consequence
-A single base changes (substitution)
-DNA of different sizes is inserted/deleted (Indel) into the middle of an existing sequence.
-If Indel is not a multiple of three then it can lead to a frameshift
Larger Changes: Less common but often greater genetic consequence
-DNA is copied a second time and/or flipped around
-Chromosomes are joined together or gained/lost (Aneuploidy)
-Entire genomes are duplicated

Question 17

Mutation rate in human

Answer 17

• Human : approximately one SNP (single nucleotide polymorphism) per 30 million base pairs (3 x 10-8)
• This figure is per genome (N)
• It has been estimated that we inherit (approximately) 100 new mutations from each of our parents, so ~200 new mutations all up (2N, as we are diploid)

Question 18

Mating Systems

Answer 18

Random Mating: Equal probability that mating will occur between any two individuals in a population
Non-Random mating: Probability bias
Assortative mating
Disassortative mating

Question 19

Assortative mating

Answer 19

Mate with individuals that share alleles
‘Like with Like’
Can result in
• Inbreeding is an extreme case
• Less genotypic diversity
• Increased homozygosity

Question 20

Disassortative mating

Answer 20

Mate with individuals that do not share alleles
‘Opposite Attract’
Can result in
• Increased genotypic diversity
• More heterozygosity

Question 21

Galapagos medium ground finch

Answer 21

• Island : Daphne Major
• Medium ground finch live their entire lives on the island
• Few plant species – producing hard or soft seeds that the birds eat
• The population shows variation in beak size
• Large beaks open larger, hard seeds faster and smaller beaks are better at smaller seed

Question 22

Natural Selection : avian attack on clay models

Answer 22

• Measuring natural selection on coat colour in oldfield mice.
• Clay models of mice were painted to resemble habitat colour and placed in either mainland or beach habitats.
• Predation was highest when coat colour provided no
camouflage.

Question 23

Requiermernt for Natural Selection

Answer 23

1. Variation
   Individuals within a population must have variation for selection to act. Variation can occur in appearance, behaviour or physiology.
2. Heredity
   Offspring need to resemble their parents more than unrelated individuals. Traits must be heritable.
3. Selection
   Some forms are more successful at reproducing in a particular environment.

Question 24

Selection can act in different ways on a population

Answer 24

Directional selection (positive selection) favours individuals on one end of the distribution of phenotypes (small fish have higher fitness than large fish)
Stabilizing selection favours individuals in the middle of the distribution of phenotypes present in a population (for example, by acting against individuals at either extreme).
Disruptive selection (right) favors individuals at either end of the distribution (shaded area).

Question 25

Selection acts on dominant alleles faster than recessive alleles

Answer 25

* Favoured dominant alleles (red line) immediately increase in frequency. * Selection is not likely to drive a dominant allele to fixation, as recessive alleles can “hide” in the heterozygous state. * Favoured recessive alleles (blue line) are not exposed to selection initially because they are likely to occur only in heterozygous genotypes. * Once recessive homozygotes begin to appear, they quickly fix in the population

Question 26

Artificial selection

Answer 26

… is similar to natural selection, except that it results from human activity. When breeders nonrandomly choose individuals with economically favourable traits to use as breeding stock, they impose strong artificial selection on those traits.

Question 27

Balancing selection, the heterozygote advantage

Answer 27

Heterozygote advantage occurs when selection favours heterozygous individuals over homozygotes

Question 28

Fitness and relative fitness

Answer 28

``` Fitness refers to the success of an organism at surviving and reproducing and thus contributing offspring to future generations. Relative fitness (w) describes the success of a genotype at producing new individuals. Relative fitness standardized by the success of other genotypes in the population and ranges from 0 to 1.0 ```

Question 29

calculate relative fitness

Answer 29

O/E than divide the number with highest value | selective advantage value: divide the two value against each other

Question 30

Genetic drift

Answer 30

-Genetic Drift involves random changes in allele frequencies that are directionless -When 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 -Allele frequency changes via genetic drift results from ‘sampling error’ • Cannot predict which allele will be fixed/lost

Question 31

Which population is most susceptible to genetic drift

Answer 31

-The effects of genetic drift occur in all populations but is most pronounced in small populations -In a small populations genetic drift is a stronger evolutionary agent of change • Outcomes are more unpredictable • Probability of large changes is greater -Large populations buffer genetic driftmaking it a less significant agent of change • Populations don’t need to be infinite size, but large enough that random sampling effects do not impact allele frequencies significantly

Question 32

• Genetic bottleneck

Answer 32

: caused by events that reduces the size and genetic diversity of a population significantly` Events that randomly impact individuals in a population - not related to Natural Selection • Impact allele frequencies in a population by chance • Populations therefore contain a smaller, mostly random sample of the alleles that were present in the original population -The chance that loosing alleles after bottleneck or founder events depend on their initial frequency plus the new population size

Question 33

Founder effect

Answer 33

-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

Question 34

what happen after bottleneck or founder effect

Answer 34

- Following a bottleneck or founder event, population size may recover quickly, but genetic diversity will not - New populations arising from a very small number of individuals can cause this population to differ considerably from the parent population

Question 35

Gene flow

Answer 35

Gene flow is the transfer of genetic information from one population to another • Gene flow occurs via migration, movement or hybridisation. • The impact of gene flow on the gene pool depends upon i. The level of migration, movement or hybridisation (how often) ii. The differences in allele frequencies between populations Gene flow also occurs when individuals share generic information via hybridisation

Question 36

gene flow effect on population

Answer 36

- Gene flow tends to homogenize more connected populations | - A lack of gene flow promotes interpopulation differentiation

Question 37

calculate the impact of gene flow

Answer 37

``` ∆p = the change in f(A) in the resident population after one generation of migration Dp = m(x-p) In residents f(A) = p f(a) = q In migrants f(A) = x f(a) = y ```

Question 38

Speciation

Answer 38

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

Question 39

Reproductive barriers

Answer 39

prevent gene flow and enable speciation 1. Pre-mating Isolation - geographical isolation - behavioural isolation 2. Pre-zygotic Isolation - mating time differences - ecological differences 3. Post-zygotic Isolation -fertilized egg/offspring inviable

Question 40

Pre-mating reproductive isolation (geographic) | Allopatric speciation

Answer 40

-Geographical isolation prevents reproduction and can enable the agents of change to drive speciation (allopatric speciation) Agents of change cause genetic divergence between populations • Mutation ->• Chromosomal/DNA differences • Selection ->• Change phenotype/behaviour • Genetic drift->• Reproductive isolation -Selection for different mating signals creates reproductive isolation in the same (sympatric) population.

Question 41

Pre-mating reproductive isolation (behaviour)

Answer 41

Genetic, behavioural, physiological, or ecological aspect preventing the sperm from one species from fertilizing eggs of another species

Question 42

Post-zygotic Isolation

Answer 42

Isolating barriers that act after a zygote begins to develop - fertilized egg fails to develop - hybrid offspring sterile

Question 43

Sympatric speciation

Answer 43

speciation in the same location

Question 44

How is a species defined?

Answer 44

Biological species concept : species are groups of actually (or potentially) interbreeding natural populations that are reproductively isolated from other such groups. Phylogenetic species concept : species are the smallest possible groups whose members are descended from a common ancestor and who all possess defining or derived characteristics that distinguish them from other such groups Ecological species concept A concept positing that species are sets of organisms that are adapted to a particular set of resources, that is, to the same ecological niche.

Question 45

Cichlid fish are an important evolutionary study system

Answer 45

1. Unparalleled degree of phenotypic and taxonomic diversity has arisen in sympatry – new species without geographical barriers 2. Speciation has occurred through macrohabitat adaptation and specialization. Mate preference traits (often colour) can cause disruptive selection 3. Adaptive radiation : very rapid evolution of many species through adapting to underutilized ecological niches

Question 46

Why is it useful to define a species

Answer 46

``` Conservation – categorizing endangered species Food – classifying fruits and vegetables Safety – e.g. Bacillus anthracis (anthrax) and Bacillus thuringiensis (pesticide) Medical – diagnose and treat infections (bacteria and viruses) Recreational – implementing catch limits when fishing ```

Question 47

Potential outcomes of hybridization

Answer 47

Adaptive introgression : inheritance of beneficial variation from related species that accelerate adaptation to, and survival in new environments

Question 48

Hybridization between Hominids

Answer 48

* DNA and fossil evidence show humans, Neanderthals, and Denisovans represent separate, parallel lineages descended from a common ancestor (★). * Molecular studies indicate that modern humans interbred with Neanderthals and Denisovans

Question 49

alternate explanation to hybridization

Answer 49

alleles pre-date speciation

Question 50

what does Genes code incolve

Answer 50

Genes code for proteins that are involved in complex biological, cellular and molecular functions that together contribute to phenotype • Evolution has been discussed from the perspective of one set of alleles and distinct phenotypic differences • In reality, many genes and their alleles are involved in determining a phenotype • Quantitative Traits

Question 51

QUALITATIVE TRAIT

Answer 51

Multiple genes contribute to a phenotype in a cumulative way • While all genes are required, some may be more important or influential than others • The alleles influence or improve a phenotype may be the subject of selection -Biological, cellular and molecular functions are part of a larger network of complex interactions and feedbacks

Question 52

Molecular genetics and genomics

Answer 52

Molecular genetics and genomics involves the sequencing and analysis of select genes or entire genomes Molecular Genetics involves the study DNA sequences encoding specific genes to understand function. Genomics is the study of the DNA sequences of all the organism's genes – called the genome

Question 53

Investigate variation using a range of approaches

Answer 53

- Compare Specific Situations - Look across the distribution of a phenotype - Look at evolutionary relationships

Question 54

Whole genome sequencing

Answer 54

Whole genome sequencing (reference genome) i) Extraction of DNA ii) Create DNA “Library” iii) Sequence iv) Assemble data (and annotation) • Collect samples • Create “Libraries” and sequence • Investigate one locus/gene or entire genome • Identify SNPs and other genetic variation

Question 55

Technological advances in genomic

Answer 55

Genomes of some organism are very big • Need a sufficient sample size to determine relationships which may involve significant sequencing • Complex analysis with big data requires bioinformatics.

Question 56

COVID-19 Spread

Answer 56

* Small genome; nucleic acid is RNA * Replicate via asexual reproduction * Replication is not accurate as in other life forms so mutations arise more rapidly * Mutations and mode of inheritance means we can fingerprint each case * The person they caught it from will appear almost identical * Transmission to additional people will likely have more differences

Question 57

Phylogenetic relationships - Cladogram

Answer 57

- Analysis of relationships between the nucleic acid sequences to create a tree of relatedness - Compare transmission and epidemiological information with the established evolutionary relationships

Question 58

how mitochondria help Indigenous Australian people’s migration into the continent

Answer 58

``` Mitochondrial Genome (Mitogenomes) • Inherited maternally and represents clonal lineages • Circular double stranded DNA molecule • Mutations occur • Haploid genome - Haplotypes ```

Question 59

Indigenous Australian people’s migration into the continent Study Methodology

Answer 59

``` Mitogenome From hair samples collected from early European settlement Locational Information Obtained at time of hair sample collection Temporal Molecular clock (mutation rates) calibrated with archaeological data ```

Question 60

Result ofPhylogenetic analysis

Answer 60

Four major haplotype groups identified which have deep splits between them Haplotype groups diverged in first 10,000 years and remained distinct for the next 40,000 years Single Rapid Migration along the East or West coasts in first 10,000 years • Regional patterning developed post continent wide settlement where little movement occurred across the landscape for next 40,000 years Continuous presence of populations in discrete geographic regions for long period Consistent with Indigenous peoples long cultural connection with land