Population Genetic Basis Of Evolutionary Change

Question 1

What is a theory? Why is evolution classed and disputed as a theory?

Answer 1

Evolution: theory and fact
- Evolution has been criticised by creationists for being just a theory
- It is indeed a theory (difference colloquial/scientific language)
- A theory is defined as a hypothesis that has been verified/supported by facts (ie empirical evidence from experiments and observations)
- Evolutionary theory has been verified in this way – by a massive amount of evidence = different sources agree with each other (consilience)
- Evolution is also predictive
- No rational minded scientists dispute the above

Question 2

Describe evolution as a process?

Answer 2

• The process of temporal change
• Ie change over time
• By which organisms come to differ (permanently) from their ancestors with respect to any heritable traits/ characteristics

Question 3

Definition of the term heritable?

Answer 3

• Characteristics passed on/ transmitted from parents to offspring
• These traits are genetic and are often (but not always) also expressed in the phenotype

Question 4

What are the 2 processes of evolutionary change? Other names for this?

Answer 4

The 2 processes of evolutionary change:
- Transformation
- Splitting/branching
Otherwise known as Anagenesis and cladogenesis

Question 5

What is anagenesis?

Answer 5

Anagenesis – evolution within a lineage, usually the ancestral form disappears as the entries species changes to a new form

Question 6

What is cladogenesis?

Answer 6

Cladogenesis – division of a lineage due to genetic divergence
- Subsequent changes (Anagenesis) occurring in both/either of the sister lineages results in further divergence

Question 7

What do division events result in?

Answer 7

Results in either –
I) 2 new lineages
II) Just one new lineage in addition to orginal

Question 8

What is meant by phylogenies/phylogenetics?

Answer 8

These branched evolutionary histories are known as phylogenies
- The study/reconstruction of phylogenies is known as phylogenetics

Question 9

What is Microevolution? What does Microevolution lead to?

Answer 9

Micro evolution is evolution at the population level
- Species are comprised of one or (usually) more populations of many individuals
- Microevolution refers to within species evolution
- Ie intraspecfic evolution
Microevolution includes the processes leading to speciation
Ie the production of new species
- Speciation occurs mainly through cladogenesis

Question 10

What is macroevolution? What 2 key things does it involve?

Answer 10

Macroevolution - evolution at the species level and above
- Eg genus and family
- Ie interspecific evolution
It involves:
1) Speciation events (splitting of lineages)
2) Subsequent divergence of species and higher taxa (genera, families etc)

Question 11

What do Anagenesis and cladogenesis explain?

Answer 11

Important points: Anagenesis and cladogenesis explain the evolutionary processes
- Nothing makes sense in biology, except in the light of evolution

Question 12

What are characters? Character states?

Answer 12

Characters: any measurable item on an organism (eg height)
Character state: alternative variants of a character (eg eye colour in humans)
Characters can also be referred to as Traits

Question 13

What is the genotype?

Answer 13

The genotype: the information stored in the DNA of 1 individual
- Observable/ measurable/ detectable characteristics of an organism

Question 14

Where is DNA found?

Answer 14

• In the nucleus of each cell, on the (linear) chromosomes
• IN the mitochondria – within the cytoplasm of each cell (lots of copies per cell) on a circular chromosome
• Mitochondria were derived from an endosymbiotic bacterium, to form the first eukaryote cell
• Chloroplasts, kinetoplasts…

Question 15

Does DNA only code for genes?

Answer 15

Junk DNA
- Note: it was once thought that most sequences (98%) in human genome) do not have a function – so are not by definition genes
- Sequences within introns of genes and those between genes
- These have been referred to as ‘junk’ DNA
- Junk is not a great name: 80% of the so called junk in humans does have a function, eg expression regulation (miRNA, snRNA)

Question 16

Why is junk DNA useful to evolutionary biologists?

Answer 16

Junk DNA is useful to evolutionary biologists
- Because true junk DNA is assumed not to be subject to natural selection
- Phylogenies and population genetics

Question 17

How is genetic variation created within individual organisms? What is a single nucleotide polymorphism? SNP

Answer 17

• Nucleotide base sequences making up that same gene may differ between individuals
• A diploid individual:
  o GCATAGCATCTAGC = chromosome copy 1
  o GCGTAGCATCTAGC = chromosome copy 2
  Single nucleotide polymorphism (SNP)
  Genotype = A/G (heterozygous)
• When nucleotide sequences differ in this manner at the same site (locus) on the paired (homologous) chromosomes
• Eg on nuclear chromosome No.4
• They are termed different alleles of the same gene
• The locus is said to be polymorphic
• There can be many more than 2 alleles (eg hair colour)

Question 18

Definition of genotype by evolutionary scientists?

Answer 18

• The information stored in all of the genes of one individual

Question 19

Definition of genotype by population geneticists?

Answer 19

• The combination of alleles at one or more studied/examined loci in one individual

Question 20

What is the phenotype?

Answer 20

The phenotype: they observable/ measurable/ detectable characteristics of an organism

Question 21

What does the phenotype comprise?

Answer 21

The phenotype comprises: ie any/all observable non-gene traits –
- External appearance
- Internal structures/tissues
- Intracellular structures
- Proteins/polypeptides

Question 22

What is morphology? Extended phenotypes?

Answer 22

Morphology: eg beak shape/ fur colour/ shell colour/ petal colour
And even behaviour, nests and other structures
- Nests are an example of the extended phenotype

Question 23

Why is the phenotype typically what scientists examine?

Answer 23

• The phenotype has been, from a practical perspective, the easiest part to record/ observe/ quantify
• In fact, until recently, it has been the only observable part of the organism
• Variation in most phenotypic traits is at least partly genetically determined (thus its heritable)

Question 24

What makes not all of the variation in a phenotypic trait heritable?

Answer 24

• Not all of the variation in a phenotypic trait is heritable
• Some variation may be due to non-genetic factors such as:
  o Wear/ trauma (damage)
  o Disease (symptoms)
  o Somatic mutation (soma=cells other than egg and sperm)

Question 25

What is the evolutionary importance of heritable trait variation?

Answer 25

- Heritable intra-population variation is essential for evolutionary change to occur - There must be a sufficient amount of such variation

Question 26

How can cloning be a problem in crops?

Answer 26

The lack of sufficient heritable trait variation is due to cloning by farmers (asexual reproduction, which produces progeny that are genetically identical to the parent)

Question 27

Describe the late potato blight and the great Irish famine.

Answer 27

- The late potato blight and the great Irish famine o Phytopthora infestans o A water mould (not a true fungus) o Capable of rapid evolution o Estimated to have caused >1 million deaths from starvation and forced 2M to emigrate from Ireland o Potatoes were of just one variety (which was vulnerable to the fungus) o And they were propagated asexually (cloned) o Had the potato population been more genetically diverse, the famine might have been averted

Question 28

Describe the black Sigatoka disease in bananas?

Answer 28

o The problem made worse by:  Cultivation of only a few banana varieties, most of which are vulnerable  These varieties are propagated asexually (cloned)  Genetic variability of fungus has allowed it to evolve resistance of fungicidal chemicals applied by farmers

Question 29

What are the 2 classifications of phenotypic variation?

Answer 29

Continuous traits – intermediates exist between 2 extremes Discontinuous traits – no intermediates exist

Question 30

What is discontinuous trait variation?

Answer 30

- One or a few gene loci involved - Usually only a few alleles involved at such loci - ‘Allele for trait’ effect clearly evident in the phenotype - Environment has little effect

Question 31

What is continuous trait evolution?

Answer 31

- Many gene loci involved - Many alleles involved - Is it harder to discern the contribution of the individual alleles to the phenotype - Environment often plays a role

Question 32

How to quantify population variation?

Answer 32

Sampling – representative (unbiased) samples needed - Take a random sample - Take a larger sample, if possible

Question 33

How do you measure variation (among individuals)?

Answer 33

- Measurement (for continuous variation) - Scoring (for discontinuous variation) Mean and variance calculated for sample – can compare with other samples (eg by T-test) - SD: standard deviation (a measure of variance around the mean)

Question 34

What is the relation between fitness and traits?

Answer 34

- adaptive traits are correlated with fitness - neutral phenotypic traits are not

Question 35

What is Microevolution?

Answer 35

- Overtime - In the relative abundance of genotypes or phenotypes

Question 36

What are the 2 processes creating genetic variation?

Answer 36

o Mutation o Recombination (shuffles genetic variation)

Question 37

What are the 2 processes removing genetic variation?

Answer 37

o Everything else (genetic drift, selection)

Question 38

What is genetic drift (demography)?

Answer 38

Genetic drift (demography) – random changes in allele frequencies - Reproduction is random - Bottleneck (random reduction in the number of breeders) - ‘Effective population size’ = number of breeders - Effect = loss of heterozygosities - Cause = inbreeding, mating between relatives

Question 39

What is selection?

Answer 39

Selection – not random changes in allele frequencies (natural, artificial) - adaptive traits are subject to selection within the population - neutral traits are usually not

Question 40

What is linkage disequilibrium/equilibrium?

Answer 40

Linkage disequilibrium: non-random association between loci - 2 loci (A and B) - 2 allele per locus - A = (A,a) B= (B,b) - LD is a correlation Linkage equilibrium: random association between loci

Question 41

Uses of hardy Weinberg and LD for population structure?

Answer 41

- Each column is an individual - Several rectangles of the same population are shown as part of a rectangle - Rectangle of the same colour represent populations (genetically) - This approach aims at reducing LD and identifying HWE

Question 42

What is adaptive evolutionary change?

Answer 42

- When subjected to natural selection or its mimic, artificial selection: o Genetically determined (=heritable) phenotypic traits correlated with fitness typically alter in frequency (% of proportion) within a population - This is directed (ie non random) change, in response to change in environmental variables

Question 43

Describe adaptive evolutionary change in the context of insects and insecticides? (Long fc )

Answer 43

- Evolution of insecticide resistance - First: consider a genetic variant under insecticide-free conditions - Next: consider what happens when insecticides are applied An insect population may contain a genetic variant (eg arising via a recent mutation) - Variant occurs as just a few individuals - Under natural, insecticide free conditions: o Variant, compared with ‘normal’ form, has shorter life span and so leaves fewer progeny - The variant, being less fit, therefore remains rare in the aphid population over successive generations o (‘fit’ being relative, the less fit variant MAY be higher fitness that another variant) - Being rare, the variant is more likely to become instinct under insecticide free conditions, due to random processes, eg bad weather However, under conditions of insecticide application the variant is resistant to insecticides: - Normal (non-resistant/susceptible) individuals either mostly die before reaching adulthood or are on average very short lived - Normals are less fit than variants - Variants has longer lifespan and leaves more progeny than normals, yet its lifespan has not increases Under insecticide conditions, variant individuals are more fit than normal ones - Ie variants contribute per head (per capita) more offspring to the next generation - The proportion of the variant within the population as a whole will increase in the next population = EVOLUTIONARY CHANGE - The variant is said to have ‘selective advantage’ over the ‘normal’ form - Selection in this case was ‘unnatural’ – human causes (ie artificial)

Question 44

What is another natural example of natural selection?

Answer 44

Predation

Question 45

What is adaptive evolutionary change?

Answer 45

- Under natural conditions, the genetic variant conferring higher fitness increases in relative abundance within the gene pool - Eg proportion of variant A increases, while proportion of variant B decreases reciprocally

Question 46

Everyday examples of adaptive evolutionary change?

Answer 46

- Insecticide resistance in head lice - Warfarin resistance in rats - Antibiotic resistance in bacteria

Question 47

What evolutionary change can take place in just a few years (ie a few generations)?

Answer 47

- Insecticide resistance - Resistance vs pathogens o Antibiotic resistance (eg MRSA) o Eg blue moon butterfly: resistance against a parasitic bacterium that kills males (males were 1% part of the population in 2001 but 40% in 2006)

Question 48

What is artificial selection and a bird example?

Answer 48

Artificial selection – mimics natural selection - Note: with artificial selection, the breeder/ experimenter decides which trait has the highest fitness o Results in adaptive evolution under artificial conditions o But it does not necessarily correspond to differential fitness under natural conditions - Eg red plumage may not correlate with greater lifetime progeny production in nature, but it does correlate in the bird breeders laboratory (by virtue of the breeder preferring red birds for breeding) - Artificial selection for red plumage results in adaptive evolution o Because it is correlated with a higher reproductive rate (=progeny production)

Question 49

Important question: are all of an organisms heritable phenotypic traits (or trait states) either adaptive or maladaptive?

Answer 49

no - They exist as selectively neutral genes (1968) - Genes whose frequencies are not influenced by natural selection - Concept developed by Motoo Kimura

Question 50

What is neutral evolutionary change?

Answer 50

- Frequencies of variants of neutral traits can change over time within a population - But it is unidirected (random) evolutionary change But note: neutral genes are known that hitch hike with (are linked to) genes that have an adaptive function - In which case they will be subject to selection - Adaptive gene (a gene which has either a positive or deleterious effect on fitness) being close to neural gene

Question 51

Examples of selectively neutral phenotypic traits

Answer 51

- Markings on clover leaves - Markings on cone shells - These seem to have to adaptive significance - The genes responsible may be selectively neutral - OR they could be adaptive (pleiotropy)

Question 52

What is pleiotropy? And examples of this in humans?

Answer 52

Pleiotropy: multiple phenotypic effects on an individual gene - The effect on one phenotypic trait can be adaptive (positive) - Whilst the effect on the other trait may be neutral, deleterious or positive - Reproduction vs ageing (= senescence)? (Antagonistic pleiotropy) - Male humans: testosterone, increases fitness early life – prostate disorders later on - Female humans: pregnancy and lactation decrease bone mineral density – osteoporosis later on

Question 53

What are the 3 kinds of selection?

Answer 53

- Negative - Positive - Balancing

Question 54

What if the selection pressures acting on an adaptive trait are completely eliminated from the environment?

Answer 54

- Eg via extinction of a major predator - In this new context, the trait will be selectively neutral - At least until a ‘new’ predator arrives

Question 55

What is phenotypic plasticity (among individuals and within individuals)?

Answer 55

- Often, a particular genotype produces a different phenotype according to the organisms particular environment - Ie the phenotypic expression of the genotype is often environmentally determined - Eg well-fed individuals grow larger than poorly fed ones - In this cases the smaller individual is likely to be less fit (it has poor survival and reproduction prospects) o Ie only some phenotypic expression of the genotype are ‘beneficial’, ie are optimal  Most others are suboptimal

Question 56

What is adaptive phenotypic plasticity and an example in humans?

Answer 56

- Each one of the different phenotypic expressions of genotype is beneficial (optimal) - Eg skin darkening and lightening in response to sun exposure in humans o Pale skin: admits UV light for vitamin D production – advantageous in winter o Dark skin: protects against too much UV – advantageous in summer o Skin darkening is reversible during the individuals lifetime, but some forms of adaptive plasticity are fixed in the individual

Question 57

What are the constraints upon evolutionary change and the 3 types of constraint?

Answer 57

Constraints upon evolutionary change: - Evolutionary change does not always happen Types of constraint: a) Insufficient genetic variation exists in the gene pool b) No selection pressure operating c) Sufficient selection pressures, but they’re constraints upon changing the blueprint of an organism

Question 58

What are blueprint constraints?

Answer 58

The genome of organisms is a coevolved, integrated assemblage of genes - It cannot be simply unravelled to produce a radically new structure to solve an environmental problem/challenge

Question 59

Example of a blue print constraint?

Answer 59

- Arachnid, myriapod and insect body size o Primarily terrestrial animals need to shed (moult) their exo skeleton o If they were very large, their bodies would collapse under their own weight at the moult - Also the respiratory mechanism of arachnids and insects: o A system of air carrying tubes would not work efficiently if maximum body size were much greater than it is o Relies upon diffusion of O2 and CO2 in/out of tissues o For these reasons, insects and terrestrial arachnids have never been, and never will be, very large

Question 60

What is meant by a phylogenetic constraint?

Answer 60

- Ie found within the entire group of descendants from a common ancestor - It cannot be undone

Question 61

Is evolution goal directed?

Answer 61

- No - Lineages do not comprise a series of prototypes culminating in a final perfected model - Generations within a lineage are adapted (or in the process of becoming adapted) to the prevailing conditions - There may be bred if phases of ‘unadaptiveness’ o In a population colonising a new habitat o If the habitat changes rapidly

Question 62

What is the red queen hypothesis in terms if evolution?

Answer 62

- “It takes all the running you can do just to stay in the same place” - To evolutionary biologists, there is no ‘purpose’ to evolution - Evolutionist speak on the design of organisms - But they do not attribute design to a supernatural creator - Some religions and philosophies teach that there is a purpose and that humans are its intended end point – ie. A teleological view