population genetics - basis of evolutionary change

Question 1

population genetics and population

Answer 1

POPULATION GENETICS: “The body of mathematical principles that explain how genetic variation changes in populations over space and time”
The study of evolution from a genetic point of view (microevolution)
To predict fate of genes over time we need to consider gene transmission in populations, change of genetic variation
Characteristics of the population such as gene frequency and population size will affect the fitness of individuals carrying particular genes

Population: “group of sexually interbreeding individuals” and has two important attributes:
i. Gene (allele) frequencies = proportion of an allele in a population
ii. Gene pool (sum of all the alleles within a population)

Question 2

causes of genetic variation

Answer 2

natural selection:
process that modifies the reproductive success of an organism in its natural environment; process through which populations of living organisms adapt and change

Migration:
gain or loss of individuals that make up the gene pool

Genetic drift:
random fluctuations in gene frequencies; small population size

Recombination:
reshuffling of genes (not new variation)

Mutation:
random change in genes that is passed on

random mating

Question 3

principles of population genetics

Answer 3

Genes occur at definite site referred to as LOCI
Loci are scattered along the chromosomes
Locus carry several variant genes called ALLELES
One allele of chromosome pair is maternally derived
The other copy is paternally inherited
These constitute a GENOTYPE (not observable)
What is observable is the PHENOTYPE

eg. blood groups:
Four blood type phenotypes (often visible):
O, A, B, AB
Four blood type genotypes (not visible):
ii, IAi or IAIA, IBi orIBIB, IAIB

Question 4

Hardy-Weinberg principle

Answer 4

• HWP states that allele and genotype frequencies in a population will remain constant from generation to generation in the absence of other evolutionary factors
• May include mate choice, mutation, selection, genetic drift, gene flow
• Describes an ideal condition

p+q=1
p(sqd.) + 2pq +q(sqd.) = 1

assuming:
Random mating
Large population
No migration
No natural selection
No mutation

Question 5

rare recessives

Answer 5

When recessive phenotypes are rare in a population it is common to find that the heterozygote “carriers” are present at high frequencies
Albinism (recessive disorder) affects about 1/20,000 humans
From this we can calculate the recessive gene frequency (q)
q2 = 0.00005; q = 0.007
And the dominant gene frequency (p): 1 – q = 1 – 0.007 = 0.993
The genotype frequency of the heterozygote carriers is:
2pq = 2 x 0.993 x 0.007 = 0.0142 (1.42 out of 100 individuals)
Thus about 1 in 70 people carry the recessive allele for albinism

Question 6

huntingtons disease and duchennes muscular dystrophy
sickle cell disease and malaria

Answer 6

Late onset
No effect on reproductive success
Short arm of chromosome 4
Autosomal dominant
Brain disorder

High mutation rates
Genes accumulate mutations at very high levels
X-linked recessive
Occurs primarily in males
Symptoms of muscle weakness
Affects the thighs and pelvis and then the arms

sickle cell disease and malaria:
AA=susceptible to malaria but no sickle cell disease
Aa=resistant to malaria and only mild sickle cell disease
aa=resistant to malaria, but fatal sickle cell disease

Question 7

gene frequencies - natural population

Answer 7

In real populations the genotype frequencies may not be available
* So, we have to rely on phenotype to calculate frequencies
In humans: ability to taste phenyl-thiocarbamide (PTC)
Controlled by a dominant allele (T)
TT or Tt = can taste PTC tt = cannot taste PTC
In a natural population of 100, 49 people cannot taste and 51 can taste
BUTTT and Tt are phenotypically indistinguishable
So, how can we determine the genotype frequencies?

• Determine the number that are tt (cannot taste PTC) = 49 out of 100
• Determine the gene frequency of T
  p = gene frequency of T Genotype frequency of TT = p2
  q = gene frequency of t Genotype frequency of tt = q2
  NB! p + q = 1. Genotype frequency of Tt = 2pq

q^2= 0.49
q = √0.49
q = 0.7
p = 1 - 0.7 = 0.3 (since p + q = 1)
Genotype frequency of TT = p2 = 0.32 = 0.09
Genotype frequency of Tt = 2pq = 2 x 0.3 x 0.7 = 0.42
From the 51 people that can taste PTC only 9 are homozygotes (TT) and the remaining 42 are heterozygotes (Tt)

Question 8

multiple alleles

Answer 8

When more than two alleles are present at a locus, the Hardy-Weinberg Principle may still be applied
In a population at equilibrium with only 3 alleles at locus A (A1, A2, A3) with respective frequencies p, q and r,
the genotype frequencies at equilibrium are:

(review on slides)

Question 9

Intro to what evolution is -theory V fact

Answer 9

*Evolution has been criticized 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 (i.e. empirical evidence from experiments, observations).
*Evolutionary theory HAS been verified in this way – by a massive amount of evidence – different sources of evidence agree with one another (= consilience)
*Evolution is also predictive
*No rational-minded scientists dispute the above.

Question 10

processes of evolution

Answer 10

*The process of temporal change,
*i.e. change over time
*by which organisms come to differ (permanently) from their ancestors with respect to any heritable trait(s) / characteristic(s)

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

2 PROCESSES
anagenesis=”transformation” and cladogenesis=”splitting/branching”

anagenesis:
Between-generation change within a single lineage (Gen. N to Gen. N+1: is usually gradual).

Evolution within a lineage. Usually the ancestral form disappears as the entire species changes to a new form

Cladogenesis(splitting/branching) - Division of a single lineage due to genetic divergence.

Division of a lineage due to genetic divergence. Subsequent changes (anagenesis) occurring in both / either of the ‘sister’ lineages results in further divergence.

Question 11

microevolution & macroevolution

Answer 11

microevolution
Microevolution: is evolution at the population level
* Species are comprised of one or (usually) more populations of many individuals
* ‘Microevolution’ refers to within-species evolution
i.e. intraspecific evolution
Microevolution includes the processes leading to speciation i.e. the production of new species.
*Speciation occurs mainly through cladogenesis.

macroevolution:
Macroevolution: evolution at the species level & above. (e.g. genus, family)
i.e. interspecific evolution It involves:
Speciation events (splitting of lineages)
Subsequent divergence of species & higher taxa (genera, families &c)

Question 12

Character and character states

Answer 12

Characters: Any measurable item on an organism (e.g. height)
Character State: Alternative variants of a character (e.g. eye colour in humans)
Characters can also be referred to as Traits

GENOTYPE:genotypic traits
PHENOTYPE:phenotypic traits

The genotype: the information stored in the DNA of one individual (e.g. genes).
The phenotype: observable / measurable / detectable characteristics of an organism

Question 13

where is the DNA

Answer 13

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 14

‘junk’ DNA - introns

Answer 14

*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, & 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, e.g. expression regulation (miRNA, snRNA…)

Junk’ DNA – is useful to evolutionary biologists
*Because ‘true’ Junk DNA is assumed not to be subject to natural selection.
*Phylogenies & Population Genetics

Question 15

genetic variation within an individual organisms

Answer 15

• Nucleotide base sequences making up the same gene may differ between individuals.
  when a base mutates A->G or C->T
  Single Nucleotide Polymorphism (SNP)
  Genotype = A/G (Heterozygote)

when nucleotide sequences differ in this manner at the same site (locus) on the paired (homologous) chromosomes e.g. on nuclear chromosome No. 4:
*They are termed different ’alleles’ of the same gene
*The locus is said to be ‘polymorphic’
*There can me many more than 2 alleles (e.g. hair colour)

Question 16

phenotype

Answer 16

The phenotype comprises (i.e. any / all observable non-gene traits):
External appearance
Internal structures / tissues
Intracellular structures
Proteins / polypeptides

Morphology: e.g. beak shape / fur colour / shell colour & pattern / petal colour / bristle number / seed colour & smoothness / body size.
& even behaviour, & nests / other structures.
Nests are an example of the ‘extended phenotype’ (sensu Dawkins)

• The phenotype is traditionally what scientists have examined, because
  (i) the phenotype has been, from a practical perspective, the easiest to observe /
  record / quantify.

(ii) variation in most phenotypic traits is at least partly genetically determined (thus, its heritable)

however:
Not all of the variation in a phenotypic trait is heritable.
Some variation may be due to non-genetic factors such as: trauma, disease, somatic mutations

Question 17

The evolutionary importance of heritable trait variation

2 examples involving pathogens of crop plants:
Potato blight + great Irish famine
Black Sigatoka disease in bananas

Answer 17

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

potato blight
Phytopthora infestans
* A ‘water mould’ (not a true fungus).
* Capable of rapid evolution.
* Estimated to have caused >1M deaths from starvation & forced 2M to emigrate from Ireland.
* Potatoes were of just one variety (which was vulnerable to the fungus).
* & they were propagated asexually (i.e. cloned).
* Had the potato population been more genetically diverse, the famine might have been averted.

black sigatoka disease:
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 to fungicidal chemicals applied by farmers).

Question 18

Continuous V discontinuous (discrete) phenotypic variation

Answer 18

Continuous Traits - intermediates exist between 2 extremes
Discontinuous/Discrete Traits - no intermediates exist

discontinuous:
* 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

continuous:
* many gene loci involved
* many alleles involved
* it is harder to discern the contribution of the individual alleles to the phenotype

Question 19

how to quantify population variation

Answer 19

Sampling
Representative (unbiased) samples needed.
* Take a random sample
* Take a large sample, if possible.

Measurement of variation among individuals
*Measurement (for continuous variation)
*Scoring (for discontinuous variation)

continuous v discrete variation
* Continuous variation in many characters, e.g. shell ‘height’.
* Discontinuous variation (polymorphism) evident in a few traits, e.g. presence/absence of stripes.

Question 20

microevolution

Answer 20

Microevolution refers to how populations (‘gene pools’) change:
over time,
in the relative abundance of genotypes OR phenotypes

Question 21

what is population genetics

Answer 21

mutation and recombination create genetic variation - these are NOT pop. genetics

What is Population Genetics? Everything else!!
Genetic Drift (demography)
random changes in allele frequencies
Selection
not random changes in allele frequencies natural
artificial

Question 22

genetic drift

Answer 22

random changes in allele frequencies within a population

Reproduction is random
Bottleneck (random reduction in the number of breeders)
“effective population size” ~ number of breeders

effect:
loss of heterozygosity

Question 23

Genetic Drift, Inbreeding and Linkage Disequilibrium

Answer 23

genetic drift and interbreding:
Inbreeding: Mating Between Relatives
cryptorchidism

Linkage Disequilibrium: Non-Random association between loci (corelation)
Linkage Equilibrium: Random association between loci (no correlation)

linkage disequilibrium:
2 loci (A and B)
2 allele per locus
A = {A,a} B = {B,b}

UNDERSTAND ON PANOPTO

If correlation-loci very close together on chromosome
Or stay. Correlation….
No correlation =no correlation segregating individually…

Question 24

Use of Hardy Weinberg Equilibrium and LD: population structure

Answer 24

Each column in an individual.
Several individuals 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 25

SELECTION and adaptive evolutionary change

Answer 25

Adaptive traits are subject to selection within the population.
Neutral traits are usually not.

adaptive evolutionary change:
When subjected to natural selection or its mimic, artificial selection:

Genetically-determined (= heritable) phenotypic traits correlated with fitness typically alter in frequency (% or proportion) within a population

directed (i.e. non-random) change
* in response to a change in environmental variable(s).

Mutations is only process that causes genetic variation

Question 26

example

Answer 26

Pineapple plantation-insecticides
Evolution of insecticide resistance.
* First: consider a genetic variant under insecticide-free conditions.
* Next: consider what happens when insecticides are applied.

e.g. an insect population may contain a genetic variant.
* e.g. arising via a recent mutation.
* Variant occurs as just a few individuals.
* Under natural, insecticide-free conditions:
* variant, compared with ‘normal’ form, has shorter average life-span.
* & so leaves fewer progeny.

The variant, being less fit*, therefore remains rare in the aphid population over successive generations.

• used in the relative, but not necessarily the absolute sense:
  because the “less fit” variant may confer higher fitness compared to yet another variant.

Being rare, the variant is more likely to become extinct under insecticide-free conditions.
* Due to random processes, e.g. 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.
* Variant has longer average life-span & leaves more progeny
Life-span female
5 days
No. of offspring/
10 (= less ‘fit’)
than ‘normals’.
* Yet its life-span has not increased.

Under insecticide conditions, variant individuals are ‘more fit’ than ‘normal’ ones.
* i.e. 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 generation = evolutionary change
* The variant has a ‘selective advantage’ over the ‘normal’ form.
* Selection in this case was ‘unnatural’ – human-caused (i.e. artificial).

Question 27

*Example involving predation (natural selection)
Everyday examples of adaptive evolutionary change

Answer 27

Insecticide resistance in head lice
* Warfarin resistance in rats
* Antibiotic resistance in bacteria.

Evolutionary change can take place in just a few years (i.e. a few generations)

*Insecticide resistance.
* Resistance vs pathogens:
* Antibiotic resistance, e.g. MRSA
* e.g. Blue moon butterfly: resistance against a parasitic
bacterium that kills males
* males were 1% of population in 2001, but 40% in 2006.