BIO SCI 94 Notes
1/8/25
Phylogenetic Tree Analysis
- Species that are separated by closer/less nodes are more closely related
- Lower range is more ancestral, higher is more recently related
Theory of Evolution by Natural Selection
- Hypothesis: populations evolve
- Predictions:
- 1. Species change through time
- Life on earth is ancient, species go extinct, traits change (transitional
features), vestigial traits are common, populations are currently evolving
- 2. Species are related by common ancestor
- Similar species are found in close proximity, related species share
homologies, new species form from pre-existing species
- What is the evidence for change through time?
- 1. Life on Earth is ancient
- Data:
- 2. Species have gone extinct
- Data: fossils
- 3. Traits change
- Data: fossils
- Transitional feature - any trait that is intermediate between the ancestral
and derived species
- There is a gradual transition
- 4. Vestigial traits
- Data: anatomical structures in fossils and in living organisms
- Vestigial trait - a reduced or incompletely developed structure that has no
function, or reduced function, but is clearly similar to the functioning
organs or structures in ancestral or closely related species
- Remnants of evolution
- What is the evidence for species being related by common ancestry?
- 1. Similar species are found in the same geographic area
- Data: geography, DNA ~> phylogeny, observations of new species arising
from hybrids
- 2. Related species share homologies
- Data:
- Homologies - similarity among organisms of different species due to
shared ancestry
- Genetic homology: similarity in DNA, RNA, or amino acid
sequence due to inheritance from common ancestor
- Developmental homology: similarity that stems from embryonic
form
, - 3. New species are currently form from preexisting species
- Data: genetic, structural, behavioural
1/10/25
Evolution Through Natural Selection
- Natural selection acts on individuality
Darwin’s Four Postulates
- 1. Variation in population
- 2. Heritable traits
- 3. Differential survival and reproduction
- 4. The fittest succeed
- Pass their genes to the next generation
- Evolution by natural selection occurs when heritable variation leads to differential
reproductive success
- artificial selection: when humans deliberately manipulate the genetic composition of a
population by allowing only individuals with desirable traits to reproduce (e.g. animal and
plant breeding)
- Created domestication
Evolution in Action
- 1. Evolution of antibiotic resistance
- Antimicrobial resistance is internal and can cause a silent pandemic
- The case of antibiotic resistance: tuberculosis (TB)
- Can be combated with mechanisms of action with rifampicin
- It actively binds to RNA polymerase which leads to the death of the
pathogen
-
- 2. Impact of drought on Galapagos Finches
, -
- The finches were not equipped to eat tough fruits (that survived the drought)
which is why their population started to decline
Common Misconceptions About Evolution & Natural Selection
- 1. Natural selection changes individuals
- natural selection DOES NOT change individuals
- The frequency of population changes
- Acclimatization or acclimation: change in an individual’s phenotype that occurs in
response to changes in the environment (NOT HERITABLE)
- Acclimation is NOT the same as adaptation
- 2. Adaptations occur because organisms want or need them
- natural selection is not goal oriented
- 3. Natural selection lead to perfection
- Adaptation is far from perfect
- Trade-off: is a compromise between two traits that cannot be optimised
simultaneously
- Adaptive traits are limited by constraints
- Environmental, genetic and historical constraints
- Environmental constraints
- Weather and vegetation can determine the adaptive
properties of a population
- Who has the advantage
- Genetic constraints
- Genetic correlation: when selection on one trait causes a
change in another trait (e.g. pleiotropy)
- One gene affects multiple traits
- Historical constraints
- Evolution is constrained by historical precedent (i.e.
evolution can only elaborate on what already exists)
1/13/25
Evolutionary Processes
- Evolution: change in allele frequencies in a population over time
- Allele: version of a gene
, - Four processes can change the allele frequencies
- natural selection
- Increases the frequency of certain alleles
- genetic drift
- Causes allele frequencies to change randomly
- gene flow
- Equalizes allele frequencies among populations
- mutation
- Introduces new alleles
- How do we know if a population is not evolving?
- We need a null hypothesis; i.e. what should be observed when the hypothesis
being tested isn’t correct
- Hardy-Weinberg Principle predicts what allele frequencies are expected
if a population is not evolving
- Hardy-Weinberg equilibrium assumes…
- Large population (no genetic drift)
- No gene flow, mutations, or natural selection
- Completely random mating
- Frequency Equations
- T = p & t = q
- Genotype frequencies: p^2+2pq+q^2=1
- Allele frequencies: p+q=1
Nonrandom Mating
- Inbreeding: mating among relatives
- Plants have self-fertilization
- Inbreeding depression is the decline in average fitness when homozygosity increases
and heterozygosity decreases in a population
- Two causes:
- 1. Recessive deleterious alleles are “exposed” in homozygotes
- 2. At many loci, homozygotes have lower fitness than heterozygotes
1/15/25
Natural Selection & Genetic Variation
- Genetic variation
- (1) the number and relative frequency of alleles present in a particular population
- natural selection relies on heritable variation to operate
- (2) the proportion of phenotypic variation in a trait due to genetic rather than
environmental factors
- Natural selection can…
Modes of Natural Selection
- Directional selection: changes the average value of a trait
1/8/25
Phylogenetic Tree Analysis
- Species that are separated by closer/less nodes are more closely related
- Lower range is more ancestral, higher is more recently related
Theory of Evolution by Natural Selection
- Hypothesis: populations evolve
- Predictions:
- 1. Species change through time
- Life on earth is ancient, species go extinct, traits change (transitional
features), vestigial traits are common, populations are currently evolving
- 2. Species are related by common ancestor
- Similar species are found in close proximity, related species share
homologies, new species form from pre-existing species
- What is the evidence for change through time?
- 1. Life on Earth is ancient
- Data:
- 2. Species have gone extinct
- Data: fossils
- 3. Traits change
- Data: fossils
- Transitional feature - any trait that is intermediate between the ancestral
and derived species
- There is a gradual transition
- 4. Vestigial traits
- Data: anatomical structures in fossils and in living organisms
- Vestigial trait - a reduced or incompletely developed structure that has no
function, or reduced function, but is clearly similar to the functioning
organs or structures in ancestral or closely related species
- Remnants of evolution
- What is the evidence for species being related by common ancestry?
- 1. Similar species are found in the same geographic area
- Data: geography, DNA ~> phylogeny, observations of new species arising
from hybrids
- 2. Related species share homologies
- Data:
- Homologies - similarity among organisms of different species due to
shared ancestry
- Genetic homology: similarity in DNA, RNA, or amino acid
sequence due to inheritance from common ancestor
- Developmental homology: similarity that stems from embryonic
form
, - 3. New species are currently form from preexisting species
- Data: genetic, structural, behavioural
1/10/25
Evolution Through Natural Selection
- Natural selection acts on individuality
Darwin’s Four Postulates
- 1. Variation in population
- 2. Heritable traits
- 3. Differential survival and reproduction
- 4. The fittest succeed
- Pass their genes to the next generation
- Evolution by natural selection occurs when heritable variation leads to differential
reproductive success
- artificial selection: when humans deliberately manipulate the genetic composition of a
population by allowing only individuals with desirable traits to reproduce (e.g. animal and
plant breeding)
- Created domestication
Evolution in Action
- 1. Evolution of antibiotic resistance
- Antimicrobial resistance is internal and can cause a silent pandemic
- The case of antibiotic resistance: tuberculosis (TB)
- Can be combated with mechanisms of action with rifampicin
- It actively binds to RNA polymerase which leads to the death of the
pathogen
-
- 2. Impact of drought on Galapagos Finches
, -
- The finches were not equipped to eat tough fruits (that survived the drought)
which is why their population started to decline
Common Misconceptions About Evolution & Natural Selection
- 1. Natural selection changes individuals
- natural selection DOES NOT change individuals
- The frequency of population changes
- Acclimatization or acclimation: change in an individual’s phenotype that occurs in
response to changes in the environment (NOT HERITABLE)
- Acclimation is NOT the same as adaptation
- 2. Adaptations occur because organisms want or need them
- natural selection is not goal oriented
- 3. Natural selection lead to perfection
- Adaptation is far from perfect
- Trade-off: is a compromise between two traits that cannot be optimised
simultaneously
- Adaptive traits are limited by constraints
- Environmental, genetic and historical constraints
- Environmental constraints
- Weather and vegetation can determine the adaptive
properties of a population
- Who has the advantage
- Genetic constraints
- Genetic correlation: when selection on one trait causes a
change in another trait (e.g. pleiotropy)
- One gene affects multiple traits
- Historical constraints
- Evolution is constrained by historical precedent (i.e.
evolution can only elaborate on what already exists)
1/13/25
Evolutionary Processes
- Evolution: change in allele frequencies in a population over time
- Allele: version of a gene
, - Four processes can change the allele frequencies
- natural selection
- Increases the frequency of certain alleles
- genetic drift
- Causes allele frequencies to change randomly
- gene flow
- Equalizes allele frequencies among populations
- mutation
- Introduces new alleles
- How do we know if a population is not evolving?
- We need a null hypothesis; i.e. what should be observed when the hypothesis
being tested isn’t correct
- Hardy-Weinberg Principle predicts what allele frequencies are expected
if a population is not evolving
- Hardy-Weinberg equilibrium assumes…
- Large population (no genetic drift)
- No gene flow, mutations, or natural selection
- Completely random mating
- Frequency Equations
- T = p & t = q
- Genotype frequencies: p^2+2pq+q^2=1
- Allele frequencies: p+q=1
Nonrandom Mating
- Inbreeding: mating among relatives
- Plants have self-fertilization
- Inbreeding depression is the decline in average fitness when homozygosity increases
and heterozygosity decreases in a population
- Two causes:
- 1. Recessive deleterious alleles are “exposed” in homozygotes
- 2. At many loci, homozygotes have lower fitness than heterozygotes
1/15/25
Natural Selection & Genetic Variation
- Genetic variation
- (1) the number and relative frequency of alleles present in a particular population
- natural selection relies on heritable variation to operate
- (2) the proportion of phenotypic variation in a trait due to genetic rather than
environmental factors
- Natural selection can…
Modes of Natural Selection
- Directional selection: changes the average value of a trait
