BIO120 Notes
Lectures 1-24, Fall 2025
,Lecture 1
Evolution is the change in heritable characteristics in organisms over generations by means of
natural selection.
The two tenets of evolution:
- Living things changing over time
- Adaptations through natural selection
Organisms on Earth have changed through time. The changes are gradual and not
instantaneous. Lineages are split by speciation, resulting in the generation of biodiversity. All
species have a common ancestor.
Biodiversity is defined as the diversity of life on Earth. It is the number and kinds of living
organisms in a given area.
Microevolution: evolutionary patterns and processes observed within species
Macroevolution: evolutionary patterns and processes observed among species
Adaptation:
- Any trait that makes an organism better able to survive or reproduce in a given
environment (state)
- The evolutionary process that leads to the origin and maintenance of such traits
(process)
Adaptations result from natural selection (Natural selection is the mechanism by which evolution
occurs)
Natural selection: the process by which organisms that are better adapted to selection
pressures/their environment survive, reproduce and pass their advantageous alleles to their
offspring, causing an increase in the allele frequency of the population.
Why is evolution relevant:
- Medicine
- Agriculture
- Environment
- Biology
Endosymbiosis
Public doubts about evolutionary biology
- Fairly recent concept (165 years is a relatively brief period)
- “Personal” implications regarding who we are and where we came from
- Violates literal interpretations of religious texts
,Lecture 2
Questions in pre-Darwinian European spheres
Where do species come from?
How can we explain complex adaptations?
Paley’s argument from design (teleological argument)
- He believed that something complex and with such a specific purpose must have
logically been the result of an intelligent designer, and could not have been by chance.
Jean-Baptiste de Lamarck (1744-1829)
- First to explicitly refer to evolution
- Hypothesized a causal mechanism: inheritance of acquired characteristics
- An organism changes during its life to adapt to its environment and passes on these
adaptations to its offspring.
August Weismann (1834-1914)
- Germplasm theory (1889)
- Inheritance only occurs in gametes, not in somatic cells
- Genetic information cannot pass from the soma to the gametes
- Genetic information flows in one direction only: from DNA to protein
Note: germline = cells that develop into gametes
Darwin and Wallace
, - Darwin developed the first comprehensive theory of evolution, but him and Wallace both
independently discovered natural selection.
- All organisms have descended with modification from a common ancestor, thus all living
things change over time.
- The process leading to evolution is natural selection, which operates in variation among
individuals.
Development of Darwin’s ideas of evolution:
1. Exploration: voyage on the HMS Beagle
2. Gradualism: (Darwin read Lyell’s “Principles of Geology” calling for uniformitarianism).
The forces and processes that shape the Earth’s surface and uniform through time. This
inspired Darwin to believe in the notion that the Earth is dynamic, not static, and that
change occurs gradually by continuously occurring mechanisms.
3. Species Vary: Galapagos mockingbirds; he saw 4 similar species endemic to the islands
descended from a mainland ancestor.
4. Struggle for Existence: Darwin read Malthus’s “An Essay on the Principle of Population”
(1798) in Sep. 1838. He noticed that favorable variations tend to be preserved and
unfavorable ones were destroyed.
Darwin’s Mechanism of Natural Selection
Variation: individual variation in a population
Heredity: progeny resemble their parents more than unrelated individuals
Differential fitness: some forms are more successful at surviving and reproducing than others in
a given environment.
Darwin proposed variational (Darwinian) evolution, in contrast to transformational (Lamarkian)
evolution.
Elements of Darwin’s theory:
- Evolution occurs at a collective level within a population, not an individual level.
- Variation isn’t directed by environment
- What constitutes as the “fittest” species is dependent on the environment
- Survival of the “fitter”
Implications of Darwin’s theory of evolution:
- Concept of a changing universe
- Phenomenon with no purpose
,Lecture 3
Sources of evidence for evolution:
● Geology
● Homology
● Biogeography
● Domestication
Darwin found the fossils of extinct mammals in Brazil, e.g. the glyptodon. Transitional fossils
provide evidence for evolution.
Geology: the study of the Earth’s structure and form.
- The Earth is very old, allowing for an immense amount of time for biological evolution.
- Intermediate forms, e.g. transitional fossils, fossils closest to the surface most resemble
the species around today
Homology: the similarity in traits between two or more individuals due to inheritance from a
common ancestor.
- Vestigial structures are features inherited from an ancestor but reduced in morphology
and function (they are no longer needed). They are homologous to functional structures
in related species.
- The anatomical features of modern-day organisms are consistent with modifications of
pre-existing structures, which would not be possible if each individual species was
optimally designed.
Biogeography:
- Colonization: when a species is introduced to a bioregion it is not native to. Remote
island biotas have a continental affinity, and many locally differentiated species, e.g. the
Galapagos giant tortoises.
- Biogeographically isolated regions have species adapted to unusual niches, e.g. the
mammal-pollinated Banksia.
- Harbor…
Lecture 4
Genotype is the genetic constitution of an organism, defined in relation to a particular gene or
combination of genes.
Phenotype is the observable characteristic or feature of an organism, resulting from the
genotype.
Genome is the entirety of an organism’s DNA including genes and non-coding regions.
3 main sources of genetic variation:
, - Mutations
- Independent assortment
- Recombination
Mutation is a stable change in the sequence of bases/triplet code in DNA. It occurs at a low rate
and varies in ways that are partially predictable. Here’s the types of mutations (Referred to as
stable because there is a low likelihood of a reversal of the change)
Mutation is random and not directed towards an outcome by the organism or by the
environment. It is random with respect to effects on fitness and not ‘summoned’ to make things
better.
Mutation rate varies across the types of different mutations and can be affected by environment,
e.g. mutagens, temperature, etc.
Point mutations (substitution) occurs in 3 types:
- Silent; amino acid sequence not altered due to degenerate nature of genetic code
- Missense; single amino acid altered, e.g. in sickle cell anemia
- Nonsense; premature stop codon (usually harmful)
Replacement mutations (insertion/deletion)
Lectures 1-24, Fall 2025
,Lecture 1
Evolution is the change in heritable characteristics in organisms over generations by means of
natural selection.
The two tenets of evolution:
- Living things changing over time
- Adaptations through natural selection
Organisms on Earth have changed through time. The changes are gradual and not
instantaneous. Lineages are split by speciation, resulting in the generation of biodiversity. All
species have a common ancestor.
Biodiversity is defined as the diversity of life on Earth. It is the number and kinds of living
organisms in a given area.
Microevolution: evolutionary patterns and processes observed within species
Macroevolution: evolutionary patterns and processes observed among species
Adaptation:
- Any trait that makes an organism better able to survive or reproduce in a given
environment (state)
- The evolutionary process that leads to the origin and maintenance of such traits
(process)
Adaptations result from natural selection (Natural selection is the mechanism by which evolution
occurs)
Natural selection: the process by which organisms that are better adapted to selection
pressures/their environment survive, reproduce and pass their advantageous alleles to their
offspring, causing an increase in the allele frequency of the population.
Why is evolution relevant:
- Medicine
- Agriculture
- Environment
- Biology
Endosymbiosis
Public doubts about evolutionary biology
- Fairly recent concept (165 years is a relatively brief period)
- “Personal” implications regarding who we are and where we came from
- Violates literal interpretations of religious texts
,Lecture 2
Questions in pre-Darwinian European spheres
Where do species come from?
How can we explain complex adaptations?
Paley’s argument from design (teleological argument)
- He believed that something complex and with such a specific purpose must have
logically been the result of an intelligent designer, and could not have been by chance.
Jean-Baptiste de Lamarck (1744-1829)
- First to explicitly refer to evolution
- Hypothesized a causal mechanism: inheritance of acquired characteristics
- An organism changes during its life to adapt to its environment and passes on these
adaptations to its offspring.
August Weismann (1834-1914)
- Germplasm theory (1889)
- Inheritance only occurs in gametes, not in somatic cells
- Genetic information cannot pass from the soma to the gametes
- Genetic information flows in one direction only: from DNA to protein
Note: germline = cells that develop into gametes
Darwin and Wallace
, - Darwin developed the first comprehensive theory of evolution, but him and Wallace both
independently discovered natural selection.
- All organisms have descended with modification from a common ancestor, thus all living
things change over time.
- The process leading to evolution is natural selection, which operates in variation among
individuals.
Development of Darwin’s ideas of evolution:
1. Exploration: voyage on the HMS Beagle
2. Gradualism: (Darwin read Lyell’s “Principles of Geology” calling for uniformitarianism).
The forces and processes that shape the Earth’s surface and uniform through time. This
inspired Darwin to believe in the notion that the Earth is dynamic, not static, and that
change occurs gradually by continuously occurring mechanisms.
3. Species Vary: Galapagos mockingbirds; he saw 4 similar species endemic to the islands
descended from a mainland ancestor.
4. Struggle for Existence: Darwin read Malthus’s “An Essay on the Principle of Population”
(1798) in Sep. 1838. He noticed that favorable variations tend to be preserved and
unfavorable ones were destroyed.
Darwin’s Mechanism of Natural Selection
Variation: individual variation in a population
Heredity: progeny resemble their parents more than unrelated individuals
Differential fitness: some forms are more successful at surviving and reproducing than others in
a given environment.
Darwin proposed variational (Darwinian) evolution, in contrast to transformational (Lamarkian)
evolution.
Elements of Darwin’s theory:
- Evolution occurs at a collective level within a population, not an individual level.
- Variation isn’t directed by environment
- What constitutes as the “fittest” species is dependent on the environment
- Survival of the “fitter”
Implications of Darwin’s theory of evolution:
- Concept of a changing universe
- Phenomenon with no purpose
,Lecture 3
Sources of evidence for evolution:
● Geology
● Homology
● Biogeography
● Domestication
Darwin found the fossils of extinct mammals in Brazil, e.g. the glyptodon. Transitional fossils
provide evidence for evolution.
Geology: the study of the Earth’s structure and form.
- The Earth is very old, allowing for an immense amount of time for biological evolution.
- Intermediate forms, e.g. transitional fossils, fossils closest to the surface most resemble
the species around today
Homology: the similarity in traits between two or more individuals due to inheritance from a
common ancestor.
- Vestigial structures are features inherited from an ancestor but reduced in morphology
and function (they are no longer needed). They are homologous to functional structures
in related species.
- The anatomical features of modern-day organisms are consistent with modifications of
pre-existing structures, which would not be possible if each individual species was
optimally designed.
Biogeography:
- Colonization: when a species is introduced to a bioregion it is not native to. Remote
island biotas have a continental affinity, and many locally differentiated species, e.g. the
Galapagos giant tortoises.
- Biogeographically isolated regions have species adapted to unusual niches, e.g. the
mammal-pollinated Banksia.
- Harbor…
Lecture 4
Genotype is the genetic constitution of an organism, defined in relation to a particular gene or
combination of genes.
Phenotype is the observable characteristic or feature of an organism, resulting from the
genotype.
Genome is the entirety of an organism’s DNA including genes and non-coding regions.
3 main sources of genetic variation:
, - Mutations
- Independent assortment
- Recombination
Mutation is a stable change in the sequence of bases/triplet code in DNA. It occurs at a low rate
and varies in ways that are partially predictable. Here’s the types of mutations (Referred to as
stable because there is a low likelihood of a reversal of the change)
Mutation is random and not directed towards an outcome by the organism or by the
environment. It is random with respect to effects on fitness and not ‘summoned’ to make things
better.
Mutation rate varies across the types of different mutations and can be affected by environment,
e.g. mutagens, temperature, etc.
Point mutations (substitution) occurs in 3 types:
- Silent; amino acid sequence not altered due to degenerate nature of genetic code
- Missense; single amino acid altered, e.g. in sickle cell anemia
- Nonsense; premature stop codon (usually harmful)
Replacement mutations (insertion/deletion)
