APS 121 – Evolution
Lecture 1 – Introduction to evolution, biodiversity and deep time
Neo-Darwinian evolution:
1859 – Origin of the species.
Reproduction: The same species can reproduce to produce viable offspring.
Excess: Always an excess of offspring are produced, more produced than can survive.
Variation: Offspring are always different.
- Asexual (e.g. bacteria): Mutation.
- Sexual: 50% of each parent’s genes, crossing over and mutation.
Environmental selection (natural selection): Environment varies over time so the ideal individual varies
over time due to the environmental conditions varying. Individuals who are better able to cope with the
environmental conditions at that point in time are more likely to survive and reproduce.
Divergence: Environment forces natural selection, certain gene combinations survive, leading to the
population diverging.
Ancestry: We can trace an ancestry for all species given the way evolution works. There is only one tree of
life.
Darwin couldn’t work out heredity so Mendel’s work in the early 1900s was very useful.
Brought together to form modern evolutionary theory.
Biodiversity:
“Biodiversity is the variety of life, in all its manifestations. It encompasses all forms, levels and combinations of
natural variation”.
Taxonomy: The science of the classification of organism.
Phylogeny: The study of evolutionary relationships.
Almost universally agreed that evolution occurs via neo-Darwinian evolution (descent with modification
through natural selection). This taxonomy and phylogeny are intimately linked as we attempt to identify
and name them, classify organisms (taxonomy) and establish their evolutionary relationships (phylogeny).
Hierarchal relationships: Order Family Genus
Deep time:
Spatial framework: Earth’s surface.
Studying biodiversity the living world (extant organisms):
- Compare it with other organisms to see how closely related they are.
- For the living world we can work out taxonomy and phylogeny easily.
- Most species that have ever lived are extinct.
Studying biodiversity the fossil record (extinct organisms):
- Can use fossils to study how closely related organisms are/were.
- Fossil record is incomplete/biased.
Environmental change through time:
- The environment of planet Earth is spatially variable today.
- The environment of planet Earth is temporally variable (diurnal, seasonal).
- But the environment has also changed over longer periods or even over vast periods of deep time.
- Variations in eccentricity, axial tilt and precession of the Earth’s orbit determined climatic patterns on the
Earth through orbital forcing.
Icehouse and greenhouse phases poles have either ice or no ice (higher sea levels).
Evolution has taken place on a variable environment – conditions change over time.
Examples of environmental change over time:
Solar luminosity
Distance between the Earth and its moon (tides)
, Continental drift
Changing atmosphere and climate change
Milankovitch cycles
Evolving biota
Rare events through time:
Tsunamis
Super eruptions
Meteorite impacts
Mass extinctions
There have been 5 big mass extinctions
Classification of Earth history:
EON ERA PERIOD MYR
Phanerozoic Cenozoic Quaternary 1.64
Neogene 23.3
Paleogene 65.0
Mesozoic Cretaceous 146
Jurassic 208
Triassic 245
Paleozoic Permian 290
Carboniferous 363
Devonian 409
Silurian 439
Ordovician 510
Cambrian 570
EON ERA BYR
Precambrian Proterozoic 0.57 2.5
Archean 3.95
Hadean 4.57
The fossil record:
Incomplete:
1. Very few of the organisms that ever live will end up being fossilized (and ultimately collected and studied).
2. Entire species or higher taxa may not be preserved in the fossil record. This is particularly true for those:
- With low preservation potential
- With small population
- That inhabit a small geographical area
- That lived for only a short period of time
Biased:
1. Certain environments are more likely to be preserved than others (i.e. those with net deposition rather
than net erosion).
- Marine organisms are more likely to be preserved than terrestrial organisms.
- Terrestrial lowland deposits (e.g. nearshore marine and floodplain) are more likely to be preserved than
upland deposits.
2. Fossils of aquatic organisms, or organisms that find their way into aquatic environments, are much more
likely to be preserved.
, 3. Organisms with recalcitrant, and therefore more readily preserved tissues, are more likely to be preserved
(e.g. bones, wood, shells versus soft bodied organisms).
Lecture 2 – Classifying life and reconstructing phylogenies
Taxonomy:
The naming of organisms.
Hierarchical system:
1. Kingdom
2. Phylum
3. Class
4. Order
5. Family
6. Genus (plural – genera)
7. Species
- No capital for species name (second word).
- Species in italics/underlined.
Phylogeny:
Introduction of evolutionary theory.
Shows evolutionary relationships between organisms.
Species diverge.
Linnaean taxonomy: Works with the way that evolution works.
Can calibrate the phylogeny to see how evolution works.
Can calibrate the phylogeny to see how evolution has worked through time.
A revolution in Biology – phylogenetic/cladistics analysis:
1970s/80s.
Before this people would use guesswork to classify organisms by looking at their internal and external
characteristics.
Should be done by phylogenetic analysis – more detailed analysis and a rigid way of identification.
Convergent evolution: The independent evolution of similar features in species of different lineages. When
things evolve similar characteristics independently of each other.
Cladistics – method of phylogenetic analysis:
Based on evolutionary relationships and classifies species according to how recently they share a common
ancestor.
Unambiguous because there is only one phylogenetic tree of living things – only one true tree of life.
Assumes that life evolved only once and the diversity of life originated through descent with modification
(neo-Darwinian evolution).
So assumes that there is a hierarchical order to life on Earth and this order is manifested in the distribution
of characters shared among organisms.
Reconstruct phylogeny through formal character analysis using parsimony analysis.
Only presence of homologous characters is used.
Diagrams are known as cladograms.
Characters may be:
Analogous: Similarity due to convergent evolution (homoplasy).
Homologous: Similarity due to common ancestry.
They are either:
Synplesiomorphies: Shared ancestral characters (e.g. backbone).
Lecture 1 – Introduction to evolution, biodiversity and deep time
Neo-Darwinian evolution:
1859 – Origin of the species.
Reproduction: The same species can reproduce to produce viable offspring.
Excess: Always an excess of offspring are produced, more produced than can survive.
Variation: Offspring are always different.
- Asexual (e.g. bacteria): Mutation.
- Sexual: 50% of each parent’s genes, crossing over and mutation.
Environmental selection (natural selection): Environment varies over time so the ideal individual varies
over time due to the environmental conditions varying. Individuals who are better able to cope with the
environmental conditions at that point in time are more likely to survive and reproduce.
Divergence: Environment forces natural selection, certain gene combinations survive, leading to the
population diverging.
Ancestry: We can trace an ancestry for all species given the way evolution works. There is only one tree of
life.
Darwin couldn’t work out heredity so Mendel’s work in the early 1900s was very useful.
Brought together to form modern evolutionary theory.
Biodiversity:
“Biodiversity is the variety of life, in all its manifestations. It encompasses all forms, levels and combinations of
natural variation”.
Taxonomy: The science of the classification of organism.
Phylogeny: The study of evolutionary relationships.
Almost universally agreed that evolution occurs via neo-Darwinian evolution (descent with modification
through natural selection). This taxonomy and phylogeny are intimately linked as we attempt to identify
and name them, classify organisms (taxonomy) and establish their evolutionary relationships (phylogeny).
Hierarchal relationships: Order Family Genus
Deep time:
Spatial framework: Earth’s surface.
Studying biodiversity the living world (extant organisms):
- Compare it with other organisms to see how closely related they are.
- For the living world we can work out taxonomy and phylogeny easily.
- Most species that have ever lived are extinct.
Studying biodiversity the fossil record (extinct organisms):
- Can use fossils to study how closely related organisms are/were.
- Fossil record is incomplete/biased.
Environmental change through time:
- The environment of planet Earth is spatially variable today.
- The environment of planet Earth is temporally variable (diurnal, seasonal).
- But the environment has also changed over longer periods or even over vast periods of deep time.
- Variations in eccentricity, axial tilt and precession of the Earth’s orbit determined climatic patterns on the
Earth through orbital forcing.
Icehouse and greenhouse phases poles have either ice or no ice (higher sea levels).
Evolution has taken place on a variable environment – conditions change over time.
Examples of environmental change over time:
Solar luminosity
Distance between the Earth and its moon (tides)
, Continental drift
Changing atmosphere and climate change
Milankovitch cycles
Evolving biota
Rare events through time:
Tsunamis
Super eruptions
Meteorite impacts
Mass extinctions
There have been 5 big mass extinctions
Classification of Earth history:
EON ERA PERIOD MYR
Phanerozoic Cenozoic Quaternary 1.64
Neogene 23.3
Paleogene 65.0
Mesozoic Cretaceous 146
Jurassic 208
Triassic 245
Paleozoic Permian 290
Carboniferous 363
Devonian 409
Silurian 439
Ordovician 510
Cambrian 570
EON ERA BYR
Precambrian Proterozoic 0.57 2.5
Archean 3.95
Hadean 4.57
The fossil record:
Incomplete:
1. Very few of the organisms that ever live will end up being fossilized (and ultimately collected and studied).
2. Entire species or higher taxa may not be preserved in the fossil record. This is particularly true for those:
- With low preservation potential
- With small population
- That inhabit a small geographical area
- That lived for only a short period of time
Biased:
1. Certain environments are more likely to be preserved than others (i.e. those with net deposition rather
than net erosion).
- Marine organisms are more likely to be preserved than terrestrial organisms.
- Terrestrial lowland deposits (e.g. nearshore marine and floodplain) are more likely to be preserved than
upland deposits.
2. Fossils of aquatic organisms, or organisms that find their way into aquatic environments, are much more
likely to be preserved.
, 3. Organisms with recalcitrant, and therefore more readily preserved tissues, are more likely to be preserved
(e.g. bones, wood, shells versus soft bodied organisms).
Lecture 2 – Classifying life and reconstructing phylogenies
Taxonomy:
The naming of organisms.
Hierarchical system:
1. Kingdom
2. Phylum
3. Class
4. Order
5. Family
6. Genus (plural – genera)
7. Species
- No capital for species name (second word).
- Species in italics/underlined.
Phylogeny:
Introduction of evolutionary theory.
Shows evolutionary relationships between organisms.
Species diverge.
Linnaean taxonomy: Works with the way that evolution works.
Can calibrate the phylogeny to see how evolution works.
Can calibrate the phylogeny to see how evolution has worked through time.
A revolution in Biology – phylogenetic/cladistics analysis:
1970s/80s.
Before this people would use guesswork to classify organisms by looking at their internal and external
characteristics.
Should be done by phylogenetic analysis – more detailed analysis and a rigid way of identification.
Convergent evolution: The independent evolution of similar features in species of different lineages. When
things evolve similar characteristics independently of each other.
Cladistics – method of phylogenetic analysis:
Based on evolutionary relationships and classifies species according to how recently they share a common
ancestor.
Unambiguous because there is only one phylogenetic tree of living things – only one true tree of life.
Assumes that life evolved only once and the diversity of life originated through descent with modification
(neo-Darwinian evolution).
So assumes that there is a hierarchical order to life on Earth and this order is manifested in the distribution
of characters shared among organisms.
Reconstruct phylogeny through formal character analysis using parsimony analysis.
Only presence of homologous characters is used.
Diagrams are known as cladograms.
Characters may be:
Analogous: Similarity due to convergent evolution (homoplasy).
Homologous: Similarity due to common ancestry.
They are either:
Synplesiomorphies: Shared ancestral characters (e.g. backbone).
