Welcome to the 2nd part of BIO1130!
A few words on the 2nd part of the course
• All lectures are in-person
• No lecture videos to watch prior to class
• Learning activities during class
• Lectures are recorded and will be posted on BrightSpace
• Material (including a few problems with their solutions will be posted ahead of the lectures)
• Additional Wooclap practice quizzes are available for Topic 8-16. They are not graded!
• Midterm 2 will cover Topic 8-12 (from Pr. Delcourt)
Pr. Delcourt's office hours will be in person - BSC 108 on...
• Monday 1pm-2pm
• Tuesday 10am-11am
• Wednesday 3-4pm
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Topic 8
The tree of life
Learning Outcomes
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Describe the 7 properties of life using an organism as an example
Justify the importance of the C, H, N, and O in organic molecules
Explain how specific properties of life emerged during the formation of protocells
List some advantages of ribonucleic acid molecules for the emergence of life
Explain how the fossil record can provide evidence for the evolution of organisms
Compare two methods used to date fossils
Describe how the Burgess Shale has contributed to our understanding of the evolution of animals
Define mass extinction, and provide an example
Define adaptive radiations, and provide an example
Analyse graphical data to infer major changes in taxonomic diversity
List different characteristics of L.U.C.A.
Name characteristics that differ between the 3 domains
Give examples of organisms for each of the 3 domains
Explain the evolution of eukaryotes from endosymbiosis
Explain the evolution of multicellularity
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https://www.wooclap.com/BIO1130
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Topic 8
The tree of life
8.1 – Life and its origin
7 properties of life
Heredity and
evolution
All living organisms share these properties
Growth and
development
Reproduction
Regulation
and
homeostasis
Energy and
metabolism
Cellular
organization
Living organism
Response to
stimuli
Virus are not considered organisms:
• No cellular organization
• No internal metabolism
• No growth or development
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First evidence of life on Earth
Age of the universe 13.8 billion years
Age of the earth 4.6 billion years
First direct evidence of life: 3.5 billion years
James Webb Telescope (deep field)
Fossil: preserved remnant or impression of an organism that lived in the past
Stromatolite: Layered rock that results from the activities of photosynthetic prokaryotes that bind thin films of
sediment together
Stromatolites – 3,500Ma (Shark Bay, AUS)
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First evidence of life on Earth
Age of the universe 13.8 billion years
Age of the earth 4.6 billion years
First direct evidence of life: 3.5 billion years
James Webb Telescope (deep field)
Fossil: preserved remnant or impression of an organism that lived in the past
Stromatolite: Layered rock that results from the activities of photosynthetic prokaryotes that bind thin films of
sediment together
Stromatolites
Stromatolites
– 3,500Ma
– 450Ma(Shark
(Ottawa,
Bay,
ON)
AUS)
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First evidence of life on Earth
Age of the universe 13.8 billion years
Age of the earth 4.6 billion years
First direct evidence of life: 3.5 billion years
James Webb Telescope (deep field)
Fossil: preserved remnant or impression of an organism that lived in the past
Stromatolite: Layered rock that results from the activities of photosynthetic prokaryotes that bind thin films of
sediment together
Cyanobacteria
Stromatolite (side view)
Stromatolite (top view)
Stromatolites
Stromatolites
– 3,500Ma
– 450Ma(Shark
(Ottawa,
Bay,
ON)
AUS)
10
First evidence of life on Earth
Age of the universe 13.8 billion years
Age of the earth 4.6 billion years
First direct evidence of life: 3.5 billion years
James Webb Telescope (deep field)
Fossil: preserved remnant or impression of an organism that lived in the past
Stromatolite: Layered rock that results from the activities of photosynthetic prokaryotes that bind thin films of
sediment together
Photosynthetic activity
Sediments trapped
Cyanobacteria
Stromatolite (side view)
Stromatolite (top view)
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Life on Earth uses carbon (C)
• Highly abundant on earth and in the atmosphere
CO2 on WASP-39 b (exoplanet)
Human body composition
Carbon (C), oxygen (O), hydrogen (H) and nitrogen (N) constitute the
majority of biological molecules:
• Carbohydrates
• Proteins
• Fatty acids
• Nucleic acids, etc.
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How did life originate on earth?
From organic molecules to protocells
Four necessary steps:
1. The abiotic synthesis of small organic molecules (monomers: amino acids, nitrogenous bases…)
2. The polymerization of small molecules into macromolecules (polymers: proteins, nucleic acids…)
3. The packaging of these molecules into protocells (precursors of cells, with only some components)
4. The origin of inheritance through the transmission of self-replicating molecules
“Primordial soup” or “prebiotic soup”: Hypothetical set of conditions that led to the transition from the abiotic
world to the biotic world (water, monomers, energy)
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Stanley Miller’s experiment (1953)
Artificial and spontaneous synthesis of organic matter under conditions mimicking the early earth’s
atmosphere (methane, ammonia, hydrogen) and lightning (energy).
à Synthesis of formaldehyde, hydrogen cyanide, amino acids and hydrocarbons… from abiotic molecules.
Similar experiments simulating volcanoes led to the synthesis of more amino acids
Re-analysis of Miller’s data
Deep-sea vents
Murchison meteorite
(18 amino acids)
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Formation of macromolecules
From monomers (1 molecule) to oligomers (2-10 repeated molecules) or polymers (>10)
Polymers of amino acids and nitrogenous bases can form spontaneously without enzymes or ribosomes.
• Precursor molecules (simple amino acids or nitrogen bases)
• Thermal energy (heat)
• Catalyst (chemical agent that selectively increases the rate of a reaction): Fe2+, Pb2+, Mg2+, etc.
Clay has been found to be a mineral catalyst for the polymerization of RNA.
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Formation of protocells
Protocell: droplet with membranes (ex: bilayer of fatty acids) that maintained an internal
chemistry different from that of the environment
Protocells were not living organisms… (lack genetic material).
Experiments have shown…
• Vesicles can divide spontaneously (reproduction)
• Replication reactions inside vesicles (internal metabolism)
• Vesicles can increase in size (growth)
• Membranes can be selectively permeable (regulation)
• Membranes can perform metabolic reactions using external molecules
(response to the environment)
à Properties of life can emerge from the abiotic world.
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Self-replication
Proteins (e.g. enzymes) are synthesized from DNA and RNA.
DNA and RNA are synthesized through enzymatic reactions.
à So which came first? Enzymes or nucleic acids?
• RNA molecules can also be catalysts and function as enzymes: ribozymes
• Ribozymes can copy other RNA molecules: self-replication
à “RNA world”
• Natural selection can favor RNA molecules that can self-replicate faster
• The passing of RNA of a splitting vesicle to daughter vesicles constitute inheritance
Given this inheritance, some error in RNA replication, some variation in replication rate...
… evolution through natural selection can proceed!
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Topic 8
The tree of life
8.2 – Using fossil records
What can fossils tell us?
The Tree of Life
• The tree of life describes the evolutionary relationship between all organisms (living or extinct)
• Similarities in morphology, anatomy or genetic sequences can be used to group species together
• The tree topology is constantly changing as it is being refined with the accumulation of new data
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Geological and fossils records
Relative and absolute age of fossils can inform us on the evolutionary history of organisms:
• Many fossils belong to species that no longer exist and that went extinct
• Some fossils resemble organisms that still exist nowadays
• Organisms can undergo very rapid morphological changes
Mary Anning (1799-1847) Plesiosaurus dolichodeirus
Duria Antiquior
Henry De la Beche (1830)
Red Dead Redemption 2
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Geological and fossils records
• Biostratigraphy: determination of relative age (imprecise and/or inaccurate) à sedimentary rocks
• Radiometric dating: determination of absolute age (precise and accurate) à magmatic rocks
Faunal succession: Specific vertical sequence of fossilized flora and fauna that can
be identified reliably over wide horizontal distances.
Grand Canyon, AZ
Specific fossil composition help
define biozones (intervals of
geological strata).
Cornwall, UK
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Geological and fossils records
• Biostratigraphy: determination of relative age (imprecise and/or inaccurate) à sedimentary rocks
• Radiometric dating: determination of absolute age (precise and accurate) à magmatic rocks
Faunal succession: Specific vertical sequence of fossilized flora and fauna that can
be identified reliably over wide horizontal distances.
Grand Canyon, AZ
Specific fossil composition help
define biozones (intervals of
geological strata).
Cornwall, UK
25
Geological and fossils records
• Biostratigraphy: determination of relative age (imprecise and/or inaccurate) à sedimentary rocks
• Radiometric dating: determination of absolute age (precise and accurate) à magmatic rocks
Faunal succession: Specific vertical sequence of fossilized flora and fauna that can
be identified reliably over wide horizontal distances.
Grand Canyon, AZ
Specific fossil composition help
define biozones (intervals of
geological strata).
Cornwall, UK
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Biostratigraphy
Species that have very specific ecological requirements, that lived for a very short geological period are
excellent biomarkers (or diagnostic species) for the chronological dating of sedimentary rocks.
Ex: Foraminifera (unicellular aquatic eukaryotes) - Cambrian 540Mya
• very wide geographical distribution
• very specific habitats
• large morphological diversity
• often well preserved (CaCO3: calcium carbonate shell)
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Radiometric dating
Steve Leonard
Radiometric dating uses changes in the isotope composition of:
• organisms during their transition into fossils
• magmatic rocks… but not sedimentary rocks
Isotopes: elements with the same # of protons different # of neutrons
à unstable (parent) isotope 14C decays into a daughter isotope (14N) at a constant known rate
à stable isotope 12C in the fossil remains constant until the fossil is discovered.
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14 C/1 C
o
i
t
Ra
Half-life: amount of time it takes for
50% of the parent isotope (14C) to
decay into a daughter isotope (14N).
Parent
isotope
Daughter
isotope
Half-life
(years)
Dating range
(years)
Carbon-14
Nitrogen-14
5,730
100 - 60,000
Potassium-40
Argon-40
1.25 Gy
10 My – 4.5 Gy
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But the fossil record is often incomplete
Many fossils were destroyed over time or not yet discovered
Bias towards species that existed for long evolutionary times and those with hard shells/skeletons.
Discontinuity in the fossil record can reflect important geological, ecological and evolutionary events:
• Plate tectonics, erosion, decrease in the rate (or halt) of sedimentation
• Changes in climate/habitat, retreat of seas and glaciers
• Species colonization, phenotypic evolution, speciation, extinction, etc.
Spinophorosaurus nigerensis (~170Ma)
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Biostratigraphy
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Topic 8
The tree of life
8.3 – Mass extinctions, adaptive radiations and key innovations
A changing world
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The Cambrian explosion
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The Cambrian explosion
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The Burgess Shale (506Mya)
Paleontological site in British Colombia (1909)
à sediments with large diversity of fossilized animals
Very different lifestyles:
• Benthic (living on the sediments)
• Endobenthic (living in the sediments)
• Nektonic (swimming freely)
Burgess Shale
Burgess Shale
(Charles Walcott)
Oryctocephalus
Ottoia
Marrella
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The Cambrian explosion
Many animal phyla we know today appeared around the same time: ~535-525 My (↑ morphological diversity)
From soft-bodied to hard shells organisms:
• defensive adaptations
• transition from grazers/suspension feeders to predators
à new body-plans, prey/predator relationships
Evolutionary success of bilateral symmetry which already existed:
• Anterior sensing organs (development of a nervous system)
• Anterior predation appendages (prey capturing and feeding)
• Posterior appendages for movement (swimming, crawling, flying, etc.)
Radial symmetry
Bilateral symmetry
Many adaptive radiations:
à Period of evolutionary change in which groups of organisms form many new
species whose adaptations allow them to fill different ecological roles in their communities.
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Mass extinctions
Geological/paleontological eras are defined by the massive changes in the abundance/composition of the
fossil record such as mass extinctions (when large number of species become extinct).
• Mass extinctions can be caused by changes in temperature, massive volcanic eruptions, meteorites, etc.
à All leading to a cascade of dramatic ecological events
à Mass extinctions are always followed by new adaptive
radiations and many new families and genera
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Mass extinctions
Geological/paleontological eras are defined by the massive changes in the abundance/composition of the
fossil record such as mass extinctions (when large number of species become extinct).
• Mass extinctions can be caused by changes in temperature, massive volcanic eruptions, meteorites, etc.
à All leading to a cascade of dramatic ecological events
3
à Mass extinctions are always followed by new adaptive
radiations and many new families and genera
1
5
5 mass extinctions.
2
4
Permian extinction (3 in the figure):
96% species lost (81% marine, 70% terrestrial vertebrates)
↓ T°C (-250m sea level) followed by large ↑ T°C, ↓O2, ↑CO2,
à ocean acidification, volcanic eruptions (Siberian Traps).
38
Mass extinctions
Geological/paleontological eras are defined by the massive changes in the abundance/composition of the
fossil record such as mass extinctions (when large number of species become extinct).
• Mass extinctions can be caused by changes in temperature, massive volcanic eruptions, meteorites, etc.
à All leading to a cascade of dramatic ecological events
3
à Mass extinctions are always followed by new adaptive
radiations and many new families and genera
1
5
5 mass extinctions.
2
4
Cretaceous - Paleogene (5 in the figure):
- 75% species
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Key innovations in the fossil record
6.5 Mya
• First cells (prokaryotes)
• Increase in atmospheric O2 concentration
485 Mya
635 Mya
• Endosymbiosis (eukaryotes)
3,500 Mya
• Sexual reproduction
• Multicellularity
1,200 Mya
• Colonization of land
1,800 Mya
2,700 Mya
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Key innovations in the fossil record
• First cells (prokaryotes)
• Increase in atmospheric O2 concentration
• Endosymbiosis (eukaryotes)
• Sexual reproduction
• Multicellularity
• Colonization of land
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Topic 8
The tree of life
8.4 – Three domains and millions of species
Number of species in the tree
Many species are still being discovered and many went extinct!
à The number of species or members of a taxonomic level
reaches an asymptote (an apparent maximum)
The number of prokaryotes species remains highly unknown!
Mora et al. 2011
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Number of species in the tree
Many species are still being discovered and many went extinct!
à The number of species or members of a taxonomic level
reaches an asymptote (an apparent maximum)
The number of prokaryotes species remains highly unknown!
Number of species predicted: >11,750,000…
…but only ~1,410,500 are described!
Of those, only ~200,000 oceanic species were described!
Mora et al. 2011
Predicted
Described
Land
Ocean
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Last Universal Common Ancestor (L.U.C.A)
• All living organisms synthesize and use only L optical isomers of amino acids
• The genetic code, is almost universal
• LUCA was not necessarily the first living organism!!
…but rather the latest organism that is ancestral to all existing living organisms we know today.
• In 2006, researchers analyzed 286,514 known proteins:
à 355 genes were likely present in LUCA’s small circular DNA genome
• LUCA was likely living near deep-sea vents, deprived of oxygen (anaerobic) but rich CO2 and H2.
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The Tree of Life – a 3 domains system
Saccharomyces cerevisiae
Pyrococcus furiosus
Escherichia coli
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The Tree of Life – a 3 domains system
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Domain of Bacteria
~700,000 species estimated (10,000 are described)
Very diverse metabolism
Photosynthetic, aerobe, and anaerobe
Can also use O2, SO42-, NO3-, NH3, H2S…
Highly resistant to harsh conditions
48
Domain of Bacteria
~700,000 species estimated (10,000 are described)
Very diverse metabolism
Photosynthetic, aerobe, and anaerobe
Can also use O2, SO42-, NO3-, NH3, H2S…
Highly resistant to harsh conditions
The most studied organism (cloning)
Easily grown in the lab on petri dish
Cell division every 20min at 37°C
Escherichia coli
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Domain of Archaea
~50,000 species estimated (500 are described)
Are considered prokaryotes but different from bacteria
Extremophiles: lives in extreme environmental conditions: acidic, hot, high salinity…
Many are methanogens: use CO2 and H2 and produce CH4 (methane)
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Domain of Archaea
~50,000 species estimated (500 are described)
Are considered prokaryotes but different from bacteria
Extremophiles: lives in extreme environmental conditions: acidic, hot, high salinity…
Many are methanogens: use CO2 and H2 and produce CH4 (methane)
70-103°C and pH~5 to 9
Source of DNA polymerase: used in molecular biology labs for its heat-resistance
à Polymerisation Chain Reaction: PCR (COVID19 testing, cloning, sequencing)
Pyrococcus furiosus
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Domain of Eukarya
~11,000,000 species estimated (1,400,000 are described)
• Evolved from prokaryotes within the Archaea branch
• Cytoskeleton, endomembrane system, nucleus
• Serial endosymbiosis: prokaryotic cells engulfed
by an ancestral archaea cell (1,800Mya).
à Mitochondrion, plastid: organelles possessing a
circular DNA, their own transcription/translation proteins,
ribosomes/membrane proteins similar to those of bacteria.
à Benefits: the cell gains a new metabolic system
(ex: aerobic respiration with increasing O2 concentrations).
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Multicellularity (1,200 Mya)
Some multicellular
All multicellular
times
5
2
d
e
v
l
Evo
dently!
n
e
p
e
d
n
i
• Colonial hypothesis: colonies form through the cooperation of
unicellular organisms of the same species
à cells fail to separate (or separate and rejoin)
à specialization can occur
Ex: colonies of cyanobacteria
Photosynthetic cells
Nitrogen fixing cells (heterocyst)
Anabaena circinalis
• Symbiosis hypothesis: cells from different species establish a mutually
beneficial and long-term association…
… not likely (requires both genomes to merge into a unique one).
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