Download Lecture 2: Origin of Earth and Life

Sept 3 2009
Lecture 2: Origin of Earth and Life
Origins of Elements and Earth
A chronological history of Earth
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4.6 bya origin of earth approximately
4.2-3.8 bya RNA world
3.8-3.75 bya Metabolism; DNA/Protein world
3.8-3.7 bya Origin of life
3.5-2.8 bya Origin of photosynthesis
2.5-2.0 bya Change from anoxygenic to oxygenic environment
1.7 bya oldest eukaryotes fossils
1.2 bya first multicellular organisms
250 mya Pangaea supercontinent forms
65 mya dinosaurs went extinct
6 mya earliest humans
Big Bang is dated 10-15 bya
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quarks - hypothetical building blocks that fuse together to form protons and neutrons which
then go on to form hydrogen and helium molecules
protostars are formed by nuclear fusion of hydrogen and helium atoms. This reaction yielded lots
of energy, which created a dense core forming elements to iron while burning.
Once the core is composed largely of iron the protostars stop burning. It had consumed most of
the fuel (h and he) once fuel is exhausted the protostar explodes to form a supernova releasing all
of the elements into space as hot gases
The sun is created
Planets around the sun form from gradual accumulation of solid matter called ‘planetisismals’
Earth was initially molten and composed of largely Fe, Mg, Si and O
Earth formed 4.6 bya
Crust forms 4.2-4.1 bya as earth cools
Meteors and comets bombard Earth 4.5-3.8 bya supplying lighter elements and frozen gases)
4.6 bya
4.2-4.1 bya
4.0 bya
crust forms
comets & meteors
Earth forms
3.7 bya
oldest fossils
Primitive Earth’s atmosphere
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Generated by volcanic out-gassing (80%) and impact bodies (20%)
CO2 (100-1000 x greater than present) N2, H20
Atmosphere reducing (reducing gases, electron taking)
NO FREE O2 in atmosphere initially – important since 02 would have prevented the build-up of
organic molecules
Very dense atmosphere (12 bar compared with 1 bar at present)
Primitive Earth’s Ocean
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Volatile substances such as the oceans remained in the atmosphere due to extreme heat
Once earth cooled to <100ºC water condensed and formed oceans
Large impact bodies would have vaporized the entire ocean, destroying any life
Earth had liquid water on it’s surface by 3.8 bya (sedimentary rocks)
LIFE AT 3.7 BYA in the form of Stromatalytes (blue green algae (cyanobacteria))
Also in form of organic matter found in rocks (C13-C12 ratio) indicates that life had
evolved by 3.7 bya
Once the oceans formed all atmospheric gases will dissolve in water due to high solubility
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These acids then dissolved rocks on land by the process of ‘chemical weathering’ and rivers
carried these salts to the ocean making it salty and adding all elements that would be used by
organisms
Characteristics of Life
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Organization
 organs, tissues, organelles to carry out specific functions
Energy use and metabolism
 To build new structures. Involves series of chemical reactions.
Homeostasis
 Maintains consistency of internal composition in spite of external environment
 Ex. ionic composition of a cell – must maintain water levels and dispose of waste
Replication/reproduction
 Exact copy of genetic material is provided to offspring
Response to environmental stimulus
 Ex. plants bending towards light
Origin of Building Blocks
Prebiotic chemistry  Pre-RNA world  RNA World  DNA/Protein World  Primordial Cell
Origin of life is known through lab research on chemical reactions that may have occurred 4.7 bya
Step 1 – Raw materials (simple organic matter such as amino acids, hydroxy acids, sugars,
purines, pyrimidines and fatty acids) Miller-Urey
Step 2 – Simple organic matter is linked together into polymers with properties of replication
RNA
Step 3 – Reverse Transcriptase copies RNA into DNA which replicates
Step 4 – RNA from DNA builds Proteins and Lipids which form spheres
Step 5 – Compartmentalization – the formation of an outer membrane that encased the
nucleic acids and proteins. Likely started with Liposomes (bubbles of lipid forming a
sealed sphere)
Miller-Urey Experiment 1953
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The experiment used water (H2O), methane (CH4), ammonia (NH3), and hydrogen (H2). The
chemicals were all sealed inside a sterile array of glass tubes and flasks connected in a loop, with
one flask half-full of liquid water and another flask containing a pair of electrodes. The liquid
water was heated to induce evaporation, sparks were fired between the electrodes to simulate
lightning through the atmosphere and water vapor, and then the atmosphere was cooled again so
that the water could condense and trickle back into the first flask in a continuous cycle.
In one week much of the C had been converted into organic compounds
17 of 20 amino acids
All purines and pyrimidines (RNA and DNA)
Panspermia: alternative hypothesis to Miller-Urey
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Organic molecules were brought to Earth from space
Supported by three lines of evidence
i. The Murchinson Meteorite was found to contain a variety of C compounds
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ii. The ALH84001 meteorite from Mars contained some evidence of microorganisms
iii. A variety of organic molecules have been identified using IF spectroscopy
Therefore we can conclude that organic matter can be synthesized abiotically throughout the
solar system
Paradox: Proteins cannot be made without nucleic acids and nucleic acids cannot be made without
proteins
Solution: Ribozymes – ribosomes which assemble proteins and store information
Scientists began to postulate that pre-biotic RNA had the capacity to self-replicate and to catalyze
every step of protein synthesis. Referred to as “RNA World”
RNA World
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Contains only RNA molecules that serve to catalyze the synthesis of themselves
Some RNA molecules that were randomly assembled on clay would acquire enzymatic properties
and replicate, creating many copies
Due to copy error the RNA sequence would be altered in some copies and such mutated
sequences may have altered the properties of the RNA increasing its rate of production
How did ribozymes originate? Three hypotheses occurring in a dilute aqueous environment where
hydrolysis occurs more readily than polymerization
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Clay catalyzed RNA synthesis (first)
Clay catalyzed RNA and protein synthesis (both first)
Protein (first) – not likely
RNA  Protein & DNA
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RNA eventually begins encoding proteins with catalytic properties
Reverse transcriptase copies RNA into DNA
DNA is better suited to store information – chemically more stable thus allows larger genomes
The first evolution of life on earth is believed to have evolved in the deep sea near hydrothermal
vents. UV radiation would have destroyed most macromolecules in sea surface as ozone was not
created until O2 was produced.
Sept 8, 2009
Lecture 3: 3.8 BYA – 1.7 BYA
Requirements for life
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Liquid water
An energy source
Elements which makes up essential biomolecules
1) Water
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Water accounts for 50-90% of an organisms mass
All chemical reactions necessary for life occur in water
Water dissolvers all elements needed by organisms
2) Energy
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The most central requirement
Used to assemble elemental building blocks (e.g. C, N, Fe) into complex molecules for the
construction of organisms + motility + nutrient transport
Organisms use one of 3 main sources of energy
o Light (photosynthesis)
o Organic molecules
o Inorganic molecules (chemosynthesis)
Autotrophs (Self-feeder) – inorganic Carbon – CO2
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Photoautotrophs - Photosynthetic (light – electromagnetic energy) par 400 – 700 nm
(photosynthetically active radiation)
Chemoautotroph – chemosynthetic (inorganic molecules  chemical bond energy) H2, H2S,
NH4+, use energy gained to synthesize organic matter
o Chemosynthesis in deep-sea organisms – worms use internal organ containing
symbiotic bacteria. Bacteria are chemoautotrophs and produce energy that the
worms use.
Among autotrophs, CO2 can be fixed by a number of pathways all of which require ribulose
bisphoshate carboxylase (RuBisCo) – the most abundant enzyme on Earth
Heterotrophs (other-feeders) – organic molecules for energy and C – (chemical bond energy)
carbohydrates, proteins, fats
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Herbivores
Carnivores
Omnivores
Detrivores
Energy Limitation
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The rate at which organisms can take in energy is limited
o The limitation may be caused by external constraints
 a shortage or reduced availability of food in the environment
 food quality
 chemical defense
o The limitation may be caused by internal constraints
 Digestion – speed may vary
 Enzyme catalysis – speed of enzymatic process may vary
General Principles
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Energy intake by organisms is limited
Organisms ‘forage’ in such a way as to maximize their rate of energy intake
Because energy intake is limited organisms cannot simultaneously maximize all of life’s functions:
ex. allocation of energy to reproduction reduces the amount of energy available for defense
(trade-off)
3) Elements
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N, P, S, Fe, Cu… are used to construct cellular constituents and in biochemical reactions that are
necessary for survival is they are for structures and catalysis
Ex. Cellulose (C, cell walls of plants) hydroxy-apatite (Ca, P, bones of vertebrates), cytochromes
(Fe, N, electron carrier proteins)
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An essential element is an element that is require by an organism to complete its life cycle –
without it the organism cannot grow (Se deficiency in humans – Keshan disease, Cu:
Wilson/Menkes diseases)
Organisms are composed of the same elements and within each organism these elements are
present in constant ratios (C:N = k)
Organisms require 28 elements, 6 of which make up the bulk: C, H, O, P, N, S.
Organisms concentrate and extract elements (aka nutrients) from their environment
The concentrations of essential elements varies among different environments and over
geological time
Acclimate – refers to a physiological change to offset a limitation
o Ex a grass may shorten it’s roots when N conc is high and lengthen when N conc is
low
Adaptation to Nutrient Availability
o During the chemical evolution of the earth the availability of many elements changed,
for example iron (Fe) in the ocean was plentiful during archaean eon (>2.5bya) but
virtually disappeared by the end of the phanerozoic (<0.54 bya)
o Green algae evolved when iron was high
o Red algae evolved when iron was low
GENERAL PRINCIPLES
o Nutrient resources may be limiting to growth of organisms in nature
o The availability of nutrients may thus affect an organism’s ecology and evolution
Given the general requirements of organisms that we have just discussed and the environmental
conditions that were thought to exist on earth 4 bya, we can hypothesis what the earliest life was like
 H2, CO2, N2, S (gases) – anaerobic, HOT
2 general hypotheses for early organisms
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A chemoautotroph that obtained both energy and C from inorganic sources (CO2) **favoured
hypothesis
A heterotroph that used organic matter that was synthesized abiotically
**old school 1920s hypothesis
Characteristics of the first organism
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Anaerobic
Hyperthermophilic and halophilic
Prokaryotic (no internal organalles – nucleus, etc)
Chemoautotroph (heterotroph)
o Ex. of early organism
Methanococcus – prokaryotes have no nucleus, organelles, or microtubules and have
70S ribosomes. They have an outer cell wall composed of petidoglycan. They are
generally small
Evidence for early chemoautotrophy on Earth
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All extant organisms near the origin of the phylogentic tree are hyperthermophiles found in 80 –
110ºC environments similar to those of early earth
These organisms use H2 as energy *chemoautotrophs
Metabolic diversification among Bacteria and Archaea
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New species exploited other energy sources – some using the products from the metabolism of
other organisms as substrates. Populations of organisms as layered one on top of the other –
biofilms
Organic compounds accumulated and allowed heterotrophic organisms to thrive
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Bacteria and archaea are the most metabolically diverse groups of organisms
Appearance of Photosynthetic Organisms
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Organisms develop pigments (bacteriocholorphyll) that are used to capture light energy
Earliest form of photosynthesis was based on sulfur (S): it was anoxygenic ( non O2 evolving)
carried out by S bacteria
Isotopic composition of organic matter 12C/13C in rocks shows photosynthesis began 3.8 bya
Oxygen evolving photosynthesis
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Fossil evidence suggests that photosynthetic cyanobacteria appeared around 3.7 bya
Co2 +H20 = CH2O + O2
H2O was an inexhaustible resource
O2 only accumulated slowly in the atmosphere because it reacted first with Fe in the sea
Consequences of O2 production
o Allowed for the evolution of aerobic metabolism: greater energy yield per mol of C
substrate consumed
o Changer ocean chemistry: S and N oxidation (SO4 2- collects in the ocean)
o Allowed for the formation of the ozone layer – O3 – protection from UV)
o Poisoned environment – anaerobic organisms became confined to refuge habitats
o Atmosphere becomes oxidizing
o Organisms had to evolve mechanisms to detoxify the noxious by products of O2 –
superoxide, hydrogen peroxide
o THE RELEASE OF O2 BY PHOTOSYNTHESIS IS THE SINGLE MOST SIGNIFICANT
EFFECT OF LIFE ON THE GEOCHEMISTRY OF EARTH
Sept 10, 2009
Origin of Eucaryotes
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Cells existing prior to 1.8 (2.7bya) were all prokayotes, bacteria and archaea
Eukaryotes appear in the fossil record 1.7 bya
Chemical markers (steranes) produced only by eucayotes are detected in rocks ~2.7 bya
Differences from prokaryotes
o Nucleus and nuclear envelope
o Internal membrane-bound organelles (mitochondria and chloroplasts)
o Generally > 2 um in diameter (100 – 10000) times larger than prokaryotes)
o 80s ribosomes
Endosymbiotic Theory for the Origin of Eucaryotes
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Theory popularized by Lynn Margulis
Mitochondria and chloroplasts of eucaryotes were at one time free-living bacteria
that were engulfed by an archaea and evolved an obligatory symbiosis
Mitochondria – proteobacterium
Chloroplast – cyanobacterium
Theory very strongly supported by data
EVIDENCE
 Organelles contain own DNA, similar to bacterial DNA, no histones, circular
 Distinct genetic code in mitochondria, like bacteria and archaea
 Surrounded by a double membrane – inner one like a bacterial membrane
 Structural similarities with free-living bacteria
 Anti-biotic sensitivity
Secondary Endosymbiosis
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In 2 groups of protists we can still see the evidence of a second
endosymbiotic event.
The Nucleomorph: a remnant of the nucleus of the endosymbiont in the
chloroplast
Lecture 4: BIODIVERSITY I
Classification
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Method for organizing information proposed by Linnaeus (1735)
Reflects the evolutionary distances and relationships among organisms
One can classify organisms by any number of criterion
Natural system of classification – based on evolutionary history
o Predict characteristics of newly described organisms
o Understand the history of life
Difficulty in Classifying Microorganims
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Morphologically simple – they have fewer obvious features that can be used to measure
relatedness of species
o RNA is proposed because it is found in all organisms
o Functions in protein biosynthesis
o Slowly changing
o Large enough to record useful info on evolutionary change
Molecular Phylogeny
RNA sequence analysis identifies 3 major lineages
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Archaea (prokaryote)
Oldest lineage of organisms. Identified by nucleotide sequences of SSU rRNA
According to this classification they are as unrelated to bacteria as the are to Eucarya
Hypothesized hosts that evolved with bacteria symbionts to become Eucarya
Three identified groups
1. Euryachaeota – inhabit extreme environments (hot springs, hydrothermal vents)
 Methanogens
o Release methane (CH4) as a waste product
 Halophils
o Live in salt water environments up to 23% NaCl
o Unique light-mediated pathway of ATP production using
bacteriorhodosporin pigment)
2. Crenarcheota – found in geothermally heated environments – most heat loving
organisms – prefer temperatures >80ºC
 Thermoacidophiles
o All use S as an electron acceptor or donor – generate sulfuric acid
(tolerate extremely acidic conditions)
3. Korarcheota (known only from rRNA sequences obtained from Obsidian Pool –
Yellowstone Nat. Park)
II. Bacteria [prokaryote)
 Divided into 12 major lineages according to rRNA sequence analysis
 Most of the groupings are based on metabolic reactions
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The most ancient bacteria are hyperthermophillic chemoautotrophs (use H2 or
reduced S as energy source)
A. Proteobacteria
 Largest group of bacteria contains heterotrophic and phototrophic genera
 Purple and green bacteria
 Photosynthesis is anoxygenic: uses H2S instead of H2O as electron donor
 Most metabolically diverse group: oxic, micro-oxis, anoxis conditions; source of
electrons H2S, H2, energy – light or inorganic compounds, C: CO2 or organics
 Common proteobacteria include E. Coli and Purple photosynthetic bacterium
B. Cyanobacteria
 Large group of phototropic bacteria that use oxygenic photosynthesis (generate O2)
 Some form specialized structures called heterocysts and are capable of N2 fixation
 The conversion of N2(g) into NH3
 Among the most important primary producers in lakes and oceans
 Prochlorophytes – a minor group of oxygenic photosynthetic bacteria
 Contain a unique chlorophyll divinyl chlorophyll a and chlorophyll b
(higher plant pigment)
 Prochlorococcus (< 1 um in size) the most abundant primary producer
 Discovered in 1988
C. Gram-positive Bacteria
 Suited to survive harsh conditions because they produce endospores “cells within
cells” that have no metabolic function and a dehydrated cytoplasm
III. Eucarya (eukaryote)
 Protoctista Kingdom
 Mostly unicellular eucaryotes
 Include parasitic forms, photosynthetic, heterotrophic
 Between 12-32 phyla are identified
A. Basal Eucaryotes – most primitive group of eucaryotes: broadly divided into those that
have mitochondria and those that don’t
 Without Mitochondria
 Ancestral to other eucaryotes
 Parasitic organisms
 Flagellated, obligate anaerobes
o Trichonnympha – a symbiotic inhabitant of termite guts that contains
cellulose degrading bacteria
o Entamoeba hystolytica – amoebic dysentery
 With Mitochondria
 Slime molds, Euglenoids, and Kinetoplastids
 Kinetoplastids have a unique structure known as kinetoplast (mass of
mitochondrial DNA, near flagellum)
o Trypanosoma – causative agent of sleeping sickness
o Leichmania – causative agent of human disease Liechmaniasis
B. The Aveolates
 Dinoflagellates, Apicomplexa, Ciliates, Formaminfera
 Common features
 Tubular mitochondrial cristae
 Flattened sacs (alveoli) beneath cell membrane
Importan group ecologically – producers and consumers of planktonic communities of
lakes and oceans
 Dinoflagellates
o Heterotrophic and phototrophic species
o Agents of toxic shellfish poisoning
o Many form dormant cyst stages
o Some species are symbionts of invertebrates (corals)
 Gonyaulax – causative agent of Red Tides. Result in paralytic
shellfish poisoning and amnesic shellfish poisonting
 Apicomplexa
o Obligate parasites of animals: complex life cycles
o Apical complex of organelles (microtubules etc) tat helps them attach
to or penetrate their host
 Plasmodium – causative agent of malaria
C. Stamenophiles
 Formerly large groups of phyla called (2 unequal flagella)
 Have unique flagellum that has hairs called mastigonemes, the other flagellum is smooth
 Includes both phototrophic and heterotrophic taxa
 Bacillariophyta – Diatoms (phototrophs)
o 10 000 species found in all aquatic environments
o produce a silica (glass) exoskeleton known as frustule
o only male gametes have flagellum
o responsible for roughly 25% of global primary production
 Oomycetes – water molds
o Filamentous growth form, but produce flagellated zoospores (asexual
spores that give rise to filaments)
o Cause many agricultural diseases including downy mildew of grapes
and potato blight
 Phaeophyta & Chrysophyta – brown and golden algae
o Vast majority are photosynthetic (some chrysophtes are heterotrophic
or mixotrophic)
o The heterotrophic forms are important consumers in lake ecosystems
o Many are multicellular (Phaeophyta) seaweeds – the largest protists
o The Phaeophyta phylum contains no unicellular representatives
D. Amastagote Algae
 No flagella
 Rhodophytes (red algae) and Gamophyta (desmids)
 Rhodophyta are mostly marine species – dulse (Palmaria palmate)
 Water soluble pigments give colour
 Complex life cycle involving three separate stages
E. Chlorophyta
 Ancestors of higher plants – some are resistant to periodic desiccation
 Contain pigments chlorophyll a and b
 Primarily freshwater species
 Sexual reproduction common: isogamy (equally sized gametes) and oogamy (large egg
fertilized by small motile sperm)
o Chlamydomonas – model organism for evolution studies, Volvox – colonial
form
o Chara – has distinct reproductive structures that contain eggs (oocyte)
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Two other important Protoctista
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Zoomastigota (zooflagellates) which include the choanoflagellates that resemble cells of sponges
(among the simplest and most ancient of animals)
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Chytridiomycota (ancestral to fungi)
Classification within each domain is based on rRNA and/or phenotypic traits
Early Classification was based on structural similarities. Biologists divided living organisms into
kingdoms:
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Bacteria (prokaryotic)
Protista (eukaryotic)
Fungi (eukaryotic)
Plant (eukaryotic)
Animal (eukaryotic)
September 15, 2009
Lecture 5: Multicellular Organisms
Evolutionary Inference – phylogeny
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Evolutionary biology is a historical science – this means we must infer history, it only happens
once
Phylogeny: the course of evolution from past to present
Phylogenetic tree: a graphical representation of the course of evolution from past to present
o Nodes
 Internal node = open circles H, F, G
 Terminal node = closed circles A-E
 Root node = open circle I
o To build a phylogenetic tree you need
 Data – from fossil record and modern taxa
 Morphology
 DNA
 Methods
 Parsimony
 Maximum likelihood
 Distance
 Bayesian methodology
Evolutionary Invention – independent evolution
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Multicellularity has been invented at least 13 independent times
Evolution is multidirectional and random
Ex Solitary vs. Colonial Choanoflagellate
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A transition to multicellularity
Possesses flagella, heterotrophs, ability to draw in food through water currents
Ex. Fungis
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Multicellularity is evolved through single cells that build hyphae network that produces a
multicellular fruiting body – a mushroom
Ex. Algae – Sea lettuce Ulva
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Single cell grows then divides without separation. Rapid division in combination with
thickening of cell wall leads to phallis
Ex. Green Algae – Volvox
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Unicellular cells are entrapped in a casing grouping them together into a colony
Ex. Colonial Diatom
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Single cells surrounded by hard silica shell. Forms a colony in which diatoms can swim
freely within the shells
Ex. Coloniale Ciliate – Zoothamnium
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Each single cell is connected by muscle thread within the stalk that permits the whole
colony to contract
Ex. Cellular Slime Mold Dictyostelium Discoideum
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Exist as individuals until food runs out, then they aggregate into fruiting bodies and broadcast
spores
Ex. Actinomycete – Streptomyces
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Grow filaments that interact with each other
Produce antibiotic Streptomycin
General Features of Multicellular inventions in evolution:
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Aquatic
 Products of cell division fail to separate
 Multicellularity allows them to stick to ideal substrates
 Increase in size prevents filter feeders from eating (Volvox)
 Allows for faster swimming
Terrestrial
 Formation of motile aggregation of cells
 Aggregation of nuclei in a multinucleate syncyitum
 Mulitcellularity allows dispersal of spores and cysts
 Feeding
 Creates an internal environment, less environmental heterogeneity
Sept 17, 2009
Lecture 6: Radiation
Consequences of Evolutionary inventions
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Adaptive Radiations: evolutionary divergence of members of a single phylogenetic lineage into a
variety of different adaptive forms over a relatively short interval of geological time
o Detected through phylogenetic trees with short early branches and later long
branches
o How/why? – to fill in previously unavailable niches, competitive release and
competitive advantage.
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Cambrian Radiation – 590-505 mya
o Cambrian explosion is the big bang of evolution
o Marks the appearance of multicellular organisms
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o Origin of all modern phyla
Devonian – 360-290 mya
o The age of fishes
o Ferns abundant, amphibians arise and diversify, bony fishes, corals, criniod; land
plants and anthropods diversify
o Acanthostega: lived most of its life on water but could venture onto land, had eight
toes. Represents important link for transition of life in water to life on land
o Lung Fish: branches closely to vertebrates on land. Can live for long periods on land.
Triassic – 205-138 mya
o Gymnosperms become dominant land plants; extensive deserts;
o First dinosaurs; first mammals
o Radiations following end Permian extinction
Eocene – 38 - 25 mya
o Mammals and flowering plants diversify
o Angiosperms (flowering plants)
Cambrian
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Appearance of all major groups including
o Mollusca, brachiopoda, ctenophore, priapulida, onychophora, anthropoda,
phoronidea, annelida, echinodermata, chordata, hemichordata, tradigrada, bryozoa
o Ediacarans
 Dickinsonia – fossil 1m diameter and 3mm thick
 Spriggina – most likely an animal
Cambrian Explosion: Burgess Shale
o located in Canada
o Contains fossils of soft bodied shells
 Hallucigenia – an early onichophoran
 Anomalocaris – predatory arthropod
 Opabinia – a predatory arthropod
 Wiwaxia – polychaete worm
 Pikaia – an early chordate
o Gould’s impression of Burgess Shale
 Chance plays an important role in evolution but the whole lineage of the
Cambrian explosion could not survive in environment
 Failed experiments in the history of life, if replayed all would be different
 Burgess shale fauna are an offshoot of modern fauna
o Conway Morris
 Early offshoots that went extinct but other lineages survived
 If life were replayed it would still be similar
o Three possiblities regarding time of origin of species in Cambrian – is it really a big
bang?
1. Yes it is a big bang all species present in Cambrian evolved during that
period
2. No, they evolved beforehand but were only fossilized in Cambrian
3. No, they evolved beforehand but only diversified and radiated during
Cambrian
 Molecular clock estimates show much deeper divergence
o As time passes mutations accumulate in a neutral way at a natural rate
o Relate genomes across species and test differences to find divergent times
between species
o Number or millions of years passed should be equivalent to number of
mutations accumulated.
September 22, 2009
Lecture 7 – Modern Diversity II
Cambrian Explosion? Studies show that animals diverged much before the Cambrian
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Molecular Clock estimates say that divergence occurred during the Proterozoic before the
Cambrian Radiation
Duchanto Formation
o Fossilized embryo found dating before the Cambrian Explosion (metazoan
embryo)
For exam: understand the concept of molecular clocks
o Calibration of molecular clock and relation to phylogenetic tree
o Controversy vs. interpretation of timing
o Relativity of fossils
Causes of Cambrian Explosion
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Molecular Clock
o Large body size
o Acquired skeletons
Fossilization
o Environmental Changes
o Increase in O2 and availability of CaCO3
o diversity
Animals have the greatest number of species of all organisms. Of Animals - Insects have the greatest
number of species.
For the exam: know evolutionary inventions of each group.
Plants: transition from water to land
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Evolved from green algae (aquatic seaweed)
Plants are multicellular eukaryotes
Possess cellulose rich cell walls
They are photoautotrophic
o get energy from the sun through
photosynthesis
Alternation of generations
4 Major Evolutionary inventions in plants
1.
2.
3.
4.
Bryophytes – non vascular lineage
Vascular Lineage – vascular seedless plants
The seed – gymnosperms
The flower - Angiosperms
Bryophythytes
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some of the earliest land plants
lack vascular tissue and true toots to transport water and nutrients
thrive in damp places although can withstand drought
lack lignan to strenthen cell walls: therefore must stay close to ground
Mosses, Hornworts, Liverworts
Pteridophytes - Seedless Vascular Plants

possess vascular tissue
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allowed plant to live in drier habitats more effectively
thrive in damp places, although can withstand drought
well developed cuticle and stomata – minimize H2O loss and regulates gas exchange
ferns are most abundants: specialized underground stem the rhizome and an aerial frond
o major divisions of pteridophytes: Ferns, Club Moss, Horsetail
Gymnosperms
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the seed is invented: provides a small capsule composed of a protective seed coat, the plant
embryo, and nutrients
pollen is invented: sperm don’t have to have water to swim to ovule – can be transported by
animals, air, moving H2O
most common are the Conifers : pine, fure, redwood, spruce, cedar
Sporophyte: large woody tree-like
Gametophyte: reduced and living in cones
Conifers, Ginkos, Cycads, Gnetophytes
Angiosperms
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Advertise their sex organs for all to see
95% of modern plants are angiosperms
the major evolution invention is the flower
complex life style: alternations of generations and double fertilization
Fungi : Absorption and Breakdown
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they are not plants, no chlorophyll or photosynthesis
cell walls built of Chitin
Absorb nutrients from substrate
Release digestive enzymes then soak up organic molecules
released
Principle decomposers in forests
o Phyla
1. Basidiomycota - mushrooms
2. Ascomycota - penicillin
3. Zygomycota – molds
Animals: Story of Ingestion
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Hypothesized evolution from Choanoflagellates
Animals obtain their energy form eating other organisms
Cells have no cell walls in stead they float in an extracellular matrix composed of collagen,
integrins, glycoproteins and proteoglycans
Parazoa – no true tissues
Porifera (Sponges) – asymmetrical
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Choanocytes – look like unicellular choanoflagellates
Marine
Eumetazoa – true animals with true tissues
Radiata - Possess radial symmetry
Cnidarians:
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“nematocysts” – have stingers
marine
diploblastic
Bilateria – possess bilaterial symmetry
Protosome – Blastopore becomes mouth
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Lophotrochzoa
o Platyhelmintes (flatworms)
o Rotifera
o Mollusca (clams, snails)
o Annelida (segmented worms)
Ecdysozoa
o Nematoda (roundworms)
o Arthropoda (crustaceans, insects)
Deuterostomes – Blastopore becomes anus
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Echinodermata (sea stars)
o Marine
o Bilaterally symmetrical larva
o Radially symmetrical adult
o triploblastic
Chordata (vertebrates)
o Marine and terrestrial
o Notochord
o Bilaterally symmetrical
o Triploblastic
Sept 24, 2009
Lecture 8 - Microevolution I
Brief History of Evolutionary Thought
Carolus Linnaeus (1707 – 1778) – Swedish biologist who devised naming system. He also firmly
abided by and promoted the view that species do not change.
J-B De Lamarck (1744-1829) – worked most of his life at the Muséum d’Histoire Naturelle. Promoted
the idea that species change, acquired characteristics = evolution. Idea was wrong but he popularized
the idea of evolution.
Charles Darwin (1809-1882) – Founder of the theory of Evolution by Natural Selection.
Darwin’s Basic Evolutionary Theory
Conditions
1.
2.
3.
Intrinsic increase in the number of individuals within a species
Competition form limited resources
Survival of the few
Mechanism: Natural Selection – Those individuals with more favorable feature would, on average, fare
better than competitors and survive, passing on to their offspring those advantageous characteristics
“Survival of the Fittest”
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Biotic – survival against interactions with other organic beings
Abiotic – physical and environmental conditions
Fitness – the relative reproductive success of individuals, within a population, in leaving offspring for
the next generation.
Phenotype vs. Genotype – Natural selection directly acts on the phenotype (individuals). Selection
only indirectly affects the genotype (alleles). Requires both survival and reproductive success
Artificial Selection – humans actively selecting certain individuals due to their phenotype (behaviour
or morphology)
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Pigeons
Dogs
Agriculture
o Corn – artificial selection through the centuries evolved the modern male tassel and
female ears of corn from wild grass.
Natural Selection

EX. Snail colour polymorphism
o Birds, such as the song thrush, hunt snails and break their shells open against “anvil
rocks” where debris collects. The snail(cepaea normalis) has several distinct color
morphs, which are camouglaged against different natural backgrounds
o Observation by Cain and Shepard
o Collected snails and found different colors vary in abundance in different habitats
o At anvil rocks found shards of rare morphs
o In deciduous forests the frequency of each morph changes by season

EX. Snake banded coloration – MUST KNOW LEARN FROM TEXT
Four Basic Types of Natural Selection
1.
2.
3.
4.
Stabilizing – extremes are eliminated, leading to a narrowing of variation (ex. baby weight)
Directional – one extreme is eliminated, shifting the curve
Disruptive – individuals with intermediate variation are eliminated producing two extremes
Sexual – Members of one sex compete for the opportunity for preferential mating with
members of the opposite sex. This is because evolutionary success is linked to reproductive
success. Explains major differences between males and females. Sexual dimorphism is
widespread through the animal kingdom
o Sexual selection isn’t survival from biotic or abiotic conditions but members of one
sex compete for the opportunity for preferential mating with members of the
opposite sex.
Mating Systems:
Monogamous – one male to one female
Polygynous – one male to many females (harem’s and alpha males)
Polyandrous – one female to many males (female choice and sperm competition)
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Ex peacock has a luxuriant tail and bright body used to attract the attentions of the female, the
peahen
Males Birds of Paradise have designs to attract females
Natural and sexual selection can be in direct conflict
Case Study in sexual dimorphism: Red-Winged Blackbirds
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Male red-winged blackbirds defend territories and in doing so attract mates
Bright colour patches (yellow and red) work as territorially displays to increase sexual selection
September 29, 2009
Lecture 9: Variation
Genetic variation is the raw material of evolution. Without variation, natural selection cannot operate
and evolution cannot occur. Darwin’s theory of natural selection was missing a mechanism of
inheritance. Mendel solved the mechanism; genetic variation comes from genes and can be generated
through sex, recombination and mutations.
Recombination
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During meiosis the chromosomes duplicate and in synapsis chromatids exchange homologs
section carrying alleles.
New combinations of alleles in daughter chromosomes lead to new variation in traits
Sex
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Independent assortment: allows a random mix of maternal and paternal genomes
Bacteria exchange genes (plasmids)
Mutations
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Mutations are the ultimate source of genetic variation
Occur at a frequency of ~1/100 000 cell divisions
Occurs during Mutagenesis (chemicals or radiation), DNA replication and synthesis
Types of mutations
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Point mutation
o Nucleotide changes such as substitutions, insertion or deletion of bases within the
DNA
o Ex. Sickle Cell Disease – a single base change in DNA results in a change in one RNA
codon, produce a protein with one substituted amino acid. The critical amino acid is
important in proper folding of the hemoglobin molecule, which becomes defective,
producing sickled cells
Gene duplication
o Unequal crossing over - During meiosis, synapsed chromosomes occasionally pair
out of register with each other. Cross over then occurs between non-homologous
sections resulting in genes being duplicated on one chromosome and deleted on the
other.
Chromosomal mutations
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o Deletion
o Translocation
o Inversion
Homeotic mutations
o Transform the identity of one body part into another
HOX genes – regulator genes that act to impart identity to regions along the body axis
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- determine the development of where paired wings form
- where legs develop
- how flower points are arranged
Sequnce of events of action of HOX genes
I. Chemical gradients in the embryo set-up symmetry, polarity, positional information
II. Deployment of HOX genes (impart identity)
III. Activation of downstream developmental regulatory genes
IV. Activation of downstream structural genes
Hox paradox: if all animals share the same genes and the functions are remarkably conserved why
is there so much diversity in animal form?
Variation following Darwinian theory favours Gradual evolution occurring in small steps such as point
mutations that occur at a much higher rate than larger mutations. “Variation proposes – Selection
disposes”
Life History Evolution – From conception to death
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Natural selection does not only act on adults. It acts on all life stages between conception and
death: fertilized egg, larva, junvenile and adult
Lizard Example
o Life history features can be seen by looking at different populations
o Difference in food, body size, females size and eggs per season between southern and
northern populations
Guppies
o Native to small streams in Venezuela and the nearby islands of Trinidad
o Guppies in different pool share different life-history characteristics induced by the
presence or absence of predators. They occupy pools separated by waterfalls. In
pools where predators are present, males are drab. Where predators are absent male
guppies are bright colored and attract females.
o Hypothesis: Predators affect life history of the male guppies
o Experiment #1: Lab – simulate natural conditions and add predators
 After several generations, guppies raised in low and high predation
environments evolve different features. As measured by the number of
bright, conspicuous spots, males become more brightly coloured (low
predation) or drab (high predation)
o Experiment #2: Wild – swap populations of guppies
 See diagram
September 30, 2009
Lecture 10 – Speciation
Kin Selection – animals cooperate and form or live in groups (Hamilton)
Darwin had a difficult time explaining cooperation in animal populations, especially ants. It defies
fitness,, the ants aren’t passing on their own genes. The individual has given up its ability to
reproduce. This defies Darwin as the ant is not maximizing its own fitness. It does apply to the idea of
family and relatedness kin selection.
Inclusive Fitness – evolutionary success is derived from your own offspring and the offspring of
those related to you
Coefficient of Relationship – is a way of mathematically expressing the degree of relatedness
between different individuals
Time allocation - Life history strategies evolve under different environmental demands.
This can be diagrammatically represented with alternative energy budget allocations. The size of the
arrow represents the size of the energy investment.
(a) Free of beetle attack, beans allocate more to Toxins and Growth than to Reproduction.
(b) Under beetle attack, beans evolved a strategy of increased Reproduction, overwhelming beetles
with a large output of seeds, but at the expense of Toxin production and vegetative Growth.
Speciation : the process by which new species arise

The evolution of a reproductive isolation within an ancestral species, resulting in two or more
decendant species
 Species: a fundamental taxonomic category to which individual specimens are assigned
o the particular concept ones uses expresses their view of the role of a species in
nature or the method used to delieate it as a matter of conveience
o species document diversity at a fundamental unit higher level taxa are arbitrary
designations, species are not
o the patter of speciation can say something about the pattern of natural selection
o
I. Biological Species Concept (BSC)
 most popular species concept applied to sexually reproducing organisms defined as a
reproductively isolated community in which all individuals potentially or actually
interbreed amongst themselves, but are genetically isolated from other groups
 ADVANTAGES: defines species on the basis of criteria important to their evolution –
reproductive isolation
 Members of the species self-define the boundaries of their own species
 DISADVANTAGES: exceptions exist, different species sometimes do interbreed. Concept
takes too much time to test and is not always feasible

II. Evolutionary Species Concept (ESC)
 an ancestral-descendant sequence of populations evolving separately from others and
with its own evolutionary role and tendencies
 looking through time for ancestors linked to intermediates
 ADVANTAGES: applicable to living and extinct groups as well as sexual and asexual
groups
 DISADVANTAGES: not operational role. Uses morphological criteria. A sequence of fossil
forms not always available due to poor preservation
III. Phenetic Species Concept (PSC)
 Individuals that are phenotypically similar (includes morphology, physiology, behavior)
 Therefore are distinguished from other species by phenotypic differences
 This includes Morphospecies- morphological species contemporary and extinct species
which form “natural” breaks in anatomical appearance
 ADVANTAGES: easily applied
 DISADVANTAGES: requires arbitrary decisions. Can be misleading - what of distantly
related species that are similar in appearance? Eg sharks and dolphins
IV. Phylogenetic Species Concept
 Monophyletic group composed of the smallest diagnosable cluster of individual
organisms within which there is parental pattern of ancestry and descent
 Includes agamospecies – based on genetic similarity
 Monophyletic groups (clusters) are defined by unique characters (DNA sequences)
 ADVANTAGES: focuses on operationally defining species
 DISADVANTAGES: the method used for reconstructing those clusters will have big effects
on outcome. The history of different genes can give different results
October 6, 2009
Lecture 11: Macro-evolution I
Process of Species Formation – using biological species concept
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The process of species formation is random
One single ancestral species gives rise to new descendant species
I. Allopatric speciation
II. Sympatric speciation
Allopatric Speciation
1.
2.
3.
4.
No barrier; one species
Geneflow interruption - Barrier allows differences to develop in two populations
Differences so great that two species are evident
When barrier is removed, species do not interbreed
Sympatric speciation arises without geographic isolation.
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Biological barrier to gene exchange has to arise within the confines of a randomly mating
population without any spatial segregation of the species.
Controversial theory with theoretical difficulties.
Uncontroversial instance of polyploidy in plants; a single instantaneous change caused by
polyploidy doubling of chromosome number that reproductively isolates a new polyploidy from
its ancestors.
Ecological isolation – follows allopatric or sympatric speciation. Separation is driven and reinforced
by selection against hybrids and competition.
Reproductively isolating mechanisms – obstacles to interbreeding between genetically distinct
species. Hybrids are not well adapted to environment; low fitness; reproductively costly to parent.
Two types:
1.
2.
3.
Prezygotic isolating mechanisms
 Geographic isolation
 Ecological isolation – species utilize different resources in the field
 Behavioral isolation – different mating habits
 Temporal isolation – mating occurs during different times of day
Sexually isolating mechanisms
 Mechanincal isolation – sexual parts do not fit
 Prevention of gamete fusion – sperm does not match with egg
Post zygotic isolating mechanisms
 Hybrid embryos don’t develop properly
 Hybrid adults do not survive in nature
 Hybrid adults are sterile or may have
reduced fertility
Ex. Ring Species – Salamanders
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Area of smooth intergradation between races
Area in which closely adjacent races hybridize
frequently
Area in which two races occupy the same territory
but do not interbreed
Latitudinal Gradients – more species exist in the
tropics because of the stable temperature; more time
and mating seasons; many habitats and niches for
species to utilize; different and varied food sources.
Brief history of Neo-Darwinism – after the discovery of mendelian genetics, some research broke
away form Darwin’s theory of natural selection.
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“Biometrical school of thought” Darwin argues that the slight differences among individuals make
up the continuous variation we see in features such as body size and height. Continuous variation
is an important source for which natural selection operates to change species gradually.
“Discrete Variation” followed by mendelians. They believed continuous variation had no genetic
basis so that only discrete variation could play a role in evolution
Mathematical theory of population genetics (Fisher, Haldane and Wright) resolves conflicts
between Darwinism and Genetics. Aka NEODARWINISM
The view that mutation, recombination, natural selection and other processes operating within
species account for the major, long-term features of evolution.
Natural selection, through gradual changes over a long period of time, has produced the variety
we see today: MICROEVOLUTION
Macroevolution
TIME – has there been enough time for microevolutionary changes via natural selection to produce
the rich diversity of organisms we see today?
Dating fossils
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Stratigrapy – places fossils in relative sequence to each other. Rocks found below are older
than those above
o Exceptions: angular unconformities and disconformities of depsositions
Index fossils
o Can build an overlapping chronological sequence longer than represented in a
single site by matching rocks from difference sites
o Allows building of chronology of fossils by correlating rocks from different sites
and matching fossils found within those rocks
Lecture 13
October 13, 2009
READINGS – pp 242-245, 249-251
The Niche
Observation: five species of warblers co-existed in the same habitat. Through careful observation it
was noticed that the warblers lived in same tree but did not spend time in the same part of the tree at
the same time. They were living in different niches
Environmental requirements of organisms
Ecology – the relationships between organisms and their environments including biological as well as
physical and chemical properties of environment
Aims of ecology are to describe and understand the distribution, abundance and production of
organisms in their environment. With the ultimate goal of being able to predict changes in
environment and organisms.; when something may occur and why.
Factors influencing where organisms live in their environment include
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Resources (N, P, Ca, etc) food
Presence/absence/quantity of light (photoautotophs are influenced by light availability)
Other species and predators
Water
Temperature
Temperature affects the metabolic activities of all organisms because the biochemistry of cells is
catalyzed by enzyme and their activity is influenced by ambient temperature. Enzyme reaction rates
are proportional to temperature, have higher catalysis rates at higher temperature. At very high
temperature enzymes will degrade and catalysis rate falls off.
On a physiological level the optimal photosynthetic temperatures vary between species.
Acclimation to temperature – physiological changes in response to temperature changes. For
example atriplex lentriformis (a desert shrub) grown at two temperatures 43/30 and 23/18
(Day/Night).
Temperature dependence of microbial growth on the organism level.
Environmental heterogeneity
Microclimate is the climate experiences at scales of kilometers, or meters, or centimeters (shade of a
tree on a sunny day). Influenced by many factors including

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altitude (T declines as high increases)
vegetation.
Soil colour
o White sand beach reflects all wavelengths of visible light
o Balck sand absorbs all wavelengths of light
Aspect (north facing vs. south face slope)
Aquatic vs. terrestrial environment (aquatic environments show less temperature variation than
terrestrial environments)
Habitat – the physical place where organisms live (eg. Tropical rainforest, bottom of a lake, hot
spring)
Niche – exist within habitiats “appropriate combination for a species to survive”. Includes physical
factors such as temperature and moisture, biological factors such as resources and predators. The
intensity of competition between species suggest the degree to which their niches overlapped
“the position it fills in its environment comprising the conditions under which it is found, the
resources it utilizes and the time it occurs there.
Law of minimums states that each species ahs a miniumum requirement for every facto cecessary to
its survival and growth. Eg. Minimum T or ligh
Law of tolerance states that even factors necessary for survival and grow th can be stressful when
present in too great an amount
1. the availability of niches within a habitat varies in times and space – which influences the
abundance and distribution of the species
Feeding niches of finches show a relationship between body size and seed size. The kinds of seeds
eaten by the bird correspond to beak size. During the drought of 77 larger birds capable of cracking
hard seeds survived at a higher rate. Consequently the population was dominated by larger birds at
the end of the drought.
2. new species (invasive species, or as a result of speciation) can spread rapidly within a habitat as
they occupy their niche. Eg. Zebra mussel (bivalve) in North America
spartina anglica is a hybrid species that arose around 1960s. unlike it’s parents it’s able to tolerate
saline habitats and water-logged soils. Hybrid species spread rapidly throughout coastal Europe,
Australia and China (where it was planted to stabilize mudflats).
Fundamental niche – defines the physical conditions under which a species might live (generally
only considers abiotic factors, temperature, moisture…)
Realized Niche is the part of the fundamental niche that an organism actually occupies (considers
bioltic interactions, which may reduce fundamental niche)
Example – chthamalus and balanus are barnalces that grow in the intertidal regions on rocky shores.
They produce larvae which settle on the rocks. The larvae grow into adults.
Realized niche of chthamalus was much smaller than that of balanus because balanus is able to
displace the fundamental niche of chtamalus.
Measurement of niche breadth