Wikinotes

Maintainer: admin

1 The Origin of Earth and Life
2 The Nature of Early Life
3 Biodiversity
4 Evolution
5 What are the consequences of independent evolution?
6 The Cambrian Explosion
7 Evo Devo
- 7.1 Pax6/eyeless gene
  - 7.1.1 Homeobox(hox) genes
- 7.2 Developmental change and evolution
8 Animals: A story of ingestion
9 Plants
10 Fungi
11 Summary
12 Variation
13 Selection
14 Speciation
15 Extinction

Between 10-15 bya
Quarks form protons and neutrons = ¹H and ⁴He ($\alpha$ and $\beta$ emission)
Expansion, condensation, formation of protostars
Protostars burn producing heavier elements (up to ²⁶Fe)
Protostar explodes as supernova - forms our solar system (4.6 bya) - sun is created
Condensation of nebular material starts forming planets. Planets around the sun form from the matter called "planetisimals"

Earth was initially molten and composed largely of: Fe, Mg, Si, O
Formed 4.6 bya
Crust forms 4.2 - 4.1 bya as Earth cools
First traces of biochemicals found from 3.85 bya
Oldest fossils found at 3.7 bya

Meteors and comets bombard Earth from 4.5 - 3.8 bya, supplying lighter elements and frozen gases
Atmosphere generated by volcanic out-gassing (80%) and impact bodies (20%)

Composition:

CO₂ at 100 - 1000 times greater than present atmosphere levels, N₂, H₂O plus trace amounts of H₂, S gases, NH₃, CH₄
Mostly reducing compounds (no oxidation)
No free O₂, because O₂ breaks down organic molecules
About 12 times the air pressure as present day

All volatile compounds remained in the atmosphere when the Earth was hot
When Earth cools below 100 deg, water condensed and formed oceans
Large impact bodies would have vaporized the entire ocean, destroying any life
Earth had liquid water on surface by 3.9 bya, evidenced by sedimentary rocks

Gases dissolve quickly in water

CO₂ + H₂O = HCO₃^- + H⁺
HCl + H₂O = H₃O⁺ + Cl^-
SO₂ + H₂O = H₂SO₃
These acids then dissolved rocks on land, and the river carried these salts to the ocean, making it salty

Graphite in quartz crystals at 3.85 bya (carbon)
Bacteria-like fossils at 3.5 bya

What is life?

Organization
Energy use and metabolism
Homeostasis
Replication/reproduction
Response to environment/stimulus

Research on the origin of life mostly consists of recreating chemical reactions that may have taken place on earth 4 bya

Organic Compounds are C-rich compounds with C-C bonded together. Amino acids, hydroxy acids, sugars, nuclear bases, fatty acids
Early experiments attempted to replicate the chemical environment of early Earth

Mix gas thought to compose the Earth's early atmosphere
17/20 amino acids, all purines/pyrimidines were formed in a week, and otehr types of organic compounds were produced in other experiments

Another hypothesis of the origin of organic matter that is supported by data
Panspermia is the hypothesis that it was brought from outer space

3 lines of evidence to support this hypothesis:

The Murchison meteorite was found to contain a variety of carbon compounds: purines/pyrimidines, polyols, amino acids
The ALH84001 meteorite from Mars contained some evidence of microorganisms (PAHs and fossils). This is refuted by some scientists
A variety of organic molecules in interstellar space have been identified using infrared spectroscopy:
- Methane
- Methanol
- Formaldehyde
- Cyanoacetylene

Simple organic molecules that were formed were subsequently linked together into large macromolecules that had some properties of life - replication
What are the important macromolecules?

All life that is know to exist on Earth today seems to be of the same form - one based on DNA genomes and protein enzymes:

DNA ---(via protein)---> RNA -> ---(via protein)---> Protein -> DNA

What came first?
Proteins cannot be made with nucleic acids and nucleic acids cannot be made without proteins

It is hypothesized that RNA had the capacity to self replicate and self catalyze chemical reactions. This is referred to as the "RNA world" which is hypothesized to have preceded the first DNA/protein life
How did the RNA polymers originate?

Thomas Cech and Sidney Altman (Nobel Prize) discovered first known ribyzyme(RNA with enyzymatic properties), which splices pre-existing RNA molecule in two

A number of hypotheses:

Clay catalyzed RNA synthesis (most popular)

Early models envisaged that life evolved in a temperate pond, however, in dilute aqueous environments, hydrolysis occurs more likely than polymerization

"One can contemplate an RNA world, containing only RNA molecules that serve to catalyze the synthesis of themselves" - Gilbert, W., 1986 - Nature 319, 618

Ribosomes which assemble proteins are ribozymes

The model proposes that some RNA molecules that were randomly ssembled on clay would acquire enzymatic properties and replicate, creating many copies.
Errors in copy would create mutations which would might increase its rate of production

Certain RNA molecules incorporate both features required of life:

Store information
Act as catalysts

No RNA molecules that direct the replication of different RNA molecules have yet been identified in nature, but it has been made to evolve to perform many functions (Joyce, 2002)

Joyce, 1992 - isolated an RNA from Tetrahymena that could cut a different RNA and attach part of the substrate to itself (required Mg²⁺ ions). He designed a system in which variants of the ribozyme that were active with Ca²⁺ were able to replicate and the Mg²⁺ form was not. (Artificial selection)

At the end of 12 rounds of synthesis the ribozyme population was dominated by the variant forms that were active with Ca₂₊

RNA may have eventually begun encoding proteins with catalytic properties, one of these enzymes could have been reverse transcriptase, which copies RNA into DNA. DNA is more chemically stable, thus allowing larger genomes. DNA -> RNA -> protein sequence established.

Liposomes (micelles) grow on solid supports and can bud off once they increase in size - forming a sealed sphere. Micelles fuse to form vesicles.

How might the association between nucleic acids and membranes lead to the formation of a stable entity that displays cellular behavior?

Osmotic stress
Creation of an electrochemical gradient (energy)

Precursor cells (Progenotes) use A as energy source
As A is depleted, those cells that evolve an enzyme to convert B into A thrive
Those progenotes that use various substrates would survive

Question: Do we have any idea of what the early energy sources are?

Yes, very likely it used hydrogen and other energy rich compounds

The environment favors those organisms that can use a variety of energy sources, and thus metabolism is created.

At this point we have covered a billion years in the history of the Earth

In a short period of time, 10 million years, the origin of life has been established.

the most popular view is that it evolved in the deep sea, near hydro thermal vents. These hydro thermal vents are like little mini volcanoes in the sense that down in the sea floor where molten rock or magma is in close proximty to the sea bed. Sea water percolates in to the sediment gets heated and boils and rises up through the hydrothermal vents.
There's lots of clays present, there's lots of metal present(metal catalysts), important in polymerization of rna on the clay template. Potential energy sources, hydrogen, sulphide, hydrogen gas that may be used. These conditions existed else where on the earth, but UV radiation was very high because there's no oxygen in the atmosphere(no ozone). Any living organism on the surface of the land will be fried by UV radiation

Question: What temperature is the deep sea vs temperature on the surface?

Who the fuck knows

Liquid water:
Ideal medium for energy reactions, polar molecule capable of H bond and stabilizing. All of our own metabolism occurs in the aqueous medium of the cytoplasm.

Energy:
Energy is used to assemble of elements into complex molecules, replication, motility, acquire other resources

Organisms use one of 3 main sources of energy:
Light, Organic molecules, Inorganic molecules(Chemosynthesis)

Organisms can be classified by how they obtain energy and carbon - C is one of the most important elements for growth

Autotroph - Inorganic C - CO₂
- Photosynthetic (light - electromagnetic energy) PAR 400-700 nm (photoautotroph)
- Chemosynthetic (inorganic molecules - chemical bond energy) H₂, H₂S, NH₄⁺, FE(II), etc, less abundant

Chemosynthesis in deep sea bacteria

No sunlight, so they need energy from hydrothermal vents. Tubeworms can grow to 2 meters in length. They rely on bacteria as food source, and the bacteria uses chemosynthesis.

Bacteria: HS^- + 2O₂ -> SO₄2- coupled with CO2 + R -> organic molecule

Heterotrophs - organic molecules for energy and C - carbohydrates, proteins, fats

Herbivores
Carnivores
Omnivores
Detritivores
Saprovores -> Dissolved organic matter

The rate at which organisms can take in energy is limited

The limitation may be caused by external constraints:
- Shortage of food in the environment(sunlight, prey)
- Food quality: Shitty food, like secondary metabolites which inhibits metabolisms
Limitation may be caused by internal constraints
- Not enough enzymes to capture the excess of energy(Not enough photosynthetic units to capture an excess of sunlight)

P_max is the maximum rate of photosynthesis, despite an increase in photon flux density.
In carnivores, there's a maximum rate in which food can be digested.

Energy is generally limited
Organisms can respond in a way to maximize their intake, a consumer can move in a way that maximize prey coverage
Organisms have to make tradeoffs because the energy is finite. The organism has to allocated for different priorities, such as reproduction.

Elements are used to construct cellular constituents and in biochemical reactions that are necessary for survival. They are used for structures and catalysis

Examples: Cellulose, hydroxy apatite(Ca, P), cytochromes(Fe, N)

Organisms don't use every element which exists

There are about 28 elements which are needed, 6 of which make up the bulk: C, H, O, P, N, S. Without these the organisms will suffer in its life
e.g. deficiency in copper = wilson's disease.

If we plot the log of element concentration in the environment vs the log of element concentration in tissue, it appears to be positively correlated. Somewhat. Most elements fall above the 1:1 line, which makes sense, since they must be more concentrated in the organism.

Organisms concentrate and extract elements from their environment. The concentrations of essential elements varies among different environments and over geological time. The change in concentration influenced the requirements of the elements required in elements.

Element	Ocean	Lake	Soil
N	420	420	45000
P	60	20	24000
S	900000	11000	480000
Ca	410000	Variable	100000
K	400000	3000	100000

Some elements may be limiting to growth

Sometimes the concentration is so low that the organism can't do anything to obtain more, the organism will Acclimate. The organism will change its developmental process to accomodate the lack of resources

An organism can also adapt to nutrient availability.

The amount of iron was very high during archaean eon(>2.5 bya), but virtually disappeared by the end of the Phanerozoic(<0.54)
Green algae evolved during archaean requires a lot of iron while the amount of iron required by the red algae, which evolved in the Phanerozoic, is half as much.

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 hypothesize what the earliest life was like.

H₂, CO₂, N₂, S gases - anaerobic, hot

First hypothesis: Chemoautotroph

H2 + 2Fe(III) <=> 2Fe(II) + 2H+
H2 + CO2 <=> CH4 + H2O
H2 + SO <=> HS- + H+

Uses hydrogen gas as energy and CO2 as carbon source. Produced methane. Evidence of the existance of methane which supports this hypothesis.

Second hypothesis(Fallen out of favor): Heterotroph that used organic matter that was synthesized abiotically. Oparin(1924)

Dilute pond model(Problem). Very very low concentration
Organic matter absorbs to clays, lived in proximity to clays and ate clay(lol)
Generally not favoured.

Other characteristic of the first organism

Anaerobic
Hyperthermophilic and halophilic(salt-loving)
Prokaryotic

First organisms may have been similar to Methanococcus(Archaea, anaerobe, lives in hydrothermal vents, uses H2, CO2, produces methane)

All extant organisms near the origin of the phylogenetic tree are hyperthermophiles that are found in hot springs and hydrothermal environments
These environments are likely similar to those of early earth
These organisms all use H2 as energy source and Fe or S as electron acceptors
Massive magnetite accumulations (Fe₃O₄) during the archaean era provide geological evidence for Fe(III) reduction

New species exploited other energy sources - some using the products from the metabolism of other organisms as substrates. Populations of organisms layered one on top of the other - biofilm. Sharing of resources, diversification of metabolic capabilities
Organic compounds accumulated and allowed heterotrophic organisms to thrive
Bacteria and Archaea are the most metabolically diverse groups of organisms

Each layer of sediment is colonized by microbes that use different energy and C sources for growth. The products from the metabolism of one organism are used by the population of organisms adjacent to it.

Organisms develop pigments(bacteriochlorophyll) that are used to capture light energy (much more plentiful than geochemical energy).
Earliest form of photosynthesis was based on sulfur (S): it was anoxygenic (non O2 evolving) carried out by S bacteria
CO2 + 2H2S = Ch2O + 2S + H2O. H2S was the electron donor

Fossil evidence suggests that photosynthetic cyanobacteria appeared around 3.2-2.4 bya
CO2 + H2O - CH2O + O2
H2O was an inexhaustible resource
O2 only accumulated slowly in the atmosphere because it reacted first with Fe in the sea
This is oxygenic photosynthesis

The earth atmosphere went from anoxic to oxic sometime between 2.5 and 2.0 bya. Oxygen reacted with all the iron in the ocean, causing it to precipitate, effectively stripping it from the ocean.

Allowed for the evolution of a new type of metabolism - aerobic metabolism: greater energy yield per mol of C substrate consumed. Glycolysis, fermentation pretty bad at generating energy
Changed ocean chemistry: S and N oxidation(SO4 2- collects in ocean). Organisms which can break down sulphate can evolve
Allowed for the formation of the ozone layer - O3 - protection from UV.
Poisoned environment - anaerobic organisms became confined to refuge habitats

Organisms had to evolve mechanisms to detoxify the noxious by-products of O2 - Superoxide, hydrogen peroxide

The release of O2 by photosynthesis is perhaps the single most significant effect of life on the geochemistry of the earth

Cells existing prior to 1.8(2.7) bya were all prokaryotes: bacteria and archaea
Eukaryotes appear in the fossil record ca. 1.8 bya.
Chemical markers (steranes) produced only by eukaryotes are detected in rocks ~2.7 bya
How did eukaryotes differ?

Prokaryotes vs Eukaryotes, rehashed for the 293872938572 time.

Theory proposed by Lynn Margulis
Mitochondria and chloroplasts of eukaryotes 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

Conceptually:

archaea engulfed the photosynthetic bacterium and an aerobic bacterium to form a chloroplast and a mitochondria. The archaea didn't digest the bacterium it had ingested, so there was a stable relationship between the host and the prey(symbiosis), eventually integrated into the host organism.

The outer membrane of eukaryotes are similar to the outer membrane of archaea, and the internal membrane of mitochondria are similar to the membrane of bacteria. The ciliate ingests chloroplasts, and it doesn't digest it, it instead uses it to make food.

Rickettsia prowazekii makes energy in the same pathways as mitochondria

Reclinomonas americana has unique DNA of its mitochondria

Organelles (chloroplasts and mitochondria):
1. contain own DNA, similar to bacterial DNA, no histones, circular.
2. surrounded by a double membrane - the inner one looks like a bacterial membrane
3. show antibiotic sensitivity, these drugs affect the metabolism of mitochondria(inhibited)
4. have ribosomes (70S) like bacteria

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

Eukaryote engulfs another eukaryote which was photosynthetic, and incorporates it.

Cryptomonad, cells which have a symbiotic relationship with a photosynthetic eukaryote. The cell inside undergoes nucleomorph(degradation of nucleus)

Method for organizing information
Grouping similar organisms together
Historically, it involved grouping organisms into different categories based on their physical characteristics (hard for microbes, convergent evolution is an issue)

Ideally it should reflect the evolutionary distances and relationships among organisms
Predict characteristics of newly described organisms
Understand the history of life

Aristotle
- Plantae (L. planta, plant) and Animalia(L. anima, breath, life)
- Structure, function, metabolism, movement
20^th century
- Single-celled organisms (prokaryotes) and single and multicelluar organisms (eukaryotes)

prokaryotes, protists, fungi, plants, animals.
Proposed by Whittaker

Morphologically simple - they have fewer obvious features that can be used to measure relatedness of species
- RNA proposed because it is found in all organisms
- Transmission of genetic information captures ancestral relationships
- The nucleotide sequence of the RNA change from organism to organism, record evolutionary progression
- Large enough to record useful info. on evolutionary change

RNA sequence analysis identifies 3 major lineages(Called domains)(Carl Woese 1977)
Bacteria (Prokaryote)
Archaea (Prokaryote)
Eucarya (Eukaryote)

Classification within each domain is based on rRNA or more recently using a number of different genes

Prokaryotes are NOT monophyletic branches of the tree of life; they are two seperate lineages that evolved similar character states (polyphyletic).

Bigger difference in genetic sequence, more apart from each other. We can use the genetic distance to generate phylogenetic tree.

What if genes were not only transferred vertically from parent to offspring (ancestor to descendent)? It would obscure the prediction of a phylogenetic tree
During endosymbiosis genes were transferred from the endosymbiont to the host genome(Endosymbiotic gene transfer). Obscures the tree of life
Horizontal gene transfer is also effected by a virus or plasmids that contains a foreign gene that can be transferred.
- 20% of ecoli genome can be traced to HGT
- 1/3 of the genome of some prokaryotic organisms has been acquired through HGT

The current tree of life has 3 accepted domains

Hypothesized to be hosts that engulfed symbionts

Three groups are identified:

Euryarchaeota
Crenarcheota
Korarcheota (Known only from rRNA sequences obtained from Obsidian Pool at Yellow Nat. Park)

Contains methanogens and halophils
The methanogens release methane (CH₄) as a waste product. In rice paddies
The halophils grow in salt water up to 23% NaCL
Extremophiles, inhabit extreme environments, hot, salty environments
Halophils have a unique light-mediated pathway of ATP production using bacteriorhodopsin (a pigment)

Divided into 12 major lineages acording to rRNA sequence analysis
The most ancient bacteria are hyperthermophilic chemoautotrophs (uses H₂ or reduced S as energy source) - Aquifex-Hydrogenobacteria group

Largest group of bacteria contains heterotrophic and phototrophic genera
Purple and green sulfur bacteria, they have an anoxygenic photosynthesis, don't use hydrogen. One green sulfur bacteria that has been found in hot vents near oceans near mexico. Photoautotroph, down in 2500 m in the sea, using the dimlight produced near hydrothermal vents as energy source
Most metabolically divers group: oxic, micro oxic, anoxic, conditions.

Common proteobacteria: Ecoli, purple photosynthetic bacterium

Large group of phototrophic bacteria that use oxygenic photosynthesis (generate O₂)
Some form specialized structures called heterocysts and are capable of using nitrogen gas(N₂) fixation, converting it to NH₃. Involves a great deal of energy, sensitive to oxygen, oxygen is toxic, which is why heterocysts are needed.
Among the most important primary producers in lakes and oceans.

Contains plants, animals, fungi, protists.
Protists
- Mostly unicellular eucaryotes
- Include parasitic, photosynthetic, heterotrophic forms
- Between 12-32 phyla are described

Parasite to humans
No common morphology
Ancestral to other eukaryotes, some lack mitochondria, but now known to have relic mito 0 mito proteins
Flagellated, obligate anaerobes
Trichonympha - a symbiotic inhabitant of termite guts, contains cellulose degrading bacteria
Entamoeba hystolytica, amoebic dysentery
Kinetoplastids, causes sleeping sickness. Have a unique structure known as kinetoplast(mass of mitochondrial DNA, near flagellum
Leichmaniasis - human disease caused by Leichmania, also contains kinetoplast.

A supergroup that contains 23 previous groups
- Algae
- Some non-photosynthetic groups
Important group ecologically - producers and consumers of planktonic communities of lakes and oceans
Includes: dinoflaellates, apicomplexa, ciliates, brown algae, diatoms

Alveolates: Dinoflagellates
Symbiotic organism with invertebrates, corals.
Heterotrophic and phototrophic species
Many form dormant cyst stage
Single living
* Produce toxins, red tide. Paralytic shellfish poisoning, amnesic shellfish poisoning

Aveolates: Apicomplexa

Obligate prasites of animals: Complex life cycles
They have an apical complex of organelles(microtubules, etc) that helps them attach to or penetrate their host
Malaria - Plasmodium sp.

Stramenophiles: Diatoms

10000 species found in all aquatic environments
Responsible for roughly 25% of global primary production
Produce a silica (glass) exoskeleton known as a frustule
Only male gametes have flagellum

Stramenophils: Oomycetes
Water molds(formerly fungi)
Filamentous growth form, but produce flagellated zoospores (asexual spores that give rise to filaments)
* Cause many agricultural diseases:
* Downy mildew of grapes
* Potato blight

Stremenophiles: Phaeophyta
Contains no unicellular representatives
Macroscopic

United only by molecular data(no distinguishing morphological features).
Heterotrophic cells that consume prokaryotes and eukaryotes.
They produce rhizopods that feed on their prey.

Include red and gree algae, land plants and charophytes

All contain plastids that arose by primary endosymbiosis

Sexual reproduction common: isogamy(equal sized gametes) and oogamy(large egg fertilized by small motile sperm). Unicellular, colonial and multicellular forms

Chlamydomonas - model organism for evolution studies, volvox, colonial form
The most advanced form have reproductive features like those of higher plants

Contains parasitic protists, slime molds, amoebae, animals, fungi
Includes choanoflagellates, previous protista. That resemble cells of sponges (among the simplest and most ancient of animals)

Descent with modifications from a common ancestor; it is a fact, but the mechanism of it is not certain, that's why some people call it a theory, but biological evolution is an observable phenomenon.

3 important principles in evolution biology:

Inferring evolutionary history: principle of phylogeny
Independent evolution: principle of convergence
Direction in evolution: does complexity linearly increase?

Evolutionary Biology is a historical science
- We must infer history: it only happens once
- Darwin didn't come up with the concept of evolution, he came up with the theory of natural selection. Through natural selection Darwin believed he can connect the dots together and find the history of phylogeny

Phylogeny: The course of evolution from past to present
Phylogenetic tree: A graphical representation of the course of evolution from past to present

The anatomy of a phylogenetic tree:

Nodes, Terminal nodes, root node

Branches, internal branchs, terminal branches

How many trees are possible for n OTU(operational taxonomical units, species, terminal nodes)

2 = 1, 3 = 3, 4 = 15, 5 = 105

Exponential function(figure out later)

Just because things are similar, it does not mean they are closely related to each other, rather, it means they evolved to solve a common problem.

Features and behaviors can both be formed by convergence evolution.

Data (from fossil record and modern taxa):
Morphology
DNA

Methods:
Parsimony
Maximum Likelihood
Distance
Bayesian methodology

wtf only half way

Step-wise evolution is influenced by the way of thinking known as 'the great chain of being' (Evolutionary Bias). The idea is that there's a scale of being where you start with a simple organism, and you go up until the most complex organism.

Step-wise evolution is sort of false. The reality is that evolution is more like a tree.

According to step-wise evolution, multicelluarity evolved once. Actually, it evolved a minimum of 13 times across different kingdoms. Thus, evolution is multidirectional.

Sponges: The evolution of multicellularity in animals remains a mystery

Solitary choanoflagellate -> Use flagella for motility, heterotrophs, draw in food through water currents

Colonial choanoflagellate -> A lot of choanoflagellates formed in a cluster above a stalk, much like a sponge(choanoflagellate-like cells)

The development of fungi looks like a stepwise process from unicellularity to multicellularity.

Development of the small mushroom Coprinus:

Spores
Spores start growing hyphae
The hyphae start touching each other and forms a network and their nuclei get shared
Mushroom forms

kill me

Within the algae there are many ways that multicellularity might have evolved

Start with a single cell
It divides and forms a wall
A large algae forms

The theory was that walls fused between neighboring unicellular algae cells (failure to divide), and it conferred an advantage, and it was naturally selected to become multicellular

Sea Lettuce Ulva
kill me

Volvox is another way multicellular might have evolved. Different volvox cells form losely together in an aggregate.

kill me

Colonial Diatom

Zoothamnium: a colonial ciliate

Cellular slime mold: Dictyostelium discoideum

Actinomycete - Streptomyces (produces antibiotic Streptomycin)

Aquatic:

Products of cell division failed to seperate

Terrestrial:

Formation of motile aggregation of cells
Aggregation of nuclei in a multinucleate synctium

Multicellularity evolved 1 bya, while organic matter came 3.5 bya.

Aquatic:

Mutation allowed them to stick to ideal substrate
Increasing in size preventing filter feeders from feeding (volvox)
Faster swimming capability

Terrestrial

Dispersal of spores, cysts
Feeding
Creates an internal environment less environmental heterogeneity

Diversity
Competition
Specialization

Evolutionary inventions can cause Adaptive Radiations

Adaptive Radiation: Evolutionary divergence of members of a single phylogenetic lineage into a variety of different adaptive forms over a relatively short interval of geological time

Short early branches diverge into long late branches

Fill previously unavailable niches
Competitive release
Competitive advantage

The Cambrian explosion - the big bang of evolution. Brief 10 mil period where massive speciation occurred.

For midterm, memorize time scale of evolution periods

IMPORTANT DATES

Proterozoic, 590 mya, ediacaran organisms, green algae
Cambrian, 505 mya, cambrian explosion, ancestor of all modern animal groups appear
Ordovician, 435 mya, jawless fishes, first land plants
Silurian, 410 mya, first vascular plants and first fish with jaws
Devonian, 360 mya, bony fishes
Carboniferous, 290 mya, amphibians arise and diversify
Triassic, 205 mya, first dinosaurs, first mammals
Jurassic, 138 mya, first birds
Cretaceous, 65 mya, first flowering plants
Eocene, 38 mya, mammals and flowering plants diversify

Lived most of its life on water - but could venture onto land - had eight toes. Important link for transition of life in water to life on land

kill me

Insects help angiosperms to dominate in speciation

600 mya, first metazoan traces (footprints)
570 mya, first metazoan body fossils

For midterm, memorize name and appearance, as well as a characteristic of a fossil

Ediacarans: Dickinsonia

Possible jellyfish

Ediacarans: Spriggina

Not sure if plant or animal

Rangeomorph frondlet (wtf??)

No basic anatomical features in any Ediacaran fossils - no eyes, mouths, anuses, intestinal tracts, or locomotory appendages.

An alternative (and earlier) evolutionary experiment in multicellularity

conditions were just right to fossilize softshelled, soft bodied organisms.
Organisms are crown taxa that already had evolved the characters that define the phyla of living animals
Morphological gaps separated these crown taxa
Origination of phyla from stem taxa has to be sought in earlier forms in older deposits

early Onychophoran.

predatory arthropod

polychaete worm

early chordate, repeated muscular segments

More and more diversity...

Interpretation
Timing

The two different interpretation of the burgess shale:

Gould - some of them died, those that survived, radiated

Conway Morris - one species remained, gave birth to the big radiation

Molecular clock estimates show much deeper divergence.

Number of AA substitutions is linearly correlated with time to common ancestor

Geological conditions
Rising oxygen levels
Predator-prey relationships - fairly absent

Questions:

How did so many body plans arise and why have so few, if any, arisen since the Early Cambrian?
Adaptive radiation? Is it a big bang or a long slow diffusion
Too specialized upon appearance in the fossil record to have originated in the cambrian?

It's accepted that burgess shale fauna is a stem group from which modern species are derived - conway morris is corrected.

Of 1.2 billion yrs of animal evolution, modern humans have been on the planet for 200k years.

For midterm understand molecular clocks and do molecular clock <-> tree conversion

There are only 35 phyla of animals - Why only 35? It is a mystery.

If the cambrian explosion is a true explosion, the animals must've originated and diversified into 35 phyla in that short period of time.
If we believe in the molecular clock, originated first, then during cambrian explosion it radiated. It's possible that they could not have fossilized before the evolution of skeletons, availability of CaCO₃ caused skeletons to form. Large body size also evolved during cambrian, maybe when they were small, it's hard to be fossilized/discovered.
It could be a larger body sized allowed animals to diversify more, as it's able to occupy previously undiscovered niches.

Radiation facilitated by highly conserved developmental genes - they are already in place during the cambrian.

Discovery of genes that control development. These genes are highly conserved across all animals.

Exampled: engrailed gene, a gene that codes for segment polarity. It is highly conserved in all animals.

It is genes that code for eye development.

In 3 organisms, fly, human, squid, all of their eyes have evolved independently. Even though all of them have different structures, they all use the same pax6 gene.
Human pax6 can be substituted in flies. You can activate it on the wings to grow eyes on the wings, on the legs, on the antennae, to grow eyes there (why the hell are biologists growing eyes everywhere)

They are used to polarize animal developments (which side is anterior/posterior). It differentiates each segments to develop specialized features.
Hox genes have homologs across all phyla of animals. Hox genes are aligned in the chromosomes in the same order they are expressed along the body. Various hox genes are often duplicated, and the entire cluster have been duplicated in vertebrates. 4 clusters in mice, with many copies of a gene in cluster. Their regulation also get changed, to create diversity.

The idea that you can take a conserved set of genes, and duplicate it, change its regulation, to create variation, is called bricolage(tinkering), a term that places the emphasis on modification of existing genes. Termed by Francois Jacob (Operon dude)

Pro tip: animals has the most number of species of all the kingdoms, and insects have the most number of species within animals.

Hypothesized to have evolved from colonial choanoflagellates
Animals obtain their energy from eating other organisms
No cell walls, secrete extracellular matrix that consists of collagen, integrins, glycoproteins, proteoglycans
Divided into parazoa (Sponges), eumetazoa
Eumetazoa divided into radiata and bilateria
Bilateria divided into protostomia, deuterostomia
Protostomes divided into lophotochozoa and ecdysozoa

Branch	Defining features
choanoflagellate	flagella, heterotrophs, draw in food through water currents
Sponges (Parazoa)	pseudoanimal, chanocytes, marine, asymmetrical, no true tissues
Eumetazoa	Has tissues, symmetry
Radiata	Jellyfish and hydra, radially symmetrical, nematocysts, marine, diploblastic(ecto and endoderm, no mesoderm)
Bilateria	Bilateral
Protostomia	Blastopore becomes the mouth
Deuterostomia	Blastopore becomes the anus
Lophotrochozoa	Trochozoa + lophophorates, some have the lophophore, some have ring of tentacles around their larvae
Ecdysozoa	Shedding of the skin
Flatworms	Free-living and parasitic, bilaterally symmetric, triploblastic
Molluscs	Shell, bilaterally symmetric, triploblastic
Annelids	Earthworm, bilateral, triploblastic
Nematodes	Roundworms, bilateral, triploblastic
Arthropod	Joint limbs, marine and aquatic
Echinodermata	Sea stars, bilaterally symmetrical larva, radially symmetrical adult, deuterostomes
Chordates	Notochord

Darwin always found plants hard to explain - "The rapid development as far as we can judge of all the higher plants within recent geological times is an abominable mystery."

Origination from green algae, a long-standing hypothesis, has received support.

They evolved from green algae, plants are multicellular eukaryotes, cellulose rich cell walls, photoautotrophic, alternation of generations.

There are 24 families of plants, 4 groups - seedless non vascular, seedless vascular, gymnosperms, angiosperms.

Unicellular green algae that had incorporated new genes through horizontal gene transfer and gained organelles by endosymbiosis, transformed into multicellular photosynthetic organisms.

Green algae and land plants share various similarities reflecting their common origins:

Green algae store their carbohydrate reserves as starch
Many species of algae have rigid, cellulose reinforced cell walls, as do all land plants
Green algae and vascular plants use similar types of pigments in metabolic pathways, both green chlorophyll (a and b) and yellow-orange carotenoids ($\alpha$ and $\beta$).

Failure of division in cells
New genes from horizontal gene transfer (endosymbiosis, gave photosynthetic ability of land plants)

All plants have have alternation of gametophyte and sporophyte generations:

Gametophyte(n) -> sperm -> syngamy -> sporophyte(2n) -> spores

Origin of plants (Silurian 430 mya)

Vascular lineage (Early devonian 390 mya)

Seed (Late dev 360 mya)

Flower (Early cretaceous 130 mya)

KNOW THIS FOR MIDTERM

Some of the earliest land plants
Lack vascular tissue & True roots to transport water & nutrients
Thrive in damp places, cannot withstand drought
Lack lignan to strengthen cell walls: Stay close to ground

Simplest of land plants: Paraphyletic group liverworts, mosses, club mosses, and hornworts

Bryophytes were important in two major transitions

Water to land
Haploid gametophyte dominated life cycle to a diploid sporophyte dominated life cycle.

Bryophytes have large gametophytes that dominate the life cycle to a parasite sporophyte

Possess vascular tissue
Live in drier habitat
Withstand drought
Well developed cuticle and stomata
Ferns are abundant plants

Vascular: Presence of conductive tissue:

Xylem enables water to reach the erect plants
Phloem enables nutrients to reach different parts of the plant

Cooksonia is the earliest plant fossil vascular plants

There are 3-4 major divisions of pteridophytes

WHY DO YOU HATE REAL GRAPHS

Club mosses, horse tails, ferns

Now sporophyte dominated.

reduce size of gametophyte
Evolution of easily dispersible pollen
Encasement of seeds

Characteristics of gymnosperms and angiosperms

Gymnosperms	Angiosperms
Naked seed plants
Non flowering	flowering
seed hidden in cones
Seed not enclosed in ovary	seed enclosed in ovary
Seed not enclosed in protective fruit	Seed enclosed in protective fruit
double fertilization	Double fertilization

Seed is invented, small capsule composed of a protective seed coat, the plant embryo, and nutrients
Pollen is invented, sperm doesn't have to travel by water
Sporophyte, woody tree like
Gametophyte, reduced and living in cones

Major groups of gymnosperms:

Gnetophytes - Cycads, Ginkos, Conifers

Advertise sex organs for all to see
95% of modern plants are angiosperms
Major evolutionary invention is the flower - allows coevolution with insects and other animals

Rapid evolution of angiosperms caused by:

evolution and elaboration of flowers as sex organs
Enabling insects and birds to pollinate them and to disperse their seed

A sister group of animals

Not plants, no chlorophyl, no photosynthesis
Cell wall of fungi are built of chitin
Fungi absorb nutrients from substrate
Release digestive enzymes then soak up organic molecules released
Principle decomposers in forests

First appeared along with first vascular plants in silurian 440 mya

They share a chanoflagellate ancestor with animals, thus more related (sister group) to animals than plants

Three major phyla:

Ascomycota - antibiotic
Zygomycota - molds
Basidiomycota - mushrooms

Why do we need variation?

First order process of evolution is variation, second order processes can happen upon the variation, such as selection, and thus lead to evolution.

What is the relationship between the genetic variation of the genotype and variation of the phenotype?
What are the mechanisms by which mutations and modifications of gene regulation serve as sources of variation?
What other sources of variation are available to populations?
What are the ecological and developmental determinants of phenotypic variation?

Two major kinds of changes:

Number of entire sets of chromosomes
Numbers of single chromosomes within a set

Repetitive doubling = polyploidy
Example:

Evolution of wheat,

Breeding the evil wheat in the lab: N tabacum (n = 24) + N glutinosa (n = 12) -> Sterile hybrid (2n = 36) -> Chromosome doubling -> N digluta ( 2n = 72, fertile)
The phenotype doesn't change that much.

One type of variation is the whole duplication of the entire set of chromosomes, it can be deleterious or beneficial.

Deletions
Duplications
Paracentric inversion
Pericentric inversion
Reciprocal translocation

The chinese and indian muntjac dear look very similar, but one has 23 pairs of chromosomes while the other has 3 pairs of genes.

Point mutations/base substitutions in protein coding region is another way to create variation; case study: sickle cell anemia

Some mutation happens in the gene regulation region.

Gene regulation in eukaryotic cells:

A mutation in the cis-regulatory region, it will change the binding type/strength of transcription factors that will bind to the regulatory region.
A mutation in the trans-regulatory region, it will change the actual protein of the transcription factor. It will change how the gene will be expressed
RNAi
Transposons
Posttranscriptional modification

Regulatory genes that act during to impart identity to regions along the body axis.

They determine:

Where paired wings form
Where legs develop
how flower parts are arranged

Conserved across the animal kingdom

Homeotic mutation: Transform the identity of one body part into another. E.g. antp, 4 winged flies

ubx is expressed to give an elongated legs, whichever legs it's expressed, will be elongated. Variations in ubx expression will give variation in mobility
In waterstriders, expression of ubx in the third pair of legs, it will make it shorter while the expression of ubx in the second pair of legs. Alternative splicing

Produce special transposase enzymes that allow it to insert copies of itself into various target sites in an organisms's nuclear genome
In primates, an Alu sequence is present in more than 1 mil copies in each diploid human cell

Variation in one species:

Queen ant and worker ants look very different, same genome. Three white dots on the head of the queen ant helps them mate.

The same species of lasius alienus in California, Florida, Netherlands, and they all look different.
There's great amount of variation across the same genus of Lasius.
Variation within the same colony -> variation within the same species -> variation within the same genus

Across different species, worker ants don't have wings, although they all don't have wings, the way wings are disabled are quite different. No variation in phenotype, but large variation in genotype.

Genotypic and phenotypic evolution are often not concordant.

Environment can also induce phenotypic variation. Butterflies in different seasons look very different, they even look like different species.

Environmental differences can be induced, implies the environment can be a selective force, and it can induce variation.

Point mutations, duplication of chromosomes. Most mutations are deleterious

Variation equation: Different types of mutation in different gene regions and different types of genes can lead to different types of genetic and phenotypic evolution

Mutations (Point mutations, chromosomal rearrangements, transpositions)
X
Gene regions (protein coding, regulatory, posttranscriptional modifications)
X
Genes (house keeping, regulatory, upstream, downstream)
X
Environment (phenotypic plasticity)
=
Different combinations of phenotypic variation

Variation proposes - selection disposes

Selection acts on populations in four ways:

Stabilizing selection
Directional selection
Disruptive selection
Sexual selection

Selection acts on variation, constrained by genetic and developmental pathways

Intrinsic increase in the number of individuals within a species
Competition of limited resources
Survival of the few

Those with more favorable features would on average, fare better than competitors and survive, passing on to their offspring those advantageous characteristics.
"Struggle for existence or survival of the fittest"

Surviving against biotic (competition, species interactions) and abiotic (climate changes, changes in the environment) factors

The relative reproductive success of individuals, within a population, in leaving offspring for the next generation
Need both survival and reproductive success

Natural selection directly acts on the phenotype, and indirectly affects the genotype through the phenotype.

Artificial selection is something that is directed by humans - fancy pigeons breeds. In artificial selection, the breeder selects the parents deemed desirable and culls the undesirable types.

Animal and plant breeders, who select for extremes of yield, productivity, or resistance to disease.

Stabilizing selection: Lowering the $\sigma$ of the normal curve, only those with the average trait will survive
Directional selection: Shifting the horizontal location of the normal curve, only either the high extreme or the low extreme will survive
Disruptive selection: Dividing the normal curve into two parts, both the high extreme and the low extreme will survive

For midterm, memorize this example!

Directional selection in the wild, color polymorphism in cepaea snails.

Study by Cain and Shepard
Collected snails and found different colors vary in abundance in different habitats
At anvil rocks found shards of rare morph
The frequencies of each morph change by season in deciduous forests

The birds hunts snails pick them up, and drop them on anvil rocks, and eat them. Those snails that camouflaged the best survive.

In beechwoodland, brown and pink snails survive the best, green are rare.
In meadows, brown and pink snails are rare, and green are common
In deciduous woodland in the spring, brown and pink are common and the green are rare, in the summer, the reverse is true

Why do we find major differences between individuals, males and females within populations?
Sexual dimorphism widespread throughout the animal kingdom: Horns in dung beetles, fur seals' sizes, male antlers are much bigger, longer tail feathers
Evolutionary success = reproductive sucess, survival is not enough

Sexual selection is not 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
- Harems & alpha males
Polyandrous - one female to many males
- Female choice and sperm competition
- Fruitflies - sperm of 2nd dislodges and poisons sperm of first
- Swamp by volume other male's sperm
- Spiders, black widow

Barn swallows are sexually dimorphic. Males have longer tails than females

Experiment 1, shorten tails by cutting
Experiement 2, lengthen tails by gluing
Controls, cutting tails and regluing, but no lengthening.

Results:

tl;dr, long tailed males are studs.

Even though sexual selection is a special case of natural selection, natural and sexual selection can be in direct conflict.

Pools without predators, the colouration is much intense to attract females, while pools with predators, the colours are much more mild.

Experiment #1: Lab - simulate natural conditions and added predators
Experiment #2: Wild - swap populations of guppies

Experiment 1:

Within a year, low predation evolves more spots and high predation evolves less spots

Experiment 2:

Within 2 years, drab guppies that were transplanted to predator free pools became colorful

At what level does natural selection operate?

DNA?
Individual?
Groups?
Species?
Lineages?

Altruistic behavior which suggests natural selection operating on a group basis, can be explained by the need to pass on genes of relatives to indirectly pass on your own genes (inclusive fitness).

Most levels of selection happen in the individual level, but some also happen with groups, species, and lineages

Speciation: The process by which new species arise. The evolution of reproductive isolation within an ancestral species, resulting in two or more descendant species

Species: a complex concept with various definitions, a fundamental taxonomic category to which individual specimens are assigned.

Biological species concept
Evolutionary species concept
Phenetic species concept
Phylogenetic species concept

The particular concept one uses expresses their view of role of species in nature or the method used to delineate it as a matter of convenience
Species document diversity at a fundamental unit - higher level taxa are arbitrary designations, species are not

The pattern of speciation say something about the pattern of natural selection
e.g. more species in the tropics than in temperate, therefore, does this mean that natural selection acts differently in these two regions?

Species under the PSC are composed of individuals that are phenotypically similar, distinguished from other species by phenotypic differences.

You look for "natural breaks", similarities and differences.

People use comparative anatomy to unite or divide different species.

Advantages:

Applied easily

Disadvantages:

Requires some arbitrary decisions
Convergence of features are difficult to detect

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 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
Takes too much time to test, not always feasible

Defined as an ancestral-descendant sequence of populations evolving separately from others and with its own evolutionary role and tendencies
Includes paleospecies, which are the chronological series of similar forms

Advantages:

Applicable to living and extinct groups and sexual and asexual organisms

Disadvantages:

Not operation - what does "evolutionary role and tendency" mean?
Uses morphological criteria in the end
Fossil forms aren't always reliable

Defined as a monophyletic group composed of the smallest diagnosable cluster of individual organisms within which there is a parental pattern of ancestry and descent
Includes Agamospecies - based on genetic similarity
Monophyletic groups (clusters) are defined by unique characters (in most cases variation in DNA sequences), that no other clusters possess.

Advantages:

Focuses on operationally defining species

Disadvantages

The method used for reconstructing those clusters will have big effect on outcome
History of different genes can give different results

Process of species formation is random
One single ancestral species gives rise to new descendant species, an occur in two principle ways:
- Allopatric
- Sympatric

Usually follwed by ecological isolation

Allopatric speciation(Geographic isolation): A physical barrier forms that split a population, and differences accumulates in the subpopulations, eventually leading into speciation.

Peripatric: A type of allopatric where a small colony is split off, into an island or whatever

Parapatric: Different adapations between two subpopulations, but there is still gene flow (No speciation)

Genetic drift: Bottleneck effect, in theory

An important debate in evolutionary biology has been whether speciation can be initiated sympatrically by mechanisms that reduce gene flow within a population in the absence of initiation geographical isolation - sympatric speciation

This means that a biological barrier to gene exchange has to arise within the confines of a randomly mating population without any spatial segregation of the species. This is very controversial with many theoretical difficulties. E.g. cichlid fishes (sexual selection leading to speciation), polyploidy in plants.

There are two types of reproductive isolation mechanisms:

Those that act before fertilization of the egg - prezygotic
Those that act after fertilization of the egg - postzygotic

Prezygotic Mechanisms:

Spatial (Geographical) isolation
Ecological isolation, species use different resources
Behavioral isolation, different mating rituals
Temporal isolation, mating season differs, or being active at different times during the day

After mating:

Mechanical separation, the key doesn't fit the lock
Prevention of gamete fusion, egg and sperm fail to attract each other

After fertilization:

Hybrid embryo does not develop properly
Hybrid adults do not survive in nature
Hybrid adults are sterile or have reduced fertility

KNOW THIS FOR THE MIDTERM

Sexual isolation in sympatric and allopatric populations

Higher the sexual isolation index, the more difficult it is to form hybrids. Sympatric species have a much higher sexual isolation index

This is because for sympatric populations, after mating and post-zygotic mechanisms must be used to prevent gene flow, thus strong sexual isolation must exist. Allopatric populations have a very strong prezygotic mechanism that separates the subpopulations before any sexual isolation have to occur.

Evolution and diversity is driven by both speciation and extinction

G.G. Simpson estimated that of all the species of plants and animals to evolve since the Cambrian 544 million years ago:

99% are extinct today!

Only a few exceptions to this rule called "living fossils": lingula, horseshoe crabs

Extinction can be considered at levels of increasing severity and impact:

Extinction may be local and specific
Extinction may eliminate an entire species
Extinction may eliminate an entire ecosystem

Uniform or background extinctions
Catastrophic or mass extinctions

Members of taxonomic groups are lost gradually over time without abrupt loss of large numbers. Most extinct species are now extinct through this fashion. It has many ecological causes.

Leigh Van Valen (1973) in his paper "a new evolutionary law" showed that extinction rate is constant.
Species must evolve quickly to keep up with competitors and change in environments, when a species falls behind, it risks becoming extinct.

Real data:

The loss of species from many different groups - it takes large numbers of species.
They occur infrequently and abruptly over short periods of geological time
There are 5 mass extinction events:

end of ordovician -12%
late devonian -14%
end of permian -52%
end of triassic -12%
end of cretaceous -11% (dinosaurs)

Extraterrestrial impacts

Extraterrestrial impacts are known to have battered the moon and earth about 4 bya
100 craters on earth
- tem meteors, each one km in diameter, are estimated to have each produced 20 km wide craters at a frequency of 1/400k years
- 50 km wide crater is produced once every 12.5 my
- 150 km wide crater is produced once every 100 my

No land vertebrate larger than a labrador dog survived, known as the KT boundary

Violent volcanic eruptions, plumes of deep mantle material also can cause this mass extinction event

Microevolution is happening constantly and is a long drawn process, we don't see immediate species because fossilization doesn't always occur

Paleontologists, however, recognized that:

1) species appear abruptly in the fossil record
2) persist for long periods of time
3) then abruptyly disappear

This was first thought to be an artifact of the fossil record; however, intermediate fossils began to be discovered.

Suggested that this pattern was real and not an artifact

Proposed the idea of Quantum evolution

Species enter adaptive zones where they undergo very rapid radiation

Microevolution: slight short term evolutionary changes within species

Macroevolution: term for the evolution of great phenotypic changes

Are micro and macro evolution driven by the same mechanisms?

Is natural selection enough to explain the diversity we see?

Course summary

1The Origin of Earth and Life¶

1.1Big Bang Theory¶

1.2Formation of Earth¶

1.3Earth's Early Atmosphere¶

1.4Earth's Ocean¶

1.4.1Sea Salt¶

1.5Biomarker and Fossil Evidence for life at 3.8 bya¶

1.6Life - definition¶

1.7The Origin of Life¶

1.7.1Making the building blocks: Simple Organic Compounds¶

1.8Miller-Urey Experiment 1953¶

1.9Alternative hypothesis¶

1.10Building Blocks - Assembly into Polymers¶

1.11A paradox¶

1.11.1Solution¶

1.11.2A Discovery¶

1.12Origin of RNA polymers?¶

1.13Crepe model¶

1.14RNA World¶

1.15Ribozymes¶

1.16Evolution of RNAs with new function¶

1.17RNA -> Protein & DNA¶

1.18Compartmentalization¶

1.19Hypothesis for the origin of metabolism¶

2The Nature of Early Life¶

2.1Where on earth did life first evo?¶

2.2Requirements of organisms¶

2.3Trophic classification of organisms¶

2.4Why is energy so important?¶

2.5General principles of consumption¶

2.5.1Elements¶

2.5.2Adaption to Nutrient Availability¶

2.6What were the earliest organisms like?¶

2.7Evidence for early chemoautotrophy on Earth¶

2.8Metabolic diversification among Bacteria and Archaea¶

2.9Extant biofilm¶

2.10Appearance of Photosynthetic Organisms¶

2.11Oxygen evolving photosynthesis¶

2.12Consequences of O2 production¶

2.13Origin of Eukaryotes¶

2.14Endosymbiotic Theory of Origin of Eukaryotes¶

2.15Evidence for endosymbiotic theory¶

2.16Secondary Endosymbiosis¶

3Biodiversity¶

3.1Classification¶

3.2Kingdoms of Organisms¶

3.2.1Two kingdom approach¶

3.2.2Five kingdom approach¶

3.3Difficulty in classifying microoganisms¶

3.4Molecular phylogeny¶

3.5Horizontal Gene Transfer and the Tree of Life¶

3.6Five became Three¶

3.7Archaea¶

3.7.1Archaea: Euryarchaeota¶

3.8Bacteria¶

3.8.1Proteobacteria¶

3.8.2Cyanobacteria¶

3.9Eukarya¶

3.9.1Excavates¶

3.9.2Chromalveolates¶

3.10Rhizaria¶

3.11Plantae (archaeplastida)¶

3.11.1Chlorophyta¶

3.12Unikonts¶

4Evolution¶

4.1What is biological evolution?¶

4.2Phylogeny and Transition to Multi-cellular organisms¶

4.3Inferring Evolutionary History¶

4.4Counting trees¶

4.5Independent evolution - Principle of Convergence¶

4.6How do we build phylogenetic trees?¶

4.7Major evolutionary transitions and lifestyles¶

4.7.1Fungi multicellularity¶

4.7.2Algae multicellularity¶

4.7.3Other examples¶

4.7.4General Features of Multicellular inventions in evolution¶

4.7.5Timeline¶

4.8Advantages of multicelluarity¶

5What are the consequences of independent evolution?¶