tree of life 2015
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TreeolifeTRANSCRIPT
Principles of Biology (01/26/15)
The tree of life Chapter 26 (Campbell, 10th ed.)
Microbiology
and Intro to Animal Biology Lectures 1 to 9 Jan 26 – Feb 25, 2014
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Patrick Eichenberger Associate Professor of Biology
Major Interests: Comparative and functional genomics of
endospore-forming bacteria
Office hours: Thursdays 3-5 pm,
Center for Genomics and Systems Biology, 12 Waverly Place,
Room 205
E-mail: [email protected]
Animal Biology
Lectures 10 to 19 Mar 02 – Apr 08, 2015
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Esteban O. Mazzoni Assistant Professor of Biology
Major Interests: Stem cell biology, cell fate differentiation,
developmental neuroscience
Plant Biology & Ecology
Lectures 20 to 23 Apr 13 – Apr 22, 2015
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Gloria Coruzzi: Plant Biology Carroll and Milton Petrie Professor
Professor of Biology
Major Interests: Plant Systems Biology and Evolutionary
Genomics
Lectures 24 to 28 Apr 27 – May 11, 2015
Katie Schneider Paolantonio: Ecology Clinical Assistant Professor of Biology
Major Interests: Community Ecology, Food Web Ecology,
Subterranean Ecosystems (Natural and man made)
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Michael J. Carrozza Clinical Assistant Professor of Biology
Major Interests:
Chromatin, Transcription, DNA damage and repair
Archaea
Bacteria
Protists
(4th lecture)
Fungi
(6th lecture)
Plants
Prof. Coruzzi
Course organization: tree of life
Prokaryotes (2nd lecture)
Viruses
(3rd lecture)
Animals
Lectures 7-9
& Prof. Mazzoni
Immunology
(5th lecture)
Eukaryotes
Ecology
Prof. Schneider
Paolantonio
The tree of life as it stands today
3 domains
Root
-origin of life?
Biogenesis and heterogenesis
Biogenesis
= every living organism comes from a pre-existing living organism
(vertical transmission)
Tree of life (one root)
Heterogenesis
=some life forms can arise spontaneously from non-living matter
(e.g. decaying matter, broth)
Spontaneous generation (many roots)
Aristotle: On the Generation of Animals
Animals and plants come into being in earth and in liquid because there is water in earth, and
air in water, and in all air is vital heat so that in a sense all things are full of soul. Therefore living
things form quickly whenever this air and vital heat are enclosed in anything.
On the Generation of Animals, Book III, Part 11
4 elements (earth, air, water, and fire) and a
fifth essence in the heavens (“quintessence” or “ether”)
Greek philosopher, student of Plato, 4th century B.C.
tutor of Alexander the Great, Laws of logic (Organon)
History of Animals, Book V, Part 1
“So with animals, some spring from parent animals according to their kind, whilst others grow
spontaneously and not from kindred stock; and of these instances of spontaneous generation
some come from putrefying earth or vegetable matter, as is the case with a number of insects,
while others are spontaneously generated in the inside of animals out of the secretions of their
several organs”
The controversy about spontaneous generation
An address delivered by Louis Pasteur
at the "Sorbonne Scientific Soirée" on April 7, 1864
“It must be acknowledged that the belief in
spontaneous generation has been with us
throughout the ages; universally accepted in
antiquity, it has become more disputed in
modern times, and especially in our own lives.
It is this belief I have come to challenge.”
Louis Pasteur
(1822-1895)
A good experiment provides high quality data
in support of a hypothesis
Novelty
Not just descriptive, but predictive power (formulation and testing of hypotheses)
Impact: universality-simplicity
Quality of the data and controls
Objectivity (validity of the interpretation)
Reproducibility
It is easy enough to conduct experiments,
it is far from easy to conduct irreproachable ones
Louis Pasteur , "Sorbonne Scientific Soirée" April 7, 1864
Jan Baptist van Helmont’s recipe for mice
“If a soiled shirt is placed in the opening of
a vessel containing grains of wheat, the
reaction of the leaven in the shirt with fumes
from the wheat will, after approximately
twenty-one days, transform the wheat into
mice
Quoted by Louis Pasteur (1864)
Flemish physician
(1579-1644)
Contemporary of Galileo
“When water from the purest spring is placed in a flask steeped in
leavening fumes, it putrefies, engendering maggots.
The fumes which rise from the bottom of a swamp produce frogs, ants,
leeches, and vegetation....”
Von Helmont quoted by Louis Pasteur, "Sorbonne Scientific Soirée" on April 7, 1864
Extension to maggots and leeches…
Physician at the court of the Medici,
Poet and naturalist
Francesco Redi (1626, Arezzo-1697, Pisa)
Bacchus in Tuscany
(1685)
A hymn to Tuscan wines
Redi’s key observation
“Belief would be vain without the confirmation of an experiment”
Francesco Redi, Experiments on the Generation of Insects
Having considered things, I began to believe that all worms found in meat were derived
directly from the droppings of flies, and not from the putrefaction of the meat,
and I was still more confirmed in this belief by having observed that, before the meat grew
wormy, flies had hovered over it, of the same kind as those that later bred in it.
The first modern experiment in biology (1668) Use of appropriate controls is critical to the quality of an experiment
Positive
control
Negative
control
“Thus the flesh of dead animals cannot engender worms
unless the eggs of the living be deposited therein”
Experiment
The tree of life as a catalog of species Encyclopedia of life on earth (all organisms, extant and extinct)
Carolus Linnaeus (aka Carl von Linne)
2) Use of binomial nomenclature
A formal classification of all living things
Two main concepts (still in use today):
1) Hierarchical organization
(1707-1778)
Linne is the father of taxonomy and systematics
Systematics = branch of biology that classifies organisms
and determines their evolutionary relationships (i.e. relatedness)
Taxonomy = ordered division and naming of organisms
taxon (plural, taxa) = taxonomic unit at any level
i.e. taxa can refer to species, genera, orders, etc
Hierarchical organization
Domain
Kingdom
Phylum
Class
Order
Family
Genus
Species
Common name: leopard
Binomial nomenclature
Baker’s yeast
Fruit fly
Mouse
Common name:
Zebrafish
Escherichia
Saccharomyces
The first part of the name is the genus
Caenorhabditis
Drosophila
Mus
Homo
Danio
The second part, called the specific epithet, is unique for each species within the genus
coli
cerevisiae
elegans
melanogaster
musculus
sapiens
rerio
Human
Species names
Example: Homo sapiens
The first letter of the genus is capitalized
and the entire species name is italicized
Broader categories (e.g. domains) are not italicized (but the first letter is capitalized)
Examples: Mammals (=class)
Animals (=kingdom)
Eukaryotes (=domain)
Building the tree
From two kingdoms to three domains
Linnaeus and his contemporaries classified all species as either Plants or Animals
(based essentially on macroscopic morphological characteristics)
19th century: Four kingdoms: Prokaryotes, Protists, Plants and Animals
20th century: Five kingdoms: Prokaryotes, Protists, Plants, Fungi, and Animals
At the end of the seventeenth century, a tremendous discovery, that of
the microscope, revealed an entire new world to Man, the world of the
infinitesimally small.
Louis Pasteur, "Sorbonne Scientific Soirée" on April 7, 1864
From two kingdoms to three domains
Three-domain system: Bacteria, Archaea, and Eukaryotes
DNA sequencing (1970s)
An organism’s genome seems to be
the ultimate record of its evolutionary history
Carl Woese (1928-2012)
The 3 domains of life
3 domains
Phylogeny
= evolutionary history of a species or group of related species
Can be represented in a phylogenetic tree
TAXA
Leo
pard
Tu
na
Vertebral column
(backbone)
Hinged jaws
Four walking legs
Amniotic (shelled) egg
Hair
(a) Character table
Hair
Hinged jaws
Vertebral column
Four walking legs
Amniotic egg
(b) Phylogenetic tree
Salamander
Leopard
Turtle
Lamprey
Tuna
Lancelet
(outgroup)
0
0 0
0
0
0
0 0
0
0
0 0
0 0 0 1
1 1
1 1 1
1
1 1
1
1
1 1
1 1
Using morphologies to determine phylogenies
Example: Vertebrates
Organisms with similar morphologies are likely to be more closely
related than organisms with different structures
Sorting homology from analogy
Homology is similarity due to shared ancestry
Analogy is similarity due to convergent evolution
Convergent evolution
When similar environmental pressures and natural selection produce
analogous adaptations in organisms from different evolutionary lineages
Homoplasies
= analogous structures that evolved independently
Importance of molecular markers to resolve ambiguities
Examples of convergent evolution
Limbless bodies
Examples of convergent evolution
Common ancestor lived 140 million years ago
Australian mole
(marsupial)
North American mole
(eutherian)
Examples of convergent evolution
Found in the soil
Forms spores
Produces antibiotics (streptomycin)
Found in the soil
Forms spores
Produces antibiotics (penicillin)
Streptomyces
Bacterium
Penicillium
Fungus
Phylogenetic analyses with DNA sequences
Using ribosomal RNA sequence (small subunit)
to determine evolutionary relationships
Archaea represent a new domain of life
Carl Woese (1928-2012)
Divergence time (millions of years)
120
90
90
60
60
30
30 0
0
A molecular clock
The higher the number of mutations, the older the divergence time
Using DNA sequence to determine phylogenies
The first step is to align the corresponding sequences
In order to account for insertions and deletions
Deletion
Insertion
Building a phylogenetic distance tree
Because more than one change
may have occurred at any given site
Lengths of the lines are proportional to the evolutionary distance
16S rRNA as an evolutionary chronometer
Ribosomal Database Project (RDP)
http://rdp.cme.msu.edu/
September 17, 2014:: 3,019,928 16S rRNAs
Sister taxa
ANCESTRAL LINEAGE
Taxon A
Polytomy Common ancestor of taxa A–F
Branch point
Taxon B
Taxon C
Taxon D
Taxon E
Taxon F
How to read a phylogenetic tree?
• A phylogenetic tree represents a hypothesis about evolutionary relationships
• Each branch point (node) represents the divergence of two species
• Sister taxa are groups that share an immediate common ancestor
• A rooted tree includes a branch to represent the last common ancestor
of all taxa in the tree
• A polytomy is a branch from which more than two groups emerge
Key points about phylogenetic trees
What we can and cannot learn from
phylogenetic trees
• Phylogenetic trees do show patterns of descent
• Phylogenetic trees do not indicate when species evolved or how much
genetic change occurred in a lineage
• It shouldn’t be assumed that a taxon evolved from the taxon next to it
Orthologs/Paralogs
Orthologous genes: different species
common functionality and ancestry
Paralogous genes: same species
gene duplication and divergence
Fig. 26-18a
Ancestral gene
Ancestral species
Speciation with divergence of gene
Species A Species B Orthologous genes
Orthologous genes
Paralogous genes
Gene duplication and divergence
Species A after many generations
Species A
Fig. 26-18b
Paralogous genes
The tree of life is a record of life on Earth
Life on Earth
Animals
Colonization of land
Humans
Origin of solar system and Earth
Prokaryotes Proterozoic Archaean
1 4
3 2
Multicellular eukaryotes
Single-celled eukaryotes
Atmospheric oxygen
So, where did life come from?
”[A] warm little pond, with all sorts of ammonia and
phosphoric salts, lights, heat, electricity, etc. present, so
that a protein compound was chemically formed ready
to undergo still more complex changes”
The concept of the primordial (or prebiotic) soup
Charles Darwin
(1809-1882)
Letter to Joseph Dalton Hooker (1871)
Alexander Oparin
(1894-1980)
Russian biochemist
The Oparin-Haldane hypothesis
Spontaneous generation of life occurred once,
when atmospheric conditions found on earth were largely different from today
J.B.S. Haldane
(1892-1964)
British biologist
Reactions leading to synthesis of amino acids (building blocks of proteins)
Primitive atmosphere made of CH4, CO2, NH3, H2 and H2O + solar radiation (UV)
A test of the hypothesis: the Miller-Urey experiment
Simulated, in the laboratory, conditions thought to be present in the early earth
Stanley Miller
(1930-2007)
Science (1953)
Chemical analysis of the compounds formed amino acids are formed
Experimental set-up
Seven amino acids are produced,
including three (glycine, alanine and aspartic acid) found
in modern organisms
The claim was never that life had been made,
but only that the necessary molecules for life could form spontaneously
Chemical analysis
Prokaryotes
4
3 2
1
Had the planet to themselves for about 80% of the time life existed on earth
History of Prokaryotes
Prokaryotes are the ancestors of all other life forms
What is a prokaryote?
By default, any organism that is not a eukaryote
[eu-karyote: Greek for “true nucleus”]
A prokaryote is an organism whose cells do not have a nucleus
(no nuclear membrane surrounding the genome)
Two domains
(Eu)bacteria
Archaea(bacteria)
[“archaios”: Greek for ancient]
Atmospheric oxygen
4
3 2
1
~2.7 billion years ago
The oxygen revolution
Most atmospheric oxygen (O2) is of biological origin (photosynthesis)
The source of O2 was likely bacteria similar to modern cyanobacteria
Tolerance to O2
Obligate aerobes cannot grow without O2 (cellular respiration)
Facultative anaerobes use O2 if present
Obligate anaerobes grow exclusively by fermentation (O2 is poisonous)
or use different electron acceptor for respiration
Nutritional modes of organisms on Earth
Carbon source?
Autotrophs
Inorganic (CO2)
Producers of the biosphere,
Synthesis of organic molecules
from CO2 and other inorganic molecules
Heterotrophs
Organic (e.g. glucose, fructose)
Consumers of the biosphere
obtain their organic material
from other organisms
Nutritional modes of organisms on earth
Source of energy?
Phototrophs
Light
Chemotrophs
Chemicals (organic or inorganic)
4 classes (all present in prokaryotes)
Photoautotrophs Plants, algae and Cyanobacteria
Chemoautotrophs unique to certain prokaryotes
Photoheterotrophs unique to certain prokaryotes
Chemoheterotrophs Animals, Fungi
and several prokaryotes (e.g. B. subtilis, E. coli)