Tree of Life 2015

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)