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Biology and
the Tree of Life

Lecture Presentation by
Cindy S. Malone, PhD,
California State University Northridge
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What Does It Mean to Say That Something Is


Alive?
All living organisms share five fundamental
characteristics:
1. Cells
All organisms are made up of membrane-bound cells

2. Replication
All organisms are capable of reproduction

3. Evolution
Populations of organisms are continually evolving

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What Does It Mean to Say That Something Is


Alive?
4. Information
All organisms process hereditary information encoded
in genes as well as information from the environment

5. Energy
All organisms acquire and use energy

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Theories
A theory is an explanation for a very general class
of phenomena or observations that are supported by
a wide body of evidence
This differs from everyday usage of the word
theory, which often carries meanings such as
speculation or guess

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Theories
Three theories form the framework for modern
biological science:
The cell theory
What are organisms made of?

The theory of evolution by natural selection


Where do organisms come from?

The chromosome theory of inheritance


How is hereditary information transmitted from one
generation to the next?

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The Cell Theory


In the late 1660s, Robert Hooke and Anton van
Leeuwenhoek were the first to observe cells
A cell is a highly organized compartment
Bounded by a plasma membrane
Containing concentrated chemicals in an aqueous
solution

The cell theory states that


All organisms are made of cells
All cells come from preexisting cells

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Figure 1.1

(a) van Leeuwenhoek built his own microscopeswhich, while


small, were powerful. They allowed him to see, for example ...

Lens

(b) ... human blood cells (this modern photo was shot through
one of van Leeuwenhoeks original microscopes).

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https://www.hhmi.org/news/imaging-techniques-set-new-standard-super-resolution-live-cells?utm_source=HHMI+News

http://www.nobelprize.org
http://www.pnas.org/content/105/38/14271.full

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http://www.microscopyu.com/

http://www.kip.uni-heidelberg.de

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The Cell Theory


In the late 1660s, Robert Hooke and Anton van
Leeuwenhoek were the first to observe cells
A cell is a highly organized compartment
Bounded by a plasma membrane
Containing concentrated chemicals in an aqueous
solution

The cell theory states that


All organisms are made of cells
All cells come from preexisting cells

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Louis Pasteurs Experiment


A hypothesis is a testable statement that explains
something observed
An experiment allows researchers to test the effect
of a factor on a particular phenomenon
A prediction is a measurable or observable result
that must be correct if a hypothesis is valid
Louis Pasteurs hypothesis:
Cells arise from cells
Cells do not arise by spontaneous generation

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Francesco Redi (1668)

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Lazarro Spallanzani (1768)

Louis Pasteur (1862)

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Figure 1.2

(a) Pasteur experiment with straight-necked flask: (b) Pasteur experiment with swan-necked flask:
1. Place nutrient broth in
swan-necked flask.

1. Place nutrient broth in


straight-necked flask.

Cells

Cells
2. Boil to sterilize the flask
(killing any living cells that
were in the broth).

2. Boil to sterilize the flask


(killing any living cells that
were in the broth).
Condensation settles in neck

No cells

Cells
3. Preexisting cells
enter flask from air.

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No cells
Cells

3. Preexisting cells
from air are trapped
in swan neck.

Implications of the Cell Theory


Because all cells come from preexisting cells
All individuals in a population of single-celled
organisms are related by common ancestry

All of the cells present in a multicellular organism


Have descended from preexisting cells
And are connected by common ancestry

First cells probably arose from non-life early in


Earths history by the process of chemical
evolution

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The Theory of Evolution by Natural Selection


In 1858, Charles Darwin and Alfred Russel Wallace
made two claims regarding the natural world:
All species are related by common ancestry
A species is a distinct, identifiable type of organism

Characteristics of species can be modified from


generation to generation
Darwin called this descent with modification

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Evolution and Natural Selection


Evolution:
It is a change in the characteristics of a population
over time
It means that species are related to one another and
can change through time

A population is
A group of individuals of the same species
Living in the same area
At the same time

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Natural Selection and Populations


Natural selection explains how evolution occurs
Two conditions must be met for natural selection to
occur in a population:
1. Individuals must vary in characteristics that are
heritablecan be passed on
2. In a particular environment, certain versions of
these heritable traits help individuals reproduce
more than other versions

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Figure 16.4

(a) Genetic information flows from DNA to RNA to proteins.

(b) Differences in genotype may cause differences in phenotype.

DNA

GENOTYPE

(information
storage)

TRANSCRIPTION

TRANSCRIPTION

TRANSLATION

TRANSLATION

mRNA
(information
carrier)

Proteins
(melanocortin
receptor)

Beach mouse

Forest mouse

PHENOTYPE
Physical traits
that are a
product of
the proteins
produced.

Mice with this DNA sequence have

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dark coats.

Mice with this DNA sequence have

light coats.

Evolutionary Change
If certain heritable traits lead to increased success in
producing offspring
These traits become more common in the population
over time

In this way, the populations characteristics change


as a result of natural selection acting on individuals
Natural selection acts on individuals
Evolutionary change occurs in populations
Speciation occurs when populations diverge to form
new species
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Fitness and Adaptation Drive Natural Selection


Fitness is
The ability of an individual to produce offspring
Individuals with high fitness produce many more
surviving offspring than do others in the population

Adaptation is
A trait that increases the fitness of an individual in a
particular environment

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Fitness and Adaptation


Example of natural selection:
Finches on a Galpagos island
Small, soft seeds abundant due to increased rainfall
Finches with small, pointed beaks had higher fitness
Small, pointed beaks were an adaptation that
increased finches ability to thrive
Finches with small, pointed beaks increased in the
population

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Artificial Selection
Helps us understand natural selection
In artificial selection
Changes in populations occur when humans select
which individuals will produce the most offspring
Repeating this process over generations results in
Changes in the characteristics of a domesticated
population over time

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cei.org
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Figure 1.3

Kernels with
high protein

Average % protein

Kernels with
low protein

Generation
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http://biologos.org/blog/evolution-basics-artificial-selection-and-the-origins-of-the-domestic-dog
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The Tree of Life


The cell theory and the theory of evolution by natural
selection imply that
All species come from preexisting species
All species, past and present, trace their ancestry to a
single common ancestor

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Life Processes Information


What is the source of heritable variation in traits?
How is information stored and transmitted from one
generation to the next?
Chromosome theory of inheritance
Provides foundation to answer these questions
Third unifying idea of biology

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Life Processes Information


Chromosomal theory of inheritance proposed in
1902 by Walter Sutton and Theodor Boveri
Hereditary or genetic information is encoded in genes
Genes are units located on chromosomes

1950s: chromosomes are molecules of


deoxyribonucleic acid, or DNA
DNA is the hereditary material
Genes are segments of DNA that code for cell
products

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Life Processes Information


James Watson and Francis Crick proposed that
DNA is a double-stranded helix

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Life Processes Information


Each strand of the double helix is made up of four
building blocks: A, T, C, and G
Sequence of this code is like letters in a word
DNA carries, or encodes, information needed for an
organisms growth and reproduction

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Life Processes Information


The two strands of the double helix are held
together by connections between the building blocks
A pairs with T
C pairs with G

This pairing allows DNA to be copied


Preserves the information encoded in the DNA

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Life Processes Information


The Central Dogma
Describes the flow of information in cells
DNA codes for ribonucleic acid, or RNA, which
codes for proteins
RNA copy made of the DNAs information
The RNA copy is read to determine what building
blocks to use to make a protein

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Figure 1.5

DNA

Messenger RNA

Messenger
RNA
Protein

Proteins determine
physical traits

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Life Processes Information


DNA is copied to pass genetic information from cell
to cell or from one organism to its offspring
Copying DNA is highly accurate
What happens when a mistake is made?
DNA sequence changes may lead to changes in
proteins
Outward appearance is a product of proteins
produced
DNA sequence changes may cause changes in
outward appearance
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Life Processes Information


At individual level, changes in DNA sequence might
increase or decrease fitness
Change in finch beak size and shape
Change in length of giraffes neck

At population level, changes in DNA sequence:


Lead to heritable variations that underlie diversity of
life
Make evolution possible

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Life Requires Energy


Chemical reactions take place inside cells, require
energy
Organisms have two fundamental nutritional needs:
1. Acquiring chemical energy in the form of adenosine
triphosphate (ATP)
2. Obtaining molecules that can be used as building
blocks to make DNA, RNA, proteins, etc.

How organisms acquire energy is central to the


diversification of life

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The Tree of Life


The tree of life is
A family tree of organisms that describes the
genealogical relationships among species with a
single ancestral species at its base

Phylogeny is
The actual genealogical relationships among all
organisms

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Using Molecules to Understand the Tree of Life


Biologists study RNA and DNA from different
organisms
Compare sequences of the building blocks (A,T,C,G)
Fewer sequence variations between two species may
indicate a closer relationship

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Using Molecules to Understand the Tree of Life


Example:
Land plant DNA:

A T A T C G A G

Green algae DNA: A T A T G G A G


Brown algae DNA: A A A T G G A C
Green algae is more closely related to land plants
than brown algae is

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Using Molecules to Understand the Tree of Life


Example:
Land plant DNA:

A T A T C G A G

Green algae DNA: A T A T G G A G


Brown algae DNA: A A A T G G A C
Green algae is more closely related to land plants
than brown algae is

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The Phylogenetic Tree of Life


A phylogenetic tree
Is used to show the relationships between species
Branches that share a recent common ancestor
represent species that are closely related
Branches that do not share recent common
ancestors represent species that are more distantly
related

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Figure 1.6

DOMAIN BACTERIA

Mycoplasma
Firmicutes
Cyanobacteria
Actinobacteria
Spirochaetes
Chlamydiae
Bacteriodetes
-Proteobacteria
-Proteobacteria
This node
represents the
common ancestor
of all organisms
alive today

-Proteobacteria
-Proteobacteria

-Proteobacteria
DOMAIN ARCHAEA

Thaumarchaeota
Crenarchaeota
Korarchaeota
This node
Euryarchaeota
represents the
common ancestor
of archaea and DOMAIN EUKARYA
eukaryotes
Slime molds
Fungi
Animals
Choanoflagellates

Euglenids
Parabasilids
Diplomonads
Red algae

Fungi,
animals,
and plants
are small
branch tips
on the
tree of life

Green algae
Land plants
Foraminiferans
Ciliates
Dinoflagellates
Apicomplexans
Water molds
Diatoms

http://tolweb.org/tree/

Brown algae

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http://www.nature.com/articles/nmicrobiol201648#f1

Interpreting the Tree of Life


The tree of life indicates three major groups of
organisms:
The eukaryotes
Eukarya

Two groups of prokaryotes


Bacteria and Archaea

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Figure 1.7

(a) Eukaryotic cells have


a membrane-bound
nucleus.

Membrane
around
nucleus

Nucleus

1 m

(b) Prokaryotic cells do not


have a membrane-bound
nucleus.

No nucleus

0.1 m
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Interpreting the Tree of Life


The tree of life shows
Fungi and animals are more closely related to each
other than either is to plants

Traditional classification schemes were often


inaccurate
The location of certain branches on the tree is hotly
debated, and the shape of the tree will continue to
change as databases expand

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Taxonomy
Taxonomy is the effort to name and classify
organisms
A taxon is a named group

Domain
Woese created this new taxonomic level
It consists of three taxa:
Bacteria
Archaea
Eukarya

A phylum is a major lineage within a domain


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Linnaeus Taxonomic System of Classification


In 1735 Carolus Linnaeus established the
classification system still in use today
Each organism is given a unique two-part scientific
name
It consists of the genus and the species
A genus is
Made up of a closely related group of species

A species is made up of
Individuals that regularly breed together
Or individuals whose characteristics are distinct from
those of other species
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Rules of Nomenclature
An organisms genus and species designation is
called
Its scientific name or Latin name
Scientific names are always italicized
Genus names are always capitalized
Species names are not capitalized
For example, Homo sapiens

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Doing Biology: The Nature of Science


All scientists ask questions that can be answered by
measuring thingsby collecting data
Science is about formulating hypotheses and finding
evidence that supports or conflicts with those
hypotheses
For example, using carefully designed experiments,
biologists test ideas about the way the natural world
works by testing the predictions made by alternative
hypotheses

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Doing Biology: The Nature of Science


On the other hand, religious faith addresses
questions that cannot be answered by data but
instead focus on why we exist and how we should
live

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Fig. 1.3

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Hypothesis Testing
Hypothesis testing is a two-step process:
1. State the hypothesis as precisely as possible and
list the predictions it makes
2. Design an observational or experimental study that
is capable of testing those predictions

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Why Do Giraffes Have Long Necks?


The food competition hypothesis argues that long
necks evolved because those with long necks can
reach food unavailable to other mammals
Predictions:
Neck length is variable among giraffes
Neck length in giraffes is heritable
Giraffes feed high in trees

Simmons and Scheepers tested the food


competition hypothesis and found
The third prediction does not hold true
Thus, there may be better alternative hypotheses to
explain neck length in giraffes
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Figure 1.8

(a) Most feeding is done at about shoulder height.


Percentage of feeding bites

40

Males

Average
height of
males

Females

Average
height of
females

Feeding height (meters)

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(b) Typical feeding posture in giraffes

The Sexual Competition Hypothesis


An alternative hypothesis is that giraffes evolved
long necks because
Longer-necked males win more fights than shorternecked males
Longer-necked males can then father more offspring

Data support this hypothesis


Data refute the food competition hypothesis
The question is not closedall hypotheses must be
tested rigorously

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E1-2

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Male widowbirds have extremely longs tails.

Why do males, but not females, have such longs tails?

Males have longs tails because females prefer to mate with long-tailed males.
If females prefer long-tailed males, males with artificially lengthened tails will
attract more mates.

Divide male birds


into four groups.

Manipulate the
tails of the males.

Cut tail end


re-glue in place.

Do not
change tail.

Cut tail to half of


original length.

Add feathers to
double tail length.

Release males,
wait a week,
count nests.

Release males,
wait a week,
count nests.

Controlled variables:
location, season,
time, weather

Release males,
wait a week,
count nests.

Release males,
wait a week,
count nests.

Average of
about one nest
per male.

Average of
about one nest
per male.

Results

Average of less
than half nest
per male.

Average of
about two nests
per male.

Control groups

E1-3

Experimental variables:
length of tail

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Experimental groups

Female widowbirds do prefer to mate with long-tailed males (and avoid mating with short-tailed males).

Nature
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Experimental DesignHow Do Ants Navigate?


Experiments are a powerful scientific tool because
They allow researchers to test the effect of a single,
well-defined factor on a particular phenomenon

Wittlinger and colleagues questioned how ants find


their way back to their nest after foraging for food

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Figure 1.9

Saharan desert ants meander long distances to find


food (insect carcasses) but then return to
the nest in a straight line.

Nest

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Food

How do they find their way back?

Experimental DesignHow Do Ants Navigate?


The pedometer hypothesis states
Ants always know how far they are from the nest
Because they track the number of steps taken
And they know length of their stride

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Experimental Setup
Wittlingers group manipulated the ants into three
groups after walking from the nest to a feeder:
1. Stumps
Legs were cut to form shorter-than-normal legs

2. Normal
Individuals were left alone with normal leg length

3. Stilts
Bristles glued on legs to form longer-than-normal legs

Then the team measured the distance the ants


traveled back to the nest via a different route
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Figure 1.10
How do desert ants find their way back to their nest?
Desert ants keep track of stride number and length to calculate how far they are from the nest.
Stride number and length have nothing to do with navigation (the ants use some other mechanism to navigate).

1. Ants walk from nest to feeder. 75 ants are collected.


Nest

1. Recapture manipulated ants from Test 1.

Feeder
stumps

normal

stilts

2. Manipulation of legs. Three treatments, 25 ants each.

Cut legs
to create
stumps

Leave
legs normal
length

Add pig
bristles as
stilts

2. The three treatments of ants walk from nest to feeder again.


Feeder

Nest

3. Ants return home from feeder and search for nest hole.

?
Feeder

3. Ants walk back home from feeder again.

Feeder

Ants with stilts will go too far; ants with stumps will stop short.

All three groups will start looking for nest after walking 10 m.

No differences among the three groups.

No difference from the observed results in Test 1.

Stilts

Normal

Stilts

Normal
Stumps

Stumps

Homebound run (m)

Homebound run (m)

Desert ants use information on stride length and number to calculate how far they are from the nest.

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Results and Conclusion


A null hypothesis specifies what we should
observe if the hypothesis being tested does not hold
Stride number and length have nothing to do with
navigation (the ants use some other mechanism to
navigate)

Results
Stumps stopped short of the nest
Normal ants returned to the nest
Stilts walked beyond the nest

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Results and Conclusion


Conclusion
Desert ants use information on stride length and
number to calculate how far they are from the nest

Supports the pedometer hypothesis

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Elements of a Well-Designed Experiment


The experiment just described is well designed
It included a control group (the normal ants) to
check for other factors that might influence the
outcome
Experimental conditions were controlled to eliminate
other variables
The test was repeated to reduce the effects of
distortion due to small sample size

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The Principles of Experimental Design


Biologists practice evidence-based decision making
Ask questions about how organisms work
Pose hypotheses to answer those questions
Use experimental or observational evidence to
decide which hypotheses are correct

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Web Activity: Introduction to Experimental


Design

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