Transcript History and Phylogeny (25 26) PPT

LECTURE PRESENTATIONS
For CAMPBELL BIOLOGY, NINTH EDITION
Jane B. Reece, Lisa A. Urry, Michael L. Cain, Steven A. Wasserman, Peter V. Minorsky, Robert B. Jackson
Chapters 25 and 26: history and diversity
of life on Earth
Lectures by
Erin Barley
Kathleen Fitzpatrick
© 2011 Pearson Education, Inc.
LECTURE PRESENTATIONS
For CAMPBELL BIOLOGY, NINTH EDITION
Jane B. Reece, Lisa A. Urry, Michael L. Cain, Steven A. Wasserman, Peter V. Minorsky, Robert B. Jackson
Ch. 25: History of Life on Earth
Lectures by
Erin Barley
Kathleen Fitzpatrick
© 2011 Pearson Education, Inc.
Figure 25.1
How do we know so much about dinosaurs? What
can we tell about them?
Figure 25.UN01
Cryolophosaurus skull
Concept 25.1: Conditions on early Earth
made the origin of life possible
• Chemical and physical processes on early Earth
may have produced very simple cells through a
sequence of stages:
1. Abiotic synthesis of small organic monomers
2. Joining of these small molecules into
macromolecules
3. Packaging of molecules into protocells or
protobionts
4. Origin of self-replicating molecules
© 2011 Pearson Education, Inc.
• In the 1920s, A. I. Oparin and J. B. S. Haldane
hypothesized that the first life forms were morn in an acidic
primordial sea (coacervates of protein and carbs)
• In 1953, Stanley Miller and Harold Urey conducted lab
experiments that showed that the abiotic synthesis of
organic monomers (amino acids) in a reducing atmosphere
is possible. Rain brings to earth and sea
© 2011 Pearson Education, Inc.
The key building blocks of life are not
hard to come by…
• Amino acids have also been found in meteorites
•RNA monomers have been produced spontaneously
from simple molecules
•In water, lipids and other organic molecules can
spontaneously form vesicles with a lipid bilayer
•Vesicles exhibit simple reproduction and
metabolism and maintain an internal chemical
environment
•Resultprotocells
© 2011 Pearson Education, Inc.
Relative turbidity,
an index of vesicle number
Figure 25.3
0.4
Precursor molecules plus
montmorillonite clay
0.2
Precursor
molecules only
0
0
20
40
Time (minutes)
60
(a) Self-assembly
Vesicle
boundary
20 m
(b) Reproduction
(c) Absorption of RNA
1 m
Self-Replicating RNA and the Dawn of
Natural Selection
• The first genetic material was probably RNA, not
DNA
• RNA molecules called ribozymes have been
found to catalyze many different reactions
– For example, ribozymes can make
complementary copies of short stretches of RNA
© 2011 Pearson Education, Inc.
Concept 25.2: The fossil record documents
the history of life
• The fossil record reveals changes in the history of
life on Earth
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Video: Grand Canyon
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Figure 25.4
Present
Dimetrodon
Rhomaleosaurus
victor
100 mya
1m
0.5 m
4.5 cm
Coccosteus
cuspidatus
175
200
Tiktaalik
270
300
Hallucigenia
375
400
1 cm
Stromatolites
2.5 cm
500
525
Dickinsonia
costata
565
600
Fossilized
stromatolite
1,500
3,500
Tappania
• The fossil record is biased in favor of species that
– Existed for a long time
– Were abundant and widespread
– Had hard parts
© 2011 Pearson Education, Inc.
How Rocks and Fossils Are Dated
• Sedimentary strata reveal the relative ages of
fossils
• The absolute ages of fossils can be determined by
radiometric dating
– A “parent” isotope decays to a “daughter” isotope at a
constant rate
– Each isotope has a known half-life, the time required
for half the parent isotope to decay
– Carbon dating is accurate, but only up to 75,000 years
© 2011 Pearson Education, Inc.
Fraction of parent
isotope remaining
Figure 25.5
1
Accumulating
“daughter”
isotope
2
Remaining
“parent”
isotope
1
1
4
1
2
3
Time (half-lives)
8
1
4
16
Reptiles
(including
dinosaurs and birds)
†Dimetrodon
Cynodonts
Therapsids
Synapsids
OTHER
TETRAPODS
†Very
late (nonmammalian)
cynodonts
Mammals
Key to skull bones
Articular
Dentary
Quadrate
Squamosal
Early cynodont (260 mya)
Temporal
fenestra
(partial view)
Synapsid (300 mya)
Hinge
Later cynodont (220 mya)
Temporal
fenestra
Hinges
Hinge
Therapsid (280 mya)
Very late cynodont (195 mya)
Temporal
fenestra
Hinge
Hinge
The evolution of unique mammalian features can be traced through gradual changes over time
Concept 25.3: Key events in life’s history
include:
- the origins of single-celled
- multicelled organisms and
- the colonization of land
© 2011 Pearson Education, Inc.
Table 25.1
Figure 25.7-1
Origin of solar
system and
Earth
4
Archaean
3
Prokaryotes
Atmospheric oxygen
Figure 25.7-2
Origin of solar
system and
Earth
Animals
Multicellular
eukaryotes
4
1
Proterozoic
2
Archaean
3
Prokaryotes
Single-celled
eukaryotes
Atmospheric oxygen
Figure 25.7-3
Cenozoic
Humans
Colonization
of land
Origin of solar
system and
Earth
Animals
Multicellular
eukaryotes
4
1
Proterozoic
2
Archaean
3
Prokaryotes
Single-celled
eukaryotes
Atmospheric oxygen
Photosynthesis and the Oxygen Revolution
• Most atmospheric oxygen (O2) is of biological
origin
– In the search for extraterrestrial life, it is our primary
target of observation
© 2011 Pearson Education, Inc.
Atmospheric O2
(percent of present-day levels; log scale)
Figure 25.8
1,000
100
10
1
0.1
“Oxygen
revolution”
0.01
0.001
0.0001
4
3
2
Time (billions of years ago)
1
0
• The early rise in O2 was likely caused by ancient
cyanobacteria
• A second increase in the rise of O2 might have
been caused by the evolution of eukaryotic cells
containing chloroplasts
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The First Eukaryotes
• Eukaryotic cells have a nuclear envelope,
mitochondria, endoplasmic reticulum, and a
cytoskeleton
– The oldest fossils of eukaryotic cells date back 2.1
billion years
• The endosymbiotic theory proposes that
mitochondria and plastids (chloroplasts and
related organelles) were formerly small
prokaryotes living within larger host cells
• An endosymbiont is a cell that lives within a host
cell
© 2011 Pearson Education, Inc.
Which was the first endsymbiotic
component,
chloroplasts or mitochondria?
Figure 25.9-1
Plasma membrane
Cytoplasm
DNA
Ancestral
prokaryote
Nucleus
Nuclear envelope
Endoplasmic
reticulum
Figure 25.9-2
Plasma membrane
Cytoplasm
DNA
Ancestral
prokaryote
Nucleus
Endoplasmic
reticulum
Nuclear envelope
Aerobic heterotrophic
prokaryote
Mitochondrion
Ancestral
heterotrophic eukaryote
Figure 25.9-3
Plasma membrane
Cytoplasm
DNA
Ancestral
prokaryote
Nucleus
Endoplasmic
reticulum
Photosynthetic
prokaryote
Mitochondrion
Nuclear envelope
Aerobic heterotrophic
prokaryote
Mitochondrion
Plastid
Ancestral
heterotrophic eukaryote
Ancestral photosynthetic
eukaryote
• What evidence would support an endosymbiotic
origin of mitochondria and plastids?
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• What evidence would support an endosymbiotic
origin of mitochondria and plastids?
– Inner membranes are similar to plasma
membranes of prokaryotes
– Division is similar in these organelles and some
prokaryotes
– These organelles transcribe and translate their
own DNA
– Their ribosomes are more similar to prokaryotic
than eukaryotic ribosomes
© 2011 Pearson Education, Inc.
The Cambrian Explosion
• The Cambrian explosion refers to the sudden
appearance of a multitude of modern body
designs (530 million years ago)
• first evidence of predator-prey interactions
© 2011 Pearson Education, Inc.
Figure 25.10
Sponges
Cnidarians
Echinoderms
Chordates
Brachiopods
Annelids
Molluscs
Arthropods
PROTEROZOIC
Ediacaran
635
PALEOZOIC
Cambrian
605
575
545
515
Time (millions of years ago)
485 0
The Colonization of Land
• Fungi, plants, and animals began to colonize land
about 500 million years ago
• Vascular tissue in plants transports materials
internally and appeared by about 420 million years
ago
• Plants and fungi today form mutually beneficial
associations and likely colonized land together
© 2011 Pearson Education, Inc.
• Arthropods and tetrapods are the most
widespread and diverse land animals
• Tetrapods evolved from lobe-finned fishes around
365 million years ago
© 2011 Pearson Education, Inc.
Concept 25.4: The rise and fall of groups of
organisms reflect differences in speciation
and extinction rates
• The history of life on Earth has seen the rise and
fall of many groups of organisms
• The rise and fall of groups depends on speciation
and extinction rates within the group
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Video: Volcanic Eruption
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Video: Lava Flow
© 2011 Pearson Education, Inc.
Cenozoic
Present
Figure 25.14
Eurasia
Africa
65.5
South
America
India
Madagascar
135
Mesozoic
Laurasia
251
Paleozoic
Millions of years ago
Antarctica
Mass Extinctions
• The fossil record shows that 99% of species that
have ever lived are now extinct
• At times, the rate of extinction has increased
dramatically and caused a mass extinction, and
is the result of disruptive global environmental
changes
© 2011 Pearson Education, Inc.
The “Big Five” Mass Extinction Events
• In each of the five mass extinction events, more
than 50% of Earth’s species became extinct
© 2011 Pearson Education, Inc.
Figure 25.15
1,100
1,000
25
800
20
700
600
15
500
400
10
300
200
5
100
Era
Period
0
E
542
O
Paleozoic
D
S
488 444 416
359
Mesozoic
P
C
299
Tr
251
J
200
Cenozoic
C
145
P
65.5
0
Q
N
0
Number of families:
Total extinction rate
(families per million years):
900
• The Permian extinction defines the boundary
between the Paleozoic and Mesozoic eras 251
million years ago
• This mass extinction occurred in less than 5
million years and caused the extinction of about
96% of marine animal species
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• A number of factors might have contributed to
these extinctions
– Intense volcanism in what is now Siberia
– Global warming resulting from the emission of
large amounts of CO2 from the volcanoes
– Reduced temperature gradient from equator to
poles
– Oceanic anoxia from reduced mixing of ocean
waters
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Is a Sixth Mass Extinction Under Way?
• Scientists estimate that the current rate of
extinction is 100 to 1,000 times the typical
background rate
• Data suggest that a sixth, human-caused mass
extinction is likely to occur unless dramatic action
is taken
© 2011 Pearson Education, Inc.
Relative extinction rate of marine animal genera
Figure 25.17
Mass extinctions
3
2
1
0
1
2
3
2
1
Cooler
0
1
Warmer
Relative temperature
2
3
4
Figure 25.16
NORTH
AMERICA
Yucatán
Peninsula
Chicxulub
crater
Positive Aspect of Mass Extinctions
• Mass extinction can pave the way for
adaptive radiations
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Concept 25.5: Major changes in body form
can result from changes in the sequences and
regulation of developmental genes
• Studying genetic mechanisms of change can
provide insight into large-scale evolutionary
change
© 2011 Pearson Education, Inc.
Heterochrony
is an
evolutionary
change in the
rate or timing
of
developmental
events
The contrasting
shapes of
human and
chimpanzee
skulls are the
result of small
changes in
relative growth
rates
Chimpanzee infant
Chimpanzee adult
Chimpanzee fetus
Chimpanzee adult
Human fetus
Human adult
Figure 25.22
•In paedomorphosis, the rate of reproductive development accelerates
compared with somatic development
•The sexually mature species may retain body features that were juvenile
structures in an ancestral species
Gills
Concept 25.6: Evolution is not goal oriented
• Evolution is like tinkering—it is a process in which
new forms arise by the slight modification of
existing forms
© 2011 Pearson Education, Inc.
Evolutionary Novelties
• Most novel biological structures evolve in many
stages from previously existing structures
• Complex eyes have evolved from simple
photosensitive cells independently many times
• Exaptations are structures that evolve in one
context but become co-opted for a different
function
– Natural selection can only improve a structure in the
context of its current utility
© 2011 Pearson Education, Inc.
Exaptations are structures that
evolve in one context but become
co-opted for a different function
LECTURE PRESENTATIONS
For CAMPBELL BIOLOGY, NINTH EDITION
Jane B. Reece, Lisa A. Urry, Michael L. Cain, Steven A. Wasserman, Peter V. Minorsky, Robert B. Jackson
Chapter 26
Phylogeny and the Tree of Life
Lectures by
Erin Barley
Kathleen Fitzpatrick
© 2011 Pearson Education, Inc.
Figure 26.1
What type of animal is this?...why do you say?
• Phylogeny is the evolutionary history of a species
or group of related species
• The discipline of systematics classifies organisms
and determines their evolutionary relationships
– Systematists use fossil, molecular, and genetic data to
infer evolutionary relationships
© 2011 Pearson Education, Inc.
Figure 26.2a
Create a
cladogram of…
Figure 26.2b
Figure 26.2c
Figure 26.2
Create a cladogram of the following
1.
2.
3.
4.
AAG CAT ATA CGT
GAG CAT ATA CAT
ACG GAT ATA CGT
ACG GGT ATA CGC
Calculate the percent similarity
1.
2.
3.
4.
ACG GGT ATA CGC
ACG GAT ATA CGT
AAG CAT ATA CGT
GAG CAT ATA CAT
Concept 26.1: Phylogenies show evolutionary
relationships
• Taxonomy is the ordered division and naming of
organisms
© 2011 Pearson Education, Inc.
Figure 26.3
Species:
Panthera pardus
Genus:
Panthera
Family:
Felidae
Order:
Carnivora
Class:
Mammalia
Phylum:
Chordata
Domain:
Bacteria
Kingdom:
Animalia
Domain:
Eukarya
Domain:
Archaea
Linking Classification and Phylogeny
• Systematists depict evolutionary relationships in
branching phylogenetic trees
© 2011 Pearson Education, Inc.
Figure 26.4
Order
Family Genus
Species
Panthera
Felidae
Panthera
pardus
(leopard)
Taxidea
Lutra
Mustelidae
Carnivora
Taxidea
taxus
(American
badger)
Lutra lutra
(European
otter)
Canis
Canidae
Canis
latrans
(coyote)
Canis
lupus
(gray wolf)
Figure 26.5
Branch point:
where lineages diverge
Taxon A
Taxon B
Taxon C
Sister
taxa
Taxon D
ANCESTRAL
LINEAGE
Taxon E
Taxon F
Taxon G
This branch point
represents the
common ancestor of
taxa A–G.
This branch point forms a
polytomy: an unresolved
pattern of divergence.
Basal
taxon
• A phylogenetic tree represents a hypothesis about
evolutionary relationships
• Each branch point represents the divergence of
two species
• Sister taxa are groups that share an immediate
common ancestor
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• A rooted tree includes a branch to represent the
last common ancestor of all taxa in the tree
• A basal taxon diverges early in the history of a
group and originates near the common ancestor of
the group
• A polytomy is a branch from which more than two
groups emerge
© 2011 Pearson Education, Inc.
Applying Phylogenies
• Phylogeny provides important information about
similar characteristics in closely related species
• A phylogeny was used to identify the species of
whale from which “whale meat” originated
© 2011 Pearson Education, Inc.
Figure 26.6
RESULTS
Minke (Southern Hemisphere)
Unknowns #1a, 2, 3, 4, 5, 6, 7, 8
Minke (North Atlantic)
Unknown #9
Humpback (North Atlantic)
Humpback (North Pacific)
Unknown #1b
Gray
Blue
Unknowns #10, 11, 12
Unknown #13
Fin (Mediterranean)
Fin (Iceland)
Concept 26.2: Phylogenies are inferred
from morphological and molecular data
• To infer phylogenies, systematists gather
information about morphologies, genes, and
biochemistry of living organisms
© 2011 Pearson Education, Inc.
Sorting Homology from Analogy
• When constructing a phylogeny, systematists
need to distinguish whether a similarity is the
result of homology or analogy
– Homology is similarity due to shared ancestry
• The more complex two similar structures are, the more likely it
is that they are homologous
– Analogy is similarity due to convergent evolution
© 2011 Pearson Education, Inc.
Figure 26.7 Convergent
evolution of analogous
burrowing characteristics.
Evaluating Molecular Homologies
• Systematists use computer programs and
mathematical tools when analyzing comparable
DNA segments from different organisms
© 2011 Pearson Education, Inc.
Figure 26.8-4
1
1
2
Deletion
2
1
2
Insertion
3
1
2
4
1
2
Concept 26.3: Shared characters are used
to construct phylogenetic trees
• Once homologous characters have been
identified, they can be used to infer a phylogeny
© 2011 Pearson Education, Inc.
Cladistics
• Cladistics groups organisms by common descent
• A clade is a group of species that includes an
ancestral species and all its descendants
– Clades can be nested in larger clades, but not all
groupings of organisms qualify as clades
© 2011 Pearson Education, Inc.
Figure 26.10
(a) Monophyletic group (clade)
(b) Paraphyletic group
(c) Polyphyletic group
A
A
B
B
C
C
C
D
D
D
E
E
F
F
F
G
G
G
A
B
Group 
Group 
Group 
E
• A valid clade is monophyletic, signifying that it
consists of the ancestor species and all its
descendants
• A shared ancestral character is a
character that originated in an ancestor of
the taxon
• A shared derived character is an
evolutionary novelty unique to a particular
clade
• What are some examples?
© 2011 Pearson Education, Inc.
Figure 26.11
Lancelet
(outgroup)
CHARACTERS
Lancelet
(outgroup)
Lamprey
Bass
Frog
Turtle
Leopard
TAXA
Lamprey
0
1
1
1
1
1
Bass
Vertebral
column
(backbone)
Hinged jaws
0
0
1
1
1
1
Four walking
legs
0
0
0
1
1
1
Amnion
0
0
0
0
1
1
Hair
0
0
0
0
0
1
Vertebral
column
Frog
Hinged jaws
Turtle
Four walking legs
Amnion
Leopard
Hair
(a) Character table
(b) Phylogenetic tree
• An outgroup is a species or group of species that
is closely related to the ingroup, the various
species being studied
– The outgroup is a group that has diverged before the
ingroup
– Systematists compare each ingroup species with the
outgroup to differentiate between shared derived and
shared ancestral characteristics
© 2011 Pearson Education, Inc.
Figure 26.12
Drosophila
Lancelet
Zebrafish
Frog
Chicken
Human
Mouse
• In some trees, the length of a branch can reflect
the number of genetic changes that have taken
place in a particular DNA sequence in that lineage
• In other trees, branch length can represent
chronological time, and branching points can be
determined from the fossil record
Drosophila
Lancelet
Zebrafish
Frog
Chicken
Human
Mouse
PALEOZOIC
542
MESOZOIC
251
Millions of years ago
CENOZOIC
65.5
Present
Systematists can never be sure of finding
the best tree in a large data set
• Maximum parsimony assumes that the tree that
requires the fewest evolutionary events
(appearances of shared derived characters) is the
most likely
• The principle of maximum likelihood states that,
given certain rules about how DNA changes over
time, a tree can be found that reflects the most
likely sequence of evolutionary events
© 2011 Pearson Education, Inc.
Figure 26.14
Human
Mushroom
Tulip
0
30%
40%
0
40%
Human
Mushroom
Tulip
0
(a) Percentage differences between sequences
15%
5%
5%
15%
15%
10%
25%
20%
Tree 1: More likely
Tree 2: Less likely
(b) Comparison of possible trees
Figure 26.15
TECHNIQUE
Species 
1
Species 
Species 
Three phylogenetic hypotheses:









1
Site
2 3
4
Species 
C
T
A
T
Species 
C
T
T
C
Species 
A
G
A
C
Ancestral sequence
A
G
T
T
2
3
1/C

1/C






1/C
4
3/A
2/T

2/T
3/A

3/A

4/C

2/T 4/C
3/A4/C
RESULTS
4/C

1/C




4/C

1/C
2/T

2/T 3/A







6 events

7 events

7 events
Phylogenetic Trees as Hypotheses
• The best hypotheses for phylogenetic trees fit the
most data: morphological, molecular, and fossil
• Phylogenetic bracketing allows us to predict
features of an ancestor from features of its
descendants (e.g. dinosaurs)
© 2011 Pearson Education, Inc.
Figure 26.16
Lizards
and snakes
Crocodilians
Common
ancestor of
crocodilians,
dinosaurs,
and birds
Ornithischian
dinosaurs
Saurischian
dinosaurs
Birds
Relationships reinforced:
• Birds and crocodiles share several features:
four-chambered hearts, song, nest building,
and brooding
• These characteristics likely evolved in a
common ancestor and were shared by all of its
descendants, including dinosaurs
• The fossil record supports nest building and
brooding in dinosaurs
© 2011 Pearson Education, Inc.
Figure 26.17
Front limb
Hind limb
Eggs
(a) Fossil remains of
Oviraptor and eggs
(b) Artist’s reconstruction of the dinosaur’s
posture based on the fossil findings
Concept 26.4: An organism’s evolutionary
history is documented in its genome
• Comparing nucleic acids works really well
– DNA that codes for rRNA changes relatively slowly and
is useful for investigating branching points hundreds of
millions of years ago
– mtDNA evolves rapidly and can be used to explore
recent evolutionary events
© 2011 Pearson Education, Inc.
Two types of homologous genes:
Formation of orthologous genes:
a product of speciation
Species A
Formation of paralogous genes:
within a species
Ancestral gene
Ancestral gene
Ancestral species
Species C
Speciation with
divergence of gene
Gene duplication and divergence
Orthologous genes
Paralogous genes
Species C after many generations
Species B
Genome Evolution
• Orthologous genes are widespread and extend
across many widely varied species
– For example, humans and mice diverged about 65
million years ago, and 99% of our genes are
orthologous
© 2011 Pearson Education, Inc.
Concept 26.5: Molecular clocks help track
evolutionary time
• A molecular clock uses constant rates of
evolution in some genes to estimate the absolute
time of evolutionary change
– In orthologous genes, nucleotide substitutions are
proportional to the time since they last shared a
common ancestor
– In paralogous genes, nucleotide substitutions are
proportional to the time since the genes became
duplicated
© 2011 Pearson Education, Inc.
Number of mutations
Mammal molecular clock
90
60
30
0
60
90
30
Divergence time (millions of years)
120
Tracking gene change works well because…
• the Neutral theory states that much evolutionary
change in genes and proteins has no effect on
fitness and is not influenced by natural selection
– Therefore change in these genes and proteins should
be regular like a clock
© 2011 Pearson Education, Inc.
Dating the origin
of HIV-1 M with
a molecular clock.
Index of base changes between HIV gene sequences
0.20
0.15
HIV
0.10
Range
Adjusted best-fit line
(accounts for uncertain
dates of HIV sequences)
0.05
0
1900
1920
1940
1960
Year
1980
2000
Concept 26.6: New information continues to
revise our understanding of the tree of life
© 2011 Pearson Education, Inc.
Animation: Classification Schemes
Right-click slide / select “Play”
© 2011 Pearson Education, Inc.
New-ish: 3 domains of life
Eukarya
Land plants
Green algae
Cellular slime molds
Dinoflagellates
Forams
Ciliates
Red algae
Diatoms
Amoebas
Euglena
Trypanosomes
Leishmania
Animals
Fungi
Green
nonsulfur bacteria
Sulfolobus
Thermophiles
(Mitochondrion)
Spirochetes
Halophiles
COMMON
ANCESTOR
OF ALL
LIFE
Methanobacterium
Archaea
Chlamydia
Green
sulfur bacteria
Bacteria
Cyanobacteria
(Plastids, including
chloroplasts)
• Horizontal gene transfer complicates efforts to
build a tree of life
– Horizontal gene transfer is the movement of genes
from one genome to another
• It occurs by exchange of transposable elements and plasmids,
viral infection, and fusion of organisms
© 2011 Pearson Education, Inc.
Is the Tree of Life Really a Ring?
Archaea
Eukarya
Bacteria