25
Phylogenies
and the
History of Life
Lecture Presentation by
Cindy S. Malone, PhD,
California State University Northridge
© 2017 Pearson Education, Inc.
Chapter 25 Opening Roadmap.
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Introduction
• Biologists use two major analytical tools to
reconstruct the history of life:
1. Phylogenetic trees
2. The fossil record
• Can be used separately or in combination
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Phylogenetic Trees
• Phylogeny - the evolutionary history of a group of
organisms.
• Phylogenetic tree - a graphical summary of this
history
• Shows evolutionary relationships among genes, and
species
• Tree of life - the most universal phylogenetic tree.
• Depicts evolutionary relationships among all
living organisms
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Phylogenetic Trees
• A branch represents a population through time
• A node (fork) represents a point where a branch splits,
most recent ancestor
• A tip (terminal node) represents the endpoint of a
branch—a living or extinct species
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Creating the Data
• The first step in inferring evolutionary relationships is
to determine which species to compare and which
characteristics to use
• A character or trait is any genetic, morphological,
physiological, or behavioral characteristic to be
studied
• Each character has two possible states: present (1)
or absent (0)
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Creating the Data
• An ancestral trait is a character that existed in an
ancestor
• A derived trait is one that is a modified form of the
ancestral trait, found in a descendant
• Originate via mutation, selection, and genetic drift
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Figure 25.1a
(a) Data matrix
Characters
Skull Limbs Hair Lactation
1
0
0
0
Lungfish (outgroup)
1
1
0
0
Lizard
1
1
1
1
Dog
1
1
1
1
Human
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Figure 25.1b
(b) Phylogenetic tree inferred from the data
Most recent
common
ancestor
Lungfish
Skull
Limbs
Hair, Lactation
Synapomorphies
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Lizard
Dog
Human
Table 25.3
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How Can Biologists Distinguish Homology from
Homoplasy?
• Homology occurs when traits are similar due to
shared ancestry
• Homoplasy occurs when traits are similar for
reasons other than common ancestry
• Convergent evolution is a common cause
of homoplasy
• Occurs when natural selection favors similar solutions
to similar environmental pressures
• Within a species, some characteristics may be
homologous with characteristics in other species,
while others may be convergent
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Are Streamlined Bodies in Dolphins and
Ichthyosaurs Homologous or Convergent?
• Ichthyosaurs (extinct aquatic reptiles) and dolphins are
very similar
• Streamlined bodies
• Large dorsal fins and flippers
• Phylogenetic analysis, however, indicates that these
similarities are not due to common ancestry
• Dolphins are in the mammal clade and ichthyosaurs are
closely related to lizards
• Sister groups to dolphins and ichthyosaurs do not have
the same traits
• The similarities result from convergent evolution
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Figure 25.3
Synapsids
Monotremes
Common dolphin
Marsupials
Dolphins
The common
ancestor of
dolphins and
ichthyosaurs
did not have
a streamlined
body or fins
and flippers
Dolphins and
ichthyosaurs
evolved their
similar traits
independently
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0.5 m
Primates
Rodents
Ichthyosaur
Dinosaurs
Ichthyosaurs
1m
Lizards
The Fossil Record
• The fossil record provides the only direct evidence
about
• What organisms that lived in the past looked like
• Where they lived
• When they existed
• A fossil is the physical evidence from an organism
that lived in the past
• The fossil record is the total collection of fossils
that have been found throughout the world
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How Do Fossils Form?
• Most of the processes that form fossils begin when
part or all of an organism is buried in some type
of sediment
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How Do Fossils Form?
• Once burial occurs, several things can happen:
• Intact fossils form when decomposition does not
occur and organic remains are preserved
• Compression fossils form when sediments
accumulate on top of the material and compress it
into a thin carbonaceous film
• Cast fossils form when the remains decompose after
burial and dissolved minerals create a cast in the
remaining hole
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How Do Fossils Form?
• Permineralized fossils form when the remains
decompose slowly and dissolved minerals slowly
infiltrate the cells’ interiors and harden into stone
• Trace fossils form when sedimentation and
mineralizations preserve indirect evidence of an
organism
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Table 25.4
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How Do Fossils Form?
• If the species is new, researchers estimate its age
based on the age of nearby rock layers
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How Do Fossils Form?
• Fossils form only under ideal conditions
• They must be buried rapidly
• They must decompose slowly
• Fossilization is an extremely rare event, and the
discovery of individual fossils is also rare
• There are 12 specimens of Archaeopteryx, the first
birdlike dinosaur to appear in the fossil record
• As far as researchers currently know, only one out
of every 200,000,000 individuals were fossilized
and discovered
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Limitations of the Fossil Record
• The fossil record has several limitations:
1. Habitat bias
• Organisms that live where sediment is actively being
deposited (e.g., beaches, swamps) are more likely to
fossilize than are organisms in other habitats
• In these habitats, burrowing organisms are more likely
to fossilize compared to organisms living aboveground
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Limitations of the Fossil Record
2. Taxonomic and tissue bias
• Some organisms (e.g., those with hard parts such as
bones or shells) are more likely to decay slowly and
leave fossil evidence
• Tissues with a tough outer coat that resists decay
(e.g., pollen) fossilize more readily
3. Temporal bias
• More recent fossils are more common than ancient
fossils
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Life’s Time Line
4. Abundance bias
• Organisms that are abundant, widespread, and
present for a long time leave evidence much more
often than do species that are rare, local, or
ephemeral
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Life’s Time Line
• It is difficult to date the origin of life precisely
• Our best estimates
• Earth started to form about 4.6 billion years ago
• Life began around 3.5 billion years ago
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Life’s Time Line
• Researchers
• Divide Earth’s history into segments called eons,
eras, periods, and epochs
• These record “evolutionary firsts” such as the
appearance of important new lineages or innovations
• The dates likely underestimate when events occurred
or lineages appeared, because species can exist for a
long time before leaving any fossil evidence
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Life’s Time Line
• Originally, geologists used distinctive rock
formations or fossilized organisms to identify the
boundaries of time intervals
• Radiometric dating allowed researchers to assign
absolute dates—expressed as years before the
present—to events and species in the fossil record
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Figure 25.5
Millions of
years ago
541
mya
Phanerozoic Eon
Eons
Present
First appearances
See Figure 25.6
First bilaterally symmetric animals
Oxygen levels begin rapid rise
First sponges
First red algae; first evidence
of sexual structures
Proterozoic
Eon
First photosynthetic eukaryotes
Precambrian
First eukaryotic fossils
First rocks containing
evidence of abundant oxygen
(in atmosphere and ocean)
First cyanobacteria
fossils
2500
First evidence of oxygenic
photosynthesis
Archaean
Eon
First evidence of photosynthetic cells
Origin of life
4000
Hadean
Eon
4570
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First oceans; heavy bombardment
(collisions with large asteroids and
other bodies) from space ends
Liquid water on Earth
Earth formation complete
Moon forms
Formation of solar system
Precambrian Era
• The Precambrian era spans the interval from
Earth’s formation (4.6 billion years ago) to the
appearance of most animal groups about 541 million
years ago (mya)
• It is divided into the Hadean, Archaean, and
Proterozoic eons
• In the Precambrian
• Life was exclusively unicellular
• Oxygen was virtually absent from the oceans and
atmosphere for about 2 billion years, until the
evolution of photosynthetic bacteria
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Phanerozoic Eon
• The Phanerozoic eon
• Spans the interval between 542 mya and the present
• Is divided into three eras—the Paleozoic, the
Mesozoic, and the Cenozoic
• These eras are divided into periods, which are divided
into epochs
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Phanerozoic Eon
• The Paleozoic (“ancient life”) era
• Begins with the appearance of most major animal
lineages
• Includes the initial diversification of animals, land
plants, and fungi
• Land animals first appear
• Ends with the obliteration of almost all multicellular
life-forms at the end of the Permian period
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Phanerozoic Eon
• The Mesozoic (“middle-life”) era
• Begins with the end-Permian extinction events and
ends with the extinction of dinosaurs between the
Cretaceous and Paleogene periods
• Dinosaurs and gymnosperms were the most
dominant terrestrial vertebrates and plants,
respectively
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Phanerozoic Eon
• The Cenozoic (“recent-life”) era
• Divided into the Paleogene, Neogene, and
Quaternary periods
• Mammals and angiosperms were the largest
terrestrial vertebrates and plants, respectively
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Figure 25.6
Periods
Cenozoic Era
Present
2.6
23
mya
Epoch
Holocene
Quaternary
Pleistocene
Pliocene
Neogene
Miocene
Oligocene
Eocene
Paleogene
Paleocene
66
Mesozoic Era
Representative organisms
Homo sapiens; first chimpanzees
Earliest hominins
Oldest pollen from daisy-family plants
First apes
First fully aquatic whales
First horses; first primates; first rabbits/hares
Cretaceous
extinction
First bee; first ant
First magnolia-family plants
First water lilies
First centric diatoms
First angiosperm (flowering plant)
Cretaceous
145
First appearances
First bird-like reptile
First placental mammals
First tyrannosaurid dinosaur
Jurassic
Triassic
extinction
201
First mammals
Triassic
Permian
extinction
Phanerozoic Eon
252
First dinosaurs
First nectar-drinking insects
First vessels in plants
Permian
299
Pennsylvanian
Origin of amniotes
Carboniferous
First basidiomycete fungi
Mississippian
Paleozoic Era
359
First seed plants; first plants with leaves
First tetrapods (amphibians)
First winged insects
Devonian
419
Devonian
extinction
First tree-sized plants
First ferns, vascular plants, ascomycete fungi, lichens
First insects
First fish with jaws
Silurian
First bony fish
443
First mycorrhizal fungi (Glomales)
Ordovician
First land plants
485
First bryozoans
(most recent origin of an animal phylum)
Cambrian
541
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Arthropods diversify; first echinoderm
First arthropods, mollusks, vertebrates, other phyla
Ordovician
extinction
Phanerozoic Eon
• We are currently in the Holocene epoch
• Many scientists have called for recognition of a new
epoch, the Anthropocene (“human-epoch”), to reflect
human-induced change on Earth
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Phanerozoic Eon
• The fundamental message of the time line is that of
constant change of life on Earth
• The water chemistry, atmosphere, climate, and
continental positions also changed dramatically
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Adaptive Radiation
• An adaptive radiation is the rapid production, from
a single lineage, of many descendant species
• These descendant species have a wide range of
adaptive forms
• May be observed as the sudden appearance of
related diverse species in the fossil record or inferred
by phylogenetic analysis
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Adaptive Radiation
• Example: The 30 species of Hawaiian silverswords,
which evolved from tarweed
• They fulfill the three hallmarks of an adaptive
radiation:
1. They are a monophyletic group
2. They speciated rapidly
3. They diversified ecologically into many niches
• The term niche describes the range of resources
that a species can use and the range of conditions
that it can tolerate
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Figure 25.7
Tarweeds
Dubautia latifolia
HAWAIIAN SILVERSWORDS
Vine
Mat
A tarweed
colonized
Hawaii here
Rosette
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Dubautia scabra
Argyroxiphium
sandwicense
Why Do Adaptive Radiations Occur?
• Two general mechanisms can trigger adaptive
radiations:
1. Extrinsic factors such as favorable new conditions in
the environment
2. Intrinsic factors such as evolution of key
morphological, physiological, or behavioral traits
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Ecological Opportunity
• Ecological opportunity—the availability of more or
new types of resources—has driven a wide array of
adaptive radiations
• Example: Few other flowering plants were on the
Hawaiian Islands 5 mya, so silverswords could
diversify into many vacant niches
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Ecological Opportunity
• Ecological opportunity—the availability of more or
new types of resources—has driven a wide array of
adaptive radiations
• Example: Few other flowering plants were on the
Hawaiian Islands 5 mya, so silverswords could
diversify into many vacant niches
• With few competitors, colonizing tarweed grew in a
range of habitats
• Some became specialized for growth in different
niches through mutation, genetic drift, and natural
selection
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Ecological Opportunity
• Example: Adaptive radiation of the 150 species of
Anolis lizards of the Caribbean islands
• These lizards
• Thrive in a wide variety of habitats
• Have diverse body sizes and shapes
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Ecological Opportunity
• Example (continued):
• In most cases, a lizard’s size and shape correlate
with its habitat
• Species that live on tree twigs have short legs and
tails to move efficiently on narrow surfaces
• Species that live on tree trunks or the ground have
long legs and tails to make them fast and agile on
broad surfaces
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Figure 25.8
(a) Short-legged lizard species spend most of
their time on the twigs of trees and bushes.
Anolis insolitus
Twig anole
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(b) Long-legged lizard species live on tree
trunks and the ground.
Anolis cybotes
Trunk/ground anole
Ecological Opportunity
• Example (continued):
• Jonathan Losos and his colleagues used DNA
sequence data to estimate Anolis phylogeny to test
the hypothesis that a mini-radiation occurred on
each Caribbean island.
• An original colonizing population encountered no
competitors
• Therefore they could diversify, which resulted in
efficient use of available resources by the
descendant species
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Ecological Opportunity
• Example (continued):
• They found that the lizards on each island were
monophyletic
• They inferred that the original colonist on each island
was specialized for a particular niche
• From different starting points, an adaptive radiation
filled the same niches on the islands
• This is an example of homoplasy by convergent
evolution
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Figure 25.8c
(c) The same adaptive radiation of Anolis has occurred on different islands, starting from a different
species of colonist.
Colonization of Island: Hispaniola
island by lizard
living on trunks
Trunk/crown
and crowns
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Colonization Island: Jamaica
of island by
lizard living
Twig
on twigs
Twig
Trunk/ground
Crown
Crown
Trunk/ground
Trunk/crown
Morphological, Physiological, or Behavioral
Innovation
• The evolution of a key trait may have triggered many
important diversification events in the history of life
• Example:
• Flowers are a unique reproductive structure that
helped trigger the diversification of angiosperms into
over 250,000 species (most species-rich lineage of
land plants)
• Feathers and wings gave some dinosaurs the ability
to fly; today the bird lineage contains about 10,000
species living in virtually every habitat on Earth
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The Cambrian Explosion
• Almost all organisms were unicellular for almost
3 billion years after life originated
• The exceptions were lineages of small multicellular algae
that appeared about 1 billion years ago
• The first animals—early sponges—appeared around
635 mya
• Then, 50 million years later, animals became larger and
more complex
• This diversification is known as the Cambrian
explosion—the most spectacular evolutionary change
in the history of life
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The Cambrian Explosion
• The Cambrian explosion is documented by three
major fossil assemblages mainly from Canada,
China, and Australia
• Each fossil assemblage records a distinctive
fauna—or collection of animal species
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Phanerozoic Eon
Cambrian Period
Cambrian
fossils
Proterozoic Eon
Ediacaran Period
Figure 25.9
Ediacaran
fossils
1 cm
1 cm
5 mm
541
mya
1 cm
Early Animal Fossils
• Microfossils from the Ediacaran period
• First animals to appear included tiny (less than 1 mm)
sponges and corals
• They were likely to have been filter feeders
• First macroscopic fossils during the Ediacaran
• Included sponges, jellyfish, comb jellies, fossilized
burrows, tracks, and traces from unidentified animals
• None have shells, limbs, heads, or feeding appendages
• They likely were burrowing, floating, or immobile filter
feeders
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Early Animal Fossils
• Cambrian macroscopic fossils
• Included sponges, jellyfish, comb jellies, wormlike
animals, arthropods, mollusks, echinoderms, and
most other major animal phyla including chordates
• These animals swam, burrowed, walked, ran,
slithered, clung, or floated
• They were predators, scavengers, filter feeders, and
grazers
• Filled many ecological niches found in marine
habitats
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Figure 25.10
Early vertebrate
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What Triggered the Cambrian Explosion?
• Most recent common ancestor of all living animals
may have arisen about 800 mya, before
diversification occurred
• Key developmental tool-kit genes likely evolved
before diversification
• So, what triggered the onset of the diversification?
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What Triggered the Cambrian Explosion?
• There are four non-mutually exclusive hypotheses:
1. Higher oxygen levels
• This made aerobic respiration more efficient
• Increased aerobic respiration is required to support
larger, more active animals
• Oxygen levels may have reached a threshold at the
start of the Cambrian explosion
2. The evolution of predation
• Predation exerted selection for shells, exoskeletons,
rapid movement, and other defenses driving
morphological divergence among prey
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What Triggered the Cambrian Explosion?
3. New niches beget more new niches
• Once animals could move off the ocean floor, they
could exploit algae and other resources
• The ability to exploit new niches created new niches
for predators, driving speciation and divergence
4. New genes, new bodies
• The earliest animals had few or no HOX genes
• Gene duplication and diversification increased the
number of Hox genes in animals
• Made it possible for larger, more complex bodies to
evolve
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What Triggered the Cambrian Explosion?
• Most or all of these hypotheses could be correct
since they are not mutually exclusive
• If increased oxygen levels resulted in larger bodies,
animals could move into new habitats off the
ocean floor
• They could become large enough to prey upon
small species
• Selection would favor mutations in HOX genes to
make the development of a large, complex
body possible
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Figure 25.11
Protist outgroup
Hox-like genes, but no Hox genes
Sponges
Boxes represent genes
within the Hox cluster
Comb jellies
Origin of
animals
Sea anemones
Acoels
Rotifers
Flatworms
Mollusks
Annelid worms
Arthropods
Roundworms
Echinoderms
Early chordates
Vertebrates
Radiation of animals
1
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2
3
4
5
6
7
8
9
10 11 12 13
Duplication of the
Hox cluster occurred
in vertebrates. Mice
and humans have
four clusters
Mass Extinctions
• A mass extinction is the rapid extinction of a large
number of diverse organisms around the world
• A mass extinction occurs when at least 60% of the
species present are wiped out within 1 million years
• Mass extinctions are caused by catastrophic events
• They are the opposite of adaptive radiation
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How Do Mass Extinctions Differ from
Background Extinctions?
• Background extinction is the lower, average rate
of extinction
• Paleontologists traditionally recognize five historic
mass extinctions (“The Big Five”)
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Figure 25.12
Present
2.6
23
Current onset
of sixth mass
extinction
Quaternary
Neogene
Paleogene
End-Cretaceous extinction
66
Cretaceous
145
201
252
299
Phanerozoic Eon
Jurassic
Late Triassic extinction
Triassic
End-Permian
extinction
Permian
Background
extinctions
Carboniferous
359
Late Devonian extinction
Devonian
419
Silurian
443
End-Ordovician extinction
Ordovician
485
Cambrian
541
mya
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0
20
40
60
Percentage of families that went extinct
How Do Background and Mass Extinctions
Differ?
• Background and mass extinctions have contrasting
causes and effects
• Background extinctions occur when certain
populations are reduced to zero because of
• Normal environmental change
• Emerging disease
• Predation pressure
• Competition with other species
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How Do Background and Mass Extinctions
Differ?
• Mass extinctions
• Result from extraordinary, sudden, and temporary
changes in the environment
• Cause extinction due to exposure to exceptionally
harsh short-term conditions, for example, volcanic
eruptions
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The End-Permian Extinction
• The largest mass extinction was the end-Permian
extinction, which resulted in the disappearance of
90% of all species
• Research on the causes of the end-Permian mass
extinction is ongoing, but several things probably
contributed to its occurrence
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The End-Permian Extinction
1. Siberian traps, flood basalts or outpourings of
molten rock, added enormous quantities of heat,
CO2, and sulfur dioxide to the atmosphere
2. High levels of atmospheric CO2 caused severe
acid rain, which devastated plants and organisms
dependent on them
3. Flood basalts ignited widespread coal fires that
released toxic ash, including mercury, into the air
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The End-Permian Extinction
4. Oceans became anoxic (lacking oxygen)
• These conditions are fatal to organisms that rely on
aerobic respiration
5. Sea level dropped dramatically during the
extinction event
• This reduced the amount of habitat available for
marine organisms
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The End-Cretaceous Extinction
• The impact hypothesis for the extinction of
dinosaurs proposes that an asteroid struck Earth
66 mya
• Resulted in the extinction of an estimated 60% to
80% of the multicellular species
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Evidence for the Impact Hypothesis
• Support for the impact hypothesis includes
• High levels of iridium were found in sedimentary
rocks formed at the Cretaceous–Paleogene (K–P)
boundary
• Iridium is rare in Earth rocks but abundant in asteroids
• Researchers also found unusual minerals found only
at impact sites
• There is a giant crater off Mexico’s Yucatán peninsula
• Dated to the K–P boundary
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Table 25.5
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Evidence for the Impact Hypothesis
• Data indicate that the asteroid was about 10 km
across—about the size of Mt. Everest
• The consequences of the impact likely included
• A hot gas fireball spreading from the impact site, resulting
in catastrophic wildfires
• The largest tsunami in the last 3.5 billion years, disrupting
ocean sediments and circulation
• Extensive acid rain from SO4 from rock reacting with water
in the atmosphere
• Dust, ash, and soot blocking the sun, leading to global
cooling and a crash in plant productivity
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Selectivity of the Extinctions
• Some evolutionary lineages escaped the effects of
the asteroid
• One hypothesis held that the K-Pg extinction was
size selective
• Based on idea that extensive darkness and cold would
affect large organisms disproportionately because they
require more food
• Data do not support this—for example, small and large
dinosaurs died
• One current hypothesis is that the organisms that could
remain inactive for long periods of time were able to
survive
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Recovery from the Extinction
• Terrestrial ecosystems around the world were radically
simplified by the extinction event
• After the asteroid impact, recovery was slow
• Marine environment diversity remained low for millions
of years
• Mammals diversified to fill the niches left empty by the
extinction of the dinosaurs
• Their diversification was not due to competitive superiority
gained through unique characters like fur and lactation
• Instead, it was due to a chance event
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The Sixth Mass Extinction?
• Many scientists propose that life on Earth is on the
verge of the sixth mass extinction
• This event is precipitated by human impacts such as
• Habitat loss
• Invasive species
• Pollution
• Climate change
• Overfishing
• Some estimate that the current extinction rate is 1000
times higher than background—the highest since the
asteroid impact
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