CHAPTER 27 Phylogenies

and the History

of Life

1
Key Concepts & Study Guide
I. Phylogenies and the fossil record are the major tools that
biologists use to study the history of life.
•What are phylogenetic trees? What are the different aspects (terminology) of
phylogenetic trees and how do these terms relate to organisms on the
phylogenetic tree?
•How does the whale example in the text exemplify problems associated with
constructing phylogenetic trees?
•How are fossils formed?
•What are the limitations of the fossil record?
•What are the biases and how can they impact our understanding of evolution?

2
Key Concepts & Study Guide
II. The Cambrian explosion was the rapid
morphological and ecological diversification of
animals that occurred during the Cambrian period.
•What are the four major eras with respect to the timeline of life?
•Can you summarize the major (basic, keep it simple) events in each era?
•What was the Cambrian explosion?
•What are the three major faunas representing the Cambrian explosion
•Genetic Mechanisms of Evolutionary Change
•Homeotic Gene Duplication
•Changes in gene expression patterns

3
Topic Outline & Study Guide

III. Adaptive radiations are a major pattern in the

history of life. They are instances of rapid
diversification associated with new ecological
opportunities and new morphological innovations.
•What is an adaptive radiation?
•Can you give an example of an adaptive radiation?
•How and why do they occur?

4
Topic Outline & Study Guide

IV. Mass extinctions have occurred repeatedly

throughout the history of life. They rapidly eliminate
most of the species alive in a relatively random
manner.
•What is a mass extinction?
•How do we define the term?
•What is the evidence for mass extinctions over the years?

Online Discussion: on BB
Is a Mass Extinction Event Underway Now?

5
Introduction
W
hat are the two major analytical tools that biologists use to reconstruct the history of
life?

P
hylogenetic trees-A phylogenetic tree or evolutionary tree is a branching diagram or
"tree" showing the inferred evolutionary relationships among various biological
species or other entities based upon similarities and differences in their physical
and/or genetic characteristics. The taxa joined together in the tree are implied to
have descended from a common ancestor.
T
he fossil record- Ever since recorded history began, and probably before, people
have noticed and gathered fossils, including pieces of rock and minerals that have
replaced the remains of biologic organisms, or preserved their external form. Fossils
themselves, and the totality of their occurrence within the sequence of Earth's rock
strata, is referred to as the fossil record. The fossil record was one of the early
sources of data relevant to the study of evolution and continues to be relevant to
the history of life on Earth. Paleontologists examine the fossil record in order to
understand the process of evolution and the way particular species have evolved.

6
Phylogenetic Trees

hylogeny
• evolutionary history of a group of organisms is called a

hylogenetic tree
• shows ancestor-descendant relationships among populations or species

onophyletic group
• and ancestor and all its descendants form a
• AKA called a clade or lineage

7
Reading a Phylogenetic Tree
• Branches
• represent populations through time
• sister taxa
• are adjacent branches
• a taxon
• Is any group of organisms
• Tips
• Are the tree’s endpoints and represent
living groups or a group’s end in
extinction
• The names at the tips can represent
species or larger groups

8
Reading a Phylogenetic Tree

odes

polytomy

n rooted phylogenies the most ancient node of the tree is ?

he location of this node is determined using an ?

9
Estimating Phylogenies
There are two general strategies for using data to estimate
trees:
•The phenetic approach is
• Based on computing a statistic that summarizes the overall
similarity among populations
•The cladistic approach
• Inferring trees focuses on synapomorphies, the shared derived characters
of the species under study.
• Said another way, a synamorphy is a trait that certain groups of organisms
•When many such traits have been measured, traits unique to
each monophyletic group are identified and the groups are
placed on a tree in the appropriate relationship to one another.

10
Synapomorphies Identify Monophyletic Groups
This is a
This is a monophyletic
monophyletic group
groups that shares a
that shares a derived
derived trait (the “c” in
trait (G, in the fifth
the thir position)
position)

1 2 3 4

B C

AAC GCT ACT AAA GGT ACT

A
Trait (in this case,
AAA GCT ACT a DNA sequence)
in the ancestral
population
11
Distinguishing Homology from Homoplasy

roblems can arise with both phenetic and cladistic analyses because
similar traits can evolve independently in two distant species rather
than from a trait present in a common ancestor.

omoplasy
• occurs when traits are similar for reasons other than common ancestry.
• Figure 27.2a shows an example comparing the similar traits of dolphins and
extinct marine reptiles called Ichthyosaurs.

omology
• Occurs when traits are similar due to shared ancestry.
• Figure 27.2b shows an example using the hox genes

12
Homoplasy
and
Homology Common dolphin Ichthyosaur

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El
The dolphin and ichthyosaur The members of lineages
lineages are far apart on the between the dolphins and
evolutionary tree, suggesting ichthyosaurs do not have
that they are not closely adaptations such as:
related – streamlined bodies
– long jaws filled with teeth
– fins and flippers

Fruit-fly Hox complex

Human Hox complex

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an ers

s,
ce id

sa sta rms
,

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ta sp

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ea de
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ec o
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ui , c
us ,

The genes in the Hox

br
(in rop

(e lid
le thw

(v rda
or

(s ino
(s us
sq ils
w

complexes of fruit flies

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h

ho
nn

ol

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at

rt

Ec
M
Fl

C
and humans have similar
A

sequences and are in the

same order on their
chromosomes

Annelids, mollusks, and

echinoderms also have
Hox genes

Infer that common

ancestor had 8
Hox genes

13
Homoplasy and Homology

Common dolphin Ichthyosaur

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Pr
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B
R

The dolphin and ichthyosaur The members of lineages

lineages are far apart on the between the dolphins and
evolutionary tree, suggesting ichthyosaurs do not have
that they are not closely adaptations such as:
related – streamlined bodies
– long jaws filled with teeth
– fins and flippers

14
Homoplasy and Homology

Fruit-fly Hox complex

Human Hox complex

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an er s

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ce i d

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nd ar s

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es
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ec o The genes in the Hox
se po

ar s
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br
le thw
(e elid

(v rda
(s ino
sq ils,
(s llus
or

( in h ro

complexes of fruit flies

w

ho
nn

h
o
rt
at

Ec
and humans have similar

C
A
A
Fl

sequences and are in the

same order on their
chromosomes

Annelids, mollusks, and

echinoderms also have
Hox genes

Infer that common

ancestor had 8
Hox genes

15
Distinguishing Homology from Homoplasy

onvergent evolution
• Occurs when natural selection factors similar solutions to the problems
posed by a similar way of life, as shown by the dolphin and ichthyosaur
• Is a common cause of homoplasy

f similar traits found in distantly related lineages are indeed similar

due to common ancestry, then similar traits should be found in
many intervening lineages on the tree of life.

16
Distinguishing Homology from Homoplasy

arsimony
• Is a principle of logic stating that the most likely explanation or patter s the
one that implies the least amount of change
• Convergent evolution and other cause of homoplasy should be rare
compared with similarity due to shared descent
• So the tree that implies the fewest overall evolutionary changes should be
the one that most accurately reflects what is happening during evolution

17
 Two changes

T T T T T
GC GC GC GG GG
A C C A A
AA AA AA AA AA
1 2 3 4 5
Choosing
among the
AC CG
Many
Possible
Trees
AAA GCT

Four changes

T T T T T
GC GC GG GC GG
A C A C A
AA AA AA AA AA
1 2 3 4 5
AC CG
CG
AC

AAA GCT
18
Whale Evolution: A Case History

raditionally, phylogenetic trees based on morphological data place

whales outside of the artiodactyls-mammals that have hooves

NA sequence data, however, suggest a close relationship between

whales and ? WHY?

19
Evidence That Whales and Hippos Form a Monophyletic Group
The astragalus is a synapomorphy that identifies artiodactyls as a monophyletic group.
Artiodactyls

Whale Camel Peccary Pig Hippo Deer Cow

Astragalus
Gain of pulley-
shaped astragalus (ankle bone)

If whales are related to hippos, then two changes occurred in the astragalus.
Artiodactyls

Camel Peccary Pig Hippo Whale Deer Cow

Loss of pulley-
shaped astragalus

Gain of pulley-
shaped astragalus

Data on the presence and absence of SINE genes support the close relationship between whales and hippos.

1 = gene present
0 = gene absent
? = still undetermined

Whales and hippos share four

unique SINE genes (4, 5, 6, and 7)

20
 Evidence That Whales and Hippos Form a Monophyletic Group

The astragalus is a synapomorphy that identifies artiodactyls as a monophyletic group.

Artiodactyls

Whale Camel Peccary Pig Hippo Deer Cow

Astragalus
Gain of pulley- (ankle bone)
shaped astragalus

21
Evidence That Whales and Hippos Form a Monophyletic Group

If whales are related to hippos, then two changes occurred in the astragalus.
Artiodactyls

Camel Peccary Pig Hippo Whale Deer Cow

Loss of pulley-
shaped astragalus

Gain of pulley-
shaped astragalus

22
Evidence That Whales and Hippos Form a Monophyletic Group
Data on the presence and absence of SINE genes support the
close relationship between whales and hippos.

1 = gene present
0 = gene absent
? = still undetermined

Whales and hippos share four

unique SINE genes (4, 5, 6, and 7)

23
Whale Evolution: A Case History

ecent data on gene sequences called short interspersed nuclear

elements (SINEs) show that whales and hippos share several SINE
genes that are absent in other artiodactyl groups.

hese SINEs are shared derived traits

nd support the hypothesis that whales and hippos are indeed

closely related

24
Tools for Studying History: The Fossil Record
fossil
• Is the physical trace left by an organism that live in the pasts

he fossil record
• is the total collection of fossils that have been found throughout the world

he fossil record provides

• The only direct evidence about what organisms that lived in the past
looked like, where they lived, and when they existed

25
How Do Fossils Form?
ost fossils form when

n organisms is buried in sediment before decomposition occurs.

our types of fossils are

ntact fossils, compression fossils, cast fossils, and premineralized

fossils.

ossilization is an extremely rare event.

26
Fossilization Preserves Traces of Past Organisms

HOW FOSSILIZATION OCCURS

Pollen Leaves
Seeds

1. A tree lives in a swampy 2. The tree falls. The trunk and

habitat. The tree drops leaves, branches break up as they rot.
pollen, and seeds into the mud,
where decomposition is slow.

27
Fossilization Preserves Traces of Past Organisms

HOW FOSSILIZATION
OCCURS

Sand and gravel

Buried material from swamp

Bedrock
3. Flooding brings in sand and
mud, burying the remains of
the tree.

28
Limitations of the Fossil Record

here are several limitations of the fossil record that need to be recognized:

• habitat bias – occurs because organisms that live in areas where sediments

are actively being deposited are more likely to form fossils than are organisms

that live in other habitats

• taxonomic bias – is due to the fact that some organisms (e.g.,

• temporal bias – occurs because more recent fossills are more common than

ancient fossils

• abundance bias –evidence much more than other species that are rare

29
Limitations of the Fossil Record

aleontologists—

ecognize that they are limited to studying tiny and scattered

segments on the tree of life, yet they also know that this is the only
way to get a glimpse of what extinct life was like.

30
Life's Timeline
ajor events in the history of life are marked on the timeline shown in Figure
27.8, which has been broken into four segments.

recambrian – encompasses the hadean, archaean, protorozoic,

aleozoic era

esozoic era

enozoic era

31
 Fo
M rma
o t
Ea on ion
rth for of
m
Li fo s sol
q u rm ar
id at sy
w i o st
at n c e
er

atmosphere.
om m

Hadean Eon
on p
Ea let
rt e
h

Millions of years ago (mya)

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Position of the continents unknown

os en
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All life is unicellular

(in t ro ni
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Proterozoic Eon

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ru irs
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in ocean and ice.
Multicellular

Fi en
Life’s Timeline: The Precambrian

rs ce
Fi t li
organisms begin

rs ch
to diversify slowly

Most of Earth is covered

sy t s en
m po -li
co me ng ke
m tr es or
pl ic ; f ga
et an irs n
el im t ism
y
ox als bila
yg ; o te
en ce ral
at an ly
ed
The Precambrian (Hadean, Archaean, and Proterozoic Eons) included the origin of life, photosynthesis, and the oxygen

32
Life’s Timeline: The Paleozoic Era
Phanerozoic Eon: The Paleozoic Era included the origin early diversification of animals, land plants, and fungi.

nd
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Carboniferous

extinction

extinction

extinction
Cambrian Ordovician Silurian Devonian Permian

Mass
Mass

Mass
Mississippian Pennsylvanian

Algae abundant, Echinoderms Coral First upland plant Insects diversify, Coal-forming swamps
marine (sea stars, sea reefs communities coal-forming swamps diminish; parts of
invertebrates urchins) diversify expand (evergreen forests), abundant, sharks Antarctica forested
diversify diversification of fish, abundant, radiation
emergence of of amphibians
amphibians

Laurentia

Pa
ng
na
wa

ea
nd ana Gondwana
Go Gondw
Supercontinent of Gondwana Climate cold; Supercontinent of Laurentia Supercontinent Pangea
forms. Oceans cover much of extensive ice to the north and Gondwana assembles. Building of
North America. Climate not in Gondwana. to the south. Climate mild. Appalachian Mountains ends.
well known. Climate warm; little variation.

33
Life’s Timeline: The Mesozoic Era
Phanerozoic Eon: The Mesozoic Era is sometimes called the Age of Reptiles.

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extinction

extinction

extinction
Mass

Mass
Mass

Triasssic Jurassic Cretaceous

Gymnosperms become dominant Gymnosperms continue Dinosaurs diversify Flowering plants diversify
land plants; extensive deserts to dominate land
Pan
Pang

Gon
gea

dwa
e

na
a

Pangea intact. Interior Pangea begins to break apart; Gondwana begins to break India separated from Madagascar,
of Pangea arid. Climate interior of continent still arid. apart; interior less arid. moves north; Rocky Mountains
very warm. form. Climate mild, temperate.

34
Life’s Timeline: The Cenozoic Era
Phanerozoic Eon: The Cenozoic Era is nicknamed the Age of Mammals.

s
le
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Fi

Fi

O
Paleogene Neogene
Paleocene Eocene Oligocene Miocene Pliocene Pleistocene

Diversification of Diversification of angiosperms Diversification of grazing mammals

mammalian orders and pollinating insects

Continents continue to drift apart. Strong drying trend in Continents close to present North and South America
Collision of India with Eurasia begins. Africa and other continents; position. Beginning of joined by land bridge.
Australia moves north from Antarctica. grasslands form. Alps and Antarctic ice cap. Opening Uplift of the Sierra Nevada.
Palms in Greenland and Patagonia. Himalayas begin to rise. of Red Sea. Worldwide glaciation.

35
The Cambrian Explosion

he first animals—sponges, jellyfish, and simple worms—appear in the

fossil record around ???? mya, at the end of the Proterozoic eon.

oon after that in geologic time, by about ?????? years later, animals had
diversified into almost all the major groups living today.

his diversification is known as the ?

his period saw what was arguably the most evolutionary change in the
history of life.
36
Cambrian Fossils: An Overview
he Cambrian explosion is documented by three major fossil
assemblages, called the

he presence of these exceptionally rich deposits before, during, and

after the Cambrian explosion makes the fossil record for this event
extraordinarily complete.

37
Fossils Document the Cambrian Explosion
A time line of early animal evolution

Doushantuo Ediacaran Burgess Shale

fossils fossils fossils

Proterozoic Cambrian

38
Doushantuo
fossils are
microscopic
• From the Doushantuo
formation in China,
researchers identified
microfossils (tiny fossils) of
sponges, cyanobacteria, and
multicellular algae in samples
dated 570–580 mya.
• They also found what they
concluded were animal
embryos in early stages.
• These were examples of the
first types of animals on Earth.
39
Small, soft-
bodied
animals from
Ediacara

n the Ediacara Hills in Australia,

paleontologists identified fossils
of sponges, jellyfish, comb
jellies, and traces of other
animals dated 544–565 mya.

hese were small, soft-bodies

animals that burrowed in
sediments, sat immobile on the
sea floor, or floated in the water. 40
 Diverse, large
animals with
hard parts from
Burgess Shale
• Virtually every major living animal
group is represented in the Burgess
Shale fossils from British Columbia,
Canada, which date to 515–525 mya.
• These fossils indicate a tremendous
increase in the size and morphological
complexity of animals, accompanied by
diversification in how they made a
living.
• This diversification filled many of the
ecological niches still found in marine
habitats today.

41
Did Gene Duplication Trigger the Cambrian Explosion?

hat is gene duplication?

hat are hox genes?

oes the phylogenetic tree of Hox genes in animals in general

supports this hypothesis?

http://evolution.berkeley.edu/evosite/evo101/IIIC6cComplexity2.shtml
http://www.nature.com/scitable/topicpage/hox-genes-in-development-the-hox-
code-41402

42
Hox Genes in Animals
The same-colored boxes within a vertical column are considered to be homologous—
meaning they are related because they are derived from the same ancestral sequence
Jellyfish

Flatworm

Earthworm

Snail

Velvet worm

Crustacean

Centipede

Fruit fly

Amphioxus

Mouse

Zebra fish

The colored boxes

along each line
represent distinct
genes within the
Hox cluster
43
Did Gene Duplication Trigger the Cambrian Explosion?

hat conclusions can be drawn from this phylogeny?

•
•
•

oth duplication of Hox genes and changes in expression and

function of existing genes have been important in making the
elaboration of animal body plans possible.

44
Adaptive Radiation

an be triggered by
• ecological opportunity
• morphological innovation.

45
 Star phylogeny (a large polytomy)
Adaptive Radiations

ense groups of bushy branches

Rapid
called
speciation
star phylogenies or polytomies
can be
observed in the tree of life
(Figure
27.11a).

hese star phylogenies represent speciation events that were so rapid

that the order of branching cannot be resolved.

f rapid speciation in a single lineage is followed by divergence into many

different adaptive forms, then a process known as adaptive radiation
has taken place.

46
Ecological Opportunity as a Trigger

ne of the most consistent triggers of adaptive radiations is ecological

opportunity, meaning

or example, biologists have documented adaptive radiations of the Anolis

lizards of the Caribbean islands.

n the two islands studied, the same four ecological types eventually evolved,
because the islands had similar varieties of habitats.

herefore, similar adaptive radiations took place independently on the two

islands, triggered by

47
The same adaptive radiation of Anolis has occurred
on different islands, starting from different types of
colonists

Trunk/crown Twig Crown Trunk/ground Twig Trunk/ground Crown Trunk/crown

Colonization of island by lizard Colonization of island

living on trunks and crowns by lizard living on twigs
HISPANIOLA JAMAICA

48
Morphological Innovation as a Trigger

orphological innovation can also be a trigger for adaptive radiation,

as was seen in the Cambrian explosion.

any of the other important diversification events in the history of

life started off with the evolution of a key morphological trait that
allowed descendents to live in new areas, exploit new food
sources, or move in new ways.

Animation: Adaptive Radiation

49
Mass Extinctions

mass extinction is the

ass extinctions are caused by

aleontologists traditionally recognize five mass extinctions ("The Big Five").

ackground extinction is the lower, average rate of extinction, representing

the normal loss of some species that always occurs.

50
The Big Five Mass Extinction Events

The catastrophic
end-Permian
extinction

Mass extinctions
Background
extinctions

51
How Do Background and Mass Extinctions Differ?

ackground extinctions typically occur when normal environmental

change, emerging diseases, or competition reduces certain
populations to zero.

ass extinctions result

ackground extinctions are thought to result from

52
What Killed the Dinosaurs?

he impact hypothesis for the extinction of dinosaurs proposes that

an asteroid struck Earth 65 mya and caused the extinction of an
estimated 60–80% of the multicellular species alive.

onclusive evidence—including iridium, shocked quartz, and

microtektites found in rock layers dated to 65 mya, as well as a
huge crater off Mexico’s Yucatán peninsula—has led researchers to
accept the impact hypothesis.

53
Evidence of an Asteroid Impact 65 MYA
Iridium is present at high concentration in Minerals that form during asteroid impacts
rocks formed 65 million years ago.
Microtektites

Normal quartz
Strong peak in iridium
in rock formed at
Cretaceous-Paleogene
boundary

Shocked quartz

The asteroid left a crater 180 km (112 miles) wide.

United States
Lat
eC
ret

Gulf of Mexico
ace
o

Crater Asteroid impact splashed

us

Yucatán material from here, forming

sho

peninsula crater…
of Mexico
reli
ne

…after striking
at an angle
here
What is now the Yucatán peninsula was
underwater when the asteroid struck
54
Selectivity

ome evolutionary lineages were better able than others to withstand

the environmental change brought on by the asteroid impact.

or example, among vertebrates, the dinosaurs, pterosaurs (flying

reptiles), and large marine reptiles perished, while the mammals,
crodilians, amphibians, and turtles survived.

esearchers are currently testing the hypothesis that organisms that

could remain inactive for long periods of time, such as by
hibernating, were able to survive.

55
Recovery
fter the asteroid impact, recovery was slow.

errestrial ecosystems around the world were radically simpified,

and the diversity of marine environments remained low for 4–8
million years afterward.

ammals diversified to fill the niches left empty by the extinction of

the dinosaurs. Within 10–15 million years, all of the major
mammalian orders living today had appeared.

56