Chapter 27: Phylogenies and the History of Life
Key Concepts
• Phylogenies and the fossil record are the major tools that biolo-
gists use to
• study the history of life
• The Cambrian explosion was the rapid morphological and ecologi-
cal
• diversification of animals that occurred during the Cambrian period
• 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
• Mass extinctions have occurred repeatedly throughout the history
of life
◦ They rapidly eliminate most of the species alive in a more or
less random manner
Section 27.1: Tools for Studying History: Phylogenetic Trees
• Phylogeny: The evolutionary history of a group of organisms
• Phylogenetic Tree: Shows ancestor–descendant relationships
among populations or species
Reading Phylogenetic Trees
• Branches: Represent populations through time
◦ Adjacent branches are sister taxa (a taxon is any named
group of organisms)
• Nodes: Occur where an ancestral group split into two or more de-
scendant groups
• Polytomy: A node where more than two descendant groups
branch off
• Tips: The tree's endpoints; represent living or extinct groups
• Rooted Phylogenies: Most ancient node of the tree is shown at the
bottom
, ◦ The location of this node is determined using an outgroup, a
taxonomic group that diverged before the rest of the taxa
being studied
• An ancestor and all its descendants form a monophyletic group
(i.e. a clade or lineage)
How Do Researchers Estimate Phylogenies?
• Morphological and/or genetic characteristics are used to estimate
phylogenetic relationships among species
• Phenetic Approach : Based on the overall similarity among popula-
tions
◦ A tree is built that clusters the most similar populations and
places more divergent populations on more distant branches
• Cladistic Approach: Focuses on synapomorphies (the shared de-
rived characteristics of the species under study; a trait that certain
populations or species have that exists in no others); when many
such traits have been measured, traits unique to each mono-
phyletic group are identified and the groups are placed on a tree in
the correct relationship to one another
How Can Biologists Distinguish Homology from Homoplasy?
• Problems can arise with both cladistic and phenetic analysis be-
cause similar traits can evolve independently in two distant species
rather than from a trait present in a common ancestor
• Homoplasy: Occurs when traits are similar for reasons other than
common ancestry
• Homology: Occurs when traits are similar due to shared ancestry.
• Convergent Evolution: Occurs when natural selection favors similar
solutions to the problems posed by a similar way of making a living
◦ A common cause of homoplasy
• If similar traits found in distantly related lineages are indeed simi-
lar due to common ancestry, then similar traits should be found in
many intervening lineages on the tree of life
• Parsimony: A principle of logic stating that the most likely explana-
tion or pattern is the one that implies the least amount of change
, • Convergent evolution and other causes of homoplasy should be
rare compared with similarity due to share descent, so the tree
that implies the fewest overall evolutionary changed should be the
one that most accurately reflects what really happened during
evolution
Whale Evolution: A Case History
• Traditionally, phylogenetic trees based on morphological data
place whales outside of the artiodactyls (mammals that have
hooves, an even number of toes, and an unusual pulley–shaped
ankle bone, i.e. an astralagus)
• DNA sequence data, however, suggests a close relationship be-
tween whales and hippos
◦ Recent data on short interspersed nuclear elements (SINEs)
show that whales and hippos share several SINE genes that
are absent in other artiodactyl groups
• These SINEs are shared derived traits (synapomor-
phies) and support the hypothesis that whales and
hippos are indeed closely related
Section 27.2: Tools for Studying History: The Fossil Record
• The fossil record provides the only direct evidence about what or-
ganisms that lived in the past looked like, where they lived, and
when they existed
• Fossil: The physical trace left by an organism that lived in the past
• Fossil Record: The total collection of fossils that have been found
throughout the world
How Do Fossils Form?
• Most fossils form when an organism is buried in sediment before
decomposition occurs
• Four types of fossils:
◦ intact fossils;
◦ compression fossils;
◦ cast fossils;
, ◦ premineralized fossils
• Fossilization is an extremely rare event
Limitations of the Fossil Record
• There are several features and limitations of the fossil record:
◦ habitat bias- occurs because organisms living in areas where
sediments are actively deposited are more likely to form fos-
sils
◦ taxonomic bias- due to the fact that some organisms (for in-
stance, those with bones) are more likely to decay slowly
and leave fossil evidence
◦ temporal bias- occurs because more recent fossils are more
common than ancient fossils
◦ abundance bias- occurs because organisms that are wide-
spread and present on Earth for a long time leave evidence
much more often than do rare, local or ephemeral species
• Paleontologists (scientists who study fossils) recognize that they
are limited to asking questions about tiny and scattered segments
on the tree of life
◦ Yet analyzing fossils is the only way scientists have of exam-
ining the physical appearance of extinct forms and inferring
how they lived
Life's Timeline
• Major events in the history of life are marked on the timeline
which has been broken into four segments:
◦ Precambrian- encompasses the Hadean, Archaean and
Proterozoic eons; almost all life was unicellular and little oxy-
gen present
◦ Paleozoic- many animal groups (including fungi, land plants
and lan animals) appeared
◦ Mesozoic (i.e. Age of Reptiles)- ended with the extinction of
dinosaurs
◦ Cenozoic (i.e. Age of Mammals)
Key Concepts
• Phylogenies and the fossil record are the major tools that biolo-
gists use to
• study the history of life
• The Cambrian explosion was the rapid morphological and ecologi-
cal
• diversification of animals that occurred during the Cambrian period
• 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
• Mass extinctions have occurred repeatedly throughout the history
of life
◦ They rapidly eliminate most of the species alive in a more or
less random manner
Section 27.1: Tools for Studying History: Phylogenetic Trees
• Phylogeny: The evolutionary history of a group of organisms
• Phylogenetic Tree: Shows ancestor–descendant relationships
among populations or species
Reading Phylogenetic Trees
• Branches: Represent populations through time
◦ Adjacent branches are sister taxa (a taxon is any named
group of organisms)
• Nodes: Occur where an ancestral group split into two or more de-
scendant groups
• Polytomy: A node where more than two descendant groups
branch off
• Tips: The tree's endpoints; represent living or extinct groups
• Rooted Phylogenies: Most ancient node of the tree is shown at the
bottom
, ◦ The location of this node is determined using an outgroup, a
taxonomic group that diverged before the rest of the taxa
being studied
• An ancestor and all its descendants form a monophyletic group
(i.e. a clade or lineage)
How Do Researchers Estimate Phylogenies?
• Morphological and/or genetic characteristics are used to estimate
phylogenetic relationships among species
• Phenetic Approach : Based on the overall similarity among popula-
tions
◦ A tree is built that clusters the most similar populations and
places more divergent populations on more distant branches
• Cladistic Approach: Focuses on synapomorphies (the shared de-
rived characteristics of the species under study; a trait that certain
populations or species have that exists in no others); when many
such traits have been measured, traits unique to each mono-
phyletic group are identified and the groups are placed on a tree in
the correct relationship to one another
How Can Biologists Distinguish Homology from Homoplasy?
• Problems can arise with both cladistic and phenetic analysis be-
cause similar traits can evolve independently in two distant species
rather than from a trait present in a common ancestor
• Homoplasy: Occurs when traits are similar for reasons other than
common ancestry
• Homology: Occurs when traits are similar due to shared ancestry.
• Convergent Evolution: Occurs when natural selection favors similar
solutions to the problems posed by a similar way of making a living
◦ A common cause of homoplasy
• If similar traits found in distantly related lineages are indeed simi-
lar due to common ancestry, then similar traits should be found in
many intervening lineages on the tree of life
• Parsimony: A principle of logic stating that the most likely explana-
tion or pattern is the one that implies the least amount of change
, • Convergent evolution and other causes of homoplasy should be
rare compared with similarity due to share descent, so the tree
that implies the fewest overall evolutionary changed should be the
one that most accurately reflects what really happened during
evolution
Whale Evolution: A Case History
• Traditionally, phylogenetic trees based on morphological data
place whales outside of the artiodactyls (mammals that have
hooves, an even number of toes, and an unusual pulley–shaped
ankle bone, i.e. an astralagus)
• DNA sequence data, however, suggests a close relationship be-
tween whales and hippos
◦ Recent data on short interspersed nuclear elements (SINEs)
show that whales and hippos share several SINE genes that
are absent in other artiodactyl groups
• These SINEs are shared derived traits (synapomor-
phies) and support the hypothesis that whales and
hippos are indeed closely related
Section 27.2: Tools for Studying History: The Fossil Record
• The fossil record provides the only direct evidence about what or-
ganisms that lived in the past looked like, where they lived, and
when they existed
• Fossil: The physical trace left by an organism that lived in the past
• Fossil Record: The total collection of fossils that have been found
throughout the world
How Do Fossils Form?
• Most fossils form when an organism is buried in sediment before
decomposition occurs
• Four types of fossils:
◦ intact fossils;
◦ compression fossils;
◦ cast fossils;
, ◦ premineralized fossils
• Fossilization is an extremely rare event
Limitations of the Fossil Record
• There are several features and limitations of the fossil record:
◦ habitat bias- occurs because organisms living in areas where
sediments are actively deposited are more likely to form fos-
sils
◦ taxonomic bias- due to the fact that some organisms (for in-
stance, those with bones) are more likely to decay slowly
and leave fossil evidence
◦ temporal bias- occurs because more recent fossils are more
common than ancient fossils
◦ abundance bias- occurs because organisms that are wide-
spread and present on Earth for a long time leave evidence
much more often than do rare, local or ephemeral species
• Paleontologists (scientists who study fossils) recognize that they
are limited to asking questions about tiny and scattered segments
on the tree of life
◦ Yet analyzing fossils is the only way scientists have of exam-
ining the physical appearance of extinct forms and inferring
how they lived
Life's Timeline
• Major events in the history of life are marked on the timeline
which has been broken into four segments:
◦ Precambrian- encompasses the Hadean, Archaean and
Proterozoic eons; almost all life was unicellular and little oxy-
gen present
◦ Paleozoic- many animal groups (including fungi, land plants
and lan animals) appeared
◦ Mesozoic (i.e. Age of Reptiles)- ended with the extinction of
dinosaurs
◦ Cenozoic (i.e. Age of Mammals)
