1. Tracing Evolutionary History
Chapter 15
Tracing Evolutionary History
slides
Lecture by Joan Sharp

2. PHYLOGENY AND THE TREE OF LIFE
PHYLOGENY AND THE TREE OF LIFE
Copyright © 2009 Pearson Education, Inc.

3. 15.14 Phylogenies are based on homologies in fossils and living organisms
Phylogeny is the evolutionary history of a species or group of species
Hypotheses about phylogenetic relationships can be developed from various lines of evidence
The fossil record provides information about the timing of evolutionary divergences
Homologous morphological traits, behaviors, and molecular sequences also provide evidence of common ancestry
Homologous and analogous relationships can be confusing for students. Simple explanations and concrete examples can serve as guides to understanding each process. Homologous relationships reflect modifications of “one form” to many “functions.” Analogous relationships reflect modifications of many “forms” for “one function.”
Student Misconceptions and Concerns
1. Homologous and analogous relationships can be confusing for students. Simple explanations and concrete examples can serve as guides to understanding each process. Homologous relationships reflect modifications of one form for many functions. Analogous relationships reflect modifications of many forms for one function.
Teaching Tips
1. Our hierarchical classification system is analogous to sorting mail first by zip code, then by street, house number, and finally individual name. Such a system of classification based upon hierarchical categories is also common in the military and many other places in our lives.
Copyright © 2009 Pearson Education, Inc.

4. 15.14 Phylogenies are based on homologies in fossils and living organisms
Analogous similarities result from convergent evolution in similar environments
These similarities do not provide information about evolutionary relationships
Marsupial and eutherian moles are very similar due to adaptation to similar burrowing life style, but are not closely related. Their last common ancestor lived 170 million years ago and was not mole-like.
Both moles have enlarged front paws for digging, small eyes, and a pad of protective thickened skin on the nose.
Student Misconceptions and Concerns
1. Homologous and analogous relationships can be confusing for students. Simple explanations and concrete examples can serve as guides to understanding each process. Homologous relationships reflect modifications of one form for many functions. Analogous relationships reflect modifications of many forms for one function.
Teaching Tips
1. Our hierarchical classification system is analogous to sorting mail first by zip code, then by street, house number, and finally individual name. Such a system of classification based upon hierarchical categories is also common in the military and many other places in our lives.
Copyright © 2009 Pearson Education, Inc.

5. Figure Convergent evolution of burrowing adaptations in Australian “mole” (top) and North American mole (bottom).

6. 15.15 Systematics connects classification with evolutionary history
Systematics classifies organisms and determines their evolutionary relationship
Taxonomists assign each species a binomial consisting of a genus and species name
Genera are grouped into progressively larger categories.
Each taxonomic unit is a taxon
Although Linnaeus recognized a hierarchical structure in the natural world, he had no natural explanation for the occurrence of such groups. One of Darwin’s greatest insights was to understand that these clusters reflect similarities due to shared ancestry and to propose a natural mechanism for the formation of new species and the generation of this diversity.
Student Misconceptions and Concerns
1. Students can be frustrated by the changing state of systematics. Some comfort can be offered by noting that this is true about many active areas of science. For example, scientists continue to learn more and revise advice regarding the causes, treatment, and prevention of heart disease and cancer.
2. Students might express concern over the need to learn scientific names, when common names already seem sufficient. Depending upon where you live, find some examples of common organisms with more than one common name. Fishermen are famous for the various names they assign to the same species, depending upon the geographic region where they fish. Have your students imagine the problems of using common names when communicating with someone in another language. Clearly, there are advantages to scientific names!
Teaching Tips
1. Although Linnaeus recognized a hierarchical structure in the natural world, he had no natural explanation for the occurrence of such groups. One might wonder why all life does not blend evenly from one form to another. One of Darwin’s greatest insights was to understand that these clusters reflect similarities due to shared ancestry, i.e., life itself is grouped into family trees. Furthermore, Darwin proposed a natural mechanism for the formation of new species and the generation of this diversity.
Animation: Classification Schemes
Copyright © 2009 Pearson Education, Inc.

7. Species: Felis catus Genus: Felis Family: Felidae Order: Carnivora
Class: Mammalia
Figure 15.15A Hierarchical classification of the domestic cat.
Phylum: Chordata
Kingdom: Animalia
Bacteria
Domain: Eukarya
Archaea

8. Order Family Genus Species Felis catus (domestic cat) Felidae Felis
Mephitis
mephitis
(striped skunk)
Mephitis
Carnivora
Mustelidae
Lutra
lutra
(European
otter)
Lutra
Figure 15.15B The relationship between classification and phylogeny.
Canis
latrans
(coyote)
Canidae
Canis
Canis
lupus
(wolf)

9. 15.16 Shared characters are used to construct phylogenetic trees
A phylogenetic tree is a hypothesis of evolutionary relationships within a group
Cladistics uses shared derived characters to group organisms into clades, including an ancestral species and all its descendents
An inclusive clade is monophyletic
Shared ancestral characters were present in ancestral groups
Consider that you are building a phylogenetic tree for tetrapods. The first tetrapod had a backbone, so the presence of a backbone is not useful in constructing a phylogenetic tree for tetrapods. By contrast, the amniotic egg and hair are traits that arose within the tetrapods. Both traits are useful in sorting out evolutionary relationships within tetrapods.
Student Misconceptions and Concerns
1. Students may struggle with many aspects of phylogenetic trees, including: (a) Students may not realize that each node/branch can be rotated to rearrange the groups without changing the nature of the relationships. For example, in Figure 15.16A, the position of the beaver and kangaroo can be reversed without changing any relationships represented in the phylogenetic tree. (b) The length of each branch is not meaningful and is not intended to be proportional to time. (c) The spacing between groups is not meaningful and does not denote the degree of divergence between them. Whether the tree is compressed or expanded in size, the information communicated in it remains the same.
Teaching Tips
1. Emphasize to students that phylogenetic trees are tentative hypotheses. As new data are collected, the hypotheses are modified or rejected outright.
Copyright © 2009 Pearson Education, Inc.

10. 15.16 Shared characters are used to construct phylogenetic trees
An important step in cladistics is the comparison of the ingroup (the taxa whose phylogeny is being investigated) and the outgroup (a taxon that diverged before the lineage leading to the members of the ingroup)
The tree is constructed from a series of branch points, represented by the emergence of a lineage with a new set of derived traits
The simplest (most parsimonious) hypothesis is the most likely phylogenetic tree
Remind students that many kinds of evidence are used to construct phylogenetic trees, including structural features, developmental features, molecular data, behavioral traits, and so on. As new data are acquired, hypotheses are revised and new trees are drawn.
Student Misconceptions and Concerns
1. Students may struggle with many aspects of phylogenetic trees, including: (a) Students may not realize that each node/branch can be rotated to rearrange the groups without changing the nature of the relationships. For example, in Figure 15.16A, the position of the beaver and kangaroo can be reversed without changing any relationships represented in the phylogenetic tree. (b) The length of each branch is not meaningful and is not intended to be proportional to time. (c) The spacing between groups is not meaningful and does not denote the degree of divergence between them. Whether the tree is compressed or expanded in size, the information communicated in it remains the same.
Teaching Tips
1. Emphasize to students that phylogenetic trees are tentative hypotheses. As new data are collected, the hypotheses are modified or rejected outright.
Animation: Geologic Record
Copyright © 2009 Pearson Education, Inc.

11. Figure 15.16A Constructing a phylogenetic tree using cladistics.
TAXA
Iguana
Duck-billed
platypus
Iguana
Kangaroo
Beaver
Duck-billed
platypus
Long
gestation 1
Hair, mammary glands
Kangaroo
CHARACTERS
Gestation 1 1
Gestation
Hair, mammary
glands 1 1 1
Beaver
Figure 15.16A Constructing a phylogenetic tree using cladistics.
Long gestation
Character Table
Phylogenetic Tree

12. TAXA Duck-billed platypus Iguana Kangaroo Beaver Long gestation 11
CHARACTERS
Gestation 1 1
Figure 15.16A Constructing a phylogenetic tree using cladistics.
Hair, mammary
glands 1 1 1
Character Table

13. Hair, mammary glands Phylogenetic Tree
Iguana
Duck-billed
platypus
Hair, mammary glands
Kangaroo
Figure 15.16A Constructing a phylogenetic tree using cladistics.
Gestation
Beaver
Long gestation
Phylogenetic Tree

14. 15.16 Shared characters are used to construct phylogenetic trees
The phylogenetic tree of reptiles shows that crocodilians are the closest living relatives of birds
They share numerous features, including four-chambered hearts, singing to defend territories, and parental care of eggs within nests
These traits were likely present in the common ancestor of birds and crocodiles
Point out to your students a number of key features of phylogenetic trees. (1) Each node/branch can be rotated to rearrange the groups, without changing the nature of the relationships. (2) The length of each branch is not meaningful and is not intended to be proportional to time. (3) The spacing between groups is not meaningful. The same phylogenetic tree squeezed onto a page or stretched wide does not denote some degree of divergence between the groups.
Remind your students that phylogenetic trees are tentative hypotheses. As new data is collected, the hypotheses are modified or outright rejected.
Student Misconceptions and Concerns
1. Students may struggle with many aspects of phylogenetic trees, including: (a) Students may not realize that each node/branch can be rotated to rearrange the groups without changing the nature of the relationships. For example, in Figure 15.16A, the position of the beaver and kangaroo can be reversed without changing any relationships represented in the phylogenetic tree. (b) The length of each branch is not meaningful and is not intended to be proportional to time. (c) The spacing between groups is not meaningful and does not denote the degree of divergence between them. Whether the tree is compressed or expanded in size, the information communicated in it remains the same.
Teaching Tips
1. Emphasize to students that phylogenetic trees are tentative hypotheses. As new data are collected, the hypotheses are modified or rejected outright.
Copyright © 2009 Pearson Education, Inc.

15. Lizards and snakes Crocodilians Pterosaurs Common ancestor of
dinosaurs,
and birds
Ornithischian
dinosaurs
Figure 15.16B A phylogenetic tree of reptiles.
Saurischian
dinosaurs
Birds

16. Front limb Hind limb Eggs
Figure Fossil remains of Oviraptor and eggs. The orientation of the bones, which surround the eggs, suggests that the dinosaur died while incubating or protecting its eggs.
Eggs

17. 15.17 An organism’s evolutionary history is documented in its genome
Molecular systematics compares nucleic acids or other molecules to infer relatedness of taxa
Scientists have sequenced more than 100 billion bases of nucleotides from thousands of species
The more recently two species have branched from a common ancestor, the more similar their DNA sequences should be
The longer two species have been on separate evolutionary paths, the more their DNA should have diverged
Teaching Tips
1. Genetic relationships provide one strong line of evidence for the ancestral relationships of life. Fossils, anatomy, embryology, and biogeography can also be used to test these same relationships. Remind students that scientists prefer to use multiple lines of evidence to test hypotheses such as phylogenies.
For the BLAST Animation DNA and RNA Compared, go to Animation and Video Files.
Copyright © 2009 Pearson Education, Inc.

18. Lesser panda Procyonidae Raccoon Giant panda Spectacled bear Ursidae
Sloth bear
Sun bear
American
black bear
Asian black bear
Figure A phylogenetic tree based on molecular data.
Polar bear
Brown bear 35 30 25 20 15 10
Pleistocene
Oligocene
Miocene
Pliocene
Millions of years ago

19. 15.17 An organism’s evolutionary history is documented in its genome
Different genes evolve at different rates
DNA coding for conservative sequences (like rRNA genes) is useful for investigating relationships between taxa that diverged hundreds of millions of years ago
This comparison has shown that animals are more closely related to fungi than to plants
mtDNA evolves rapidly and has been used to study the relationships between different groups of Native Americans, who have diverged since they crossed the Bering Land Bridge 13,000 years ago
Genetic relationships provide one strong line of evidence for the ancestral relationships of life. Fossils, anatomy, embryology, and biogeography can also be used to test these same relationships. Remind students that scientists prefer to use multiple lines of evidence to test hypotheses such as phylogenies.
Teaching Tips
1. Genetic relationships provide one strong line of evidence for the ancestral relationships of life. Fossils, anatomy, embryology, and biogeography can also be used to test these same relationships. Remind students that scientists prefer to use multiple lines of evidence to test hypotheses such as phylogenies.
Copyright © 2009 Pearson Education, Inc.

20. 15.17 An organism’s evolutionary history is documented in its genome
Homologous genes have been found in organisms separated by huge evolutionary distances
50% of human genes are homologous with the genes of yeast
Gene duplication has increased the number of genes in many genomes
The number of genes has not increased at the same rate as the complexity of organisms
Humans have only four times as many genes as yeast
Teaching Tips
1. Genetic relationships provide one strong line of evidence for the ancestral relationships of life. Fossils, anatomy, embryology, and biogeography can also be used to test these same relationships. Remind students that scientists prefer to use multiple lines of evidence to test hypotheses such as phylogenies.
Copyright © 2009 Pearson Education, Inc.

21. 15.18 Molecular clocks help track evolutionary time
Some regions of the genome appear to accumulate changes at constant rates
Molecular clocks can be calibrated in real time by graphing the number of nucleotide differences against the dates of evolutionary branch points known from the fossil record
Molecular clocks are used to estimate dates of divergences without a good fossil record
For example, a molecular clock has been used to estimate the date that HIV jumped from apes to humans
Teaching Tips
1. Genetic relationships provide one strong line of evidence for the ancestral relationships of life. Fossils, anatomy, embryology, and biogeography can also be used to test these same relationships. Remind students that scientists prefer to use multiple lines of evidence to test hypotheses such as phylogenies.
2. Molecular clocks reveal the usefulness of corroborative data, since they can be made more precise through calibration against the fossil record or other evidence. This is not much different from the accuracy of a watch set to a time standard every week, every year, or every ten years.
Copyright © 2009 Pearson Education, Inc.

22. Differences between HIV sequences
0.20
0.15
Differences between HIV sequences
0.10
Computer model
of HIV
0.05
Figure Dating the origin of HIV-1 M with a molecular clock. The data points in the upper-right corner represent different HIV samples taken at known times.
Explain that Figure shows how a molecular clock has been used to date the 1930s origin of HIV infection in humans. Samples of virus from different points in the epidemic were collected and compared.
1900
1920
1940
1960
1980
2000
Year

23. 15.19 Constructing the tree of life is a work in progress
An evolutionary tree for living things has been developed, using rRNA genes
Life is divided into three domains: the prokaryotic domains Bacteria and Archaea and the eukaryote domain Eukarya (including the kingdoms Fungi, Plantae, and Animalia)
Molecular and cellular evidence indicates that Bacteria and Archaea diverged very early in the evolutionary history of life
The first major split was divergence of Bacteria from other two lineages, followed by the divergence of the Archaea and Eukarya
For some students, the discussion of the ambiguous relationships of early life and the three domains can be unsettling. Students who expect clear answers and sharp definitions may be uncomfortable with such ambiguity.
Teaching Tips
1. The authors reference Module for information on horizontal gene transfer. If this module was not previously addressed, consider covering it in your final discussion of the early evolution of life.
2. For some students, the discussion of the ambiguous relationships of early life and the three domains can be unsettling. Students who expect clear answers and sharp definitions from science may be uncomfortable with such ambiguity.
3. The National Center for Science Education is an organization working to support the teaching of evolution and defend it against sectarian attack. Its website, contains a great deal of useful information
Copyright © 2009 Pearson Education, Inc.

24. Most recent common ancestor of all living things1
Most recent common ancestor of all living things 2
Gene transfer between mitochondrial ancestor
and ancestor of eukaryotes 3
Gene transfer between chloroplast ancestor
and ancestor of green plants
Bacteria 3 2 1
Eukarya
Figure 15.19A A phylogenetic tree depicting the origin of the three domains of life.
Archaea 4 3 2 1
Billions of years ago

25. Eukarya Bacteria Archaea
Figure 15.19B Is the tree of life really a ring?

26. 15.19 Constructing the tree of life is a work in progress
There have been two major episodes of horizontal gene transfer over time, with transfer of genes between genomes by plasmid exchange, viral infection, and fusion of organisms:
Gene transfer between a mitochondrial ancestor and the ancestor of eukaryotes,
Gene transfer between a chloroplast ancestor and the ancestor of green plants
We are the descendents of Bacteria and Archaea
Teaching Tips
1. The authors reference Module for information on horizontal gene transfer. If this module was not previously addressed, consider covering it in your final discussion of the early evolution of life.
2. For some students, the discussion of the ambiguous relationships of early life and the three domains can be unsettling. Students who expect clear answers and sharp definitions from science may be uncomfortable with such ambiguity.
3. The National Center for Science Education is an organization working to support the teaching of evolution and defend it against sectarian attack. Its website, contains a great deal of useful information
Copyright © 2009 Pearson Education, Inc.

27. 2.1 bya:
First eukaryotes (single-celled)
1.2 bya:
First multicellular eukaryotes
500 mya:
Colonization
of land by
fungi, plants,
and animals
3.5 bya:
First prokaryotes (single-celled) 4
3.5 3
2.5 2
1.5 1 .5
Billions of years ago (bya)

29. (a)
(b)
(c)
(d)

30. Systematics evolutionary relationships (a) (b) cladistics nucleotide
traces
generates
hypotheses for
constructing
evolutionary
relationships
shown in
(a)
based on
using
(b)
cladistics
seen in
analysis identifies
nucleotide
sequences
must
distinguish
from
shared
ancestral
characters
(f)
using
determine
sequence of
branch points
(c)
(d)
(e)

31. Outgroup