1. PHYLOGENY AND THE TREE OF LIFE
PHYLOGENY AND THE TREE OF LIFE
© 2012 Pearson Education, Inc. 1

2. 15.14 Phylogenies based on homologies reflect evolutionary history
Phylogeny is the evolutionary history of a species or group of species.
Phylogeny can be inferred from
the fossil record,
morphological homologies, and
molecular homologies.
Student Misconceptions and Concerns
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. 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.
2. 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.
© 2012 Pearson Education, Inc. 2

3. 15.14 Phylogenies based on homologies reflect evolutionary history
Homologies are similarities due to shared ancestry, evolving from the same structure in a common ancestor.
Generally, organisms that share similar morphologies are closely related.
However, some similarities are due to similar adaptations favored by a common environment, a process called convergent evolution.
A similarity due to convergent evolution is called analogy.
Student Misconceptions and Concerns
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. 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.
2. 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.
© 2012 Pearson Education, Inc. 3

4. Figure 15.14
Figure Australian “mole” (top) and North American mole (bottom) 4

5. 15.15 Systematics connects classification with evolutionary history
Systematics is a discipline of biology that focuses on
classifying organisms and
determining their evolutionary relationships.
Carolus Linnaeus introduced taxonomy, a system of naming and classifying species.
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. 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.
2. 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.
© 2012 Pearson Education, Inc. 5

6. 15.15 Systematics connects classification with evolutionary history
Biologists assign each species a two-part scientific name, or binomial, consisting of
a genus and
a unique part for each species within the genus.
Genera are grouped into progressively larger categories.
Each taxonomic unit is a taxon.
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. 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.
2. 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.
© 2012 Pearson Education, Inc. 6

7. Species: Felis catus Genus: Felis Family: Felidae Order: Carnivora
Figure 15.15A
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 7

8. 15.15 Systematics connects classification with evolutionary history
Biologists traditionally use phylogenetic trees to depict hypotheses about the evolutionary history of species.
The branching diagrams reflect the hierarchical classification of groups nested within more inclusive groups.
Phylogenetic trees indicate the probable evolutionary relationships among groups and patterns of descent.
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. 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.
2. 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.
© 2012 Pearson Education, Inc. 8

9. Order Family Genus Species Felis catus (domestic cat) Felidae Felis
Figure 15.15B
Order
Family
Genus
Species
Felis catus
(domestic
cat)
Felidae
Felis
Mustela
frenata
(long-tailed
weasel)
Mustela
Mustelidae
Carnivora
Lutra lutra
(European
otter)
Lutra
Figure 15.15B Relating classification to phylogeny
Canis
latrans
(coyote)
Canidae
Canis
Canis lupus
(wolf) 9

10. 15.16 Shared characters are used to construct phylogenetic trees
Cladistics
is the most widely used method in systematics and
groups organisms into clades.
Each clade is a monophyletic group of species that
includes an ancestral species and
all of its descendants.
Student Misconceptions and Concerns
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. 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.
2. Emphasize to students that phylogenetic trees are tentative hypotheses. As new data are collected, the hypotheses are modified or rejected outright.
© 2012 Pearson Education, Inc. 10

11. 15.16 Shared characters are used to construct phylogenetic trees
Cladistics is based on the Darwinian concept that organisms share characteristics with their ancestors and differ from them. Thus, there are two main types of characters.
1. Shared ancestral characters group organisms into clades.
2. Shared derived characters distinguish clades and form the branching points in the tree of life.
Student Misconceptions and Concerns
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. 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.
2. Emphasize to students that phylogenetic trees are tentative hypotheses. As new data are collected, the hypotheses are modified or rejected outright.
© 2012 Pearson Education, Inc. 11

12. 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
outgroup (a taxon that diverged before the lineage leading to the members of the ingroup),
to identify the derived characters that define the branch points in the phylogeny of the ingroup.
Student Misconceptions and Concerns
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. 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.
2. Emphasize to students that phylogenetic trees are tentative hypotheses. As new data are collected, the hypotheses are modified or rejected outright.
© 2012 Pearson Education, Inc. 12

13. 15.16 Shared characters are used to construct phylogenetic trees
As an example, consider
a frog representing the outgroup and
four other tetrapods representing the ingroup.
The presence or absence of traits is indicated as
1 if the trait is present or
0 if the trait is absent.
Student Misconceptions and Concerns
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. 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.
2. Emphasize to students that phylogenetic trees are tentative hypotheses. As new data are collected, the hypotheses are modified or rejected outright.
© 2012 Pearson Education, Inc. 13

14. Figure 15.16A
TAXA
Frog
Duck-billed
platypus
Kangaroo
Beaver
Iguana
Iguana
Frog
Amnion 1 1 1 1
Duck-billed
platypus
Amnion
Hair,
mammary
glands 1 1 1
CHARACTERS
Hair,
mammary
glands
Kangaroo
Gestation 1 1
Figure 15.16A Constructing a phylogenetic tree using cladistics
Long
gestation
Gestation 1
Beaver
Long gestation
Character Table
Phylogenetic Tree 14

15. 15.16 Shared characters are used to construct phylogenetic trees
In our example, the phylogenetic tree is constructed from a series of branch points, represented by the emergence of a lineage with a new set of derived traits.
When constructing a phylogenetic tree, scientists use parsimony, looking for the simplest explanation for observed phenomena.
Systematists use many kinds of evidence. However, even the best tree represents only the most likely hypothesis.
Student Misconceptions and Concerns
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. 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.
2. Emphasize to students that phylogenetic trees are tentative hypotheses. As new data are collected, the hypotheses are modified or rejected outright.
© 2012 Pearson Education, Inc. 15

16. 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, crocodiles, and dinosaurs.
Student Misconceptions and Concerns
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. 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.
2. Emphasize to students that phylogenetic trees are tentative hypotheses. As new data are collected, the hypotheses are modified or rejected outright.
© 2012 Pearson Education, Inc. 16

17. Lizards and snakes Crocodilians Pterosaurs* Common ancestor of
Figure 15.16B
Lizards
and snakes
Crocodilians
Pterosaurs*
Common
ancestor of
crocodilians,
dinosaurs,
and birds
Ornithischian
dinosaurs*
Figure 15.16B A phylogenetic tree of reptiles (* indicates extinct lineages)
Saurischian
dinosaurs*
Birds 17

18. Front limb Hind limb Eggs Figure 15.16C
Figure 15.16C Fossil remains of Oviraptor and eggs
Eggs 18

19. 15.17 An organism’s evolutionary history is documented in its genome
Molecular systematics uses DNA and other molecules to infer relatedness.
Scientists have sequenced more than 110 billion bases of DNA from thousands of species.
This enormous database has fueled a boom in the study of phylogeny and clarified many evolutionary relationships.
Teaching Tips
1. 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.
2. 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.
© 2012 Pearson Education, Inc. 19

20. Figure 15.17 A phylogenetic tree based on molecular data
Red
panda
Weasel
Raccoon
Giant panda
Spectacled bear
Sloth bear
Sun bear
American
black bear
Figure A phylogenetic tree based on molecular data
Asian black
bear
Polar bear
Brown bear 35 30 25 20 15 10
Oligocene
Miocene
Pliocene
Millions of years ago
Pleistocene 20

21. 15.17 An organism’s evolutionary history is documented in its genome
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. 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.
2. 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.
© 2012 Pearson Education, Inc. 21

22. 15.17 An organism’s evolutionary history is documented in its genome
Different genes evolve at different rates.
DNA coding for ribosomal RNA (rRNA)
changes slowly and
is useful for investigating relationships between taxa that diverged hundreds of millions of years ago.
In contrast, DNA in mitochondria (mtDNA)
evolves rapidly and
is more useful to investigate more recent evolutionary events.
Teaching Tips
1. 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.
2. 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.
© 2012 Pearson Education, Inc. 22

23. 15.17 An organism’s evolutionary history is documented in its genome
The remarkable commonality of molecular biology demonstrates that all living organisms share many biochemical and developmental pathways and provides overwhelming support of evolution.
The genomes of humans and chimpanzees are amazingly similar.
About 99% of the genes of humans and mice are detectably homologous.
About 50% of human genes are homologous with those of yeast.
Teaching Tips
1. 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.
2. 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.
© 2012 Pearson Education, Inc. 23

24. 15.18 Molecular clocks help track evolutionary time
Molecular clocks
rely on genes that have a reliable average rate of change,
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,
are used to estimate dates of divergences without a good fossil record, and
have been used to date the origin of HIV infection in humans.
Teaching Tips
1. 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.
2. 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.
3. 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.
© 2012 Pearson Education, Inc. 24

25. Differences between HIV sequences
Figure 15.18
0.20
0.15
HIV
Differences between HIV sequences
0.10
Range
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.
Line of best fit
to data points
1900
1920
1940
1960
1980
2000
Year 25

26. 15.19 Constructing the tree of life is a work in progress
Molecular systematics and cladistics are remodeling some trees.
Biologists currently recognize a three-domain system consisting of
two domains of prokaryotes: Bacteria and Archaea, and
one domain of eukaryotes called Eukarya including
fungi,
plants, and
animals.
Teaching Tips
1. 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.
2. The authors reference Modules and 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.
3. 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.
© 2012 Pearson Education, Inc. 26

27. 15.19 Constructing the tree of life is a work in progress
Molecular and cellular evidence indicates that
Bacteria and Archaea diverged very early in the evolutionary history of life and
Archaea are more closely related to eukaryotes than to bacteria.
Teaching Tips
1. 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.
2. The authors reference Modules and 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.
3. 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.
© 2012 Pearson Education, Inc. 27

28. 15.19 Constructing the tree of life is a work in progress
Comparisons of complete genomes from all three domains show that
there have been substantial interchanges of genes between organisms in different domains and
these took place through horizontal gene transfer, a process in which genes are transferred from one genome to another through mechanisms such as plasmid exchange and viral infection.
Some biologists suggest that the early history of life may be best represented by a ring, from which the three domains emerge.
Teaching Tips
1. 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.
2. The authors reference Modules and 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.
3. 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.
© 2012 Pearson Education, Inc. 28

29. Most recent common ancestor of all living things
Figure 15.19A 1
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 Two major episodes of horizontal gene transfer in the history of life (dates are uncertain)
Archaea 4 3 2 1
Billions of years ago 29

30. Archaea Eukarya Bacteria Figure 15.19B
Figure 15.19B Is the tree of life really a ring of life? In this model, eukaryotes arose when an early archaean fused with an early bacterium.
Bacteria 30

31. 4 3.5 3 2.5 2 1.5 1 .5 Present Billions of years ago First
Figure 15.UN01
First
multicellular
eukaryotes
Colonization of
land by fungi,
plants, and animals
First prokaryotes
(single-celled)
First eukaryotes
(single-celled) 4
3.5 3
2.5 2
1.5 1 .5
Present
Billions of years ago
Figure 15.UN01 Reviewing the Concepts,15.4 31

32. Systematics evolutionary history (e) (a) (b) cladistics nucleotide
Figure 15.UN04
Systematics
traces
generates
hypotheses for
constructing
evolutionary
history
shown in
called
(e)
based on
(a)
using
(b)
cladistics
seen in
analysis identifies
nucleotide
sequences
must
distinguish
from
Figure 15.UN04 Connecting the Concepts, question 2
shared ancestral
characters
(g)
using
determine
sequence of
branch points
(c)
(d)
(f) 32

33. Figure 15.UN05
Outgroup
Figure 15.UN05 Applying the Concepts, question 17 33