2. 15.14 Phylogeny and the Tree of Life
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
 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.
 The National Center for Science Education is an organization working to support the teaching of evolution and defend it against sectarian attack. Its website, ncse.com, contains a great deal of useful information.
Active Lecture Tips
• See the Activity Video Review: YouTube – Bang Goes the Theory: Evolution Made Simple at the Instructor Exchange in the MasteringBiology instructor resource area or the at the following address.
• See the Activity Vertebrate Phylogeny on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity.

3. Phylogeny and the Tree of Life

4. 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
 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.
 The National Center for Science Education is an organization working to support the teaching of evolution and defend it against sectarian attack. Its website, ncse.com, contains a great deal of useful information.
Active Lecture Tips
• See the Activity Video Review: YouTube – Bang Goes the Theory: Evolution Made Simple at the Instructor Exchange in the MasteringBiology instructor resource area or the at the following address.
• See the Activity Vertebrate Phylogeny on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity.

5. 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
 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.
 The National Center for Science Education is an organization working to support the teaching of evolution and defend it against sectarian attack. Its website, ncse.com, contains a great deal of useful information.
Active Lecture Tips
• See the Activity Video Review: YouTube – Bang Goes the Theory: Evolution Made Simple at the Instructor Exchange in the MasteringBiology instructor resource area or the at the following address.
• See the Activity Vertebrate Phylogeny on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity.

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

7. 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
 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.
 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
 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.
 The National Center for Science Education is an organization working to support the teaching of evolution and defend it against sectarian attack. Its website, ncse.com, contains a great deal of useful information.
Active Lecture Tips
• See the Activity Video Review: YouTube – Bang Goes the Theory: Evolution Made Simple at the Instructor Exchange in the MasteringBiology instructor resource area or the at the following address.
• See the Activity Vertebrate Phylogeny on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity.

8. 15.15 Systematics connects classification with evolutionary history
Taxonomy is like a filing system with sub files and sub-sub files and so on. The order, from largest grouping to smallest is:
Domain
Kingdom
Phyla
Class
Order
Family
Genus
Species
Organisms go by their genus and species within the genus. Called Bionomial Nomenclature.
Student Misconceptions and Concerns
 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.
 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
 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.
 The National Center for Science Education is an organization working to support the teaching of evolution and defend it against sectarian attack. Its website, ncse.com, contains a great deal of useful information.
Active Lecture Tips
• See the Activity Video Review: YouTube – Bang Goes the Theory: Evolution Made Simple at the Instructor Exchange in the MasteringBiology instructor resource area or the at the following address.
• See the Activity Vertebrate Phylogeny on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity.

9. Animation: Classification Schemes

10. 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

11. 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 the pattern of descent from the last common ancestors.
Student Misconceptions and Concerns
 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.
 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
 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.
 The National Center for Science Education is an organization working to support the teaching of evolution and defend it against sectarian attack. Its website, ncse.com, contains a great deal of useful information.
Active Lecture Tips
• See the Activity Video Review: YouTube – Bang Goes the Theory: Evolution Made Simple at the Instructor Exchange in the MasteringBiology instructor resource area or the at the following address.
• See the Activity Vertebrate Phylogeny on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity.

12. 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
Carnivora
Mustelidae
Lutra lutra (European otter)
Lutra
Figure 15.15b Relating classification to phylogeny
Canis latrans (coyote)
Canidae
Canis
Canis lupus (wolf)

13. 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.
(You are not expected to know each phylogenic tree shown [slide 13, 15, 18, 25] but you do need to understand how they show branching of newly evolved species.)
Student Misconceptions and Concerns
 Students may struggle with many aspects of phylogenetic trees. Here are three examples. (1) Students may fail to 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. (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 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
 Emphasize to students that phylogenetic trees are tentative hypotheses. As new data are collected, the hypotheses are modified or rejected outright.
 The National Center for Science Education is an organization working to support the teaching of evolution and defend it against sectarian attack. Its website, ncse.com, contains a great deal of useful information.
Active Lecture Tips
• See the Activity Video Review: YouTube – Bang Goes the Theory: Evolution Made Simple at the Instructor Exchange in the MasteringBiology instructor resource area or the at the following address.
• See the Activity Vertebrate Phylogeny on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity.

14. Frog Iguana Duck-billed platypus Amnion Kangaroo Hair, mammary glands
Figure 15.16a-2
Frog
Iguana
Duck-billed platypus
Amnion
Kangaroo
Hair, mammary glands
Figure 15.16a-2 Constructing a phylogenetic tree using cladistics (part 2)
Gestation
Beaver
Long gestation
Phylogenetic Tree

15. 15.16 Shared characters are used to construct phylogenetic trees
As new data accumulate, hypotheses are revised and new trees drawn.
The phylogenetic tree of reptiles shows that crocodilians are the closest living relatives of birds.
They share numerous features:
they have four-chambered hearts,
they “sing” to defend territories, and
they build 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. Here are three examples. (1) Students may fail to 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. (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 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
 Emphasize to students that phylogenetic trees are tentative hypotheses. As new data are collected, the hypotheses are modified or rejected outright.
 The National Center for Science Education is an organization working to support the teaching of evolution and defend it against sectarian attack. Its website, ncse.com, contains a great deal of useful information.
Active Lecture Tips
• See the Activity Video Review: YouTube – Bang Goes the Theory: Evolution Made Simple at the Instructor Exchange in the MasteringBiology instructor resource area or the at the following address.
• See the Activity Vertebrate Phylogeny on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity.

16. Common ancestor of crocodilians, dinosaurs, and birds
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. 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
 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.
 The National Center for Science Education is an organization working to support the teaching of evolution and defend it against sectarian attack. Its website, ncse.com, contains a great deal of useful information.
Active Lecture Tips
• See the Activity Video Review: YouTube – Bang Goes the Theory: Evolution Made Simple at the Instructor Exchange in the MasteringBiology instructor resource area or the at the following address.
• See the Activity Vertebrate Phylogeny on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity.

18. 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 is expected to have diverged.
Teaching Tips
 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.
 The National Center for Science Education is an organization working to support the teaching of evolution and defend it against sectarian attack. Its website, ncse.com, contains a great deal of useful information.
Active Lecture Tips
• See the Activity Video Review: YouTube – Bang Goes the Theory: Evolution Made Simple at the Instructor Exchange in the MasteringBiology instructor resource area or the at the following address.
• See the Activity Vertebrate Phylogeny on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity.

19. Red panda Weasel Raccoon Giant panda Spectacled bear Sloth bear
Figure
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 5
Millions of years ago

20. 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 relatively 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
can be used to investigate more recent evolutionary events.
Teaching Tips
 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.
 The National Center for Science Education is an organization working to support the teaching of evolution and defend it against sectarian attack. Its website, ncse.com, contains a great deal of useful information.
Active Lecture Tips
• See the Activity Video Review: YouTube – Bang Goes the Theory: Evolution Made Simple at the Instructor Exchange in the MasteringBiology instructor resource area or the at the following address.
• See the Activity Vertebrate Phylogeny on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity.

21. 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 for Darwin’s theory of “descent with modification.”
Teaching Tips
 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.
 The National Center for Science Education is an organization working to support the teaching of evolution and defend it against sectarian attack. Its website, ncse.com, contains a great deal of useful information.
Active Lecture Tips
• See the Activity Video Review: YouTube – Bang Goes the Theory: Evolution Made Simple at the Instructor Exchange in the MasteringBiology instructor resource area or the at the following address.
• See the Activity Vertebrate Phylogeny on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity.

22. 15.18 Molecular clocks help track evolutionary time
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, and
can be used to estimate the dates of other evolutionary episodes not documented in the fossil record.
Teaching Tips
 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.
 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 than the accuracy of a watch set to a time standard every week, every year, or every ten years.
 The National Center for Science Education is an organization working to support the teaching of evolution and defend it against sectarian attack. Its website, ncse.com, contains a great deal of useful information.
Active Lecture Tips
• See the Activity Video Review: YouTube – Bang Goes the Theory: Evolution Made Simple at the Instructor Exchange in the MasteringBiology instructor resource area or the at the following address.
• See the Activity Vertebrate Phylogeny on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity.

23. 15.18 Molecular clocks help track evolutionary time
Molecular clocks have been used to date a wide variety of events.
In one fascinating example published in 2011, researchers studied the divergence of human body lice from head lice and estimated that people began to wear clothing between 83,000 and 170,000 years ago.
Teaching Tips
 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.
 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 than the accuracy of a watch set to a time standard every week, every year, or every ten years.
 The National Center for Science Education is an organization working to support the teaching of evolution and defend it against sectarian attack. Its website, ncse.com, contains a great deal of useful information.
Active Lecture Tips
• See the Activity Video Review: YouTube – Bang Goes the Theory: Evolution Made Simple at the Instructor Exchange in the MasteringBiology instructor resource area or the at the following address.
• See the Activity Vertebrate Phylogeny on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity.

24. 15.18 Molecular clocks help track evolutionary time
Some biologists are skeptical about the accuracy of molecular clocks because the rate of molecular change may vary
at different times,
in different genes, and
in different groups of organisms.
Teaching Tips
 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.
 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 than the accuracy of a watch set to a time standard every week, every year, or every ten years.
 The National Center for Science Education is an organization working to support the teaching of evolution and defend it against sectarian attack. Its website, ncse.com, contains a great deal of useful information.
Active Lecture Tips
• See the Activity Video Review: YouTube – Bang Goes the Theory: Evolution Made Simple at the Instructor Exchange in the MasteringBiology instructor resource area or the at the following address.
• See the Activity Vertebrate Phylogeny on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity.

25. 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 the kingdoms
Fungi,
Plantae, and
Animalia.
Teaching Tips
 The authors reference Modules and for information on horizontal gene transfer. If these modules were not previously addressed, consider covering them in your final discussion of the early evolution of life.
 The National Center for Science Education is an organization working to support the teaching of evolution and defend it against sectarian attack. Its website, ncse.com, contains a great deal of useful information.
Active Lecture Tips
• See the Activity Video Review: YouTube – Bang Goes the Theory: Evolution Made Simple at the Instructor Exchange in the MasteringBiology instructor resource area or the at the following address.
• See the Activity Vertebrate Phylogeny on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity.

26. 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

27. 15.19 Constructing the tree of life is a work in progress
Comparisons of complete genomes from all three domains show that especially during the early history of life, 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.
How could this apply to the fact that mtDNA evolves quickly, prokaryotes have three ways to alter their genome, and the idea of endosymbionts? (Be able to answer this)
Teaching Tips
 The authors reference Modules and for information on horizontal gene transfer. If these modules were not previously addressed, consider covering them in your final discussion of the early evolution of life.
 The National Center for Science Education is an organization working to support the teaching of evolution and defend it against sectarian attack. Its website, ncse.com, contains a great deal of useful information.
Active Lecture Tips
• See the Activity Video Review: YouTube – Bang Goes the Theory: Evolution Made Simply at the Instructor Exchange in the Mastering Biology instructor resource area or the at the following youtube address.
• See the Activity Vertebrate Phylogeny on the Instructor Exchange. Visit the Instructor Exchange in the Mastering Biology instructor resource area for a description of this activity.