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BIO102: Introduction to Evolutionary Biology and Ecology

Unit 6: Phylogeny and Taxonomy   Now that we generally understand how natural selection and evolution work, we will take a look at the study of phylogeny, the field of biology that studies the evolutionary development and diversification of a species (also known as phylogenesis).  You might think of phylogenesis as an evolutionary tree, where the tree trunk is the common ancestor of all life on Earth.  Over time, species have branched off the main tree trunk to form their own “branches.”  As you might imagine, this tree of life is full of branches and sub-branches!  Phylogeny can also help us explain how animals share certain common features while being quite different from one another (for example, how cats, dogs, bears, and humans have four limbs but are clearly distinct from one another).
 
Meanwhile, taxonomy deals with the question of how we classify these different types of animals.  Carl Linnaeus answered this question with the invention of the binomial nomenclature system, a formal system for naming different species.  Scientists have now categorized all living organisms into six kingdoms.  Every living organism has a scientific name derived from Linnaeus’s original work.

Unit 6 Time Advisory
This unit should take approximately 11.25 hours to complete.

☐    Subunit 6.1: 2.5 hours
 
☐    Subunit 6.2: 1.75 hours
 
☐    Subunit 6.3: 0.75 hours

☐    Subunit 6.4: 2.25 hours
 
☐    Subunit 6.5: 0.75 hours
 
☐    Subunit 6.6: 0.75 hours
 
☐    Subunit 6.7: 0.5 hours
 
☐    Subunit 6.8: 1.5 hours

☐    Assessment: 0.5 hours

Unit6 Learning Outcomes
Upon successful completion of this unit, the student will be able to: - Demonstrate an understanding of experiments done to simulate the Big Bang, that is, the creation of organic matter from inorganic chemicals. - Demonstrate an understanding of the Endosymbiotic Theory. - Understand the process involved in making a phylogenetic tree and recognize related terms. - Describe relatedness by referring to a cladogram or tree - Demonstrate an understanding of homologies and analogies. - Understand the basics of what distinguishes organisms in one kingdom from those in another.

6.1 Origin of Life on Earth   - Lecture: Yale University: Stephen C. Stearns’ Principles of Evolution, Ecology, and Behavior: “Key Events in Evolution” Link: Yale University: Stephen C. Stearns’ Principles of Evolution, Ecology, and Behavior“Key Events in Evolution” (YouTube)

 Also available in:  
 [MP4](http://www.archive.org/details/KeyEventsInEvolution)  

[MP3](http://oyc.yale.edu/ecology-and-evolutionary-biology/eeb-122/lecture-17)  
 [iTunes U
Audio](http://deimos3.apple.com/WebObjects/Core.woa/Browse/yale.edu.2413658053.02413658061.2564124701?i=1407803913)  
 [iTunes U
Video](http://deimos3.apple.com/WebObjects/Core.woa/Browse/yale.edu.2413658053.02471197475.2687092912?i=1634628176)  

 Instructions: Please click on the link above and watch the lecture.
 This lecture covers the material in sub-subunits 6.1.1 and 6.1.2.  

 Watching this lecture and pausing to take notes should take
approximately 1 hour.  

 *Note: Although the term “endosymbiotic theory” is not used, the
origin of eukaryotic cells that Professor Stearns describes is in
fact an articulation of that theory.*  

 Terms of Use: This resource is licensed under a [Creative Commons
Attribution-NonCommercial-ShareAlike 3.0 United States
License](http://creativecommons.org/licenses/by-nc-sa/3.0/us/).  It
is attributed to Stephen C. Stearns and Yale University's [Open Yale
Courses](http://oyc.yale.edu/).  The original version can be found
[here](http://oyc.yale.edu/ecology-and-evolutionary-biology/eeb-122/lecture-17).

6.1.1 Miller-Urey Experiment   - Reading: John Kimball’s Biology Pages: “The Origin of Life” Link: John Kimball’s Biology Pages: “The Origin of Life” (HTML)

 Also available in:  

[EPUB](http://www.saylor.org/site/wp-content/uploads/2011/08/BIO102-6.1.1-The-Origin-of-Life-John-Kimball.epub)  

 Instructions: Please click on the link above and read the section
titled “Abiotic Synthesis of Organic Molecules” and all its
sub-sections.  Please note that the author labels the experiment
“Miller’s Experiment.” However, the experiment is often contributed
to both authors Stanley Miller and Harold Urey and is usually known
as the “Miller-Urey” experiment.  

 Reading this section and taking notes should take approximately 30
minutes.  

 Terms of Use: This resource has been reposted by the kind
permission of Professor John Kimball and can be viewed in its
original form
[here](http://docs.google.com/a/saylor.org/document/edit?id=1vUDGntV_TQy6-LhDoHUg_gPRth1jy_J1d3TSOKsa2aI&hl=en). 
Please note that this material is under copyright and may not be
reproduced in any capacity without the explicit permission of the
copyright holder.

6.1.2 Endosymbiotic Theory   - Reading: Indiana University-Purdue University, Indianapolis: Kathleen A. Marrs’ “Endosymbiotic Theory” Link: Indiana University-Purdue University, Indianapolis: Kathleen A. Marrs’ “Endosymbiotic Theory” (HTML)

 Instructions: Please click on the link above and read the entire
webpage.  Do not concern yourself with the details of the chart in
Section I or the “Objectives” assignment.  

 Reading this webpage and taking notes should take approximately 15
minutes.  

 Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.
  • Reading: The Saylor Foundation’s “Endosymbiotic Theory” Link: The Saylor Foundation’s “Endosymbiotic Theory” (PDF)

    Instructions: Please click on the link above and read the entire article.

    Reading this article and taking notes should take approximately 15 minutes.

  • Reading: John Kimball’s Biology Pages: “Endosymbiosis and the Origin of Eukaryotes”

    Link: John Kimball’s Biology Pages:Endosymbiosis and the Origin of Eukaryotes” (HTML)

     

    Instructions: Please click on the link above and read the entire webpage, which covers endosymbiosis and the beginning of eukaryotes.

    Reading this webpage and taking notes should take approximately 30 minutes.

     

    Terms of Use: This resource has been reposted by the kind permission of Professor John Kimball and can be viewed in its original form here.  Please note that this material is under copyright and may not be reproduced in any capacity without the explicit permission of the copyright holder.

6.2 Phylogeny   - Reading: Dr. Michael J. Farabee’s Online Biology Book: Chapter 44: “Biological Diversity I” Link: Dr. Michael J. Farabee’s Online Biology Book: “Chapter 44: Biological Diversity I” (HTML)

 Instructions: Read this entire chapter.  

 Reading this chapter and taking notes should take approximately 30
minutes.  

 Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.
  • Lecture: Yale University: Stephen C. Stearns’ Principles of Evolution, Ecology, and Behavior: “Phylogeny and Systematics” Link: Yale University: Stephen C. Stearns’ Principles of Evolution, Ecology, and Behavior“Phylogeny and Systematics” (YouTube)

    Also available in:
    MP4

    MP3
    iTunes U Audio
    iTunes U Video

    Instructions: Please click on the link above and watch the lecture.

    Watching this lecture and taking notes should take approximately 1 hour.

    Terms of Use: This resource is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 United States License.  It is attributed to Stephen C. Stearns and Yale University's Open Yale Courses.  The original version can be found here.

  • Lecture: YouTube: Paul Anderson’s Bozeman Biology: “Cladograms”

    Link: YouTube: Paul Anderson’s Bozeman Biology“Cladograms” (YouTube)

    Instructions: Please watch the entire lecture.  Cladograms are diagrams that show an evolutionary relationship between organisms.

    Watching this lecture and pausing to take notes should take approximately 15 minutes.

    Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

6.3 Linnaeus and Taxonomy   - Lecture: YouTube: Khan Academy’s “Taxonomy and the Tree of Life” and “Species” Links: YouTube: Khan Academy’s “Taxonomy and the Tree of Life” and “Species” (YouTube)

 Instructions: Please click on the links above and watch the two
lectures for an introduction to taxonomy and species.   

 *Note: Defining species is a complicated task.  Using sexual
reproduction to produce viable offspring, as discussed in the
“Species” video is one criteria of defining a species.  However,
this definition cannot then be applied to non-sexually reproducing
organisms or to extinct organisms.*  
    
 Watching these lectures and pausing to take notes should take
approximately 30 minutes.  

 Terms of Use: This resource is licensed under a [Creative Commons
Attribution-NonCommercial-ShareAlike 3.0 United States
License](http://creativecommons.org/licenses/by-nc-sa/3.0/us/). It
is attributed to Salman Khan and [Khan
Academy](http://www.khanacademy.org/).
  • Lecture: Paul Anderson’s Bozeman Biology: “The Three Domains of Life”

    Link: Paul Anderson’s Bozeman Biology: “The Three Domains of Life” (YouTube)

    Instructions: Please watch the entire lecture.  The three-domain system is a biological classification that divides all organisms into three major groups; archaea, bacteria, and eukarya.

    Watching this lecture and pausing to take notes should take approximately 15 minutes.

    Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

6.4 Kingdoms Eubacteria and Archaebacteria (Formerly Known as Kingdom Monera)   - Reading: The University of Arizona’s “Tree of Life Web Project”

Link: The University of Arizona’s [“Tree of Life Web
Project”](http://tolweb.org/tree/phylogeny.html) (HTML)  

 Instructions: Read the introductory paragraphs on the Tree of Life
main page and “browse” the tree, either by clicking on one or more
of the links on the left side of the page or by clicking on one of
the icons on the tree image (flowering plants, terrestrial
vertebrates, etc.).  Follow at least three links in the tree in
order to get a sense of the diversity of life and the relationships
within and among groups.  

 Reading this webpage and completing this activity should take
approximately 30 minutes.  

 Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.
  • Reading: University of California Museum of Paleontology’s “Phylogeny of Life,” “Systematics of the Bacteria,” and “Systematics of the Archaea”

    Link: University of California Museum of Paleontology’s “Phylogeny of Life”“Systematics of the Bacteria”, and “Systematics of the Archaea” (HTML)

    Instructions: Read each short page in its entirety in order to gain a better understanding of the current taxonomic and phylogenetic systems under which living things are classified.

    Reading these webpages and taking notes should take approximately 20 minutes.

    Terms of Use: Please respect the copyright and terms of use displayed on the webpages above.

  • Lecture: YouTube: Paul Anderson’s Bozeman Biology: “Archaea”

    Link: YouTube: Paul Anderson’s Bozeman Biology:  “Archaea” (YouTube)

    Instructions: Please watch the entire lecture.  Archaea are potentially the oldest life forms on earth.  Originally Archaea were grouped with bacteria; however, scientists later discovered through DNA and RNA comparison testing that these organisms are a distinct group.

    Watching this video and pausing to take notes should take approximately 15 minutes.

    Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

  • Reading: John Kimball’s Biology Pages: “Archaea”

    Reading: John Kimball’s Biology Pages“Archaea” (HTML)
     

    Instructions: Read this webpage, which will cover Archaea.

    Reading this webpage and taking notes should take approximately 15 minutes.

    Terms of Use: The linked material above has been reposted by the kind permission of Professor John W. Kimball, and can be viewed in its original form here.  Please note that this material is under copyright and cannot be reproduced in any capacity without explicit permission from the copyright holder.

  • Lecture: YouTube: Paul Anderson’s Bozeman Biology: “Bacteria”

    Link: YouTube: Paul Anderson’s Bozeman Biology“Bacteria” (YouTube)

    Instructions: Please watch the entire lecture.  Bacteria are a diverse group of microorganisms.  Some are free living, while others live symbiotically with other organisms such as humans.  This relationship can be beneficial: for example, there are bacteria in your gut that produce vitamin K.  Other bacteria can cause serious illness such as food poisoning.

    Watching this video and pausing to take notes should take approximately 15 minutes.

    Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

  • Reading: John Kimball’s Biology Pages: “Bacteria”

    Link: John Kimball’s Biology Pages: Bacteria (HTML)

    Instructions: Read this webpage, which will cover Bacteria.

    Reading this webpage and taking notes should take approximately 45 minutes.

    Terms of Use: The linked material above has been reposted by the kind permission of Professor John W. Kimball, and can be viewed in its original form here.  Please note that this material is under copyright and cannot be reproduced in any capacity without explicit permission from the copyright holder.

6.5 Kingdom Protista   - Reading: University of California Museum of Paleontology’s “Systematics of the Eukaryota”

Link: University of California Museum of Paleontology’s
[“Systematics of the
Eukaryota”](http://www.ucmp.berkeley.edu/alllife/eukaryotasy.html) (HTML)  

 Instructions: Read each short page in its entirety in order to gain
a better understanding of the current taxonomic and phylogenetic
systems under which living things are classified.  

 Reading this webpage and taking notes should take approximately 10
minutes.  

 Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.
  • Lecture: YouTube: Paul Anderson’s Bozeman Biology: “Protists” Link: Paul Anderson’s Bozeman Biology“Protists” (YouTube)

    Instructions: Please watch this lecture.  Protists are a diverse group of eukaryotic microorganisms.  This group has often been considered the “catch-all” in which organisms that did not fit characteristically into other groups were placed.

    Watching this lecture and pausing to take notes should take approximately 5 minutes.

    Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

  • Reading: John Kimball's Biology Pages: “The Protists”

    Link: John Kimball’s Biology Pages: “The Protists” (HTML)

     

    Instructions: Read this webpage, which will cover Protista.

    Reading this webpage and taking notes should take approximately 30 minutes.

     

    Terms of Use: This resource has been reposted by the kind permission of Professor John Kimball and can be viewed in its original form here.  Please note that this material is under copyright and may not be reproduced in any capacity without the explicit permission of the copyright holder.

6.6 Kingdom Plantae   - Lecture: YouTube: Paul Anderson’s Bozeman Biology: “Plants”

Link: YouTube: Paul Anderson’s *Bozeman Biology*:
[“Plants”](http://www.youtube.com/watch?v=X4L3r_XJW0I&list=PL7A750281106CD067&index=49&feature=plpp_video) (YouTube)  

 Instructions: Please watch this lecture.  Plants are multicellular
organisms that, for the most part, produce their own food through
the process of photosynthesis.  

 Watching this video and pausing to take notes should take
approximately 15 minutes.  

 Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.
  • Reading: John Kimball’s Biology Pages: “Plants”

    Link: John Kimball’s Biology Pages“Plants (HTML)

     

    Instructions: Read this webpage, which will cover the Plant Kingdom.

    Reading this webpage and taking notes should take approximately 30 minutes.

     

    Terms of Use: This resource has been reposted by the kind permission of Professor John Kimball and can be viewed in its original form here.  Please note that this material is under copyright and may not be reproduced in any capacity without the explicit permission of the copyright holder.

6.7 Kingdom Fungi   - Lecture: YouTube: Paul Anderson’s Bozeman Biology: “Fungi”

Link: YouTube: Paul Anderson’s *Bozeman Biology*:
[“Fungi”](http://www.youtube.com/watch?v=dj9m7Oc36wM&list=PL7A750281106CD067&index=50&feature=plpp_video) (YouTube)  

 Instructions: Please watch this lecture.  The Kingdom Fungi
consists of unicellular and multicellular organisms.  While fungal
cells have cell walls, similar to plants, they lack photosynthetic
capabilities and are heterotrophic, deriving their energy from
external sources.  They play a major role in nutrient cycling within
ecosystems.  

 Watching this lecture and pausing to take notes should take
approximately 15 minutes.  

 Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.
  • Reading: John Kimball’s Biology Pages: “Fungi”

    Link: John Kimball’s Biology Pages: “Fungi (HTML)

     

    Instructions: Read this webpage, which will cover the Fungi Kingdom.

    Reading this webpage and taking notes should take approximately 15 minutes.

     

    Terms of Use: This resource has been reposted by the kind permission of Professor John Kimball and can be viewed in its original form here.  Please note that this material is under copyright and may not be reproduced in any capacity without the explicit permission of the copyright holder.

6.8 Kingdom Animalia (Invertebrates and Vertebrates)   - Lecture: YouTube: Paul Anderson’s Bozeman Biology: “Animals”

YouTube Link: Paul Anderson’s Bozeman Biology:
[“Animals”](http://www.youtube.com/watch?v=wd-QnKlfZHI&list=PL7A750281106CD067&index=48&feature=plpp_video) (YouTube)  

 Instructions: Please watch the entire lecture.  Animals are
multicelluar, eukaryotic organisms.  All animals are heterotrophic,
meaning they obtain their energy from consuming other organisms. 
Watching this video and taking notes should take you approximately
10 minutes.  

 Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.
  • Reading: John Kimball’s Biology Pages: “The Invertebrate Animals”

    Link: John Kimball’s Biology Pages“The Invertebrate Animals (HTML)

     

    Instructions: Please read this webpage, which will cover the invertebrates.

    Reading this webpage and taking notes should take approximately 45 minutes.

    Terms of Use: The linked material above has been reposted by the kind permission of Professor John W. Kimball, and can be viewed in its original form here.  Please note that this material is under copyright and cannot be reproduced in any capacity without explicit permission from the copyright holder.

  • Reading: John Kimball’s Biology Pages: “The Vertebrates”

    Link: John Kimball’s Biology Pages“The Vertebrates” (HTML)

    Instructions: Please read this webpage, which will cover the vertebrates.

    Reading this webpage and taking notes should take approximately 30 minutes.
    .
    Terms of Use: The linked material above has been reposted by the kind permission of Professor John W. Kimball, and can be viewed in its original form here.  Please note that this material is under copyright and cannot be reproduced in any capacity without explicit permission from the copyright holder.

Unit 6 Review and Assessment   - Assessment: The Saylor Foundation’s “Unit 6 Review” Link: The Saylor Foundation’s “Unit 6 Review” (PDF)

 Instructions: Please click on the link above and work through all
of the questions. When you are finished, check your work against The
Saylor Foundation’s [“Unit 6 Review Answer
Key”](http://www.saylor.org/site/wp-content/uploads/2012/11/BIO102_Unit_6_Review-ANSWER-KEY-FINAL.pdf)
(PDF).  

 Completing this assessment should take approximately 30 minutes.
  • Assessment: The Saylor Foundation’s “Unit 6 Assessment” Link: The Saylor Foundation’s “Unit 6 Assessment” (HTML)

    Instructions: Please complete the linked assessment.
     
    You must be logged into your Saylor Foundation School account in order to access this quiz.  If you do not yet have an account, you will be able to create one, free of charge, after clicking the link.