Cladistics Prelab Assignment 1

Dear Parents and Students,

All of my notes, calendars and tutorials are posted on SCHOOLOGY.  The information posted on this webpage is derived from the older curriculum and can be considered as extra information available for students who desire extra help.  Please sign in to your SCHOOLOGY ACCOUNT to receive this year's notes and lessons by clicking on the following link:   




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    •   National Pass Rate:    63.2%
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Welcome Students. The First section lists a ton of study sites for you to use as a reference throughout the year with practice AP exams and quizzes.  After the photos section is each unit's information, in order with support materials.



  Please feel free to email me @  if you have any questions.


STUDY TOOLS FOR YOU! (ALL Individual Unit Information begin after photos)



  -Lab Tutorials and Pre-lab Animations and Questions
      (Lab Bench AP Lab Tutorials)
 2)  AP BIOLOGY FLASH CARDS (all terms from each chapter!!)
        (chapters are off by one...our chapter 24 is their chapter 23)


 3)  BIOCOACH ACTIVITIES (helps review major concepts from each unit with quiz)



  4) PRACTICE TESTS AND QUIZZES FOR EACH UNIT!!! (check this out; worth doing!!




















   11)  Review AP Exams from REVIEW BOOKS

       - CampaignID=9248


  12) Cummulative list of ALL VOCAB TERMS/ALL CHAPTERS:   see how many you know!!




  1. Hamster Research Links
  • Hamster Genetics  (use this link for genetic info: we have Dwarf Campbell Russians...follow "Genetics" links to determine which traits are dominant).
  • Additional Hamster Genetics  (Hamster Genetics Direct Link)

AP Biology Dunes Succession Field Study, MILLER DUNES/PAUL H. DOUGLAS CENTER in Gary, Indiana. (September 23, 2011)

(AP Biology Macroinvertebrate Field Study, Bartel Grasslands and Frankfort Square
October, 2010)




(AP Biology Students at Indiana Dunes, Oct. 1, 2012 and Prairie, Yankee Woods

and Bartel Grasslands, November 20, 2012)




INTRODUCTION UNIT:  Themes/Experimental Design & Statistics

a) Chapter 1 Scientific Inquiry/Data Analysis

  • Emergence Video NOVA                                                                                                                                                                                

b)  StatisticsTutorials (Khan Academy) 


c) Statistics Labs with M&M's

d)  Practice Test Questions (Click on the

Unit I:  Biochemistry (Chapters 2-5)

Chapter 2:  Basic Chemistry Review 
 -Chapter 2 NOTES

 -Chapter 2 Powerpoint Notes
 -Chapter 2 Homework Study Guide
 -Chapter 2 Activity
- Emergent Properties Video
-Animations and Tutorials  (bonding, atomic number, ect)      

 -Bozeman Biology Tutorials                                                                                                                                                                  


  -Chapter 2 Practice Test   (click on chapter; select maximum question number 0f 40 )                                                                                                                                                                                                                                                                                    
Chapter 3:  Properties of Water
  • -Water Powerpoint
  • -Chapter 3 Notes Water Chemistry
  •  -Chapter 3 Homework Study Guide
  • -Water Properties Activity (Book)
  • -Bozeman Biology Tutorials                                                                                                                                                                                                           
- Chapter 3 Animations 
  • -pH Animation
  • -pH Tutorial
  • -Buffer Animation
  • - Lecture on Acid/Base/Buffers and pKa
  • -Cat drinking water
  • -Dog drinking water 


    • Chapter 3 Practice Test   (click on chapter; select maximum of 40 )                                                                                                                                                                                                       


Chapter 4:  Carbon Chemistry


Chapter 5 Macromolecules


Carbs Notes

Carbs Study guide

Lipid Notes

Lipid Studyguide

Protein Notes

Protein Study Guide

Nucleic Acids Notes

Nucleic Acid Study Guide



Extra Worksheets

Worksheet 4/5.1 Identify Macromolecules

Worksheet 4/5.2 Macromolecules

Chart Cheat Sheet for Macromolecules
Amino acids chart

ANIMATIONS Of Biological Molecules (Lipids, Proteins, Carbs, Nucleic Acids)
macromolecules animation
step by step biomolecules tutorial with quiz
types of chemical reactions animation
hydrolysis/dehydration synthesis animation 1
hydrolysis/dehydration synthesis animation 2
You tube animation of biomolecules (good one)
Protein Folding (know this one1)
Protein Folding and pH Animation
Protein Folding Again
Advanced Protein Folding
Amino Acids and pH animation

Review Self-Quizzes
Chapter 5 Practice quiz (Choose Chapter)
Functional groups Quiz Interactive
DNA vs. RNA quiz

Unit II:  Cell Energy  (Chapters 8-10)


Chapter 8 Thermodynamics/Enzymes



  1. Gibbs Energy and Thermodynamics Online Tutorials
  1. ENZYMES Animations and Tutorials


  1. Enzyme Lab #2:  One of the "Big 13" 





Chapter 9 Respiration


Chapter 10 Photosynthesis  

         look at all of the photosynthesis quizzez and take them...use the animations for photosynthesis under "Web Links" as

         a wonderful tutorial.  These worksheets and quizzez will be used in class as study tools. 



Unit III: Ecology Unit (CHAPTERS 51-55)

  • Chapter 51 Animal Behavior


  • Chapter 50 and 52:  Introduction to the Biosphere and Population Ecology


  • Chapter 52 Video Lecture:  Population Ecology   
      • Watch Population Ecology:  Unlimited Resources
      • Watch Population Ecology:  Limited Resources
      • Watch Population Ecology:  r versus K
      • Watch Pop. Ecol:  Intraspecific competition
      • Watch Pop. Ecol:  Interspecific competition
      • Watch Pop. Ecol:  Predation
      • Watch Pop. Ecol:  Niches and ALSO symbiosis!!



Chapter 53:  Community Ecology 


Semester 1 Ecology Review Question Answers (1-44)

Sem1 Ecology Sample Questions Review Answers


Unit IV:   Cell Biology Ch. 6,7,11,12


  • Cell Video Lectures Cell Techniques   (if you can't find video directly through link, search under my mindbites)


  • Cell Video Lectures, Cell Structure and Organelles

Chapter 7 Cell Membranes/Transport

Assignment 5: Classification and Dichotomous Keys

Work sheet for assignment 5
Work sheet as a pdf file(in case you cannot open a doc file)

Before you attempt this exercise you should have a thorough understanding of the material in the topicPhylogeny and Taxonomy.


Introduction to the tree of life

Categorizing organisms into related groups allows us to study the organisms with more ease. You rely on categorization in nearly every aspect of life. For example, similar foods are kept in the same section of a grocery store. You would not expect food items to be displayed in some random fashion with every store displaying different patterns. Under these conditions, how would you find a specific food item without spending hours searching every shelf? Similarly, scientists depend on classification or categorization schemes to organize life forms in meaningful ways.

You should be aware of a current project that attempts to bring together all biologists working on classification, so that all new information, especially with regard to larger groupings, such as kingdoms, phyla or classes, can be found in one place. The project is known as the Tree of Life webProject. Check it out at this website, then view the video that describes the project.

Video: The Tree of Life Project

As you watch the video, prepare to answer questions 1-3 on your work sheet.

Background on schools of classification

Biologists have always agreed that classification systems should reflect phylogeny, or evolutionary history, in some way, and that they should embody aspects of the scientific method. Biologist have not, however, agreed on the best way to do this. In this exercise, you will learn about three approaches that are currently being used. You will then work with one approach that allows you to test hypotheses about taxa (biological categories such as phylum, class, order, etc.) and their relationships to one another.  

The oldest approach to classification is known as classic, traditional or even evolutionary phylogeny. (The latter name is confusing, since all classification schemes attempt to produce evolutionary groupings.) Classically, taxon (taxa is plural) designations are based on homologous characters, traits that resemble each other because they are descended from a common ancestor. All traits that are homologous are considered to be have been molded by natural selection or genetic drift. For example, cytochrome c is a protein found in almost all organisms and is used as a character (a feature defining a taxon, taxonomic category, or group of organisms). Changes have occurred in the amino acid composition of this protein in an almost clockwork fashion. Since these changes appear with such regular timing, they are probably driven, for the most part, by genetic drift. Many of the higher taxa (family and above) have been defined according to characters that signify major lifestyle changes among related organisms, or adaptations to different environments. For example, birds and mammals are descended from reptilian ancestors, yet current reptiles, birds and mammals are all considered classes by the traditional approach, mostly characterized by features they exhibit for life on land.  

The classic school of classification has been criticized because some scientists feel that the characters used are somewhat arbitrary: the “pick” of experts in a given area of study.   Experts have disagreed about which characters best represent a group’s ancestry. They also disagree on the type of characters (molecular, behavioral, structural, etc.) to use, since different types of characters may conflict, or indicate different relationships among groups. There may also be disagreement over how to define or "weigh" a character. For example, assume you are dealing with a group that has several species that differ in whether or not they possess wings, and the number of wings present (one to four). Would you be a “lumper,” simply grouping species on the basis of having wings or not; or would you be a “splitter,” grouping species on the basis of having zero, one, two, etc. wings?  You can see that the lumper ends up with two groups while the splitter ends up with several groups.

The second school of classification is known as phenetics or numeral taxonomy and grew out of an effort to make classification more quantitative. It was very popular as computer use grew in the 1970s and 80s but has been replaced by cladistic efforts, the approach we will discuss next.Biologists who utilize phenetics attempt to use all data regarding similarities of organisms without much consideration of homology. They may consider similar features that are a result of convergent evolution, a process characterized by similarities arising independently among distantly related groups that exploit similar environments but do not share a common ancestor.  An example would be  insect wings and bird wings, which are of similar shape, yet have developed independently in the two groups. The logic behind this classification scheme is that, if large enough numbers of characters are used, then true homologies will obscure convergent features.  An index of similarity, based mainly on the number of characters shared, can be calculated for any two groups. Because of the large amount of data used in this system, pheneticists use the help of computers to compare a given group to any group that could possibly be related and then divide the organisms into appropriate taxa. There are rules, of course, governing exactly how the computer software chooses the groups to be compared and the order in which they are compared. Phenetics is still used by behaviorists and ecologists because computers can pick out associations on a multi-dimensional grid within any large number of characters, and so enable these biologists to pick out important relationships quickly by seeing which characters always cluster together.

The third school of classification is known as phylogenetic systematics, or cladistics. Within this school of classification, shared derived characters are the main evidence for phylogenetic relationships. A shared derived character is a special type of character that is shared by a particular group of species and its ancestor. If you find a character that is present in an ancestor but not in all of its descendants, then that character cannot, according to this school, be used to divide organisms into taxa. For example, feathers, and certain other skeletal features are used by the traditional school of classification to place birds into a separate class from their reptilian ancestors. However, many reptilian ancestors that have these same features gave rise to organisms other than birds. For that reason, cladists do not agree with this classification scheme because they do not believe these features to be derived characters. Also, other descendants evolving from the same basic reptilian ancestors, at about the same time as birds, do not have these features. Under the cladistic scheme, birds are considered simply a subgroup of the larger class Reptilia.

The cladistics system emphasizes how recently species shared an ancestor. In some sense, this system tries to step back through time and feature the splitting events, or the emergence of shared derived characters.  The relationships in trees that are developed through cladistics are called clades. This is the classification school adopted by your textbook because of its very precise way of grouping organisms.Cladistics tries to use as many derived characteristics as possible, including molecular distinctions. Therefore, practitioners of this school feel that they are providing a way for even non-experts to judge the accuracy of the relationship-groups (clades) that are produced.  

"Phylogeneticists differ from traditional systematists in that we employ empirical methods to reconstruct phylogenies and strictly evolutionary principles to form classifications rather than relying on intuition or authority. We differ from pheneticists in that our methods seek to find the genealogic relationships among the taxa we study rather than the phenetic or overall similarity relationships." (Wiley, E.O., D. Siegel-Causey, D.R. Brooks and V.A. Funk. 1991. The Complete Cladist. A Primer of Phylogenetic Procedures.. The University of Kansas Museum of Natural History Special Publication No. 19.)

The tree of life project uses the cladistic approach which explains why the branches on its phylogenetic trees are all terminal. You will see more of these cladograms later. Note that cladistics is now the most widely accepted classification scheme. 

In this activity, you will first borrow the idea of classifying organisms based on an index of similarity from the pheneticists because this is the easiest way for students to build relationship trees. This system provides you with a defined way to group the organisms being compared, and to test hypotheses about their relationships based on the number of similarities that they share. Also, it does not require knowledge about the evolutionary history of the organisms (fossils, molecular sequences, etc.) as would a cladistic approach.   To be able to construct indexes of similarity so that you can ask questions about relationships, given certain characters, you will be limited to comparing four groups at a time. This is because you will also have to determine all possible relationships for the groups under comparison (as a computer would). Your goal will be to select the relationship scheme that explains the greatest numbers of characters shared by at least two groups. 

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