Difference between revisions of "Evolutionary Biology Fall 2012"

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<span style="font-size: small">'''Meeting Time:''' Tuesdays and Thursdays, 12:30-1:45 in BRAUN 124<br>
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<span style="font-size: small">'''Meeting Time:''' Tuesdays and Thursdays, 12:30-1:45 in UTEB 150<br>
  
'''Instructor:'''  Chris Simon, Professor EEB <br>
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'''Instructor:'''  Chris Simon, Professor EEB, Office: Biopharm 305D, phone 6-4640, Lab: Biopharm 323 & 325, phone 6-3947;   <br>
'''Office:''' Biopharm 305D, phone 6-4640 <br>
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'''Lab:''' Biopharm 323 & 325, phone 6-3947  <br>
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'''e-mail:''' chris.simon@uconn.edu [e-mail is the best place to leave messages.]<br>
 
'''e-mail:''' chris.simon@uconn.edu [e-mail is the best place to leave messages.]<br>
  
Office hours: Flexible except in the morning before our class.  See me after class or send me an e-mail to arrange a meeting.  I encourage quick questions by electronic mail.  With longer questions or many questions, please come to see me or your TA, Colin Carlso. Don’t wait until the day before an exam!
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'''Office hours:''' Flexible except in the morning before our class.  See me after class or send me an e-mail to arrange a meeting.  I encourage quick questions by electronic mail.  With longer questions or many questions, please come to see me or your TA, Colin Carlson. Don’t wait until the day before an exam!
  
Teaching Assistant:  Colin Carlson
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'''Teaching Assistant:''' Colin Carlson, e-mail:  colin.carlson@uconn.edu
e-mail:  colin.carlson@uconn.edu
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Class Website:  http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Category:EEB_Courses
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'''Class Website:  http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Category:EEB_Courses
  
Grade: The goal of this class is to teach you the basic principles of evolution and to give you an appreciation for the science. It is important to me that you learn the material. I hate to assign grades but they are required.  Therefore I am trying an experiment this semester to try to lessen the pressure on the midterm and enhance your learning experience. Each Friday I will post a Study Guide and ask you a few questions from that study guide as a quiz at the end of class on the following Thursday. Each Wednesday, TA Colin Carlson will run a study guide review session. We’ll grade the quizzes and return them to you by the following Thursday.  Hopefully these quizzes will serve to prepare you for the first midterm and to ensure that your grade is not based on your performance on only the midterm and the final.
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'''Grade:''' The goal of this class is to teach you the basic principles of evolution and to give you an appreciation for the science. It is important to me that you learn the material. I hate to assign grades but they are required.  Therefore I am trying an experiment this semester to try to lessen the pressure on the midterm and enhance your learning experience. Each Friday I will post a Study Guide. Each Wednesday, TA Colin Carlson will host a study guide review session. Each Thursday at the end of class, as a quiz, I will ask you a few questions from that study guide. We’ll grade the quizzes and return them to you by the following Thursday.  Hopefully these quizzes will serve to prepare you for the first midterm and to ensure that your grade is not based on your performance on only the midterm and the final.
  
EEB 245: There will be a series of ten quizzes (as described above) and two one-hour exams covering each half of the course (listed on the syllabus) and a comprehensive one-hour synthetic final exam.  The second one-hour exam will be given in the same two-hour time block as the synthetic final.  The quizzes will count 15% of your total grade, the first exam 35% and the second hour exam plus the final will count 25% each.
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'''EEB 245:''' There will be a series of ten quizzes (as described above) and two one-hour exams covering each half of the course (listed on the syllabus) and a comprehensive one-hour synthetic final exam.  The second one-hour exam will be given in the same two-hour time block as the synthetic final.  The quizzes will count 10% of your total grade, the first exam 40% and the second hour exam plus the final will count 25% each.  
  
EEB  245W: If you are registered for EEB 245W, 75% of the final  course grade will be determined by your lecture exams (as above) and 25% by your term  paper.  As required by University regulations, an F in the W part of the course will result in an  F for  the  entire course.  At least two drafts of your writing assignment  must be  successfully completed to pass the course.  A detailed set of instructions will  be provided and W students will be assigned a W instructor during  the first week of class.
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'''EEB  245W:''' If you are registered for EEB 245W, 75% of the final  course grade will be determined by your lecture exams (as above) and 25% by your term  paper.  As required by University regulations, an F in the W part of the course will result in an  F for  the  entire course.  At least two drafts of your writing assignment  must be  successfully completed to pass the course.  A detailed set of instructions will  be provided and W students will be assigned a W instructor during  the first week of class.
  
Text: Futuyma, D. J. 2009.  Evolution. Second Edition.  Sinauer Publications, Sunderland, Mass. http://www.sinauer.com/detail.php?id=2238.  The UCONN coop should have lots of used copies.  Please read assigned chapters prior to the class for which they are scheduled.  Additional supplementary readings may be assigned during the semester.  See also new value options from Sinauer: http://www.sinauer.com/detail.php?id=2238#tions
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'''Text:''' Futuyma, D. J. 2009.  Evolution. Second Edition.  Sinauer Publications, Sunderland, Mass. http://www.sinauer.com/detail.php?id=2238.  The UCONN coop should have lots of used copies.  Please read assigned chapters prior to the class for which they are scheduled.  Additional supplementary readings may be assigned during the semester.  See also new value options from Sinauer: http://www.sinauer.com/detail.php?id=2238#tions <br>
  
The syllabus always evolves.  I will periodically send updated versions which track our true progress and introduce late breaking topics.
 
  
==Evolution in the News==
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'''Syllabus:'''  Download the PDF.  The syllabus always evolves.  I will periodically send updated versions which track our true progress and introduce late breaking topics. <br>
  
[http://www.physorg.com/news/2012-02-evolutionary.html '''Peppered moths vindicated!'''] - 28 February 2012<br>
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Syllabus%20EEB%202245%20F%202012%2029%20Nov%2012.rtf}}Syllabus EEB 2245 F 2012 29 Nov 12.rtf
[http://blogs.nature.com/news/2012/01/darwins-long-forgetten-fossils-unearthed.html '''Darwin's long-lost fossils'''] - 17 January 2012
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<br><br>
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==<span style="font-size: small"><font color="#FF3300">'''NEW'''</font></span> Visiting Evolutionary Biologists and Friends==
 
  
[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Visiting_Scientists_in_Evolutionary_Biology_Spring_2012 '''Our guests this semester''']<br><br>
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'''Quiz Keys:'''
  
==Lecture Syllabus==
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Quiz%201.%20%20History%2C%20Creationism.%20Key.docx}}Quiz 1.  History, Creationism. Key.docx
'''''Please read assigned chapters, as indicated below, prior to class'''''
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{| border="1" cellpadding="1"
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!width="40"|
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!width="40"|Day
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!width="150"|Date
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!width="350"|Topic
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!width=''450''|Text Readings
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|-
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| '''Part I''' || ||'''Jan 17 - Mar 1''' || <span style="font-size: large">'''Patterns of Evolution'''</span> || '''Dr. Janine Caira'''
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Quiz%202%2C%20Fall%2012%20Key.docx}}Quiz 2, Fall 12 Key.docx
| 1 || T || Jan 17 || Introduction to the Geological Time Scale; the Fossil Record || Ch. 4 (pgs 73-77)
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|-
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/EEB%202245.%20Quiz%203%20F%2012%20key%20rev.docx}}Quiz 3 F 12 key rev.docx
| 2 || Th || Jan 19 || Life in the Precambrian; Evolution of the Metazoa || Ch. 5 (pgs 101-108)
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|-
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|-
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Quiz%204.%20Load%2C%20Levels%20of%20Selection%2C%20Plasticity%20key.docx}}Quiz 4. Load, Levels of Selection, Plasticity key.docx
| 3 || T || Jan 24 || Cambrian explosion & Life in the Paleozoic || Ch. 5 (pgs 108-115)
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|-
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|-
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Quiz%205%2C%20F12%20EEB%202245%20key.docx}}Quiz 5, F12 EEB 2245 key.docx
| 4 || Th || Jan 26 || Life in the Mesozoic || Ch. 5 (pgs 115-121)
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|-
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|-
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Quiz%206%20F12%20Systematics%20%20Key.docx}}Quiz 6 F12 Systematics  Key.docx
| 5 || T || Jan 31 || Life in the Cenozoic || Ch. 5 (pgs 121-131)
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|-
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|-
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Quiz%207%2C%20F12%2C%20Molecules%20%26%20Clocks%20key.docx}}Quiz 7, F12, Molecules & Clocks key.docx
| 6 || Th || Feb 2 || Evolution of primates || Ch. 4 (pgs 88-91) &<br> Ch. 6 (pgs 147-150)
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|-
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|-
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Quiz%208.%20%20Life%20overview%2C%20Novelties%20%20Key.docx}}Quiz 8. Life overview, Novelties  Key.docx
| || '''''M''''' || '''''Feb 6''''' || '''''Review Session for Exam 1 <br>6-8 PM''''' || '''''BioPhysics Building Rm 131'''''
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|-
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|-
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Quiz%209.%20novelties%2C%20fossils%20to%20permian%20Key.docx}}Quiz 9. novelties, fossils to permian Key.docx
| 7 || T || Feb 7 || Evolution of biodiversity & extinction || Ch. 7
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|-
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|-
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'''Midterm Answer Key:'''
|  || '''''T''''' || '''''Feb 7''''' || '''''Review Session for Exam 1 <br>6-8 PM''''' || '''''BioPhysics Building Rm 131'''''
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|-
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|-
 
|<span style="font-size: small"><font color="#FF3300">'''8'''</font></span>||<span style="font-size: small"><font color="#FF3300">'''Th'''</font></span>||<span style="font-size: small"><font color="#FF3300">'''Feb 9'''</font></span>||<span style="font-size: small"><font color="#FF3300">'''EXAM #1'''<br>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Exam%20I%20S10%20version%201.pdf}} Example of Exam 1 (from 2010)</font></span><br><span style="font-size: small"><font color="#FF3300">{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Study_Guide_exam_1_2012_final.pdf}} Final Study Guide for Exam 1</font></span>||<span style="font-size: small"><font color="#FF3300">'''Covers Lectures 1-6'''</font></span>
 
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| 9 || T || Feb 14 || Characters, homology & homoplasy || Ch. 3
 
|-
 
  
|-
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'''Study Guides, Handouts:'''
| 10 || Th || Feb 16 || Systematics & reconstructing evolutionary history || Ch. 2
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|-
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|-
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Study%20Guide%20I%20EEB%202245%20F%2012%20.doc}}Study Guide I EEB 2245 F 12 .doc
| 11 || T || Feb 21 || Systematics & reconstructing evolutionary history (cont'd) || Ch. 2
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|-
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|-
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Darwin%20Chronology%20and%20Pus}}Darwin Chronology and Pubs (handout)
| 12 || Th || Feb 23 || Biogeography & major patterns of distribution || Ch. 6
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|-
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|-
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Architects%20of%20the%20Modern%20Synthesis}}Architects of the Modern Synthesis (Handout)
|  || '''''M''''' || '''''Feb 27''''' || '''''Review Session for Exam 2<br> 6-8 PM''''' || '''''BioPhysics Building Rm 131'''''
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|-
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|-
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Study%20Guide%202.%20EEB%202245%20%20Fall%2012Hardy%20Weinberg.rtf}}Study Guide 2. EEB 2245  Fall 12Hardy Weinberg.rtf
| 13 || T || Feb 28 || Continental drift & historical biogeography || Ch. 6
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|-
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|-
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Study%20Guide%203.%20EEB%202245%20%20Fall%2012%20Bottlenecks%2C%20Founders%2C%20Selection.rtf}}Study Guide 3. EEB 2245 Fall 12 Bottlenecks, Founders, Selection.rtf
| || '''''T''''' || '''''Feb 28''''' || '''''Review Session for Exam 2<br> 6-8 PM''''' || '''''BioPhysics Building Rm 131'''''
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|-
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Natural%20Selection%20Review%20Table.pdf}}Natural Selection Review Table.pdf
| '''Part II''' || || '''Mar 6 - Apr 26''' || <span style="font-size: large">'''Processes of Evolution'''</span> || '''Dr. Charles Henry'''
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|-
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Study%20Guide%204.%20F12%20Selection%20II%20rev.doc}}Study Guide 4. F12 Selection II rev.doc
| <span style="font-size: small"><font color="#FF3300">'''14'''</font></span> ||<span style="font-size: small"><font color="#FF3300">'''Th''' </font></span>||<span style="font-size: small"><font color="#FF3300"> '''Mar 1''' </font></span>|| <span style="font-size: small"><font color="#FF3300">'''EXAM #2'''</font></span><span style="font-size: small"><font color="#FF3300"><br><span style="font-size: small"><font color="#FF3300">{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Exam%202%20S2010.pdf}} Example of Exam 2 (from 2010)</font></span><span style="font-size: small"><font color="#FF3300"><br>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Study%20Guide%20Exam%202_2012_final.pdf}}FINAL Study Guide for Exam 2</font></span><br><span style="font-size: small"><font color="#FF3300">{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/EEB%202245_W_S12_tree_exercises_rev.pdf}} Tree Exercises for Exam 2 (with answers)</font></span>|| <span style="font-size: small"><font color="#FF3300">'''Covers Lectures 7 & 9-13'''</font></span>
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|-
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|-
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Study%20Guide%205.%20F12%20variation%20isolation%20speciation.doc}}Study Guide 5. F12 variation isolation speciation.doc
| 15 || T || Mar 6 || Populations, variation, & the Hardy-Weinberg principle
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/EEB2245_12_lec1_variation.pdf}} '''Populations, Variation, and H-W Lecture'''
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|| Ch. 1 (pp 7-11) & Ch. 9
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|-
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|-
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Study%20Guide%206%20Hybridization.docx}}Study Guide 6 Hybridization.docx
| 16 || Th || Mar 8 || Microevolution and the origin of variation: mutation & gene flow
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/EEB2245_12_lec2_popgen_muta%26migra.pdf}} '''Mutation and Gene Flow (Migration) Lecture'''
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|| Ch. 8
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|-
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|-
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Lect%2015.%20Handout%20Constructing%20Evolutionary%20Trees%202012.pdf}}Lect 16. Handout Constructing Evolutionary Trees 2012.pdf
|  || '''T''' || '''Mar 13''' || '''SPRING BREAK - no class'''||
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|-
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|-
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Study%20Guide%207.%20Systematics.%20F%2012.pdf}}Study Guide 7. Systematics. F 12.pdf
|  || '''Th''' || '''Mar 15''' || '''SPRING BREAK - no class''' ||
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|-
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|-
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Study%20Guide%207%20answers%20systematics%20%20F%2012.rtf}}Study Guide 7 answers systematics F 12.rtf
| 17 || T || Mar 20 || Agents of evolutionary change: migration and genetic drift
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/EEB2245_12_lec3_genetic_drift.pdf}} '''Migration (concl.) & Genetic Drift Lecture'''
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  || Ch. 9 & 10
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|-
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|-
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Study%20Guide%208%20Clocks%2C%20Life%20F%2012.docx}}Study Guide 8 Clocks, Life F 12.docx
| 18 || Th || Mar 22 || Charles Darwin and natural selection
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/EEB2245_12_lec4_selection1.pdf}} '''Darwin & Natural Selection Lecture, Part 1'''
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|| Ch. 1 & 11
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|-
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|-
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Study%20Guide%209%2C%20F12%2C%20Novelties.docx}}Study Guide 9, F12, Novelties.docx
| 19 || T || Mar 27 || Natural selection and phenotypic evolution
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/EEB2245_12_lec5_selection2.pdf}} '''Natural Selection Lecture, Part 2'''
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|| Ch. 12 & 13
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|-
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|-
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Study%20Guide%20Lect%2021%20Paleozoic%20F%2012.rtf}}Study Guide 10, Fossil Overview & Paleozoic F 12.rtf
| 20 || Th || Mar 29 || Adaptation; introduction to life-history evolution
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/EEB2245_12_lec6_adaptation.pdf}} '''Adaptation & Life History Lecture, Part 1'''
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|| Ch. 11, 14, & 22
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|-
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|-
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Study%20Guide%2011.%20Mesozoic%20%20F%2012.rtf}}Study Guide 11. Mesozoic F 12.rtf
| || '''''M''''' || '''''Apr 2''''' || '''''Review Session for Exam 3 <br>6-8 PM''''' || '''''BioPhysics Building Rm 131'''''
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|-
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|-
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Study%20Guide%2012.%20Cenozoic%20and%20Fossil%20Record%20Summary%20F12.doc}}Study Guide 12. Cenozoic and Fossil Record Summary F12.doc
| 21 || T || Apr 3 || Life history evolution
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/EEB2245_12_lec7_lifehistory.pdf}} '''Life History Evolution, Part 2'''
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|| Ch. 14
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|-
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|-
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Study%20guide%2013.%20Human%20Evolution%20Biodiversity%20Biogeography.rtf}}Study guide 13. Human Evolution Biodiversity Biogeography.rtf
|  || '''''T''''' || '''''Apr 3''''' || '''''Review Session for Exam 3 <br>6-8 PM''''' || '''''BioPhysics Building Rm 131'''''
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|-
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|-
 
| <span style="font-size: small"><font color="#FF3300">'''22'''</font></span> || <span style="font-size: small"><font color="#FF3300">'''Th'''</font></span> || <span style="font-size: small"><font color="#FF3300">'''Apr 5'''</font></span> || <span style="font-size: small"><font color="#FF3300">'''EXAM #3'''</font></span><span style="font-size: small"><font color="#FF3300"><br><span style="font-size: small"><font color="#FF3300">'''You may bring a calculator (NO iphone/smartphone)'''</font></span><br><span style="font-size: small"><font color="#FF3300">{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Exam_Studyguide1_Henry_2245.pdf}} FINAL Study Guide for Exam 3 (first 7 lectures) </font></span><span style="font-size: small"><font color="#FF3300"><br>|| <span style="font-size: small"><font color="#FF3300">'''Covers Lectures 15-21'''</font></span>
 
|-
 
  
|-
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'''Lecture notes:'''  
| 23 || T || Apr 10 || Sexual selection
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/EEB2245_12_lec8_sex%26sexselec.pdf}} '''Sexual Selection Lecture'''
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|| Ch. 15
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|-
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 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/EEB%202245%20Lecture%201%202012.pdf}}EEB 2245 Lect. 1 Intro (four per page) 2012.pdf
  
|-
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/EEB%202245%20Lecture%201%202012%20-%20lines%20for%20notes.pdf}}EEB 2245 Lect. 1 Intro 2012 (with lines).pdf
| 24 || Th || Apr 12 || Levels of selection; cooperation & altruism
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/EEB2245_12_lec9_levels%26cooperation.pdf}} '''Multi-level Selection Lecture'''
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|| Ch. 11 & 16
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|-
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|-
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/EEB%202245%20Lecture%202%202012%20-%20lines%20for%20notes.pdf}}EEB 2245 Lec. 2 Evidence 2012 (with lines).pdf
| 25 || T || Apr 17 || Macroevolution: species and species concepts
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/EEB2245_12_lec10_species.pdf}} '''Species and Species Concepts Lecture'''
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|| Ch. 17 & 18
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|-
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|-
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/EEB%202245%20Lecture%203%202012%20%28with%20lines%29.pdf}}EEB 2245 Lect. 3 History 2012 (with lines).pdf
| 26 || Th || Apr 19 || Ecotypes, clines, and allopatric speciation
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/EEB2245_12_lec11_speciation1.pdf}} '''Lecture on Speciation, Part 1'''
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|| Ch. 17 & 18
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|-
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|-
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Lect%203.%20History%20%286%20per%20page%29%20EEB2245.pdf}}EEB 2245 Lect 3. History (6 per page) EEB2245.pdf
| 27 || T || Apr 24 || Allopatric & non-allopatric speciation
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/EEB2245_12_lec12_speciation2.pdf}} '''Lecture on Speciation, Part 2'''
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|| Ch. 18
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|-
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|-
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Lecture%204.%20Population%20Biology%2C%20HW.pdf}}  EEB 2245 Lect. 4. Population Biology, HW (4 per page).pdf
| 28 || Th || Apr 26 || The mystery of sexual reproduction; coevolution
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/EEB2245_12_lec13_sex%26coevol.pdf}} '''Sexual Reproduction and Coevolution Lecture'''
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  || Ch. 15 & 19
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|-
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|-
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/EEB%202245%20Lecture%204%202012%20%28with%20lines%29.pdf}}EEB 2245 Lect. 4 Population Biology 2012 (with lines).pdf
|  || '''''M''''' || '''''Apr 30''''' || '''''Review Session for Final Exam <br>6-8 PM''''' || '''''BioPhysics Building Rm 131'''''
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|-
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|-
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:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Lecture%205.%20%20Deviations%20from%20HW%20F12.pdf}}EEB 2245 Lect. 5.  Deviations from HW F12.pdf
|  || '''''T''''' || '''''May 1''''' || '''''Review Session for Final Exam <br>6-8 PM''''' || '''''BioPhysics Building Rm 131'''''
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|-
+
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/EEB%202245%20Lect%206.%20H-W%20selection%2C%20%20Inbreeding%20%26%20Drift%20Geneflow.pdf}}EEB 2245 Lect 6. H-W selection,  Inbreeding & Drift Geneflow.pdf
 +
 
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/EEB%202245%20Lecture%205%202012%20%28with%20lines%29.pdf}}EEB 2245 Lecture 5 2012 (with lines).pdf
 +
 
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/EEB%202245%20Lecture%206%20%28with%20lines%29.pdf}}EEB 2245 Lect. 6 (with lines).pdf
 +
 
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/EEB%202245%20Lect%207.%20Inbreeding%2C%20gene%20flow%2C%20selection.pdf}}EEB 2245 Lect 7. Inbreeding, gene flow, selection.pdf
 +
 
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/EEB%202245%20Lecture%207%202012%20%28with%20lines%29.pdf}}EEB 2245 Lect. 7 2012 (with lines).pdf
 +
 
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/EEB%202245%20Lect.%208.%20%20Selection%20I%20revised%20F12.pdf}}EEB 2245 Lect. 8.  Selection I revised F12.pdf
 +
 
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Lect.%209.%20%20Natural%20Selection%20II%20%20F12.pdf}}EEB 2245 Lect. 9. Natural Selection II plasticity coevolution F12.pdf
 +
 
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/9-25%20lecture.pdf}}EEB 2245 Lect. 9. (with lines).pdf
 +
 
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Lect.%2010.%20Geographic%20Variation.pdf}}EEB 2245 Lect. 10. Load, Geographic Variation.pdf
 +
 
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Lecture%2010%20%28with%20lines%29.pdf}}Lecture 10 (with lines).pdf
 +
 
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Lect.%2011%20%20Factors%20reducing%20geneflow%20F%2012.%20Speciation.pdf}}EEB 2245 Lect. 11 Geog. Var. (cont) Factors reducing geneflow.pdf
 +
 
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Lecture%2011%20%28with%20lines%29.pdf}}Lecture 11 (with lines).pdf
 +
 
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/EEB%202245%20Lect.%2012%20Isolation%2C%20species%20concepts.pdf}}EEB 2245 Lect. 12 Isolation, species concepts.pdf
 +
 
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Lecture%2012%20%28with%20lines%29.pdf}}Lecture 12 (with lines).pdf
 +
 
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Lect.%2013.%20Speciation%20Mechanisms.pdf}}EEB 2245 Lect. 13. Speciation Mechanisms.pdf
 +
 
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Lecture%2013%20%28with%20lines%29.pdf}}Lecture 13 (with lines).pdf
 +
 
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Lect%2014.%20Hybridization.pdf}}EEB 2245 Lect 14. Hybridization.pdf
 +
 
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Lecture%2014%20%28with%20lines%29.pdf}}Lecture 14 (with lines).pdf
 +
 
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Lect.%2015.%20Systematics%20EEB%202245%20F%202012.pdf}}Lect. 15. Systematics EEB 2245 F 2012.pdf
 +
 
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Lect.%2016%20F12%20Building%20Trees%2023Oct12.pdf}}Lect. 16 F12 Building Trees 23Oct12.pdf
 +
 
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Lecture%2016.pdf}}Lecture 16 (with lines).pdf
 +
 
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Lect.%2017%20F12%20Building%20Trees%20Morph.%20Molec.%20Evolution%20Rev%20F12.pdf}}Lect. 17 F12 Building Trees Morph. Molec. Evolution Rev F12.pdf
 +
 
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Lecture%2018%20with%20lines.pdf}}Lecture 18 with lines.pdf
 +
 
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/EEB%202245%20Lect%2019.%20pt%201.%20Overview%20of%20life.pdf}}EEB 2245 Lect 19. pt 1. Overview of life.pdf
 +
 
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/EEB%202245%20Lect.%2019%20pt%202%2C%20overview%20of%20life.pdf}}EEB 2245 Lect. 19 pt 2, Overview of life.pdf
 +
 
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Lect%2020.%20Part%20I.%20Evolutionary%20Novelties%20F%2012.pdf}}Lect 20. Part I. Evolutionary Novelties F 12.pdf
 +
 
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Lect%2020.%20Part%202.%20Evolutionary%20Novelties%20F%2012-2.pdf}}Lect 20. Part 2. Evolutionary Novelties F 12-2.pdf
 +
 
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Lecture%2021.%20Novelties%20Fossil%20overview.pdf}}Lecture 21. Novelties Fossil overview F12.pdf
 +
 
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Lect.%2022.%20Paleozoic%20F12.pdf}}Lect. 22. Paleozoic F12.pdf
 +
 
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Lect.%2023.%20Mesozoic%20Part%201%20F12.pdf}}Lect. 23. Mesozoic Part 1 F12.pdf
 +
 
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/%20Lect.%2023.%20Part%202.%20Mesozoic%20F12.pdf}} Lect. 23. Part 2. Mesozoic F12.pdf
 +
 
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Lect.%2024.%20Cenozoic%20%28Paleocene-Eocene%29%2029%20Nov%20F12-2.pdf}}Lect. 24. Cenozoic (Paleocene-Eocene) 29 Nov F12-2.pdf
 +
 
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Lect.%2025.%20Cenozoic%20%26%20Human%20Evolution%20Part%201.pdf}}Lect. 25. Cenozoic & Human Evolution Part 1.pdf
 +
 
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Lect.%2025.%20Part%202%20Cenozoic%20%26%20Human%20Evolution.pdf}}Lect. 25. Part 2 Cenozoic & Human Evolution.pdf
 +
 
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Lecture%2025.%26%2026.%20%20Human%20Evolution.pdf}}Lecture 25.& 26.  Human Evolution.pdf
 +
 
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Lect%2026%20Biodiversity%20%26%20Biogeography%20F12.pdf}}Lect 26 Biodiversity & Biogeography F12.pdf
 +
 
 +
 
 +
==Evolution in the News, Scientific Literature, and You Tube==
 +
 
 +
[http://www.sheffield.ac.uk/news/nr/family-tree-birds-evolution-sheffield-university-1.220940?utm_source=facebook&utm_medium=social%2Bmedia&utm_content=famiy-tree-birds&utm_campaign=generic '''Bird Tree of Life''']- 30 Oct 2012
 +
 
 +
[http://www.youtube.com/watch?feature=player_embedded&v=9GgAbyYDFeg '''Watch your back mate! Courtship of peacock spider <i> Maratus volans </i> from Australia''']- 23 Mar 2011
 +
 
 +
[http://www.npr.org/2012/09/26/161817096/mammalian-surprise-african-mouse-can-regrow-skin '''African mouse sheds patches of skin and hair to escape predators''']- 26 Sep 2012
 +
 
 +
[http://www.npr.org/blogs/thetwo-way/2012/09/13/161097374/monkey-new-to-science-found-in-central-africa?ps=rec&ec=mostpopularnews'''Cool Looking Monkey New to Science Found in Congo''']- 14 Sep 12
 +
 
 +
[http://www.physorg.com/news/2012-02-evolutionary.html '''Peppered moths vindicated!'''] - 28 February 2012<br>
 +
[http://blogs.nature.com/news/2012/01/darwins-long-forgetten-fossils-unearthed.html '''Darwin's long-lost fossils'''] - 17 January 2012
 +
 
 +
[http://simbio.com/blog/post/a-case-suspended-animation'''H1N1- A case of suspended animation''']- 29 Aug 2012 
 +
 
 +
Tool use evolution
 +
 
 +
[http://onlinelibrary.wiley.com/doi/10.1046/j.1461-0248.2002.00370.x/full'''Tool Use Evolution''']- Sept 2002
 +
 
 +
“Tool-use is commonly attributed to humans and other primates. However, several bird species are also known to use tools habitually. Egyptian vultures (Neophron percnopterus) are famous for dropping stones on ostrich eggs (Van Lawick-Goodall & Van Lawick-Goodall 1966), green-backed herons (Butroides striatus) use bait to catch fish (Walsh et al. 1985), satin bower birds (Ptilonorhynchus violaecus) use bark-wads to paint their bower (Chaffer 1945), and New Caledonian crows (Corvus moneduloides) make and use two forms of tools to capture prey (Hunt 1996). The woodpecker finch (Cactospiza pallida), one of 15 species of Darwin's Finches, is perhaps the most famous example of a tool-using bird. It uses twigs or cactus spines to pry arthropods from tree-holes and crevices (Eibl-Eibesfeldt 1961; Eibl-Eibesfeldt & Sielman 1962)…. social learning is not an important mechanism in the acquisition of tool-use in the woodpecker finch (Tebbich et al. 2001).”
 +
 
 +
<br><br>
  
|-
 
| 29 ||<span style="font-size: small"><font color="#FF3300"> '''Th'''</font></span> || <span style="font-size: small"><font color="#FF3300">'''May 3, 8 AM - 10AM'''<br></font></span> || <span style="font-size: small"><font color="#FF3300">'''FINAL EXAM'''</font></span><span style="font-size: small"><font color="#FF3300"><br><span style="font-size: small"><font color="#FF3300">'''NO calculators, NO iphone/smartphone'''</font></span><br><span style="font-size: small"><font color="#FF3300">:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Exam_Studyguide_2245_final_exam.pdf}} FINAL Study Guide for Exam 4 (last 6 lectures) </font></span><span style="font-size: small"><font color="#FF3300"><br>|| <span style="font-size: small"><font color="#FF3300">'''Covers Lectures 23-28'''</font></span>
 
|-
 
  
|- |-]}
 
 
<br>
 
<br>
[[Category:EEB Courses]]
 

Latest revision as of 13:28, 13 April 2017

EEB 2245: Evolutionary Biology


Meeting Time: Tuesdays and Thursdays, 12:30-1:45 in UTEB 150

Instructor: Chris Simon, Professor EEB, Office: Biopharm 305D, phone 6-4640, Lab: Biopharm 323 & 325, phone 6-3947;
e-mail: chris.simon@uconn.edu [e-mail is the best place to leave messages.]

Office hours: Flexible except in the morning before our class. See me after class or send me an e-mail to arrange a meeting. I encourage quick questions by electronic mail. With longer questions or many questions, please come to see me or your TA, Colin Carlson. Don’t wait until the day before an exam!

Teaching Assistant: Colin Carlson, e-mail: colin.carlson@uconn.edu

Class Website: http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Category:EEB_Courses

Grade: The goal of this class is to teach you the basic principles of evolution and to give you an appreciation for the science. It is important to me that you learn the material. I hate to assign grades but they are required. Therefore I am trying an experiment this semester to try to lessen the pressure on the midterm and enhance your learning experience. Each Friday I will post a Study Guide. Each Wednesday, TA Colin Carlson will host a study guide review session. Each Thursday at the end of class, as a quiz, I will ask you a few questions from that study guide. We’ll grade the quizzes and return them to you by the following Thursday. Hopefully these quizzes will serve to prepare you for the first midterm and to ensure that your grade is not based on your performance on only the midterm and the final.

EEB 245: There will be a series of ten quizzes (as described above) and two one-hour exams covering each half of the course (listed on the syllabus) and a comprehensive one-hour synthetic final exam. The second one-hour exam will be given in the same two-hour time block as the synthetic final. The quizzes will count 10% of your total grade, the first exam 40% and the second hour exam plus the final will count 25% each.

EEB 245W: If you are registered for EEB 245W, 75% of the final course grade will be determined by your lecture exams (as above) and 25% by your term paper. As required by University regulations, an F in the W part of the course will result in an F for the entire course. At least two drafts of your writing assignment must be successfully completed to pass the course. A detailed set of instructions will be provided and W students will be assigned a W instructor during the first week of class.

Text: Futuyma, D. J. 2009. Evolution. Second Edition. Sinauer Publications, Sunderland, Mass. http://www.sinauer.com/detail.php?id=2238. The UCONN coop should have lots of used copies. Please read assigned chapters prior to the class for which they are scheduled. Additional supplementary readings may be assigned during the semester. See also new value options from Sinauer: http://www.sinauer.com/detail.php?id=2238#tions


Syllabus: Download the PDF. The syllabus always evolves. I will periodically send updated versions which track our true progress and introduce late breaking topics.

Pdficon small.gifSyllabus EEB 2245 F 2012 29 Nov 12.rtf


Quiz Keys:

Pdficon small.gifQuiz 1. History, Creationism. Key.docx
Pdficon small.gifQuiz 2, Fall 12 Key.docx
Pdficon small.gifQuiz 3 F 12 key rev.docx
Pdficon small.gifQuiz 4. Load, Levels of Selection, Plasticity key.docx
Pdficon small.gifQuiz 5, F12 EEB 2245 key.docx
Pdficon small.gifQuiz 6 F12 Systematics Key.docx
Pdficon small.gifQuiz 7, F12, Molecules & Clocks key.docx
Pdficon small.gifQuiz 8. Life overview, Novelties Key.docx
Pdficon small.gifQuiz 9. novelties, fossils to permian Key.docx

Midterm Answer Key:


Study Guides, Handouts:

Pdficon small.gifStudy Guide I EEB 2245 F 12 .doc
Pdficon small.gifDarwin Chronology and Pubs (handout)
Pdficon small.gifArchitects of the Modern Synthesis (Handout)
Pdficon small.gifStudy Guide 2. EEB 2245 Fall 12Hardy Weinberg.rtf
Pdficon small.gifStudy Guide 3. EEB 2245 Fall 12 Bottlenecks, Founders, Selection.rtf
Pdficon small.gifNatural Selection Review Table.pdf
Pdficon small.gifStudy Guide 4. F12 Selection II rev.doc
Pdficon small.gifStudy Guide 5. F12 variation isolation speciation.doc
Pdficon small.gifStudy Guide 6 Hybridization.docx
Pdficon small.gifLect 16. Handout Constructing Evolutionary Trees 2012.pdf
Pdficon small.gifStudy Guide 7. Systematics. F 12.pdf
Pdficon small.gifStudy Guide 7 answers systematics F 12.rtf
Pdficon small.gifStudy Guide 8 Clocks, Life F 12.docx
Pdficon small.gifStudy Guide 9, F12, Novelties.docx
Pdficon small.gifStudy Guide 10, Fossil Overview & Paleozoic F 12.rtf
Pdficon small.gifStudy Guide 11. Mesozoic F 12.rtf
Pdficon small.gifStudy Guide 12. Cenozoic and Fossil Record Summary F12.doc
Pdficon small.gifStudy guide 13. Human Evolution Biodiversity Biogeography.rtf


Lecture notes:

Pdficon small.gifEEB 2245 Lect. 1 Intro (four per page) 2012.pdf
Pdficon small.gifEEB 2245 Lect. 1 Intro 2012 (with lines).pdf
Pdficon small.gifEEB 2245 Lec. 2 Evidence 2012 (with lines).pdf
Pdficon small.gifEEB 2245 Lect. 3 History 2012 (with lines).pdf
Pdficon small.gifEEB 2245 Lect 3. History (6 per page) EEB2245.pdf
Pdficon small.gif EEB 2245 Lect. 4. Population Biology, HW (4 per page).pdf
Pdficon small.gifEEB 2245 Lect. 4 Population Biology 2012 (with lines).pdf
Pdficon small.gifEEB 2245 Lect. 5. Deviations from HW F12.pdf
Pdficon small.gifEEB 2245 Lect 6. H-W selection, Inbreeding & Drift Geneflow.pdf
Pdficon small.gifEEB 2245 Lecture 5 2012 (with lines).pdf
Pdficon small.gifEEB 2245 Lect. 6 (with lines).pdf
Pdficon small.gifEEB 2245 Lect 7. Inbreeding, gene flow, selection.pdf
Pdficon small.gifEEB 2245 Lect. 7 2012 (with lines).pdf
Pdficon small.gifEEB 2245 Lect. 8. Selection I revised F12.pdf
Pdficon small.gifEEB 2245 Lect. 9. Natural Selection II plasticity coevolution F12.pdf
Pdficon small.gifEEB 2245 Lect. 9. (with lines).pdf
Pdficon small.gifEEB 2245 Lect. 10. Load, Geographic Variation.pdf
Pdficon small.gifLecture 10 (with lines).pdf
Pdficon small.gifEEB 2245 Lect. 11 Geog. Var. (cont) Factors reducing geneflow.pdf
Pdficon small.gifLecture 11 (with lines).pdf
Pdficon small.gifEEB 2245 Lect. 12 Isolation, species concepts.pdf
Pdficon small.gifLecture 12 (with lines).pdf
Pdficon small.gifEEB 2245 Lect. 13. Speciation Mechanisms.pdf
Pdficon small.gifLecture 13 (with lines).pdf
Pdficon small.gifEEB 2245 Lect 14. Hybridization.pdf
Pdficon small.gifLecture 14 (with lines).pdf
Pdficon small.gifLect. 15. Systematics EEB 2245 F 2012.pdf
Pdficon small.gifLect. 16 F12 Building Trees 23Oct12.pdf
Pdficon small.gifLecture 16 (with lines).pdf
Pdficon small.gifLect. 17 F12 Building Trees Morph. Molec. Evolution Rev F12.pdf
Pdficon small.gifLecture 18 with lines.pdf
Pdficon small.gifEEB 2245 Lect 19. pt 1. Overview of life.pdf
Pdficon small.gifEEB 2245 Lect. 19 pt 2, Overview of life.pdf
Pdficon small.gifLect 20. Part I. Evolutionary Novelties F 12.pdf
Pdficon small.gifLect 20. Part 2. Evolutionary Novelties F 12-2.pdf
Pdficon small.gifLecture 21. Novelties Fossil overview F12.pdf
Pdficon small.gifLect. 22. Paleozoic F12.pdf
Pdficon small.gifLect. 23. Mesozoic Part 1 F12.pdf
Pdficon small.gif Lect. 23. Part 2. Mesozoic F12.pdf
Pdficon small.gifLect. 24. Cenozoic (Paleocene-Eocene) 29 Nov F12-2.pdf
Pdficon small.gifLect. 25. Cenozoic & Human Evolution Part 1.pdf
Pdficon small.gifLect. 25. Part 2 Cenozoic & Human Evolution.pdf
Pdficon small.gifLecture 25.& 26. Human Evolution.pdf
Pdficon small.gifLect 26 Biodiversity & Biogeography F12.pdf


Evolution in the News, Scientific Literature, and You Tube

Bird Tree of Life- 30 Oct 2012

Watch your back mate! Courtship of peacock spider Maratus volans from Australia- 23 Mar 2011

African mouse sheds patches of skin and hair to escape predators- 26 Sep 2012

Cool Looking Monkey New to Science Found in Congo- 14 Sep 12

Peppered moths vindicated! - 28 February 2012
Darwin's long-lost fossils - 17 January 2012

H1N1- A case of suspended animation- 29 Aug 2012

Tool use evolution

Tool Use Evolution- Sept 2002

“Tool-use is commonly attributed to humans and other primates. However, several bird species are also known to use tools habitually. Egyptian vultures (Neophron percnopterus) are famous for dropping stones on ostrich eggs (Van Lawick-Goodall & Van Lawick-Goodall 1966), green-backed herons (Butroides striatus) use bait to catch fish (Walsh et al. 1985), satin bower birds (Ptilonorhynchus violaecus) use bark-wads to paint their bower (Chaffer 1945), and New Caledonian crows (Corvus moneduloides) make and use two forms of tools to capture prey (Hunt 1996). The woodpecker finch (Cactospiza pallida), one of 15 species of Darwin's Finches, is perhaps the most famous example of a tool-using bird. It uses twigs or cactus spines to pry arthropods from tree-holes and crevices (Eibl-Eibesfeldt 1961; Eibl-Eibesfeldt & Sielman 1962)…. social learning is not an important mechanism in the acquisition of tool-use in the woodpecker finch (Tebbich et al. 2001).”