Difference between revisions of "Evolutionary Biology Spring 2011"

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<span style="font-size: medium">EEB2245/2245W: The objectives of this course are to familiarize students with the mechanisms of evolutionary change (processes of evolution), major patterns of evolution, and the history of the diversity of life.</span><br>
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<span style="font-size: large">EEB2245/2245W: </span><br><span style="font-size: medium">The objectives of this course are to familiarize students with the mechanisms of evolutionary change (processes of evolution), major patterns of evolution, and the history of the diversity of life.</span><br>
  
 
== Course Overview ==
 
== Course Overview ==
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<td></td><td>[http://news.uconn.edu/emergency_closings.php Emergency closing information]</td>
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<td></td><td>[http://today.uconn.edu/?page_id=1041 Emergency closing information]</td>
 
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<td>Web site:</td><td> [http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/EEB_2245/2245W_Evolutionary_Biology_Spring_2011 http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/EEB_2245/2245W_Evolutionary_Biology_Spring_2011]</td>
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<td></td><td> (can be purchased at discount as an e-book or in loose leaf sections)</td>
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<br>
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Revised Syllabus for second half of semester {{pdf|http://hydrodictyon.eeb.uconn.edu/people/ewade/EEB2245/EEB2245_Syllabus_Revised.pdf}}  <br>
  
 
=== EEB 2245W ===
 
=== EEB 2245W ===
 
In addition to this web site those of you who are enrolled in the W part of the course will want to refer to the [http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/EEB2245W_%28Spring_2011%29 EEB 2245W web site] for information about W assignments and requirements.
 
In addition to this web site those of you who are enrolled in the W part of the course will want to refer to the [http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/EEB2245W_%28Spring_2011%29 EEB 2245W web site] for information about W assignments and requirements.
 +
<br><br>
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 +
==Announcements==
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 +
 +
'''Study Sessions for Exam 2/Final Exam'''<br>
 +
Friday April 29 2:30-4:30pm TLS 313<br>
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Monday May 2 7:30-9:30pm BPB 130<br>
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Tuesday May 3 2-4pm<br>
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<span style="font-size: small"><font color="#FF3300">'''Room Change for Tuesday study session to Physics Building  Room 36'''</font></span> <span style="font-size: small">
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<br>
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 +
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'''Study Guide for first half of semester'''<br>
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A number of you have emailed to ask advice on preparing for my part of final exam, so I've put together a {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/eeb245W/EEB2245FinalExamStudyGuide_S2011.pdf }}'''Study Guide''' that lists many of the major concepts and applications we covered.  Note that the study guide is not intended to be comprehensive (e.g., it doesn't cover specific examples), but going through it should provide a good refresher.  I also highly recommend working some practice problems again.
 +
 +
Good luck!<br>
 +
Prof. Jockusch
  
 
==Instructors==
 
==Instructors==
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Office: Biology/Pharmacy 305B<br>
 
Office: Biology/Pharmacy 305B<br>
 
Phone: (860) 486-4452<br>
 
Phone: (860) 486-4452<br>
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Office hours: , and by appointment<br><br>
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Office hours: 11-12 on Tuesdays and by appointment<br><br>
  
 
'''[mailto:chris.simon@uconn.edu Dr. Chris Simon]'''<br>
 
'''[mailto:chris.simon@uconn.edu Dr. Chris Simon]'''<br>
 
Office: Biology/Pharmacy 305D<br>
 
Office: Biology/Pharmacy 305D<br>
 
Phone: (860) 486-4640<br>
 
Phone: (860) 486-4640<br>
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Office hours:  pm and by appointment<br><br>
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Office hours:  anytime by appointment<br><br>
  
 
'''[mailto:elizabeth.wade@uconn.edu Beth Wade]''' (Teaching Assistant)<br>
 
'''[mailto:elizabeth.wade@uconn.edu Beth Wade]''' (Teaching Assistant)<br>
 
Office: Torrey Life Sciences 461<br>
 
Office: Torrey Life Sciences 461<br>
 
Phone: (860) 486-3947<br>
 
Phone: (860) 486-3947<br>
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Office hours:  and by appointment<br><br>
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Office hours:  10-11 on Wednesdays and by appointment<br><br>
  
 
==Grading==
 
==Grading==
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'''Quiz 1'''                         = 50 points (12.5%)<br>
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<table>
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'''Midterm Exam 1'''         = 100 points (25%)<br>
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<tr>
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'''Quiz 2'''                           = 50 points (12.5%)<br>
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<td>'''Quiz 1'''</td><td>50 points (12.5%)</td>
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'''Midterm Exam 2'''         = 100 points (25%) <br>
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</tr>
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'''Final Exam'''                                                       = 100 points (25%)<br>
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<br>
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<td>'''Exam 1'''</td><td>100 points (25%)</td>
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</tr>
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<td>'''Quiz 2'''</td><td>50 points (12.5%)</td>
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<td>'''Exam 2'''</td><td>100 points (25%)</td>
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</tr>
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<td>'''Comprehensive Final Exam'''</td><td>100 points (25%)</td>
  
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</tr>
  
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</table>
  
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'''EEB 2245: ''Your final grade of the course will be calculated as above.''''' University regulations require that students who miss the final exam without an excuse from the Dean of Students receive an F for that exam. Thus, you are required to take the final exam.
 
  
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'''EEB 2245W:''''' Your final grade in the lecture portion of the course will be calculated as above.  This grade will constitute 75% of your final course grade.  Your grade in the '''W part''' of the course, as determined by your “W” instructor, will constitute the remaining 25% of your final course grade, except that '''''an F in the W part of the course will result in an F for the entire course. An F in the lecture part of the course will also result in an F for the entire course.'''''  Refer to the 2245W handout and [ website]  for further information. Dr. Kent Holsinger (PBB 305A; tel: 486-4059; kent.holsinger@uconn.edu) is the coordinator of the W part of the course.
 
  
 +
'''EEB 2245: '''Your final grade of the course will be calculated as above. The second exam will be given on the same day as the comprehensive final.
 +
 +
'''EEB 2245W: '''Your final grade in the lecture portion of the course will be calculated as above.  This grade will constitute 75% of your final course grade.  Your grade in the '''W part''' of the course, as determined by your “W” instructor, will constitute the remaining 25% of your final course grade, except that '''an F in the W part of the course will result in an F for the entire course. An F in the lecture part of the course will also result in an F for the entire course.'''  Refer to the 2245W handout and [http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/EEB2245W_%28Spring_2011%29 EEB 2245W web site]  for further information. [mailto:kent.holsinger@uconn.edu Dr. Kent Holsinger] is the coordinator of the W part of the course.
 +
<br><br>
 
==Course Policies==
 
==Course Policies==
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'''Lecture Expectations:'''
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*Arrive on time and stay until the end.  If you must come late or leave early, sit by the back door.
 +
*Turn cell phones OFF and store them out of sight.
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*Use laptops only for taking notes or other activity directly related to class.
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<br>
 
'''Missed Exams:'''<br>
 
'''Missed Exams:'''<br>
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Any student who does not attend an exam and fails to receive permission [[in advance]] will receive a 0 for the exam.  Approval of any request to miss an exam requires, [[but is not guaranteed by]], verifiable written documentation of the reason.  A student who receives approval to miss an exam will have his or her grade for the missed exam prorated based on his or her performance on the remainder of the exams.  We will not give make-up exams.  Every student must take the final (exam 3).  Permission to reschedule the final can only be obtained through procedures determined by the [http://www.ossa.uconn.edu/ Office of Student Services and Advocacy].
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Any student who misses a quiz or exam without <U>advance permission</U> will receive a 0 for the assessment.  Permission to miss a quiz or exam requires, <U>but is not guaranteed by,</U> verifiable written documentation of the reason.  A student who receives permission to miss a quiz or exam will have his or her grade for the missed work prorated based on his or her performance on the remainder of the assessments.  <U>We will not give make-ups.</U> Every student must take the final exam (and second exam) during the scheduled final exam period unless permission to reschedule is obtained through the [http://www.ossa.uconn.edu/ Office of Student Services and Advocacy].
 
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<br>
  
 
'''Academic Integrity:'''<br>
 
'''Academic Integrity:'''<br>
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Plagiarism and cheating are violations of the student conduct code, and may be punished by failure in the course or, in severe cases, dismissal from the University.  For more information, see [http://www.dosa.uconn.edu/student_code_partiv.html Section IV of the Student Conduct Code].<br>
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Plagiarism and cheating are violations of the student conduct code, and may be punished by failure in the course or, in severe cases, dismissal from the University.  For more information, see [http://www.community.uconn.edu/student_code_appendixa.html Appendix A of the Student Conduct Code].<br>
 
<br>
 
<br>
 
'''Disabilities:'''<br>
 
'''Disabilities:'''<br>
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!width="400"|Topic
 
!width="400"|Topic
 
!width="185"|Readings
 
!width="185"|Readings
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!width="300"|Problem Sets/ Study Questions
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!width="250"|Problem Sets/ Study Questions
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!width=''300''|Lecture PDFs
  
 
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|-  
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| || '''Part I: Jan 18 - Mar 3, Dr. Elizabeth Jockusch''' || || ||
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| || '''Part I: Jan 18 - Mar 3, Dr. Elizabeth Jockusch''' || ||  
 
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|-  
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|-
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| Jan 18 || Snow Day- Class canceled || ---------||
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|-  
 
|-  
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| Jan 18 || Class Organization, Introduction to the study of evolutionary biology || ---------||
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| Jan 20 || Class Organization, Introduction to the study of evolutionary biology || Ch 1|| [http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Evolutionary_Biology_Spring_2011_Study_Questions#Lecture_1_.28Jan_20.2C_2011.29 Study Questions]
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|-  
 
|-  
  
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| Jan 20 || Hardy Weinberg and mutation ||----||
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| Jan 25 || Variation and the Hardy-Weinberg equilibrium ||pp 215-225||[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Evolutionary_Biology_Spring_2011_Study_Questions#Lecture_2_.28Jan_25.2C_2011.29 Study Questions]
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||
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{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/eeb245W/HardyWeinbergDerivation.pdf}} '''Hardy-Weinberg Handout'''<br>
 +
'''Hardy-Weinberg Problem Answer Key'''<br>
 
|-   
 
|-   
  
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| Jan 25 || Genetic Drift ||----||
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| Jan 27 || Snow Day- Class canceled ||---------||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/eeb245W/ProblemSet1.pdf}} '''Problem Set 1'''<br>
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||  
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 +
'''Problem Set 1 Answer Key (Revised)'''
 +
|-
 +
| Feb 1|| Snow Day- Class canceled ||---------|| <br>
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|-
 +
| Feb 3|| Mutation and Genetic Drift ||Ch 8, pp 255-266||[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Evolutionary_Biology_Spring_2011_Study_Questions#Lecture_3_.28Feb_3.2C_2011.29 Study Questions]<br>
 +
[http://pandasthumb.org/archives/2009/03/population-gene.html Simulate Genetic Drift]  Suggestion:  explore different starting allele frequencies
 +
 
|-
 
|-
  
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| Jan 27 || Migration and non-random mating ||----||
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|Feb 3|| Study Group 1-4pm TLS 311||||
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||  
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|-
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|Feb 4|| Study Group 1:30-4pm TLS 313||||{{pdf|http://hydrodictyon.eeb.uconn.edu/people/ewade/EEB2245/ProblemSet2.pdf}} '''Problem Set 2'''  <br> '''Problem Set 2 Answer Key'''
 
|-
 
|-
  
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| Feb 1 || Natural selection and adaptation ||----||
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| Feb 8 || Migration||pp 244-246||[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Evolutionary_Biology_Spring_2011_Study_Questions#Lecture_4_.28Feb_8.2C_2011.29 Study Questions]
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||  
+
[http://darwin.eeb.uconn.edu/simulations/drift-migration.html Simulate drift and migration]
 +
 +
|-
 +
|Feb 8|| Review for Quiz  1-4pm TLS 313 and 7:30-10:30pm PBP 130||||
 
|-
 
|-
  
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| <span style="font-size: small"><font color="#FF3300">'''Feb 3'''</font></span>|| <span style="font-size: small">Natural Selection, con't. & <font color="#FF3300">'''Quiz 1'''</font></span>|| --------- ||||  
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| <span style="font-size: small"><font color="#FF3300">'''Feb 10'''</font></span>|| <span style="font-size: small">Non-random mating & <font color="#FF3300">'''Quiz 1'''</font></span>|| pp 225-229 || '''Quiz 1 Answer Key'''<br>[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Evolutionary_Biology_Spring_2011_Study_Questions#Lecture_5_.28Feb_10.2C_2011.29 Study Questions]
 +
 
|-  
 
|-  
  
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| Feb 15 || Natural selection ||Ch 11||[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Evolutionary_Biology_Spring_2011_Study_Questions#Lecture_6_.28Feb_15.2C_2011.29 Study Questions]
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| Feb 8 || Examples of natural selection ||----||
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||
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|-
 
|-
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|Feb 17 || Genetics of natural selection ||Ch 12||[http://darwin.eeb.uconn.edu/simulations/selection.html  Simulate Selection] <br> [http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Evolutionary_Biology_Spring_2011_Study_Questions#Lecture_7_.28Feb_17.2C_2011.29 Study Questions]
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| Feb 10|| Genetics of natural selection ||----||
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|-
 
|-
  
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| Feb 15|| Modes of natural selection ||----||
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| Feb 22|| Modes of natural selection ||Ch 12 & 13||[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Evolutionary_Biology_Spring_2011_Study_Questions#Lecture_8_.28Feb_22.2C_2011.29 Study Questions]
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|-
 
|-
  
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| Feb 17|| Sexual selection and female choice ||----||
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| Feb 24 || Heritability, Sexual selection ||pp. 237-241, Ch 13 & 15||[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Evolutionary_Biology_Spring_2011_Study_Questions#Lecture_9_.28Feb_24.2C_2011.29 Study Questions]
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||
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|-
 
|-
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| Feb 24 || ''Study Group 1:30-3:30pm TLS 311'' ||||
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| Feb 22|| Genetic conflict and levels of selection ||----||
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| Feb 25 || ''Study Group 1:30-3:30pm TLS 313'' ||||{{pdf|http://hydrodictyon.eeb.uconn.edu/people/ewade/EEB2245/Problem_Set_3.pdf}} '''Problem Set 3'''
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| Feb 24|| Geographic variation and speciation ||----||
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||  
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|-
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|Mar 1|| Sexual selection; geographic variation and speciation ||Ch 15, pp 241-251||[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Evolutionary_Biology_Spring_2011_Study_Questions#Lecture_10_.28March_1.2C_2011.29 Study Questions]
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 +
|-
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| Mar 1 || ''Study Group 1:30-3:30pm TLS 313 and 7:30-9:30pm BPB 130''|||| '''Problem Set 3 Answer Key'''
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|-
  
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| Mar 1|| Mechanisms of speciation ||----||
 
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| <span style="font-size: small"><font color="#FF3300">'''Mar 3'''</font></span>|| <span style="font-size: small"><font color="#FF3300">'''Midterm EXAM 1'''</font></span> covers all material from the first half of the course || --------- ||||
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| <span style="font-size: small"><font color="#FF3300">'''Mar 3'''</font></span>|| <span style="font-size: small"><font color="#FF3300">'''EXAM 1'''</font></span> covers all material from the first half of the course || --------- || '''Exam 1 Answer Key'''
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|-  
 
|-  
  
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| ||'''Part II: Mar 15 - May 5, Dr. Chris Simon'''        ||  ||  
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| ||'''Part II: Mar 15 - May 5, Dr. Chris Simon'''        ||  ||||
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|-  
 
|-  
  
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| Mar 15|| ----||----||
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| Mar 15||Geographic variation, continued. Factors that inhibit gene flow- pre- and post mating isolation, natural selection at the molecular level.  ||Ch 17 & 18||[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Evolutionary_Biology_Spring_2011_Study_Questions#Part_II:_Mar_15-May_5.2C_Dr._Simon Study Questions]||{{pdf|http://hydrodictyon.eeb.uconn.edu/people/ewade/EEB2245/Lect_11_Sp_11_EEB2245_Geogr_Var_Factors_reducing_geneflow.pdf}} '''Lecture 11 PDF'''
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||
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|-
 
|-
  
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| Mar 17|| ----||----||
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| Mar 17|| Species concepts in space and time.  The origin of biodiversity.||Ch 17 & 18||[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Evolutionary_Biology_Spring_2011_Study_Questions#Lecture_12_.28March_17.2C_2011.29 Study Questions]||{{pdf|http://hydrodictyon.eeb.uconn.edu/people/ewade/EEB2245/Lect.%2012.%20EEB%202245%20Species%20concepts,%20Speciation%20mech.pdf}} '''Lecture 12 PDF'''
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||  
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|-
 
|-
  
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| Mar 22|| ----||----||
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||  
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| Mar 22|| Speciation mechanisms, Hybridization, reproductive character displacement, and speciation.||Ch 17 & 18||[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Evolutionary_Biology_Spring_2011_Study_Questions#Lecture_13_.28March_22.2C_2011.29 Study Questions] ||{{pdf|http://hydrodictyon.eeb.uconn.edu/people/ewade/EEB2245/Lect.%2013.%20EEB%202245%20Sp%2011%20Speciation%20Mech.%20&%20Hybridiz.pdf}} '''Lecture 13 PDF'''
 +
 
|-
 
|-
  
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| Mar 24|| ----||----||
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|Mar 24||Systematics, the study of biodiversity and its origins. Problems in constructing relationships: polymorphisms and homoplasy.||Ch 2 &3||[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Evolutionary_Biology_Spring_2011_Study_Questions#Lecture_14_.28March_24.2C_2011.29 Study Questions]||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Lects_14%2B15.pdf}} '''Lecture 14 & 15 PDF'''
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||  
+
 
|-
 
|-
  
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| Mar 29|| ----||----||
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| Mar 29|| Homoplasy (continued):  convergence, parallelisms, and reversals in evolution. Tree thinking.||Ch 2 & 3||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Handout_Constructing_Evolutionary_Trees%202011.pdf}}'''Constructing Trees Handout'''<br>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Lect15Worksheet.pdf}}'''Trees Worksheet'''<br>[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Evolutionary_Biology_Spring_2011_Study_Questions#Lecture_15_.28March_29.2C_2011.29 Study Questions]||
−
||  
+
 
|-
 
|-
  
−
| Mar 31|| ----||----||
+
| Mar 31|| Reconstructing evolutionary trees from morphological and molecular data.||Ch 2 & 3||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/ProblemSet4.pdf}}'''Problem Set 4'''<br>[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Evolutionary_Biology_Spring_2011_Study_Questions#Lecture_16_.28March_31.2C_2011.29 Study Questions]||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Lect16.pdf}} '''Lecture 16 PDF'''
−
||  
+
 
|-
 
|-
  
−
| Apr 5|| ----||----||
+
| Apr 5|| The tempo of molecular evolution; is there a molecular clock?  ||Ch 2 ||'''Problem Set 4 Answer Key'''<br>[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Evolutionary_Biology_Spring_2011_Study_Questions#Lecture_17_.28April_5.2C_2011.29 Study Questions]||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Lect1718.pdf}}'''Lect 17 & 18 PDF'''
−
||  
+
 
 +
 
|-
 
|-
  
−
| Apr 7|| ----||----||
+
 
−
||  
+
 
 +
| <span style="font-size: small"><font color="#FF3300">'''Apr 7'''</font></span>|| <span style="font-size: small">A review of the tree of life and the major innovations in animal evolution. & <font color="#FF3300">'''Quiz 2'''</font></span>|| Review intro bio || [http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Evolutionary_Biology_Spring_2011_Study_Questions#Lecture_18_.28April_7.2C_2011.29 Study Questions]||
 +
 
|-
 
|-
  
−
| Apr 12|| ----||----||
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| Apr 12|| The origin of evolutionary novelties:  Body plans, constraints; pre-adaptation, modification of existing traits:  gene duplication, gene regulation.||Ch 21 & 22||[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Evolutionary_Biology_Spring_2011_Study_Questions#Lecture_19_.28April_12.2C_2011.29 Study Questions]||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Lect%2019.pdf}} '''Lecture 19 PDF'''
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||  
+
 
|-
 
|-
  
−
| Apr 14|| ----||----||
+
| Apr 14|| Evolutionary novelties (continued) Homeobox genes, Master control genes. Flies with eyes on their wings. Ontogeny and phylogeny, Allometry.||Ch 21 & 22|| '''Quiz 2 Answer Key'''<br>[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Evolutionary_Biology_Spring_2011_Study_Questions#Lecture_20_.28April_14.2C_2011.29 Study Questions]||
−
||  
+
{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Lect20reduce.pdf}}'''Lect 20 PDF'''
 +
 
 +
 
|-
 
|-
  
−
| Apr 19|| ----||----||
+
| Apr 19|| Overview of the fossil record. Paleozoic:  Cambrian explosion?  Origin of vertebrates, invasion of land. Ordovician (age of jawless vertebrates), Silurian (first life on land), Devonian (age of fishes). Carboniferous (clubmoss forests); Permian.  Origin of mammals.  The Permo-Triassic boundary mass extinction||Ch 4 & 5 (plus 168-171 and Box 7A)||[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Evolutionary_Biology_Spring_2011_Study_Questions#Lecture_21_.28April_19.2C_2011.29 Study Questions]||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Lect21_Pt1.pdf}}'''Lecture 21 Part 1 PDF''' <br>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Lect21_Pt2.pdf}}'''Lecture 21 Part 2 PDF'''
−
||  
+
 
|-
 
|-
  
−
| Apr 21|| ----||----||
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| Apr 21|| Mesozoic:  The age of reptiles. Pangea, Laurasia & Gondwanaland. Origin of birds; insects and angiosperms radiate. K-T Boundary: extinction of the dinosaurs.  Birds and mammals cross the boundary  ||Ch 4 & 5 & 6||[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Evolutionary_Biology_Spring_2011_Study_Questions#Lecture_22_.28April_21.2C_2011.29 Study Questions]||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Lect22.pdf}}'''Lecture 22 PDF'''
−
||  
+
 
|-
 
|-
  
−
| Apr 26|| ----||----||
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| Apr 26|| The Cenozoic: Greenhouse to Icehouse. Continental drift, land bridges, mountain building.  Modern biogeographic distributions take shape.  The great American interchange.  Primate evolution.||Ch 4, 5 & 6||[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Evolutionary_Biology_Spring_2011_Study_Questions#Lecture_23_.28April_26.2C_2011.29 Study Questions]||
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{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Lect231.pdf}}'''Lecture 23 PDF Part 1'''<br>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Lec%20232.pdf}}'''Lecture 23 PDF Part 2'''
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| Apr 28|| ----||----||
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| Apr 28|| Human evolution; Mitochondrial Eve and her relatives. Africa, our most diverse continent. Humans invade Asia and the Pacific and later North America. Biogeography and Biodiversity||Ch 4, 5 & 6||[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Evolutionary_Biology_Spring_2011_Study_Questions#Lecture_24_.28April_29.2C_2011.29 Study Questions]||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evolution/restricted/Lect24.pdf}}'''Lecture 24 PDF'''
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| <span style="font-size: small"><font color="#FF3300">'''May 5''' (tentative)</font></span>|| <span style="font-size: small"><font color="#FF3300">'''Midterm EXAM 2 and FINAL EXAM'''</font></span>|| --------- ||||  
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| <span style="font-size: small"><font color="#FF3300">'''May 5''' </font></span>|| <span style="font-size: small"><font color="#FF3300">'''EXAM 2 and COMPREHENSIVE FINAL EXAM'''</font></span> (8 am)|| --------- ||||
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Latest revision as of 18:09, 20 January 2015

EEB2245/2245W:
The objectives of this course are to familiarize students with the mechanisms of evolutionary change (processes of evolution), major patterns of evolution, and the history of the diversity of life.

Course Overview

Lectures:Tu,Th 9:30-10:45, Biological Sciences/Physics 130
Emergency closing information
Textbook:Futuyma, D. J. 2009. Evolution, 2nd ed. Sinauer Associates, Sunderland, MA
(can be purchased at discount as an e-book or in loose leaf sections)

Revised Syllabus for second half of semester Pdficon small.gif

EEB 2245W

In addition to this web site those of you who are enrolled in the W part of the course will want to refer to the EEB 2245W web site for information about W assignments and requirements.

Announcements

Study Sessions for Exam 2/Final Exam
Friday April 29 2:30-4:30pm TLS 313
Monday May 2 7:30-9:30pm BPB 130
Tuesday May 3 2-4pm

Room Change for Tuesday study session to Physics Building Room 36


Study Guide for first half of semester
A number of you have emailed to ask advice on preparing for my part of final exam, so I've put together a Pdficon small.gifStudy Guide that lists many of the major concepts and applications we covered. Note that the study guide is not intended to be comprehensive (e.g., it doesn't cover specific examples), but going through it should provide a good refresher. I also highly recommend working some practice problems again.

Good luck!
Prof. Jockusch

Instructors

Dr. Elizabeth Jockusch
Office: Biology/Pharmacy 305B
Phone: (860) 486-4452
Office hours: 11-12 on Tuesdays and by appointment

Dr. Chris Simon
Office: Biology/Pharmacy 305D
Phone: (860) 486-4640
Office hours: anytime by appointment

Beth Wade (Teaching Assistant)
Office: Torrey Life Sciences 461
Phone: (860) 486-3947
Office hours: 10-11 on Wednesdays and by appointment

Grading

Quiz 150 points (12.5%)
Exam 1100 points (25%)
Quiz 250 points (12.5%)
Exam 2100 points (25%)
Comprehensive Final Exam100 points (25%)


EEB 2245: Your final grade of the course will be calculated as above. The second exam will be given on the same day as the comprehensive final.

EEB 2245W: Your final grade in the lecture portion of the course will be calculated as above. This grade will constitute 75% of your final course grade. Your grade in the W part of the course, as determined by your “W” instructor, will constitute the remaining 25% of your final course grade, except that an F in the W part of the course will result in an F for the entire course. An F in the lecture part of the course will also result in an F for the entire course. Refer to the 2245W handout and EEB 2245W web site for further information. Dr. Kent Holsinger is the coordinator of the W part of the course.

Course Policies

Lecture Expectations:

  • Arrive on time and stay until the end. If you must come late or leave early, sit by the back door.
  • Turn cell phones OFF and store them out of sight.
  • Use laptops only for taking notes or other activity directly related to class.


Missed Exams:
Any student who misses a quiz or exam without advance permission will receive a 0 for the assessment. Permission to miss a quiz or exam requires, but is not guaranteed by, verifiable written documentation of the reason. A student who receives permission to miss a quiz or exam will have his or her grade for the missed work prorated based on his or her performance on the remainder of the assessments. We will not give make-ups. Every student must take the final exam (and second exam) during the scheduled final exam period unless permission to reschedule is obtained through the Office of Student Services and Advocacy.

Academic Integrity:
Plagiarism and cheating are violations of the student conduct code, and may be punished by failure in the course or, in severe cases, dismissal from the University. For more information, see Appendix A of the Student Conduct Code.

Disabilities:
If you have a disability for which you may be requesting an accommodation, you should contact a course instructor and the Center for Students with Disabilities (Wilbur Cross Building, Room 201) within the first two weeks of the semester.

Lecture Schedule & Materials

Date Topic Readings Problem Sets/ Study Questions Lecture PDFs
Part I: Jan 18 - Mar 3, Dr. Elizabeth Jockusch
Jan 18 Snow Day- Class canceled ---------


Jan 20 Class Organization, Introduction to the study of evolutionary biology Ch 1 Study Questions
Jan 25 Variation and the Hardy-Weinberg equilibrium pp 215-225 Study Questions

Pdficon small.gif Hardy-Weinberg Handout

Hardy-Weinberg Problem Answer Key
Jan 27 Snow Day- Class canceled --------- Pdficon small.gif Problem Set 1
Problem Set 1 Answer Key (Revised)
Feb 1 Snow Day- Class canceled ---------
Feb 3 Mutation and Genetic Drift Ch 8, pp 255-266 Study Questions

Simulate Genetic Drift Suggestion: explore different starting allele frequencies

Feb 3 Study Group 1-4pm TLS 311
Feb 4 Study Group 1:30-4pm TLS 313 Pdficon small.gif Problem Set 2
Problem Set 2 Answer Key
Feb 8 Migration pp 244-246 Study Questions

Simulate drift and migration

Feb 8 Review for Quiz 1-4pm TLS 313 and 7:30-10:30pm PBP 130
Feb 10 Non-random mating & Quiz 1 pp 225-229 Quiz 1 Answer Key
Study Questions
Feb 15 Natural selection Ch 11 Study Questions
Feb 17 Genetics of natural selection Ch 12 Simulate Selection
Study Questions
Feb 22 Modes of natural selection Ch 12 & 13 Study Questions
Feb 24 Heritability, Sexual selection pp. 237-241, Ch 13 & 15 Study Questions
Feb 24 Study Group 1:30-3:30pm TLS 311
Feb 25 Study Group 1:30-3:30pm TLS 313 Pdficon small.gif Problem Set 3
Mar 1 Sexual selection; geographic variation and speciation Ch 15, pp 241-251 Study Questions
Mar 1 Study Group 1:30-3:30pm TLS 313 and 7:30-9:30pm BPB 130 Problem Set 3 Answer Key
Mar 3 EXAM 1 covers all material from the first half of the course --------- Exam 1 Answer Key
Part II: Mar 15 - May 5, Dr. Chris Simon
Mar 15 Geographic variation, continued. Factors that inhibit gene flow- pre- and post mating isolation, natural selection at the molecular level. Ch 17 & 18 Study Questions Pdficon small.gif Lecture 11 PDF
Mar 17 Species concepts in space and time. The origin of biodiversity. Ch 17 & 18 Study Questions Pdficon small.gif Lecture 12 PDF
Mar 22 Speciation mechanisms, Hybridization, reproductive character displacement, and speciation. Ch 17 & 18 Study Questions Pdficon small.gif Lecture 13 PDF
Mar 24 Systematics, the study of biodiversity and its origins. Problems in constructing relationships: polymorphisms and homoplasy. Ch 2 &3 Study Questions Pdficon small.gif Lecture 14 & 15 PDF
Mar 29 Homoplasy (continued): convergence, parallelisms, and reversals in evolution. Tree thinking. Ch 2 & 3 Pdficon small.gifConstructing Trees Handout
Pdficon small.gifTrees Worksheet
Study Questions
Mar 31 Reconstructing evolutionary trees from morphological and molecular data. Ch 2 & 3 Pdficon small.gifProblem Set 4
Study Questions		 Pdficon small.gif Lecture 16 PDF
Apr 5 The tempo of molecular evolution; is there a molecular clock? Ch 2 Problem Set 4 Answer Key
Study Questions		 Pdficon small.gifLect 17 & 18 PDF


Apr 7 A review of the tree of life and the major innovations in animal evolution. & Quiz 2 Review intro bio Study Questions
Apr 12 The origin of evolutionary novelties: Body plans, constraints; pre-adaptation, modification of existing traits: gene duplication, gene regulation. Ch 21 & 22 Study Questions Pdficon small.gif Lecture 19 PDF
Apr 14 Evolutionary novelties (continued) Homeobox genes, Master control genes. Flies with eyes on their wings. Ontogeny and phylogeny, Allometry. Ch 21 & 22 Quiz 2 Answer Key
Study Questions

Pdficon small.gifLect 20 PDF


Apr 19 Overview of the fossil record. Paleozoic: Cambrian explosion? Origin of vertebrates, invasion of land. Ordovician (age of jawless vertebrates), Silurian (first life on land), Devonian (age of fishes). Carboniferous (clubmoss forests); Permian. Origin of mammals. The Permo-Triassic boundary mass extinction Ch 4 & 5 (plus 168-171 and Box 7A) Study Questions Pdficon small.gifLecture 21 Part 1 PDF
Pdficon small.gifLecture 21 Part 2 PDF
Apr 21 Mesozoic: The age of reptiles. Pangea, Laurasia & Gondwanaland. Origin of birds; insects and angiosperms radiate. K-T Boundary: extinction of the dinosaurs. Birds and mammals cross the boundary Ch 4 & 5 & 6 Study Questions Pdficon small.gifLecture 22 PDF
Apr 26 The Cenozoic: Greenhouse to Icehouse. Continental drift, land bridges, mountain building. Modern biogeographic distributions take shape. The great American interchange. Primate evolution. Ch 4, 5 & 6 Study Questions

Pdficon small.gifLecture 23 PDF Part 1
Pdficon small.gifLecture 23 PDF Part 2


Apr 28 Human evolution; Mitochondrial Eve and her relatives. Africa, our most diverse continent. Humans invade Asia and the Pacific and later North America. Biogeography and Biodiversity Ch 4, 5 & 6 Study Questions Pdficon small.gifLecture 24 PDF
May 5 EXAM 2 and COMPREHENSIVE FINAL EXAM (8 am) ---------
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