Biology of the Vertebrates

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<span style="font-size: x-large">EEB 2214, Fall 2014</span><br><br>
<span style="font-size: x-large">EEB 2214, Fall 2012</span><br>
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<span style="font-size: large">''The evolution of form, function, & diversity of the vertebrates''</span><br>
<span style="font-size: large">''The evolution of form, function,<br> & diversity of the vertebrates''</span><br>
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<br><span style="font-size: small">'''Meeting Time: Tuesdays and Thursdays, 12:30-1:45 in BPB130'''<br>
<span style="font-size: small">'''Meeting Time: Tuesdays and Thursdays, 12:30-1:45 in BPB130'''<br>
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'''Textbook: <font color="#FF3300">Vertebrate Life</font>, by Pough F. H., C. M. Janis, and J. B. Heiser. 2012. ''9th Edition.'' Pearson/Benjamin Cummings ''(8th edition also acceptable)''''' <br><br>
 
==Instructors==
 
==Instructors==
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[[Image:Female_with_hatchlings.JPG|right]]
  
 
'''[mailto:elizabeth.jockusch@uconn.edu Dr. Elizabeth Jockusch]'''<br>
 
'''[mailto:elizabeth.jockusch@uconn.edu Dr. Elizabeth Jockusch]'''<br>
Office: Biology/Pharmacy 305B<br>
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Office: Pharmacy/Biology 305B<br>
 
Phone: (860) 486-4452<br>
 
Phone: (860) 486-4452<br>
Office hours: Thursdays 2-3 pm and by appointment<br><br>
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Office hours: Thursdays 2-3 pm and by appointment <br>
 +
[http://jockusch.eeb.uconn.edu/ Jockusch Lab Website] <br><br>
  
'''[mailto:kristiina.hurme@uconn.edu Dr. Kristiina Hurme]'''<br>
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'''[mailto:margaret.rubega@uconn.edu Dr. Margaret Rubega]'''<br>
Office: TLS 379<br>
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Office: Pharmacy/Biology 500<br>
Phone: (860) 486-5434<br>
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Phone: (860) 486-4502<br>
Office hours: TBA and by appointment<br><br>
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Office hours: TBA and by appointment <br>
 +
[http://rubegalab.eeb.uconn.edu/ Rubega Lab Website] <br><br>
  
'''[mailto:alejandro.rico@uconn.edu Alejandro Rico]''' (Teaching Assistant)<br>
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'''[mailto:kevin.burgio@uconn.edu Kevin Burgio]''' (Teaching Assistant)<br>
Office: Biology/Pharmacy 404<br>
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Office: Pharmacy/Biology 402<br>
Phone:(860) 486-0309<br>
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Office hours: Tuesdays 2-3 pm and by appointment <br>
Office hours: Tuesdays 2-3 pm and by appointment<br><br>
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[http://monkparakeetresearch.org/ Monk Parakeet Research Website] <br><br>
 +
 
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<span style="font-size: medium"><font color="#FF3300">'''Note: All emails must contain "EEB2214" in the subject line to avoid being filtered out and deleted'''</font></span>
 +
<br><br>
  
 
==Grading==
 
==Grading==
'''Exam 1'''                         = 100 points<br>
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[[Image:MonkParakeet01.jpeg|325 px|right]]
'''Exam 2'''                 = 100 points<br>
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'''Exam 1''' (Thursday, Sept. 25) = 100 points <br>
'''Final Exam'''                           = 150 points<br>
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'''Exam 2''' (Thursday, Oct. 30) = 100 points <br>
'''[[#Research Reviews]]'''                           = 30 points<br>
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'''Final Exam''' (Friday, Dec. 12, TENTATIVE) = 125 points <br>
'''[[#Tree Quizzes]]'''                           = 15 points<br>
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'''[[#Research Reviews]]''' (Tuesdays)  = 30 points total<br>
'''[[#Collections Tour]]'''         = 5 points<br>
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'''[[#Quizzes]]''' = 50 points total<br>
 
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'''[[#Collections Tour]]''' = 5 points<br>
There will be two one-hour, non-cumulative, exams scheduled during the lecture hour.  The final exam will be cumulative, with an emphasis on material from the final third of the course.  <br>
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<br>
 
<br>
 
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There will be two one-hour, non-cumulative, exams scheduled during the lecture hour. The final exam will be cumulative, with an emphasis on material from the final third of the course.<br>
== Research Reviews ==
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<br>
As a research field, vertebrate biology is alive and well, with discoveries being made constantly.  Each week, we will select one paper from the primary scientific literature that describes a study relevant to vertebrate biology. On Tuesdays, class will include a short in-class written exercise, in which we ask you to answer three standard questions about the paper:<br>
+
12 research reviews (3 points each) and quizzes (5 points each) will be offered over the course of the semester.  10 of these will count towards the final course grade (the best 5 of 6 from each half of the semester, as determined by the combined quiz + research review grade.)  Because two scores are dropped, '''no make-ups will be given for research reviews or quizzes'''.<br>
* What was the major new result?<br>
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* How does this change what we think?<br>
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* Why does it matter?<br>
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<span style="font-size: medium"><font color="#FF3300">'''The written exercise will be followed by a brief discussion of the paper, during which we will call on pre-determined, but randomly selected, students to talk about the paper.'''</font></span><br><br>
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<br>
 
<br>
 
In-class assessments are worth 3 points each.  11 will be offered over the course of the semester, and the best 10 counted towards the final course grade.  There will be no paper selected for the first week, or the weeks of the first and second exams.  <br>  <br>
 
 
All papers will be available electronically.  A link to each paper will be posted on the course schedule below, next to the date of the in-class exercise.  While many articles in scientific journals are now made available free to everyone ("open access" articles), access to other articles requires a subscription, which the UConn library buys.  On campus, you should not encounter difficulty accessing the full text of selected articles.  From off-campus, the easiest way to access articles that require a subscription is using the [http://www.lib.uconn.edu/about/ezproxy-blurb.html EZProxy].  If you get a message saying that you may purchase access to the paper, then try again through the proxy.  In some cases, it may also be necessary to quit and restart your browser.  Alternative ways to access the articles via UConn's subscription are to configure the proxy within your web browser and to use the [http://security.uconn.edu/services/vpn/ VPN].  It is your responsibility to test that you have access in a timely fashion.  Course instructors will not respond to requests to provide the article directly to individuals.  <br><br>
 
 
== Tree Quizzes==
 
On several of the research response days, we will incorporate additional questions about the phylogenetic tree of vertebrates into the written exercise.  These will be worth a total of 15 points over the course of the semester.  As with the research responses, you must be present to receive credit and no make-ups will be given.  If you have a valid, documented reason for missing class on the day of a tree quiz, and have followed the policy on missed exams, then your quiz score will be prorated.<br><br>
 
 
== Collections Tours ==
 
 
Every student is expected to visit the [http://hydrodictyon.eeb.uconn.edu/department/collections/index.html EEB Biological Collections] for a tour that will introduce you to the resources and opportunities in the collection. We will offer 8 different opportunities, on different days and times. You will need to sign in at the collection; at the end of the semester, everyone who has signed in will have 5 points added to their grade. '''Tours will take about 45 minutes; they meet at the south end of the Biology/Physics building lobby on the hour'''. You are responsible for finding a day and time to attend from the options below; if your class schedule prohibits you from attending any of these, you are responsible for letting us know that you will need an alternative opportunity AT LEAST TWO WEEKS PRIOR TO THE FINAL TOUR. If you have already toured the collections (e.g., in a previous class), provide us with documentation to that effect, and we will just add the points to your grade without you needing to tour the collections again.
 
 
'''Available tour days/times:'''<br>
 
TBA
 
<br><br>
 
  
 
==Course Policies==
 
==Course Policies==
 
'''Missed Exams'''<br>
 
'''Missed Exams'''<br>
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.  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 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.  Permission to reschedule the final can only be obtained through procedures determined by the [http://dos.uconn.edu Dean of Students Office].
 
<br><br>
 
<br><br>
 
+
 
 
'''Other Absences'''<br>
 
'''Other Absences'''<br>
No make-ups will be given for research responses or tree quizzes.  The first research response from which a student is absent will be dropped. If a student misses a second one, then he or she will receive a zero.  For tree quizzes, the missed exam policy applies. 
+
No make-ups will be given for research reviews or quizzes.  Instead, the lowest research review/quiz grade from each half of the semester will be dropped.  
 
<br><br>
 
<br><br>
 +
 
'''Academic Integrity'''<br>
 
'''Academic Integrity'''<br>
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://community.uconn.edu/the-student-code-part-iv Section IV of the Student Conduct Code].<br>
 
<br>
 
<br>
 
'''Disabilities'''<br>
 
'''Disabilities'''<br>
If you have a disability for which you may be requesting an accommodation, you should contact a course instructor and the [http://www.csd.uconn.edu Center for Students with Disabilities] (Wilbur Cross Building, Room 201) within the first two weeks of the semester.<br>
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If you have a disability for which you may be requesting an accommodation, you should contact a course instructor and the [http://www.csd.uconn.edu Center for Students with Disabilities] (Wilbur Cross Building, Room 201), within the first two weeks of the semester.<br>
 
<br>
 
<br>
 
'''Classroom Conduct'''<br>
 
'''Classroom Conduct'''<br>
We expect all students to behave in a way that is respectful of others.  The  {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/EEB2214ClassroomConduct.pdf}}''' classroom conduct form''', which describes our expectations in more detail, must be signed and returned to the teaching assistant by the end of the 2nd week of class.<br>
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We expect all students to behave in a way that is respectful of others.  The  {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/EEB2214_F2014_ClassroomConduct.pdf}}''' classroom conduct form''', which describes our expectations in more detail, must be signed and returned to the teaching assistant by the end of the 2nd week of class.<br>
 
*Arrive on time and stay until the end.  If you must come late or leave early, sit by the back door.   
 
*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.
 
*Turn cell phones OFF and store them out of sight.
Line 80: Line 68:
 
:'''[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Biology_of_the_Vertebrates_Honors_Conversion Can I convert this course to honors?''']<br><br>
 
:'''[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Biology_of_the_Vertebrates_Honors_Conversion Can I convert this course to honors?''']<br><br>
  
==Help Resources==
+
== Research Reviews ==
The secret of success to this course is to not let yourself fall behind.  Be sure to fill gaps in your notes and navigate blocks in your understanding as soon as possibleShould you run into trouble with the material, below we have listed some steps for obtaining assistance.  While we welcome any and all questions on the material, before you contact us, please first check the resources below to see if your question has already been answered. If/when you do contact us, please understand that we will respond as quickly as we can, but we do have other obligations that might prevent this from happening as urgently as you may need (like 3:00 am the day of an exam...).
+
As a research field, vertebrate biology is alive and well, with discoveries being made constantlyEach week, we will select one paper from the primary scientific literature that describes a study relevant to vertebrate biology. On Tuesdays, class will include a short in-class written exercise, in which we ask you to answer three standard questions about the paper:<br>
<br><br>
+
* What was the major new result?<br>
 +
* How does this change what we think?<br>
 +
* Why does it matter?<br>
 +
<span style="font-size: medium"><font color="#FF3300">'''The written exercise will be followed by a brief discussion of the paper, during which we will call on pre-determined, but randomly selected, students to talk about the paper.'''</font></span><br>
 +
<br>
  
'''Study Materials:'''<br>
+
In-class research review assessments are worth 3 points each.  12 will be offered over the course of the semester, and 10 (of 12) will count towards the final course grade (the best 5 of 6 from each half of the semester, as determined by the combined quiz + research review grade).  There will be no paper selected for the first or eighth week of class.  You must be present to receive credit and no make-ups will be given.  Also, if you are selected for the discussion, but do not participate, you will receive a 0. <br>  
The textbook for this course is Pough F. H., C. M. Janis, and J. B. Heiser. 2009. Vertebrate Life, 8th Edition. Prentice HallThree copies of the textbook are available at the library iDeskAsk for call numbers XR5, XR6 and XR7.   We strongly encourage you to read the assigned sections before lecture.<br>
+
<br>
 +
All papers will be available electronically.  A link to each paper will be posted on the course schedule below, next to the date of the in-class exercise. While many articles in scientific journals are now made available free to everyone ("open access" articles), access to other articles requires a subscription, which the UConn library buys. On campus, you should not encounter difficulty accessing the full text of selected articles. From off-campus, the easiest way to access articles that require a subscription is using the [http://www.lib.uconn.edu/about/ezproxy-blurb.html EZProxy]If you get a message saying that you may purchase access to the paper, then try again through the proxyIn some cases, it may also be necessary to quit and restart your browser. Alternative ways to access the articles via UConn's subscription are to configure the proxy within your web browser and to use the [http://security.uconn.edu/services/vpn/ VPN].  It is your responsibility to test that you have access in a timely fashion.  Course instructors will not respond to requests to provide the article directly to individuals. <br><br>
  
[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Biology_of_the_Vertebrates_Study_Questions_F2012 Study questions] will be posted online after every lecture.  These are intended to help you think about and synthesize information. They are not intended to provide a comprehensive study guide. <br>
+
{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/EEB2214_ReadingScientificLiterature.pdf}}'''This handout''' offers some helpful suggestions for how to navigate your way through the primary literature.<br>
 +
<br>
  
{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/EEB2214F12Exam1studyguide.pdf}}<span style="font-size: small"><font color="#FF3300"> '''Exam 1 Study Guide'''</font></span>
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==Quizzes==
 +
This course incorporates weekly quizzes which will be completed at the same time as the written portion of the research review, unless another schedule is announced.  The quizzes will use a variety of formats and are designed to help prepare you for exams.  Each quiz will be worth 5 points.  10 (of 12) will count towards the final course grade (the best 5 of 6 from each half of the semester, as determined by the combined quiz + research review grade).  As with the research reviews, you must be present to receive credit and no make-ups will be given.<br><br>
 +
 
 +
== Collections Tour ==
 +
Every student is expected to visit the [http://hydrodictyon.eeb.uconn.edu/department/collections/index.html EEB Biological Collections] for a tour that will introduce you to the resources and opportunities in the collection. We will offer 8 different opportunities, on different days and times. You will need to sign in at the collection; at the end of the semester, everyone who has signed in will have 5 points added to their grade. '''Tours will take about 45 minutes; they meet at the south end of the Biology/Physics building lobby on the hour'''. You are responsible for finding a day and time to attend from the options below; if your class schedule prohibits you from attending any of these, you are responsible for letting us know that you will need an alternative opportunity AT LEAST TWO WEEKS PRIOR TO THE FINAL TOUR. If you have already toured the collections (e.g., in a previous class), provide us with documentation to that effect, and we will just add the points to your grade without you needing to tour the collections again. <br><br>
 +
Collections tour times will be posted here and announced in class once the schedule is set.<br><br>
 +
 
 +
==Help Resources==
 +
The secret of success to this course is to not let yourself fall behind.  Be sure to fill gaps in your notes and navigate blocks in your understanding as soon as possible.  Should you run into trouble with the material, below we have listed some steps for obtaining assistance.  While we welcome any and all questions on the material, before you contact us, please first check the resources below to see if your question has already been answered.  If/when you do contact us, please understand that we will respond as quickly as we can, but we do have other obligations that might prevent this from happening as urgently as you may need (like 3:00 am the day of an exam...).
 
<br><br>
 
<br><br>
  
'''Phylogenetic Tree Resources:'''<br>
+
'''Study Materials'''<br>
The {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/VertebratePhylogeny.pdf}} '''phylogenetic tree of vertebrates''' provides the backbone for this course.<br>  {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/Phyl_tut_pptshow2010.ppt}}''' This phylogeny tutorial''' is designed to help students review their knowledge of trees.<br>
+
The textbook for this course is Pough F. H., C. M. Janis, and J. B. Heiser. 2012. Vertebrate Life, 9th Edition. Prentice Hall. (The 8th edition is also acceptable; we have posted readings for both.)  We strongly encourage you to read the assigned sections before lecture.<br>
Test your ability to interpret phylogenetic trees with this {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/EEB214F06treequiz.pdf}}'''Tree Quiz'''.<br>
+
{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/EEB214F06treequizAnswers.pdf}} '''Tree Quiz Answers'''
+
  
 +
[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Biology_of_the_Vertebrates_Study_Questions_F2014 Study questions] will be posted online after every lecture.  These are intended to help you think about and synthesize information.  They are not intended to provide a comprehensive study guide. <br>
 
<br>
 
<br>
 
+
'''Review Sessions'''<br>
'''Research Reviews:'''<br>
+
Use {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/EEB2214ReadingScientificLiterature.pdf}}''' this handout''' to help navigate your way through the primary literature.
+
<br><br>
+
'''Review Sessions:'''<br>
+
 
A review session will be held before each exam.  Dates and times will be posted once they are set.<br>
 
A review session will be held before each exam.  Dates and times will be posted once they are set.<br>
<span style="font-size: small"><font color="#FF3300">'''Exam 1 Review session''': Tuesday, Sept. 25, 5-7 pm in BPB131</font></span>
 
<br><br>
 
'''Links to External Resources:'''<br>
 
:'''[http://digimorph.org/index.phtml DigiMorph]''' - Excellent source of 2 & 3D images of internal & external structures of various organisms
 
:'''[http://www.arkive.org/ ARKive]''' - a unique collection of thousands of wildlife videos, images and fact-files, with a special focus on the world's threatened species
 
 
<br>
 
<br>
  
==Vertebrates in the News==
+
'''Research Reviews'''<br>
'''[http://news.bbc.co.uk/earth/hi/earth_news/newsid_9281000/9281424.stm Lampreys feed on whales]'''<br>
+
Use {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/EEB2214_ReadingScientificLiterature.pdf}}''' this handout''' to help navigate your way through the primary literature.<br>
 +
<br>
  
'''[http://www.nbc.com/saturday-night-live/video/lampreys/1354563 SNL lamprey skit]''' If you were science advisor to the show, which line(s) would you change?<br>
+
'''Syllabus'''<br>
 
+
{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/EEB2214_F2014_Syllabus.pdf}} Syllabus distributed on the first day of class.  The lecture schedule and readings are subject to change, and will be updated below.<br>
'''[http://species.asu.edu/2012_species01 New species of Snub-nose Monkey found in Burma '''30 August 2011''']'''<br>
+
<br>
 
+
:'''[http://www.google.com/hostednews/ap/article/ALeqM5hAZWFUc6F33zcJHk6hP4YcUGRDvgD9HQVM680 Pea-sized frog found in Borneo '''30 August 2010''']'''<br>
+
[[Image:Pea-sized Frog.jpg]]<br>
+
  
 
==Lecture Schedule & Materials==
 
==Lecture Schedule & Materials==
 
+
The lecture schedule below will be updated regularly.  A link to each research review paper will be posted next to the date of the in-class exercise.  Generally, these will be posted by the weekend prior to the exercise.  After lectures, study questions and links to supplemental materials will be added.<br>
 +
<br>
 
{| border="1" cellpadding="1"
 
{| border="1" cellpadding="1"
 
!style="background:#F0F9E8;" width="75"|Date
 
!style="background:#F0F9E8;" width="75"|Date
!style="background:#BAE4BC;" width="400"|Topic
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 +
!style="background:#BAE4BC;" width="350"|Topic
 
!style="background:#7BCCC4;" width="185"|Textbook Readings
 
!style="background:#7BCCC4;" width="185"|Textbook Readings
 
!style="background:#43A2CA;" width="300"|Supplemental Materials
 
!style="background:#43A2CA;" width="300"|Supplemental Materials
!style="background:#0868AC;" width="300"|Research Review Reading
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!style="background:#0868AC;" width="300"|<font color="#FFFFFF">Research Review Reading</font>
  
 
|-  
 
|-  
| || '''Part I: Aug 28 - Oct 11, Dr. Elizabeth Jockusch''' || || ||
+
| || '''Part I: Aug 26 - Oct 9, Dr. Elizabeth Jockusch''' || || ||<br>
|-
+
  
 
|-  
 
|-  
| Aug 28 || Vertebrate Diversity || ---------|| '''[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Biology_of_the_Vertebrates_Study_Questions_F2012#Lecture_1_.2828_August_2012.29 Study Questions'''] <br>[http://www.arkive.org/galapagos-marine-iguana/amblyrhynchus-cristatus/video-06b Marine Iguana Running]<br> [http://www.arkive.org/komodo-dragon/varanus-komodoensis/video-06a Komodo Dragon Walking - Breathing (Buccal pumping)]<br>[http://debanlab.org/movies/ Salamander feeding videos] <br> [http://www.youtube.com/watch?v=7oSseAl_dW0 Ballistic tongue salamander: Cold-proof bow and arrow mechanism]  ||
+
| Aug 26 || Vertebrate diversity || || [http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Biology_of_the_Vertebrates_Study_Questions_F2014#Lecture_1_.26_August_2014.29 '''Study Questions'''] <br>[http://www.arkive.org/galapagos-marine-iguana/amblyrhynchus-cristatus/video-06b Marine Iguana Running]<br> [http://www.arkive.org/komodo-dragon/varanus-komodoensis/video-06a Komodo Dragon Walking - Breathing (Buccal pumping)]<br>[http://debanlab.org/movies/ Salamander feeding videos] <br> [http://www.youtube.com/watch?v=7oSseAl_dW0 Ballistic tongue salamander: Cold-proof bow and arrow mechanism]  ||<br>
|-  
+
 
 +
|-
 +
| Aug 28 || Chordates and vertebrate origins|| Chapters 1 & 2 || [http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Biology_of_the_Vertebrates_Study_Questions_F2014#Lecture_2_.28_August_2014.29 '''Study Questions'''] ||<br>
  
| Aug 30 || Chordate and Vertebrate Origins || Ch. 1, 2 || '''[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Biology_of_the_Vertebrates_Study_Questions_F2012#Lecture_2_.2830_August_2012.29 Study Questions'''] <br>
 
||
 
 
|-   
 
|-   
  
| Sept 4 || Chordates and Living Jawless Vertebrates || Ch. 3 || '''[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Biology_of_the_Vertebrates_Study_Questions_F2012#Lecture_3_.284_September_2012.29 Study Questions'''] <br>
+
| Sept 2 || Living jawless vertebrates || Chapter 3 || || Zintzen et al. (2011) Sci. Rep. 1:131 on [http://ezproxy.lib.uconn.edu/login?url=http://www.nature.com/srep/2011/111027/srep00131/full/srep00131.html Hagfish behavior] <br>
[http://www.youtube.com/watch?v=Gh9OOlgrHyA Urochordate heart beat]<br>
+
 
[http://www.nature.com/srep/2011/111027/srep00131/extref/srep00131-s1.mov Hagfish defense]<br>
+
[http://www.nature.com/srep/2011/111027/srep00131/extref/srep00131-s2.mov Predation by hagfish]<br>
+
|| McGuire and Ratcliffe (2010) Biol. Lett. 7:233-236 on [http://ezproxy.lib.uconn.edu/login?url=http://rsbl.royalsocietypublishing.org/content/7/2/233.full Bat brains]
+
 
|-  
 
|-  
  
| Sept 6 || Living Jawless Vertebrates, cont.|| Ch. 3 || '''[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Biology_of_the_Vertebrates_Study_Questions_F2012#Lecture_4_.286_September_2012.29 Study Questions'''] <br>[http://www.youtube.com/watch?v=pmaal7Hf0WA Hagfish Slime]<br>[http://www.youtube.com/watch?v=letqkpG3b5Q Hagfish on sea floor]<br>[http://jeb.biologists.org/content/vol210/issue22/images/data/3897/DC1/JEB006940Movie1.mov Hagfish feeding]<br>[http://www.arkive.org/river-lamprey/lampetra-fluviatilis/video-07.html Lamprey Spawning]
+
| Sept 4 || Early vertebrate fossils || Chapter 3 || || <br>
||
+
 
 
|-  
 
|-  
  
| Sept 11 || Early Vertebrate Fossils || Ch. 3 || '''[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Biology_of_the_Vertebrates_Study_Questions_F2012#Lecture_5_.2811_September_2012.29 Study Questions''']
+
| Sept 9 || Chondrichthyans || Chapter 5 || ||<br>
|| Sansom et al. (2010) Nature 463:797-800 on [http://ezproxy.lib.uconn.edu/login?url=http://www.nature.com/nature/journal/v463/n7282/full/nature08745.html Interpreting fossils]
+
 
 
|-  
 
|-  
  
| Sept 13 || Chondrichthyans|| Ch. 5 || '''[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Biology_of_the_Vertebrates_Study_Questions_F2012#Lecture_6_.2813_September_2012.29 Study Questions'''] <br>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/SampleQuestions.pdf}} '''Sample Questions'''<br>[http://www.arkive.org/sand-tiger-shark/carcharias-taurus/video-09.html Male Sand Tiger Shark Swimming]<br>[http://www.arkive.org/whitetip-reef-shark/triaenodon-obesus/video-09.html Whitetip Reef Sharks Mating]<br>[http://www.arkive.org/leopard-shark/stegostoma-fasciatum/video-09.html Leopard Shark Courtship]<br>[http://www.arkive.org/lemon-shark/negaprion-brevirostris/video-09a.html Lemon shark giving birth]
+
| Sept 11 || Osteichthyan origin and diversification || Chapter 6 || ||<br>
||
+
 
 
|-  
 
|-  
  
| Sept 18 || <span style="font-size: small"><font color="#FF3300">'''Tree Quiz 1'''</font></span><br>Chondrichthyans, con't, Diversification of jaws and feeding|| Ch. 5|| '''[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Biology_of_the_Vertebrates_Study_Questions_F2012#Lecture_7_.2818_September_2012.29 Study Questions''']<br>[http://www.arkive.org/tiger-shark/galeocerdo-cuvier/video-08.html Shark Feeding on Albatross]<br> [http://www.arkive.org/whale-shark/rhincodon-typus/video-08b.html Whale Shark Feeding]<br>[http://www.arkive.org/spotted-eagle-ray/aetobatus-narinari/video-08.html Eagle Ray Feeding/Locomoting]<br>[http://www.arkive.org/manta-ray/manta-birostris/video-08b.html Manta Ray Feeding]<br>[http://www.amnh.org/learn/pd/fish_2/fish_skull/index.html Jaw protrusion animations]<br> [http://www.youtube.com/watch?v=TbGILi8p5Y8&feature=related Fish Suction Feeding]<br>[http://www.youtube.com/watch?v=pDU4CQWXaNY&NR=1&feature=endscreen Jaw protrusion champion]<br>
+
| Sept 16 || Actinopterygians || Chapter 6 || || <br>
|| Myers et al. (2007) Science 315:1846-1850 on [http://ezproxy.lib.uconn.edu/login?url=http://www.sciencemag.org/content/315/5820/1846.full Effects of shark overfishing]
+
 
 +
|-
 +
 
 +
| Sept 18 || Sarcopterygii & evolution of tetrapods || pp. 125-128 & 196-211 (8th ed.)/153-156 & 189-201 (9th ed.) || ||<br>
 +
 
 
|-  
 
|-  
  
| Sept 20 || Osteichthyan Origins and Living Actinopterygians|| Ch. 6 (except pp. 125-134)|| {{pdf|http://hydrodictyon.eeb.uconn.edu/eebedia/images/1/12/Quiz1key.pdf}} '''Tree Quiz 1 Key''' <br>  '''[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Biology_of_the_Vertebrates_Study_Questions_F2012#Lecture_8_.2820_September_2012.29 Study Questions'''] <br>  
+
| Sept 23 || Amphibian diversity and decline || Chapter 10 || ||<br>
[http://www.youtube.com/watch?v=MF5Qq9mhrrw Paddlefish Feeding]<br>
+
 
[http://www.youtube.com/watch?v=utuxlfvlLEQ Moray Eel Feeding (with Pharyngeal Jaw)]<br>[http://www.mbari.org/news/homepage/2012/chaunacops/chaunacops.html anglerfish]<br>[http://www.mbari.org/news/news_releases/2009/barreleye/barreleye.html barreleye video] <br>[http://www.mbari.org/education/video/bigteeth.html deep sea fish]<br>
+
||
+
 
|-  
 
|-  
  
| Sept 25 ||Sarcopterygii and Evolution of Tetrapods <br>
+
| <span style="font-size: small"><font color="#FF3300">'''Sept 25'''</font></span> || <b><span style="font-size: small"><font color="#FF3300">'''EXAM 1'''</font></span> ||  || || <br>
<span style="font-size: small"><font color="#FF3300">'''Exam 1 Review session''': 5-7 pm in BPB131</font></span>
+
 
|| Ch. 6 (pp. 125-134); Ch. 9 (pp. 196-211)
+
|| '''[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Biology_of_the_Vertebrates_Study_Questions_F2012#Lecture_9_.2825_September_2012.29 Study Questions'''] <br> [http://www.arkive.org/coelacanth/latimeria-chalumnae/video-06.html Coelacanth]<br>[http://www.arkive.org/shoebill/balaeniceps-rex/video-08.html Lungfish vs. Bird] <br> [http://tiktaalik.uchicago.edu/meetTik.html Tiktaalik]||None
+
 
|-  
 
|-  
  
| <span style="font-size: small"><font color="#FF3300">'''Sept 27'''</font></span>|| <span style="font-size: small"><font color="#FF3300">'''EXAM 1'''</font></span> includes material through the origin of tetrapods (but not amphibian diversity)|| --------- ||{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/EEB2214F12Exam1studyguide.pdf}}<span style="font-size: small"><font color="#FF3300"> '''Study Guide'''</font></span>||
+
| Oct 2 || Amniote origins || pp. 211-218 (8th ed.)/pp. 201-208 (9th ed.) || ||<br>
 +
 
 
|-  
 
|-  
  
| Oct 2 || Amphibian Diversity || Ch. 10 ||'''[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Biology_of_the_Vertebrates_Study_Questions_F2012#Lecture_10_.282_October_2012.29 Study Questions'''] <br> [http://www.youtube.com/watch?v=B9h1tR42QYA Tiktaalik]<br> [http://www.nature.com/nature/journal/vaop/ncurrent/extref/nature11124-s2.mov Ichthyostega] ||King et al. (2011) PNAS 108:21146-21151 on the [http://ezproxy.lib.uconn.edu/login?url=http://www.pnas.org/content/108/52/21146.long Origin of tetrapod gaits]
+
| Oct 7 || Amniote diversity / desert adaptations || Chapter 13 || ||<br>
 +
 
 
|-  
 
|-  
  
 +
| Oct 9 || Snakes || pp. 339-349 (8th ed.)/pp. 317-327 (9th ed.) || || <br>
  
| Oct 4 || Amphibian Diversity|| Ch. 10  || '''[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Biology_of_the_Vertebrates_Study_Questions_F2012#Lecture_11_.284_October_2012.29 Study Questions'''] <br> [http://www.youtube.com/watch?v=6K6szXrBHwM Caecilian Feeding]<br>[http://video.google.com/videoplay?docid=1983266083446767772#docid=-5359004945508340113 Salamander Pheromone Delivery]<br>[http://video.google.com/videoplay?docid=1983266083446767772# Salamander Sperm Transfer]<br>[http://www.arkive.org/chinese-giant-salamander/andrias-davidianus/video-06.html Giant Salamander]<br>
 
||
 
 
|-  
 
|-  
  
| Oct 9 || Amniote Origins and Diversity || Ch. 9 (pp. 211-218); Ch. 13 || || Vredenburg et al. (2010) PNAS 107:9689-9694 on [http://ezproxy.lib.uconn.edu/login?url=http://www.pnas.org/content/107/21/9689.long Amphibian extinctions]
+
| || '''Part 2: Oct 14 - Dec 12, Dr. Margaret Rubega'''  || || ||<br>
  
 
|-  
 
|-  
  
| Oct 11 || Desert Adaptations & Snakes || Ch. 13 ||
+
| Oct 14 || Turtles || Chapter 12 || || no research review<br>
||  
+
 
 
|-  
 
|-  
  
| || '''Part II: Oct 16 - Dec 14, Dr. Kristiina Hurme'''      || || ||  
+
| Oct 16 || Turtles cont'd & Archosaurs || Chapter 16 || ||<br>
 +
 
 
|-  
 
|-  
  
| Oct 16 || Turtles || Ch. 12 || ||  
+
| Oct 21 || Crocodilians & friends || Chapter 16 || ||<br>
 +
 
 
|-  
 
|-  
  
| Oct 18 || Introduction to Archosaurs & Crocodilians|| Ch. 16 ||
+
| Oct 23 || Dinosaurs and other Mesozoic diapsids || Chapter 16 || ||<br>
||  
+
|-
+
  
| Oct 23 || Archosaurs: Pterosaurs || Ch. 16 || ||
 
 
|-  
 
|-  
  
| Oct 25 || Dinosaurs and Other Mesosoic Diapsids || Ch. 16 || ||  
+
| Oct 28 || Dinosaurs II || Chapter 16 || || <br>
 +
 
 
|-  
 
|-  
  
|| <span style="font-size: small"><font color="#FF3300">'''Oct 30'''</font></span>|| <span style="font-size: small"><font color="#FF3300">'''EXAM 2'''</font></span> includes material beginning with Lissamphibia and ending on Saurichia (includes all of Thursday's lecture material)|| --------- ||||
+
| <span style="font-size: small"><font color="#FF3300">'''Oct 30'''</font></span> || <span style="font-size: small"><font color="#FF3300">'''EXAM 2'''</font></span> || || || <br>
|-
+
  
| Nov 1 || Dinosaurs II - Theropods || Ch. 16 ||
 
||
 
|-
 
 
| Nov 6 || Birds: Avian Origins || Ch. 16 (pp. 439-443)  ||||
 
 
|-  
 
|-  
  
| Nov 8 || Birds: Feeding, Morphology, and Reproduction || Ch. 17 ||||  
+
| Nov || Birds: Avian origins || pp. 439-443 (8th ed.)/pp. 407-410 (9th ed.) || ||<br>
 +
 
 
|-  
 
|-  
  
| Nov 13 || Birds: Reproduction, and Introduction to Mammals || Ch. 17 ||||  
+
| Nov 6 || Birds: Feeding || Chapter 17 || ||<br>
 +
 
 
|-  
 
|-  
  
|Nov 15 || Mammals: Origins and Radiation  || Ch. 18 ||
+
| Nov 11  || Birds:Morphology and Reproduction || Chapter 17 || ||<br>
||
+
 
 
|-  
 
|-  
  
| Nov 27 || Mammals: Primate Evolution and Human Diversity || Ch. 24  ||
+
| Nov 13  || Mammals: Origins and radiations || Chapter 18 || ||<br>
||
+
 
 
|-  
 
|-  
  
| Nov 29 || Mammals: Primate Evolution continued and Mammal Diversity<br> || Ch. 20 ||
+
| Nov 18  || Mammals: Primate evolution and human origins || Chapter 24 || ||<br>
||  
+
 
 
|-  
 
|-  
  
| Dec. 4 || Vertebrate Mass Extinctions, Past and Present|| Ch. 21 ||||
+
| Nov 20 || Mammals: Diversity || Chapter 20 || || <br>
 +
 
 
|-  
 
|-  
  
| Dec 6 || Vertebrate Mass Extinctions, Past and Present || Ch. 25  ||||  
+
| Dec || Mammals: Morphology and Behavior || Chapter 21 || ||<br>
 +
 
 
|-  
 
|-  
  
|<span style="font-size: small"><font color="#FF3300">'''Dec 14'''</font></span>||<span style="font-size: small"><font color="#FF3300">'''FINAL EXAM 10:30 am-12:30 pm '''</font></span>|| --------- ||||  
+
| Dec 4  || Vertebrate mass extinctions, past and present || Chapter 25 || || <br>
 +
 
 +
|-
 +
 
 +
| <span style="font-size: small"><font color="#FF3300">'''Dec 12'''</font></span> ||<span style="font-size: small"><font color="#FF3300"> '''Final Exam 10:30 - 12:30 (Tentative)''' </font></span>|| Chapter 25 || ||<br>
 +
 
 +
|- |-
 
|- |-}
 
|- |-}
  
 
[[Category:EEB Courses]]
 
[[Category:EEB Courses]]

Latest revision as of 06:15, 29 August 2014

EEB 2214, Fall 2014

The evolution of form, function, & diversity of the vertebrates

Meeting Time: Tuesdays and Thursdays, 12:30-1:45 in BPB130

Textbook: Vertebrate Life, by Pough F. H., C. M. Janis, and J. B. Heiser. 2012. 9th Edition. Pearson/Benjamin Cummings (8th edition also acceptable)

Contents

Instructors

Female with hatchlings.JPG

Dr. Elizabeth Jockusch
Office: Pharmacy/Biology 305B
Phone: (860) 486-4452
Office hours: Thursdays 2-3 pm and by appointment
Jockusch Lab Website

Dr. Margaret Rubega
Office: Pharmacy/Biology 500
Phone: (860) 486-4502
Office hours: TBA and by appointment
Rubega Lab Website

Kevin Burgio (Teaching Assistant)
Office: Pharmacy/Biology 402
Office hours: Tuesdays 2-3 pm and by appointment
Monk Parakeet Research Website

Note: All emails must contain "EEB2214" in the subject line to avoid being filtered out and deleted

Grading

MonkParakeet01.jpeg

Exam 1 (Thursday, Sept. 25) = 100 points
Exam 2 (Thursday, Oct. 30) = 100 points
Final Exam (Friday, Dec. 12, TENTATIVE) = 125 points
#Research Reviews (Tuesdays) = 30 points total
#Quizzes = 50 points total
#Collections Tour = 5 points

There will be two one-hour, non-cumulative, exams scheduled during the lecture hour. The final exam will be cumulative, with an emphasis on material from the final third of the course.

12 research reviews (3 points each) and quizzes (5 points each) will be offered over the course of the semester. 10 of these will count towards the final course grade (the best 5 of 6 from each half of the semester, as determined by the combined quiz + research review grade.) Because two scores are dropped, no make-ups will be given for research reviews or quizzes.

Course Policies

Missed Exams
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. Permission to reschedule the final can only be obtained through procedures determined by the Dean of Students Office.

Other Absences
No make-ups will be given for research reviews or quizzes. Instead, the lowest research review/quiz grade from each half of the semester will be dropped.

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 Section IV 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.

Classroom Conduct
We expect all students to behave in a way that is respectful of others. The Pdficon small.gif classroom conduct form, which describes our expectations in more detail, must be signed and returned to the teaching assistant by the end of the 2nd week of class.

  • 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.
  • Recording is prohibited without the written permission of instructors.
  • Course materials are the intellectual property of the course instructors. Students may not make these materials (including handouts, exams and quizzes) available electronically.


Honors Conversion

Can I convert this course to honors?

Research Reviews

As a research field, vertebrate biology is alive and well, with discoveries being made constantly. Each week, we will select one paper from the primary scientific literature that describes a study relevant to vertebrate biology. On Tuesdays, class will include a short in-class written exercise, in which we ask you to answer three standard questions about the paper:

  • What was the major new result?
  • How does this change what we think?
  • Why does it matter?

The written exercise will be followed by a brief discussion of the paper, during which we will call on pre-determined, but randomly selected, students to talk about the paper.

In-class research review assessments are worth 3 points each. 12 will be offered over the course of the semester, and 10 (of 12) will count towards the final course grade (the best 5 of 6 from each half of the semester, as determined by the combined quiz + research review grade). There will be no paper selected for the first or eighth week of class. You must be present to receive credit and no make-ups will be given. Also, if you are selected for the discussion, but do not participate, you will receive a 0.

All papers will be available electronically. A link to each paper will be posted on the course schedule below, next to the date of the in-class exercise. While many articles in scientific journals are now made available free to everyone ("open access" articles), access to other articles requires a subscription, which the UConn library buys. On campus, you should not encounter difficulty accessing the full text of selected articles. From off-campus, the easiest way to access articles that require a subscription is using the EZProxy. If you get a message saying that you may purchase access to the paper, then try again through the proxy. In some cases, it may also be necessary to quit and restart your browser. Alternative ways to access the articles via UConn's subscription are to configure the proxy within your web browser and to use the VPN. It is your responsibility to test that you have access in a timely fashion. Course instructors will not respond to requests to provide the article directly to individuals.

Pdficon small.gifThis handout offers some helpful suggestions for how to navigate your way through the primary literature.

Quizzes

This course incorporates weekly quizzes which will be completed at the same time as the written portion of the research review, unless another schedule is announced. The quizzes will use a variety of formats and are designed to help prepare you for exams. Each quiz will be worth 5 points. 10 (of 12) will count towards the final course grade (the best 5 of 6 from each half of the semester, as determined by the combined quiz + research review grade). As with the research reviews, you must be present to receive credit and no make-ups will be given.

Collections Tour

Every student is expected to visit the EEB Biological Collections for a tour that will introduce you to the resources and opportunities in the collection. We will offer 8 different opportunities, on different days and times. You will need to sign in at the collection; at the end of the semester, everyone who has signed in will have 5 points added to their grade. Tours will take about 45 minutes; they meet at the south end of the Biology/Physics building lobby on the hour. You are responsible for finding a day and time to attend from the options below; if your class schedule prohibits you from attending any of these, you are responsible for letting us know that you will need an alternative opportunity AT LEAST TWO WEEKS PRIOR TO THE FINAL TOUR. If you have already toured the collections (e.g., in a previous class), provide us with documentation to that effect, and we will just add the points to your grade without you needing to tour the collections again.

Collections tour times will be posted here and announced in class once the schedule is set.

Help Resources

The secret of success to this course is to not let yourself fall behind. Be sure to fill gaps in your notes and navigate blocks in your understanding as soon as possible. Should you run into trouble with the material, below we have listed some steps for obtaining assistance. While we welcome any and all questions on the material, before you contact us, please first check the resources below to see if your question has already been answered. If/when you do contact us, please understand that we will respond as quickly as we can, but we do have other obligations that might prevent this from happening as urgently as you may need (like 3:00 am the day of an exam...).

Study Materials
The textbook for this course is Pough F. H., C. M. Janis, and J. B. Heiser. 2012. Vertebrate Life, 9th Edition. Prentice Hall. (The 8th edition is also acceptable; we have posted readings for both.) We strongly encourage you to read the assigned sections before lecture.

Study questions will be posted online after every lecture. These are intended to help you think about and synthesize information. They are not intended to provide a comprehensive study guide.

Review Sessions
A review session will be held before each exam. Dates and times will be posted once they are set.

Research Reviews
Use Pdficon small.gif this handout to help navigate your way through the primary literature.

Syllabus
Pdficon small.gif Syllabus distributed on the first day of class. The lecture schedule and readings are subject to change, and will be updated below.

Lecture Schedule & Materials

The lecture schedule below will be updated regularly. A link to each research review paper will be posted next to the date of the in-class exercise. Generally, these will be posted by the weekend prior to the exercise. After lectures, study questions and links to supplemental materials will be added.

Date Topic Textbook Readings Supplemental Materials Research Review Reading
Part I: Aug 26 - Oct 9, Dr. Elizabeth Jockusch
Aug 26 Vertebrate diversity Study Questions
Marine Iguana Running
Komodo Dragon Walking - Breathing (Buccal pumping)
Salamander feeding videos
Ballistic tongue salamander: Cold-proof bow and arrow mechanism

Aug 28 Chordates and vertebrate origins Chapters 1 & 2 Study Questions
Sept 2 Living jawless vertebrates Chapter 3 Zintzen et al. (2011) Sci. Rep. 1:131 on Hagfish behavior
Sept 4 Early vertebrate fossils Chapter 3
Sept 9 Chondrichthyans Chapter 5
Sept 11 Osteichthyan origin and diversification Chapter 6
Sept 16 Actinopterygians Chapter 6
Sept 18 Sarcopterygii & evolution of tetrapods pp. 125-128 & 196-211 (8th ed.)/153-156 & 189-201 (9th ed.)
Sept 23 Amphibian diversity and decline Chapter 10
Sept 25 EXAM 1
Oct 2 Amniote origins pp. 211-218 (8th ed.)/pp. 201-208 (9th ed.)
Oct 7 Amniote diversity / desert adaptations Chapter 13
Oct 9 Snakes pp. 339-349 (8th ed.)/pp. 317-327 (9th ed.)
Part 2: Oct 14 - Dec 12, Dr. Margaret Rubega
Oct 14 Turtles Chapter 12 no research review
Oct 16 Turtles cont'd & Archosaurs Chapter 16
Oct 21 Crocodilians & friends Chapter 16
Oct 23 Dinosaurs and other Mesozoic diapsids Chapter 16
Oct 28 Dinosaurs II Chapter 16
Oct 30 EXAM 2
Nov 4 Birds: Avian origins pp. 439-443 (8th ed.)/pp. 407-410 (9th ed.)
Nov 6 Birds: Feeding Chapter 17
Nov 11 Birds:Morphology and Reproduction Chapter 17
Nov 13 Mammals: Origins and radiations Chapter 18
Nov 18 Mammals: Primate evolution and human origins Chapter 24
Nov 20 Mammals: Diversity Chapter 20
Dec 2 Mammals: Morphology and Behavior Chapter 21
Dec 4 Vertebrate mass extinctions, past and present Chapter 25
Dec 12 Final Exam 10:30 - 12:30 (Tentative) Chapter 25
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