Difference between revisions of "Biology of the Vertebrates"

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[[Image:Elaphe_obsoleta,_head,I_JP1822.jpg|thumb|right|'']] [[Image:Hyla_cinerea,_Green_Treefrog,I_JP6639_1-1.jpg|thumb|right|'']][[Image:Untitled,I_TP2877.jpg|thumb|right|'']][[Image:Untitled,I_TP2576.jpg|thumb|right|'']]<span style="font-size: x-large">EEB 2214, Fall 2009</span>
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<span style="font-size: x-large">EEB 2214, Fall 2014</span><br><br>
<span style="font-size: large">''The evolution of form, function, and diversity of the vertebrates''</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: small">'''Tuesdays and Thursdays, 12:30-1:45 in BSP130'''<br>
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<span style="font-size: small">'''Textbook: TBA''' <br>
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<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>
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==<span style="font-size: large"><font color="#FF3300"> '''Announcements'''</font></span><br>==
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'''12/5/14'''<br>
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The final exam review session will be on Thursday Dec. 11 from 2 - 4pm in TLS, Room 301. This review will primarily focus on the material covered since the last exam.<br>
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'''9/24/14''' <br>
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For a detailed and thorough phylogenetic tree, please check the appendix of your text book! Though, be sure to check it against your notes, as some things have changed since the book has been published (e.g. position of conodonts).<br>
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Kevin produced a short instructional video on phylogenetic tree basics! See it [http://www.screencast.com/t/ycbUEphh48 '''here.''']<br>
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Here is the official {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/EEB2214F14Exam1studyguide.pdf}}<span style="font-size: small"><font color="#FF3300"> '''Exam 1 Study Guide!'''</font></span><br>
  
 
==Instructors==
 
==Instructors==
  
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[[Image:Female_with_hatchlings.JPG|right]]
  
Dr. Kentwood D. Wells<br>
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'''[mailto:elizabeth.jockusch@uconn.edu Dr. Elizabeth Jockusch]'''<br>
Office: Torrey Life Science Room 312<br>
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Office: Pharmacy/Biology 305B<br>
Phone: (860) 486-4319<br>
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Phone: (860) 486-4452<br>
E-mail: [mailto:kentwood.wells@uconn.edu kentwood.wells@uconn.edu]<br>
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Office hours: Thursdays 2-3 pm and by appointment <br>
Office hours: TBA
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[http://jockusch.eeb.uconn.edu/ Jockusch Lab Website] <br><br>
  
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'''[mailto:margaret.rubega@uconn.edu Dr. Margaret Rubega]'''<br>
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Office: Pharmacy/Biology 500<br>
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Phone: (860) 486-4502<br>
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Office hours: 11:30 - 12:20 a.m., Thurs, IN the BPB cafe, and by appointment <br>
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[http://rubegalab.eeb.uconn.edu/ Rubega Lab Website] <br><br>
  
Dr. Margaret Rubega<br>
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'''[mailto:kevin.burgio@uconn.edu Kevin Burgio]''' (Teaching Assistant)<br>
Office: Biology/Pharmacy 500<br>
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Office: Pharmacy/Biology 402<br>
Phone: 486-4502<br>
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Office hours: Tuesdays 2-3 pm and by appointment <br>
E-mail: [mailto:margaret.rubega@uconn.edu margaret.rubega@uconn.edu]<br>
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[http://monkparakeetresearch.org/ Monk Parakeet Research Website] <br><br>
Office hours: by appointment<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>
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<br><br>
  
Diego Sustaita (Teaching Assistant)<br>
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==Grading==
Office: BioPharm 402<br>
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[[Image:MonkParakeet01.jpeg|325 px|right]]
Phone: 486-0309<br>
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'''Exam 1''' (Thursday, Sept. 25) = 100 points <br>
E-mail: [mailto:diego.sustaita@uconn.edu diego.sustaita@uconn.edu]<br>
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'''Exam 2''' (Thursday, Oct. 30) = 100 points <br>
Office hours: TBA
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'''Final Exam''' (Friday, Dec. 12, TENTATIVE) = 125 points <br>
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'''[[#Research Reviews]]''' (Tuesdays)  = 30 points total<br>
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'''[[#Quizzes]]'''  = 50 points total<br>
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'''[[#Collections Tour]]'''  = 5 points<br>
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<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>
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<br>
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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>
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<br>
  
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==Course Policies==
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'''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.  Permission to reschedule the final can only be obtained through procedures determined by the [http://dos.uconn.edu Dean of Students Office].
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<br><br>
  
==Grading==
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'''Other Absences'''<br>
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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.
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<br><br>
  
<span style="font-size: large"><font color="#FF3300">Under construction</font></span>
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'''Academic Integrity'''<br>
<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>
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<br>
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'''Disabilities'''<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>
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<br>
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'''Classroom Conduct'''<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>
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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. 
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*Turn cell phones OFF and store them out of sight.
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*Use laptops only for taking notes.
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*Recording is prohibited without the written permission of instructors.
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*Course materials are the intellectual property of the course instructors.  Students may not make these materials (including handouts, exams and quizzes) available electronically.
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<br>
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'''Honors Conversion'''<br>
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:'''[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Biology_of_the_Vertebrates_Honors_Conversion Can I convert this course to honors?''']<br><br>
  
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== Research Reviews ==
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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>
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* 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>
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<br>
  
<span style="font-size: larger">'''Missed exams and Concerns about Finals'''</span>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/FinalsInstructions.pdf}}<br>
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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>  
Any student who does not attend an exam and fails to receive permission in advance will receive a 0 for the examApproval of any request to miss an exam requires, but is not guaranteed by, verifiable written documentation of the reasonA student who receives approval to miss an exam will, at the discretion of the instructor, either take a make-up exam or have his or her course grade prorated based on performance in the remainder of the course.
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<br>
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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 exerciseWhile 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 buysOn 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>
  
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{{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>
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<br>
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==Quizzes==
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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>
  
<span style="font-size: larger">'''Academic integrity'''</span><br>
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== Collections Tour ==
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] available at the web site of the Dean of Students.
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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>
  
  
<span style="font-size: larger">'''Disabilities'''</span><br>
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'''Collection Tour Schedule'''<br><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:
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Mon. Nov. 3: 2:00 - 2:45 pm <br>
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Tues. Nov. 4: 11:30 - 12:15 pm <br>
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Wed. Nov. 5: 1:00 - 1:45 pm <br>
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Thur. Nov. 6: 9:30 - 10:15am <br>
  
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Mon. Nov. 10: 9:15 - 10:00am <br>
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Tues. Nov. 11: 3:00 - 3:45pm <br>
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Wed. Nov. 12: 2:00 - 2:45pm <br>
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Thur. Nov. 13: 11:00 - 11:45am <br><br>
  
==Vertebrates in the News==
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'''Please email Kevin ASAP with your preferences! Each slot is limited to ~10 students.'''
  
[http://www.nytimes.com/2008/10/16/science/16fossil.html?_r=1&oref=slogin ''Tiktaalik'' Article]<br>
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==Help Resources==
[http://www.nytimes.com/2008/10/07/science//07mammal.html Mammals Threatened with Extinction]<br>
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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...).
[http://news.bbc.co.uk/2/hi/science/nature/7684796.stm New Feathered Dinosaur Discovered]<br>
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<br><br>
[http://www.nytimes.com/2008/11/04/science/04obbats.html?ref=science Bat Disease Fungus Identified]<br>
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[http://www.washingtonpost.com/wp-dyn/content/article/2008/11/03/AR2008110303042.html?hpid=topnews Marine Protected Areas Proposed]<br>
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[http://www.nytimes.com/2008/12/02/science/02obturtle.html?ref=science New Turtle Fossil with Partial Shell]
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'''Study Materials'''<br>
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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>
  
'''Exam Information'''<br>
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[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>
Go through the powerpoint[http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/Phyl_tut_pptshow2.ppt PHYLOGENY TUTORIAL ] and then test your tree knowledge with this PRACTICE QUIZ{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/EEB214F06treequiz.pdf}}<br>
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Practice Quiz Answers{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/EEB214F06treequizAnswers.pdf}}
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<br>
 
<br>
Study guide for Exam 1{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/EEB214F06Exam1studyguide.pdf}}<br> Practice Multiple Choice Questions{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/MultipleChoiceQuestions.pdf}}<br>
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{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/EEB2214F14Exam1studyguide.pdf}}<span style="font-size: small"><font color="#FF3300"> '''Exam 1 Study Guide'''</font></span><br><br>
An answer key for exam 1 is posted outside of Dr. Jockusch's Office, BioPharm 305B.<br>
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An answer key for exam 2 is posted outside of Dr. Rubega's Office, BioPharm 500.<br>
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==Review Session Information and Additional Office Hours==
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'''Tree Resources'''<br>
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{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/EEB2214F14_Phylogeny.pdf}} This is the backbone of the '''vertebrate phylogeny''' we will be using in this class.  Note that it differs from the textbook tree in the placement of turtles and in how lampreys and hagfishes are related to each other.  We will be expanding the terminal taxa and adding fossils to this tree throughout the semester.<br>
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{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/Phyl_tut_pptshow.pptx}} This '''phylogeny tutorial''' is designed to help students review their knowledge of trees.<br>{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/EEB2214_TreeTerminology.pdf}} A primer of '''tree terminology'''<br>
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{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/SampleTreeQuiz.pdf}} An example of a previous '''tree quiz'''<br>
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{{pdf|https://mcdb.colorado.edu/courses/4350/2012/articles/TreeThinkingChallenge.pdf}} the '''Tree Thinking Quiz''' we went over during the study sessions. Make sure you scroll down for the quiz and answers. <br>
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[http://www.screencast.com/t/ycbUEphh48 '''Kevin's "Phylogenetic Tree Basics" Video''']
  
'''REVIEW SESSION FOR THE FINAL EXAM will be held on FRIDAY, DEC. 5th, 4-6, BPB130'''
 
*Additional Office Hours on MONDAY, DEC. 8: Maria 11-1pm
 
  
=='''Questions''' (from students) and Answers  (note: I will respond to questions received up to, but not after, Monday 8 December, at 12 p.m.)==
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'''Review Sessions'''<br>
   
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A review session will be held before each examDates and times will be posted once they are set.<br>
'''In our slides since the last exam the only slides that actaully have the title synapamorphies on them have to do with mammals and carnivora. Does this mean the only synapamorphies we have are those of mammals and carnivores and everything else every other group has is a characteristic or are there more synapamorphies we have to know?''' There has certainly been a great deal of anxiety about synapomorphies, and what should and should not be on your lists to memorize....The most important thing, for starters, is to understand what a synapomorphy is, and is not. Thus, many of the "groups" we have talked about in the Synapsida are paraphyletic groups --- by definition, they are not defined by synapomorphies. Secondly, complete lists of synapomorphies are not likely to help you if you don't understand the significance of when and in which taxa certain characteristics evolved. We did not give you complete lists of synapomorphies for every, or even perhaps any, group, because most groups are defined by a collection of characteristics, and not infrequently the majority of the list consists of features whose significance is obscure to everyone but a specialist. If you can reproduce for us, in most cases, the most significant characteristics of a lineage and why they are important, you'll do well, whether your list of synapomorphies is complete or not.  
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<br>
  
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'''Research Reviews'''<br>
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Use {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/EEB2214_ReadingScientificLiterature.pdf}}''' this handout''' to help navigate your way through the primary literature.<br>
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<br>
  
'''On the slide that discusses locomotion during breathing from the 11/13lecture, the difference between positive pressure breathing and negative pressure breathing. Which taxa does positive pressure breathing refer to and which does negative pressure breathing refer to?''' The slide in question shows positive and negative pressure symbols superimposed on the lung (areas) of a running cheetah. If you look closely at the slide, you'll see that the pressure changes at different parts of the stride cycle -- when the animal is "bunched" up, the pressure is positive, when stretched out, the pressure is negative. This is not a taxonomic thing: all respiration via lungs requires this cycling of pressure from negative to positive and back again. The point that was being made in that lecture is that a flexible spine contributes to the ability of the animal to force those pressure changes to occur rapidly, and thus to heighten respiration rates, by moving the viscera forward (where it presses the diaphragm forward and increasing air pressure in the lungs) and backward (where they pull the diaphragm after them, thus decreasing air pressure in the lungs).  
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'''Syllabus'''<br>
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{{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>
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<br>
  
'''Are fur and mammary glands the only synapomorphies of mammals? What about diphyodonty, anisognathy, and nasal turbinates? Are those just common characteristic?''' Fur and mammary glands are synapomorphies of living mammals --- only mammals have them. Because they are "soft" tissues that do not fossilize well, exactly which extinct taxa had them is uncertain. The others you list are synapomorphies, but not all those that characterize Mammalia; there is a list on page 488 of your textbook which details which other "hard" (bony) characters are synapomorphies for Mammalia.
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==Lecture Schedule & Materials==
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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>
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<br>
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{| border="1" cellpadding="1"
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!style="background:#F0F9E8;" width="75"|Date
  
'''We have to identify the five major groups of Eutherians.  I would say Edentata, Glires, Archonta, Carnivora and Ungulata are the major groups.We also mention Insectivora though and so I'm not sure what they would count as?''' Good catch: we actually discussed SIX, and yes that includes the Insectivora.
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!style="background:#BAE4BC;" width="350"|Topic
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!style="background:#7BCCC4;" width="185"|Textbook Readings
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!style="background:#43A2CA;" width="300"|Supplemental Materials
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!style="background:#0868AC;" width="300"|<font color="#FFFFFF">Research Review Reading</font>
  
'''The question also wants us to explain some important morphological attributes of the groups.  I can't seem to find any attributes that are common among all Archonta. I know there are some synapomorhpies and traits for certain species within the group, but I'm wondering if I'm missing some sort of general characteristic that all Archonta have?''' Another good catch: I find that I failed to give you the synapomorphies for Archonta; they are 1) a pendulous penis (i.e., one that is not tucked up or retracted into the body when not in use, and 2)certain details of the structure of the ankle.
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|-
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| || '''Part I: Aug 26 - Oct 9, Dr. Elizabeth Jockusch''' ||  ||  ||<br>
  
'''When you explained the shifting of bones in the lower jaw, I am assuming that occured in all therapsids? (not only/excluding non-cynodont therapsids?)''' As I explained in class, the shift in size and location of the bones of the jaws is a TREND --- it didn't happen at one, easily identifiable part of the tree at one point in time --- but was completed by the time you get to mammals.  
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|-
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| Aug 26 || Vertebrate diversity ||  || [http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Biology_of_the_Vertebrates_Study_Questions_F2014#Lecture_1_.2826_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>
  
'''On the pelycosaur slide, you wrote that "synapsids exhibit the primitive amniote conditions", I just wanted to be clear that these are exhibited in all synapsids and not just present (or further developed in some way) in pelycosaurs?''' That's right. All synapsids have (or had) an inability to excrete uric acid, relatively poor color vision, and glandular skin without scales.
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|-
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| 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_.2828_August_2014.29'''Study Questions'''] ||<br>
  
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|- 
  
'''What exactly is this difference in the pubis orientation between ornithischians and saurischians?'''
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| Sept 2 || Chordates, con't.; Living jawless vertebrates || Chapter 3 ||[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Biology_of_the_Vertebrates_Study_Questions_F2014#Lecture_3_.282_Sept_2014.29'''Study Questions'''] <br>
This is illustrated, and better looked at than described, in Fig. 16.8 in your book, and in at least one of the diagrams on the handout from the dinosaur lecture.  
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[http://www.youtube.com/watch?v=Gh9OOlgrHyA Urochordate heart beat]<br>
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[http://www.nature.com/srep/2011/111027/srep00131/extref/srep00131-s1.mov Hagfish defense]<br>
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[http://www.nature.com/srep/2011/111027/srep00131/extref/srep00131-s2.mov Predation by hagfish]<br>
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[http://www.youtube.com/watch?v=pmaal7Hf0WA Hagfish slime]<br>
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[http://www.youtube.com/watch?v=Bb2EOP3ohnE&feature=youtu.be Hagfish slime #2--what happened to the water?]
 +
|| 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>
  
'''You spoke more in-depth about the estrus cycle in marsupials versus eutherians, how much about this do we need to know?''' You need to know what I covered in class --- that marsupial pregnancies are short because they have not evolved the means to suppress their estrus cycles, so that embryos are expelled from the uterus relatively early in development.
+
|-  
  
 +
| Sept 4 ||Living jawless vertebrates, con't.  || Chapter 3 ||
 +
[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Biology_of_the_Vertebrates_Study_Questions_F2014#Lecture_4_.284_Sept_2014.29'''Study Questions'''] <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] <br>
 +
|| <br>
  
'''In the lecture on Pterosaurs we discussed Pterosaurian adaptations to flight and hollow bones were given as an example. How can this be if hollow bones are a synapomorphy for Theropoda, which comes later in the tree?'''
 
This is an excellent question, and points out the issue of using certain morphological features to define groups when convergence may cause those features to arise in multiple places, independently, on a phylogenetic tree. The shortest answer is that hollow bones arose independently in the Pterosauria and then later in the Dinosauria; and thus hollow bones are useful for distinguishing Theropods from other Dinosauria -- they are a synapomorphy within the Dinosauria part of the tree, but require more careful definition in the larger Vertebrate tree to be useful as a group-defining characteristic.
 
  
'''What types of morphological features and synapomorphies do we need to know for sauropodomorpha, tyrannosaurids, ornithomimids and
+
|-  
manirapturians as separate groups?''' You need to know '''all''' the synapomorphies that were given AS synapomorphies for any group (e.g. Sauropodomorpha) defined in class by synapomorphies. These will generally appear on the handouts provided in class on slides titled, "Synapomorphies of...." For groups where characteristics were given, but synapomorphies not listed (e.g. Maniraptorans -- note the spelling, which counts), you need to know which morphological features were important in an evolutionary sense -- e.g., in Maniraptorans, swiveling shoulder and hand joints made the evolution of flight in birds possible, by making the arm movements that would become necessary for flapping flight possible).
+
  
'''Is the palatal valve a synapomorphy for crocodiles?'''
+
| Sept 9 || Early vertebrate fossils || Chapter 3 || [http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Biology_of_the_Vertebrates_Study_Questions_F2014#Lecture_5_.289_Sept_2014.29'''Study Questions'''] <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 biased fossil decay]<br>
The palatal valve is a feature of the soft-tissue found in all living crocodylians. Because we can't be sure of soft-tissue morphology in extinct forms, we can't say for sure that it's a synapomorphy for the whole group, but it is an important feature that allows crocodiles to breathe when most of their bodies are underwater.  
+
  
'''Is the perforate acetabulum a dinosaur synapomorphy or specifically a saurischian synapomorphy?'''
+
|-
The perforate acetabulum is a DINOSAUR synapomorphy.
+
  
'''what exactly does the term food caching mean? Does it involve the movement of the head that the bird uses to get its food? Then with the tool use I have that the Bristle-thighed curlew throws rocks at the eggs to break and that the New Caledonian crows us "handedness" but I'm not clear on that term either.''' Food caching is a behavior in which the animal stores food for consumption at a later date, sometimes by burying it, sometimes by other means. I gave Acorn Woodpeckers, who make holes in dead trees to store acorns, as an example. Both curlews and New Caledonian crows use tools -- the curlews use rocks, and the crows use twigs as probes -- but the New Caledonia crows exhibit handedness the way a human does; individuals always hold the twig either to the left or right to use it, in the same way an individual human always uses either their left or right hand to manipulate a tool.  
+
| Sept 11 || Early gnathostomes; Chondrichthyans || Chapters 3, 5||[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Biology_of_the_Vertebrates_Study_Questions_F2014#Lecture_6_.2811_Sept_2014.29 '''Study 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://oceanexplorer.noaa.gov/okeanos/explorations/ex1304/logs/july14/media/rhino-video.html Rhinochimera swimming above the ocean floor] <br>
 +
[http://sharkdevocean.wordpress.com/tag/australia/ Blog entry about Chimaera biology ] <br>
  
'''What should we know about the Darwin's finches experiments? I am assuming it will be in terms of their implications on the importance of beak shape to feeding... just that each species has a highly specific, highly adapted beak form to one certain type of food, and that this specificity was demonstrated when some species died off in the drought periods when their usual food source disappeared?'''
+
||<br>
The first thing to know about Darwin's finches are that they don't represent any experiment in the sense of a human manipulation of conditions to test an idea. The diversity of beak shapes among Darwin's finches were an important hint to Charles Darwin about how differences among closely-related animals might evolve. The populations of these birds, over the last 50 years or so, has also served to provide a real, ongoing test of the idea that evolution happens through natural selection. As conditions have changed on the Galapagos islands, where the birds live, the beak shape that works best on the food available under those conditions changes, and we have seen that the prevalence of one kind of beak or another changes as conditions change. When hard seed are all that's available, beaks that are good for hard seeds become more common, as the birds with beaks good for softer seed fail to survive.
+
  
 +
|-
  
'''I have a question about the phylogeny of birds. I understand that birds evolved from the therapod group and the therapod dinosaurs broke up into the tyrannosaurids, ornithomimids and manirapturians, but I am confused about which group exactly gave rise to birds.'''
+
| Sept 12 || <font color="#7D1B7E">'''Phylogenetic Tree Study Sessions'''</font> || || 10 - 11am: PharmBio Rm 404 <br> 2 - 3pm: Math-Science Building (MSB) Rm 407 <br> ||<br>
The ''Maniraptoran'' (note the spelling, which counts) theropods gave rise to birds.
+
  
'''is polygyny the most common mating system among birds or is that just the most common polygamous mating system?'''
+
|-
Polygyny is the most common form of ''polygamy''; the most common mating system in birds overall is (social) monogamy.
+
+
'''Is promiscuity is the most rare condition?'''
+
Yes.
+
+
'''a synapomorphy for birds doesn't include feathers....because we think its actually a synapomorphy for theropods?'''
+
It isn't a synapomorphy for birds because animals that we don't define as birds have feathers. Whether it is a synapomorphy for all theropods depends on two things: 1)was it present in all lineages of theropods? and 2) was it absent in all other lineages of archosaurs? We lack the fossil information we'd need to answer those two questions definitively, but feathers are beginning to look widespread in the Theropoda, so may eventually be considered a synapomorphy for that group.
+
+
'''when did most of the neornithin(e) lineages come about?'''
+
Most of the modern orders of birds arose about 60 million years ago.
+
 
+
'''and 5-10 mya that most modern  genera were around?'''
+
yes.
+
  
'''What was the advantage/significance of the phytosaur's nostrils being located so high on its head? Does it indicate something about their terrestrial lifestyle?'''
+
| Sept 16 ||Chondrichthyans, con't. ||Chapters 5 ||
The present position of nostrils on extant crocodylians --- on the tip of their snout -- along with their secondary palate, allows them to be entirely submerged, except for the nostrils, and still breathe. The phytosaur's nostril position, which would require most of the head to be out of any water if the animal was to breathe, is just one of several morphological hints that it was more, and perhaps completely, terrestrial.  
+
[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Biology_of_the_Vertebrates_Study_Questions_F2014#Lecture_7_.2816_Sept_2014.29 '''Study Questions'''] <br>
 +
[http://www.arkive.org/lemon-shark/negaprion-brevirostris/video-09a.html Lemon shark giving birth] <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.arkive.org/tiger-shark/galeocerdo-cuvier/video-08.html Shark Feeding on Albatross]<br>
 +
||Feldheim et al. (2014) Mol. Ecol. 23:110-117 on [http://ezproxy.lib.uconn.edu/login?url=http://onlinelibrary.wiley.com/doi/10.1111/mec.12583/full shark philopatry] <br>
  
 +
|-
  
'''What was the name of the gigantic crocodylian ancestor we talked about in class?'''  
+
| Sept 18 || Osteichthyan origin and diversification; Actinopterygians || Chapter 6  ||
I showed you pictures of the skulls of Deinosuchus and Sarchosuchus, both of which were very large.
+
[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Biology_of_the_Vertebrates_Study_Questions_F2014#Lecture_8_.2818_Sept_2014.29 '''Study Questions''']<br>
 +
[http://www.arkive.org/tiger-shark/galeocerdo-cuvier/video-08.html Shark Feeding on Albatross] <br>
 +
[http://www.youtube.com/watch?v=MF5Qq9mhrrw Paddlefish Feeding]<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>
 +
[http://www.amnh.org/learn/pd/fish_2/fish_skull/index.html Jaw protrusion animations]<br>
 +
||<br>
  
'''In terms of Pterosaurs form of flying (flapping vs. gliding), the location of wing attachment varies and may indicate flight form. Should we extrapolate that attachment closer to the foot (ie. a larger wing base)would assist in gliding, while a more narrow wing assists in active flapping?'''
+
|-
The relationship of wing area and shape to flight style are more complicated than this question would imply. For instance, albatrosses (a kind of bird) have extremely long, narrow wings, not wide ones, but they glide almost all the time. The size (especially weight) of the body in relation to total wing area is an important factor, so in each case, you'd have to know that to make a decision for a particular pterosaur. In general, though, a large wing area in relation to body weight increases the animal's capacity to glide without having to flap.
+
  
 +
| Sept 23 || Sarcopterygii || pp. 125-128 (8th ed.)/153-156 (9th ed.) ||
  
'''The morphological diversity of pterosaurs was said in lecture to indicate they were also "ecologically diverse". What exactly does this mean?'''  
+
[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Biology_of_the_Vertebrates_Study_Questions_F2014#Lecture_9_.2823_Sept_2014.29 '''Study Questions'''] <br>
It means that they inhabited a wide range of kinds of habitats, and made a living in a wide range of ways: eating different foods, living up in trees, or down on the ground, living near the water or far away.....
+
[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>
 +
[https://www.youtube.com/watch?v=C0mgFGDEFRM Lungfish locomotion] <br>
 +
||Dixson and Hay (2012) Science  338:804-807 on [http://ezproxy.lib.uconn.edu/login?url=http://www.sciencemag.org/content/338/6108/804.long coral-fish mutualism]<br>
  
 +
|-
  
'''Were the giant sauropods endotherms or ectotherms? We talked in class about the body heat probably produced by their liver while making all the enzymes necessary to break down their food; does this indicate homeothermy? It would be hard to shed that amount of heat.'''  
+
| Sept 24 || <font color="#7D1B7E">'''Exam Study Session''' ||  || 6:00 - 8:00pm: BioPhysics Room 131 ||<br>
No one knows for sure if the giant sauropods were endotherms or ectotherms. In this case your notes have misled you; we talked in class about how, IN ENDOTHERMS, body heat is produced by enzymes produced by the liver, but we don't know that this happened in sauropods. We did talk about how muscle activity, in both endo- and ectotherms, makes waste heat that is lost easily in small animals, not lost so easily in big animals. In any case, a big animal like a sauropod would have had a somewhat stable body temperature just because it was big, and therefore didn't lose heat very rapidly.
+
  
'''should I focus more on the notes and handouts or possibly the readings in the textbook for Tuesday's exam?'''
+
|-
In general, you should certainly have a strong grasp of the notes and handouts from lecture, and use them as a guide to what is most important in the textbook. So, for instance, if I told you in class to ignore a diagram in your book, you'd want to ignore it; if I lecture for 3 days on dinosaur relationships, you want to know the textbook material on dinosaur relationships, as well as the notes, pretty well.
+
  
'''I was wondering if we have to know the relationships within Paleognathaes
+
| <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>
and Neognathaes for the exam.'''
+
If there is a grey box printed over the names on your handout, you don't need to know the relationships among them. If there isn't, you do. Thus: you need to know the two major groups in the paleognathae (Tinamiformes and Struthioniformes) but not the groups inside the Struthioniformes.
+
  
 +
|-
  
'''what exactly is a pair bond? '''  
+
| Sept 30 ||  Origin of tetrapods || pp. 196-211 (8th edition)/ pp. 189-201 (9th edition)|| [http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Biology_of_the_Vertebrates_Study_Questions_F2014#Lecture_10_.2830_Sept_2014.29 '''Study Questions''']
It is a social association of two individuals for the purposes of reproduction. Thus, two birds who spend time together defending a territory where they will build a nest have a pair bond; two birds who travel together in the same feeding flock in the winter do not.  
+
||Gerlach et al. Proc. R. Soc. B 281:20140787 on [http://ezproxy.lib.uconn.edu/login?url=http://rspb.royalsocietypublishing.org/content/281/1787/20140787.long fluorescent signaling in fish]<br>
  
'''Were pterosaurs the first vertebrates to gain the ability of powered flight?'''
+
|-
Yes.  
+
| Oct 2 || Amphibians ||Chapter 10  ||
 +
[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Biology_of_the_Vertebrates_Study_Questions_F2014#Lecture_11_.282_Oct_2014.29 '''Study Questions'''] <br>
 +
[http://www.nature.com/nature/journal/vaop/ncurrent/extref/nature11124-s2.mov Ichthyostega]<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>
 +
||<br>
  
'''How does the pevlic arrangement differ between ornithischia and saurischia (I understand the pubis orientation but I got confused with pelvis'''
+
|-  
The pelvis consists of three principle bony elements: the ischium, the ilium and the pubis. What differs about the pelvis between ornithischian and saurischian dinosaurs IS the orientiation of the pubis. There is also some difference in the overall shape of the ilium, in that in ornithischian dinosaurs, it has a more elongated anterior (front) projection.
+
+
'''what is the relationship between body size and herbivory (bigger animals are herbivores?)'''
+
In general, in order to perform successfully as a herbivore, an animal must be relatively large bodied, because plants are difficult to digest, and therefore have to be held in the gut (stored inside the body) for longer. A large gut, with lots of storage space, requires a large container. This does not preclude predators from growing very large -- a blue whale is a predator, not a herbivore --- but it does mean that dedicated herbivores cannot be small.
+
  
'''synapomorphies of birds which distinguish them from arch. and non avian dinosaurs (is that the keeled sternum, pygostyle, etc.?)'''
+
| Oct 7 || Amniotes origins; Lepidosaurs  || Chapter 13; pp. 211-218 (8th ed.)/pp. 201-208 (9th ed.) ||
Synapomorphies of birds include: a pygostyle, fusion of the hand elements, a keeled sternum, and a toothless beak. At one time the list would have included feathers, but we now know that a number of other theropod dinosaurs which we would not consider birds had feathers, so feathers cannot uniquely identify birds among the dinosaurs.  
+
[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Biology_of_the_Vertebrates_Study_Questions_F2014#Lecture_12_.287_Oct_2014.29 '''Study Questions''']<br>
 
+
[http://www.arkive.org/tomato-frog/dyscophus-antongilii/video-10.html Frog vs. Snake]<br>
'''WAIR- i'm confused about how it is a theory of flight; is it that they flap to climb but then they use it to fly?'''
+
||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]<br>
WAIR (Wing-assisted incline running) is an actual behavior exhibited by many species of birds: when they are chased up a slope, they climb or run up it by using their wings in a flapping motion that increases the traction of their feet against the slope. We think about it as a theory of flight in that it illustrates, directly, one way in which we can envision how a ground-dwelling theropod dinosaur could have benefited from limb motions and an increase in the surface area of the limbs; once the motions and the surface area had been enhanced through natural selection (because they were good for tree-climbing) then they were available (and happened also to be useful) for generating lift to get off the ground and fly.  
+
  
'''What was the reason for birds having higher body temperatures? I remember the causes of this, such as needing to feed often, but I don’t know what the cause of it is.'''
+
|-  
An excellent question: did the warm body temperatures ''cause'' the need to feed often (if you are burning energy all the time, you need to keep feeding the furnace), or did warm body temperatures evolve because of the advantages of being warm all the time for an active predator?  We don't know what came first: we know there is an association between being an active predator and being warm-bodied (i.e., able to move around quickly at any time), and between being warm-bodied and high feeding rates. There is also an association between being very warm-bodied (as birds are) and being small (as birds are, in general) that results from the higher rates of heat loss for a small animal than for a large one.
+
  
 +
| Oct 9 || Snakes || pp. 339-349 (8th ed.)/pp. 317-327 (9th ed.) ||
  
'''What were the things that helped diversify feeding? I got loss of teeth and flight allowed them to go into any habitat, but I don’t have the third.'''
+
[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Biology_of_the_Vertebrates_Study_Questions_F2014#Lecture_13_.289_Oct_2014.29 '''Study Questions''']<br>
An additional factor is that the jaws are covered with a rhamphotheca, a continuously-growing horny covering that is more easily modified in shape than are the underlying bones.
+
[http://www.arkive.org/namaqua-chameleon/chamaeleo-namaquensis/video-10.html Namib Chameleon]<br>
 +
[http://www.youtube.com/watch?v=5-qEt1J5LDU Snake Eating Crab]<br>
 +
[http://www.californiaherps.com/movies/emmulticarinatatail310.mov Tail Autonomy]<br>
 +
|| <br>
  
==Lecture Schedule, Review Questions, and Video Links==
+
|-
  
 +
| || '''Part 2: Oct 14 - Dec 12, Dr. Margaret Rubega'''  || ||  ||<br>
  
{| border="1" cellpadding="1"
+
|-
!width="75"|Date
+
 
!width="90"|Instructor
+
| Oct 14 || Turtles || Chapter 12 ||  
!width="350"|Topic
+
[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Biology_of_the_Vertebrates_Study_Questions_F2014#Lecture_14_.2814_Oct_2014.29 '''Study Questions''']<br>
!width="75"|Readings
+
[http://www.arkive.org/green-turtle/chelonia-mydas/video-09c.html This looks like work: female Green Turtle laying eggs] <br>
 +
[http://www.arkive.org/green-turtle/chelonia-mydas/video-11b.html It's hard to be a hatchling Green turtle!] <br>
 +
[http://www.arkive.org/galapagos-giant-tortoise/chelonoidis-nigra/video-ho06.html Galapagos giant tortoise]<br>
 +
|| no research review<br>
  
 
|-  
 
|-  
| Aug. 26 || Jockusch || Vertebrate diversity {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/08.26.08reviewquestions.pdf}}<br> [http://www.autodax.net/feedingmovieindex.html Salamanders Feeding]<br> [http://www.arkive.org/species/GES/reptiles/Amblyrhynchus_cristatus/Amblyrhynchus_crist_09d.html?offset=0px Marine Iguana Running]<br> [http://www.arkive.org/species/GES/reptiles/Varanus_komodoensis/Varanus_komodoensis_06a.html Komodo Dragon Walking]|| --- ||
+
 
 +
| Oct 16 || Archosaurs: Crocodilians || Chapter 16 ||
 +
[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Biology_of_the_Vertebrates_Study_Questions_F2014#Lecture_15_.2816_Oct_2014.29 '''Study Questions''']<br>
 +
[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Biology_of_the_Vertebrates#Collections_Tour '''Collections Tour Schedule''']<br>
 +
[http://www.arkive.org/american-crocodile/crocodylus-acutus/video-06.html American Crocodile, belly walking and upright walking]<br>
 +
[https://www.youtube.com/watch?v=iwThAki0j7U Crocodile galloping on land] <br>
 +
[http://www.arkive.org/american-crocodile/crocodylus-acutus/video-09b.html female crocodile moving hatchlings to water] <br>
 +
[http://www.arkive.org/nile-crocodile/crocodylus-niloticus/video-08e.html It's hard to be a wildebeast: Nile crocodile catching prey, group spin-feeding]<br>
 +
||
 +
 
 
|-  
 
|-  
| Aug. 28 || Jockusch || Chordates and vertebrate origins {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/08.28.08reviewquestions.pdf}} || Ch. 1, Ch. 2 ||
+
 
 +
| Oct 21 || Archosaurs: Pterosaurs || Chapter 16 ||
 +
[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Biology_of_the_Vertebrates_Study_Questions_F2014#Lecture_16_.2821_Oct_2014.29 '''Study Questions''']<br>
 +
||Dinets (2014)Ethology, Ecology & Evolution [http://ezproxy.lib.uconn.edu/login?url=http://www.tandfonline.com/doi/pdf/10.1080/03949370.2014.915432#.VEEtIPldVEI Apparent coordination and collaboration in cooperatively hunting crocodilians]<br>
 +
 
 
|-  
 
|-  
| Sept. 2 || Jockusch || Living jawless vertebrates {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/09.02.08reviewquestions.pdf}}<br> [http://www.youtube.com/watch?v=Bb2EOP3ohnE Hagfish Sliming] || pp. 48-53 ||
 
|-
 
| Sept. 4 || Jockusch || Early vertebrate fossils {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/09.04.08reviewquestions.pdf}}|| pp. 43-48, 53-71 || 
 
|-                     
 
| Sept. 9 || Jockusch || Chondrichthyans {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/09.09.08reviewquestions.pdf}}<br> [http://www.youtube.com/watch?v=JHUm6cgLbYY Shark Mating]<br> [http://www.arkive.org/species/GES/fish/Rhincodon_typus/Rhincodon_typus_08b.html Whale Shark Feeding]<br>[http://www.arkive.org/species/GES/fish/Manta_birostris/Manta_birostris_08c.html Manta Ray Feeding]<br> [http://www.arkive.org/species/GES/fish/Aetobatus_narinari/Aetobatus_narinari_08.html Eagle Ray Feeding]|| Ch. 5 ||
 
|-
 
| Sept. 11 || Jockusch || Actinopterygians {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/09.11.08reviewquestions2.pdf}}<br>[http://www.youtube.com/watch?v=QjjG9_gGakA&feature=related Paddlefish Feeding]<br>[http://www.youtube.com/watch?v=QrQDFMFvXEc Moray Eel Eating]<br> [http://research.myfwc.com/images/articles/26398/indivsblackdrum_4838.wav Listen to a Black Drum]|| pp. 124-150 ||
 
|-
 
| Sept. 16 || Jockusch || Fish conservation {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/09.16.08reviewquestions.pdf}}<br> [http://www.arkive.org/species/GES/fish/Phycodurus_eques/Phycodurus_eques_09.html Leafy Seadragon Babies Hatching]<br> [http://www.youtube.com/watch?v=ElZ3xGuA-qo Mangrove Killifish in Log]<br>[http://science.readigg.com/description/16137.html Pictures of Deep Sea Fishes]<br> [http://video.google.com/videoplay?docid=5446451367745063142&q=bottom+trawling Bottom Trawling]|| pp. 150-155 ||
 
|-
 
| Sept. 18 || Jockusch || Fish conservation, Sarcopterygii {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/09.18.08reviewquestions.pdf}}<br> [http://www.mbayaq.org/cr/SeafoodWatch/web/sfw_regional.aspx Guide to Sustainable Seafood Choices]--|| pp. 118-124||
 
|-
 
| Sept. 23 || Jockusch || The origin of tetrapods {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/09.23.08reviewquestions.pdf}}|| pp. 196-210||
 
|-
 
| Sept. 25 || Jockusch || Lissamphibian diversity {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/09.25.08reviewquestions.pdf}}<br> [http://oregonstate.edu/~arnoldst/shermani%20slapping.avi Salamander Courtship--Headslap]<br> [http://oregonstate.edu/~arnoldst/shermani%20transter.avi Salamander Sperm Transfer]<br> [http://www.arkive.org/species/GES/amphibians/Andrias_davidianus/Andrias_davidianus_06.html Chinese Giant Salamander (''Andrias'')]<br> [http://www.arkive.org/species/GES/amphibians/Litoria_aurea/Litoria_aurea_08.html Frog Eats Frog]|| Ch. 10||
 
|-
 
| '''Sept. 30''' || Jockusch || '''Exam 1''' || ||
 
|-
 
| Oct. 2 || Jockusch || Lissamphibian diversity continued {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/10.02.08reviewquestions.pdf}}<br> [http://www.arkive.org/species/GES/amphibians/Dyscophus_antongilii/Dyscophus_antongilii_10.html Frog defenses-In Snake's Mouth]<br>[http://people.bu.edu/kwarken/KWvideo.html Escape Hatching from Snake Attack]|| Ch. 10 ||
 
|-
 
| Oct. 7 || Jockusch || Amniote diversity/desert adaptations{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/10.07.08reviewquestions.pdf}} || pp. 327-336, 341-374 ||
 
|-
 
| Oct. 9 || Jockusch || Evolution of snakes {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/10.09.08reviewquestions.pdf}}<br> [http://www.arkive.org/species/GES/reptiles/Chamaeleo_namaquensis/Chamaeleo_namaquen_10.html Heat Avoidance in Desert Chameleon]<br>[http://www.youtube.com/watch?v=yeomSH_w8gw Horned Lizard Defense (Spurting Blood!)] <br>[http://www.arkive.org/species/ARK/reptiles/Natrix_natrix/Natrix_natrix_08a.html Snake Jaw in Action]|| pp. 336-341 ||
 
|-
 
| Oct. 14 || Rubega || Turtles {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/10.14.08reviewquestions.pdf}}<br> [http://www.arkive.org/kemps-ridley-turtle/lepidochelys-kempii/video-09a.html Kemp's Ridley turtle digging a nest]<br>[http://www.arkive.org/kemps-ridley-turtle/lepidochelys-kempii/video-09b.html?offset=0pt Kemp's Ridley turtle laying eggs]<br> [http://www.arkive.org/kemps-ridley-turtle/lepidochelys-kempii/video-09c.html?offset=0pt Kemp's Ridley turtle eggs hatching]<br>[http://www.arkive.org/kemps-ridley-turtle/lepidochelys-kempii/video-09d.html?offset=0pt Kemp's Ridley turtle hatchlings making their way to the sea after hatching]  || Ch. 12 ||
 
|-
 
| Oct. 16 || Rubega || Diapsids: Archosaurs; Crocodilians {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/10.16.08reviewquestions.pdf}}<br>
 
[http://www.arkive.org/american-crocodile/crocodylus-acutus/video-09b.html Crocodile Parental Care]  || pp. 397-407 ||
 
|-
 
| Oct. 21 || Rubega || Archosaurs: Pterosaurs to Dinosaurs {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/10.21.08reviewquestions.pdf}} || pp. 407 - 436 ||
 
|-
 
| Oct. 23 || Rubega || Dinosaurs II {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/10.23.08reviewquestions.pdf}} || pp. 407-436 ||
 
|-
 
| Oct. 28 || Rubega || Birds: Avian origins {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/10.28.08reviewquestions.pdf}}<br> [http://www.youtube.com/watch?v=5Rjin-tjOxU Wing-assisted Incline Running in birds]<br> [http://www.youtube.com/watch?v=e81J915TEXg&NR=1 WAIR in a variety of birds]  || pp. 426-436 ||
 
|-
 
| Oct. 30 || Rubega || Birds: Feeding {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/10.30.08reviewquestions.pdf}}<br> [http://www.youtube.com/watch?v=BGPGknpq3e0 Crows use cars as a feeding tool!]  ||pp. 458 -463 ||
 
|-
 
| Nov. 4 || Rubega || Birds: Morphology and Reproduction {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/11.04.08reviewquestions.pdf}} || pp.443-448, 453-458, 463-478  ||
 
|-
 
| Nov. 6 || Rubega || Birds: Reproduction {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/11.06.08reviewquestions.pdf}}  <br> [http://www.youtube.com/watch?v=GPbWJPsBPdA Australian Bowerbird Behavior]  || Chap 18 ||
 
|-
 
| '''Nov. 11''' || Rubega || '''Exam 2''' ||  ||
 
|-
 
| Nov. 13 || Rubega || Mammals: Diversity {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/11.13.08reviewquestions.pdf}}    || pp. 519-543||
 
|-
 
| Nov. 18 || Rubega || Mammals: Morphology and Behavior {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/11.18.08reviewquestions.pdf}}  || Ch. 21 ||
 
|-
 
| Nov. 20 || Rubega ||Mammals: Primate evolution and human origins {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/11.20.08reviewquestions.pdf}} [http://www.youtube.com/watch?v=yrO2Qc1KyZc Muybridge movie showing the ungulate foot as a spring] || Chapter 24 ||
 
|-
 
| Dec. 2 || Rubega || Mammals: Primate evolution and human origins continued{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/12.02.08reviewquestions.pdf}}  || Ch. 24 ||
 
|-
 
| Dec. 4 || Rubega || Vertebrate mass extinctions, past and present; Vertebrate Conservation {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB2214/12.04.08reviewquestions.pdf}} || pp.663-671 ; 671-687 ||
 
|-
 
|-
 
| Dec. 5 || Maria || Review Session, 4-6pm, BSB 130 ||  ||
 
|-
 
| '''Dec. 8''' || || '''Final Exam 3:30-5:30 pm (TENTATIVE)'''||  ||
 
  
 +
| Oct 23 || Dinosaurs and other Mesozoic diapsids || Chapter 16 ||
 +
[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Biology_of_the_Vertebrates_Study_Questions_F2014#Lecture_17_.2823_Oct_2014.29 '''Study Questions''']<br>
 +
||<br>
 +
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|-
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| Oct 27 || <font color="#7D1B7E">'''Exam II Study Session'''  ||  || 6:00 - 8:00pm: Laurel Hall Room 101 || <br>
 +
 +
|-
 +
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| Oct 28 || Dinosaurs II || Chapter 16 ||
 +
[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Biology_of_the_Vertebrates_Study_Questions_F2014#Lecture_18_.2828_Oct_2014.29 ''' Study Questions''']<br>
 +
|| Erickson et al. (2001) Nature [http://ezproxy.lib.uconn.edu/login?url=http://www.nature.com/nature/journal/v412/n6845/abs/412429a0.html Dinosaurian growth patterns and rapid avian growth rates] <br>
 +
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|-
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| <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>
 +
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|-
 +
 +
| Nov 4  || Birds: Avian origins || pp. 439-443 (8th ed.)/pp. 407-410 (9th ed.) ||[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Biology_of_the_Vertebrates_Study_Questions_F2014#Lecture_19_.284_Nov_2014.29 '''Study Questions''']<br>
 +
|| Brussatte et al. (2014) Current Biology [http://ezproxy.lib.uconn.edu/login?url=http://www.sciencedirect.com/science/article/pii/S0960982214010471 Rapid rates of Evolution across the Dinosaur-Bird Transition]<br>
 +
 +
|-
 +
 +
| Nov 6 || Birds: Feeding || Chapter 17 || [http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Biology_of_the_Vertebrates_Study_Questions_F2014#Lecture_20_.286_Nov_2014.29 '''Study Questions'''] ||<br>
 +
 +
|-
 +
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| Nov 11  || Birds:Morphology and Reproduction || Chapter 17 ||
 +
[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Biology_of_the_Vertebrates_Study_Questions_F2014#Lecture_21_.2811_Nov_2014.29 '''Study Questions''']<br>
 +
||Foth et al. 2014, Nature [http://ezproxy.lib.uconn.edu/login?url=http://www.nature.com/nature/journal/v511/n7507/full/nature13467.html Evolution of Feathers]<br>
 +
 +
|-
 +
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| Nov 13  || Mammals: Origins and radiations || Chapter 18 ||
 +
[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Biology_of_the_Vertebrates_Study_Questions_F2014#Lecture_22_.2813_Nov_2014.29 '''Study Questions''']<br>
 +
||<br>
 +
 +
|-
 +
 +
| Nov 18  || Mammals: Primate evolution and human origins || Chapter 24 ||
 +
[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Biology_of_the_Vertebrates_Study_Questions_F2014#Lecture_23_.2818_Nov_2014.29 '''Study Questions''']<br>
 +
||Archetti 2013, Journal of Theoretical Biology [http://ezproxy.lib.uconn.edu/login?url=http://www.sciencedirect.com/science/article/pii/S0022519312005929 Evolution of polygamous marriage by maximization of inclusive fitness] ONLY Introduction and Discussion are required reading. <br>
 +
 +
|-
 +
 +
| Nov 20 || Mammals: Diversity || Chapter 20 ||
 +
[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Biology_of_the_Vertebrates_Study_Questions_F2014#Lecture_24_.2820_Nov_2014.29 '''Study Questions''']<br>
 +
|| <br>
 +
|-
 +
 +
| Dec 2  || Mammals: Morphology and Behavior || Chapter 21 ||
 +
[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Biology_of_the_Vertebrates_Study_Questions_F2014#Lecture_25_.282_Dec_14.29 '''Study Questions''']<br>
 +
|| Barnosky et al. 2011, Nature [http://ezproxy.lib.uconn.edu/login?url=http://www.nature.com/nature/journal/v471/n7336/full/nature09678.html Has the Earth’s sixth mass extinction already arrived?]<br>
 +
 +
|-
 +
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| Dec 4  || Vertebrate mass extinctions, past and present || Chapter 25 ||
 +
[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Biology_of_the_Vertebrates_Study_Questions_F2014#Lecture_26_.284_Dec_14.29 '''Study Questions''']<br>
 +
|| <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>
  
 +
|- |-
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|- |-}
  
 
 
[[Category:EEB Courses]]
 
[[Category:EEB Courses]]

Latest revision as of 17:03, 5 December 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)

Announcements

12/5/14
The final exam review session will be on Thursday Dec. 11 from 2 - 4pm in TLS, Room 301. This review will primarily focus on the material covered since the last exam.


9/24/14
For a detailed and thorough phylogenetic tree, please check the appendix of your text book! Though, be sure to check it against your notes, as some things have changed since the book has been published (e.g. position of conodonts).
Kevin produced a short instructional video on phylogenetic tree basics! See it here.
Here is the official Pdficon small.gif Exam 1 Study Guide!

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: 11:30 - 12:20 a.m., Thurs, IN the BPB cafe, 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.


Collection Tour Schedule

Mon. Nov. 3: 2:00 - 2:45 pm
Tues. Nov. 4: 11:30 - 12:15 pm
Wed. Nov. 5: 1:00 - 1:45 pm
Thur. Nov. 6: 9:30 - 10:15am

Mon. Nov. 10: 9:15 - 10:00am
Tues. Nov. 11: 3:00 - 3:45pm
Wed. Nov. 12: 2:00 - 2:45pm
Thur. Nov. 13: 11:00 - 11:45am

Please email Kevin ASAP with your preferences! Each slot is limited to ~10 students.

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.

Pdficon small.gif Exam 1 Study Guide

Tree Resources
Pdficon small.gif This is the backbone of the vertebrate phylogeny we will be using in this class. Note that it differs from the textbook tree in the placement of turtles and in how lampreys and hagfishes are related to each other. We will be expanding the terminal taxa and adding fossils to this tree throughout the semester.
Pdficon small.gif This phylogeny tutorial is designed to help students review their knowledge of trees.
Pdficon small.gif A primer of tree terminology
Pdficon small.gif An example of a previous tree quiz
Pdficon small.gif the Tree Thinking Quiz we went over during the study sessions. Make sure you scroll down for the quiz and answers.
Kevin's "Phylogenetic Tree Basics" Video


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 Chordates, con't.; Living jawless vertebrates Chapter 3 Study Questions

Urochordate heart beat
Hagfish defense
Predation by hagfish
Hagfish slime
Hagfish slime #2--what happened to the water?

Zintzen et al. (2011) Sci. Rep. 1:131 on hagfish behavior
Sept 4 Living jawless vertebrates, con't. Chapter 3

Study Questions
Hagfish feeding
Lamprey Spawning



Sept 9 Early vertebrate fossils Chapter 3 Study Questions
Sansom et al. (2010) Nature 463:797-800 on biased fossil decay
Sept 11 Early gnathostomes; Chondrichthyans Chapters 3, 5 Study Questions

Male Sand Tiger Shark Swimming
Whitetip Reef Sharks Mating
Rhinochimera swimming above the ocean floor
Blog entry about Chimaera biology


Sept 12 Phylogenetic Tree Study Sessions 10 - 11am: PharmBio Rm 404
2 - 3pm: Math-Science Building (MSB) Rm 407

Sept 16 Chondrichthyans, con't. Chapters 5

Study Questions
Lemon shark giving birth
Eagle Ray Feeding/Locomoting
Manta Ray Feeding
Shark Feeding on Albatross

Feldheim et al. (2014) Mol. Ecol. 23:110-117 on shark philopatry
Sept 18 Osteichthyan origin and diversification; Actinopterygians Chapter 6

Study Questions
Shark Feeding on Albatross
Paddlefish Feeding
Fish Suction Feeding
Jaw protrusion champion
Jaw protrusion animations


Sept 23 Sarcopterygii pp. 125-128 (8th ed.)/153-156 (9th ed.)

Study Questions
Coelacanth
Lungfish vs. Bird
Lungfish locomotion

Dixson and Hay (2012) Science 338:804-807 on coral-fish mutualism
Sept 24 Exam Study Session 6:00 - 8:00pm: BioPhysics Room 131
Sept 25 EXAM 1
Sept 30 Origin of tetrapods pp. 196-211 (8th edition)/ pp. 189-201 (9th edition) Study Questions Gerlach et al. Proc. R. Soc. B 281:20140787 on fluorescent signaling in fish
Oct 2 Amphibians Chapter 10

Study Questions
Ichthyostega
Caecilian Feeding
Salamander Pheromone Delivery
Salamander Sperm Transfer
Giant Salamander


Oct 7 Amniotes origins; Lepidosaurs Chapter 13; pp. 211-218 (8th ed.)/pp. 201-208 (9th ed.)

Study Questions
Frog vs. Snake

Vredenburg et al. (2010) PNAS 107:9689-9694 on Amphibian extinctions
Oct 9 Snakes pp. 339-349 (8th ed.)/pp. 317-327 (9th ed.)

Study Questions
Namib Chameleon
Snake Eating Crab
Tail Autonomy


Part 2: Oct 14 - Dec 12, Dr. Margaret Rubega
Oct 14 Turtles Chapter 12

Study Questions
This looks like work: female Green Turtle laying eggs
It's hard to be a hatchling Green turtle!
Galapagos giant tortoise

no research review
Oct 16 Archosaurs: Crocodilians Chapter 16

Study Questions
Collections Tour Schedule
American Crocodile, belly walking and upright walking
Crocodile galloping on land
female crocodile moving hatchlings to water
It's hard to be a wildebeast: Nile crocodile catching prey, group spin-feeding

Oct 21 Archosaurs: Pterosaurs Chapter 16

Study Questions

Dinets (2014)Ethology, Ecology & Evolution Apparent coordination and collaboration in cooperatively hunting crocodilians
Oct 23 Dinosaurs and other Mesozoic diapsids Chapter 16

Study Questions


Oct 27 Exam II Study Session 6:00 - 8:00pm: Laurel Hall Room 101
Oct 28 Dinosaurs II Chapter 16

Study Questions

Erickson et al. (2001) Nature Dinosaurian growth patterns and rapid avian growth rates
Oct 30 EXAM 2
Nov 4 Birds: Avian origins pp. 439-443 (8th ed.)/pp. 407-410 (9th ed.) Study Questions
Brussatte et al. (2014) Current Biology Rapid rates of Evolution across the Dinosaur-Bird Transition
Nov 6 Birds: Feeding Chapter 17 Study Questions
Nov 11 Birds:Morphology and Reproduction Chapter 17

Study Questions

Foth et al. 2014, Nature Evolution of Feathers
Nov 13 Mammals: Origins and radiations Chapter 18

Study Questions


Nov 18 Mammals: Primate evolution and human origins Chapter 24

Study Questions

Archetti 2013, Journal of Theoretical Biology Evolution of polygamous marriage by maximization of inclusive fitness ONLY Introduction and Discussion are required reading.
Nov 20 Mammals: Diversity Chapter 20

Study Questions


Dec 2 Mammals: Morphology and Behavior Chapter 21

Study Questions

Barnosky et al. 2011, Nature Has the Earth’s sixth mass extinction already arrived?
Dec 4 Vertebrate mass extinctions, past and present Chapter 25

Study Questions


Dec 12 Final Exam 10:30 - 12:30 (Tentative) Chapter 25