Biology of the Vertebrates
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)
Please email Kevin to sign up for a collections tour! The schedule can be found here
Exams were returned in class today. Please double check your point totals. If you find any mistakes in our arithmetic, hand your exam back in with a note explaining the error. Also, if you believe that any questions were incorrectly graded, you may submit your exam with a written explanation of what you believe the error to be, and we will evaluate it. All requests for regrading must be received by October 14, 2014.
Course evaluations for Dr. Jockusch are now available through the online course evaluation system. Your feedback is appreciated!
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 Exam 1 Study Guide!
Note: All emails must contain "EEB2214" in the subject line to avoid being filtered out and deleted
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.
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.
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.
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.
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.
We expect all students to behave in a way that is respectful of others. The 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.
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.
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.
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.
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...).
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.
Exam 1 Study Guide
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.
This phylogeny tutorial is designed to help students review their knowledge of trees.
A primer of tree terminology
An example of a previous tree quiz
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
A review session will be held before each exam. Dates and times will be posted once they are set.
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
|| Zintzen et al. (2011) Sci. Rep. 1:131 on hagfish behavior |
|Sept 4||Living jawless vertebrates, con't.||Chapter 3|| |
|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
|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||Feldheim et al. (2014) Mol. Ecol. 23:110-117 on shark philopatry |
|Sept 18||Osteichthyan origin and diversification; Actinopterygians||Chapter 6|
|Sept 23||Sarcopterygii||pp. 125-128 (8th ed.)/153-156 (9th ed.)||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|
|Oct 7||Amniotes origins; Lepidosaurs||Chapter 13; pp. 211-218 (8th ed.)/pp. 201-208 (9th ed.)||Vredenburg et al. (2010) PNAS 107:9689-9694 on Amphibian extinctions|
|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||Dinets (2014)Ethology, Ecology & Evolution Apparent coordination and collaboration in cooperatively hunting crocodilians|
|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|