Biology of the Vertebrates

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EEB 2214, Fall 2014

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


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

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

Contents

Announcements

10/20/14
Kevin will be leading a review session for Exam II on Monday Oct. 27th, from 6 - 8 pm in Room 101 in Laurel Hall. Anyone with suggestions for the format of this session, please feel free to email Kevin (unless your suggestion is: "tell us what to study and/or what's going to be on the exam").

10/16/14
Please email Kevin to sign up for a collections tour! The schedule can be found here

10/7/14
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.

10/5/14
Course evaluations for Dr. Jockusch are now available through the online course evaluation system. Your feedback is appreciated!

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
Oct 27 Exam II Study Session 6:00 - 8:00pm: Laurel Hall Room 101
Oct 28 Dinosaurs II Chapter 16
Oct 30 EXAM 2
Nov 4 Birds: Avian origins pp. 439-443 (8th ed.)/pp. 407-410 (9th ed.)
Nov 6 Birds: Feeding Chapter 17
Nov 11 Birds:Morphology and Reproduction Chapter 17
Nov 13 Mammals: Origins and radiations Chapter 18
Nov 18 Mammals: Primate evolution and human origins Chapter 24
Nov 20 Mammals: Diversity Chapter 20
Dec 2 Mammals: Morphology and Behavior Chapter 21
Dec 4 Vertebrate mass extinctions, past and present Chapter 25
Dec 12 Final Exam 10:30 - 12:30 (Tentative) Chapter 25
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