Biology of the Vertebrates Fall 2012
EEB 2214, Fall 2012
The evolution of form, function,
& diversity of the vertebrates
Meeting Time: Tuesdays and Thursdays, 12:30-1:45 in BPB130
Exam 3 Study guide posted below
Exam Review, BPB 131, Dec. 12th, 5-7pm
Dr. Elizabeth Jockusch
Office: Biology/Pharmacy 305B
Phone: (860) 486-4452
Office hours: by appointment
Dr. Kristiina Hurme
Office: TLS 379
Phone: (860) 486-5434
Office hours: Thursdays 2-3 pm and by appointment
Alejandro Rico (Teaching Assistant)
Office: Biology/Pharmacy 404
Office hours: Tuesdays 2-3 pm and by appointment
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.
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 assessments are worth 3 points each. 11 will be offered over the course of the semester, and the best 10 counted towards the final course grade. There will be no paper selected for the first week, or the weeks of the first and second exams.
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.
On several of the research response days, we will incorporate additional questions about the phylogenetic tree of vertebrates into the written exercise. These will be worth a total of 15 points over the course of the semester. As with the research responses, you must be present to receive credit and no make-ups will be given. If you have a valid, documented reason for missing class on the day of a tree quiz, and have followed the policy on missed exams, then your quiz score will be prorated.
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 10 different opportunities, on different days and times. You will need to sign in at the collection; at the end of the semester, everyone who has signed in will have 5 points added to their grade. Tours will take about 45 minutes; they meet at the south end of the Biology/Physics building lobby on the hour. You are responsible for finding a day and time to attend from the options below; if your class schedule prohibits you from attending any of these, you are responsible for letting us know that you will need an alternative opportunity AT LEAST TWO WEEKS PRIOR TO THE FINAL TOUR. If you have already toured the collections (e.g., in a previous class), provide us with documentation to that effect, and we will just add the points to your grade without you needing to tour the collections again.
Available tour days/times:
Susan Hochgraf (860) 486-8945
Thursday October 18th at 10 am
Thursday November 1st at 11 am
Thursday November 8th at 2 pm
Thursday December 6th at 4 pm
Alejandro Rico (860) 486-0309
Monday November 12th at 11 am
Tuesday November 13th at 9:30 am
Wednesday November 14th at 12 pm
Tuesday November 27th at 2 pm
Wednesday November 28th at 3 pm
Friday November 30th at 1 pm
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 Office of Student Services and Advocacy.
No make-ups will be given for research responses or tree quizzes. The first research response from which a student is absent will be dropped. If a student misses a second one, then he or she will receive a zero. For tree quizzes, the missed exam policy applies.
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.
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. 2009. Vertebrate Life, 8th Edition. Prentice Hall. Three copies of the textbook are available at the library iDesk. Ask for call numbers XR5, XR6 and XR7. 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.
Phylogenetic Tree Resources:
The phylogenetic tree of vertebrates provides the backbone for this course.
This phylogeny tutorial is designed to help students review their knowledge of trees.
Test your ability to interpret phylogenetic trees with this Tree Quiz.
Tree Quiz Answers
Use this handout to help navigate your way through the primary literature.
A review session will be held before each exam. Dates and times will be posted once they are set.
Exam 1 Review session: Tuesday, Sept. 25, 5-7 pm in BPB 131
Exam 2 Review session: Monday, Oct. 29, 5-7 pm in BPB 131 - CANCELED DUE TO UNIVERSITY CLOSING
Exam 3 Review session: Wednesday, Dec. 12, 5-7 pm in BPB 131
Links to External Resources:
- DigiMorph - Excellent source of 2 & 3D images of internal & external structures of various organisms
- ARKive - a unique collection of thousands of wildlife videos, images and fact-files, with a special focus on the world's threatened species
- iNaturalist - an online database for logging observations of plants and animals. Go to project UConn Vert Bio!
Vertebrates in the News
SNL lamprey skit If you were science advisor to the show, which line(s) would you change?
Lecture Schedule & Materials
|Date||Topic||Textbook Readings||Supplemental Materials||Research Review Reading|
|Part I: Aug 28 - Oct 11, Dr. Elizabeth Jockusch|
|Aug 28||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 30||Chordate and Vertebrate Origins||Ch. 1, 2|| Study Questions
|Sept 4||Chordates and Living Jawless Vertebrates||Ch. 3|| Study Questions
||McGuire and Ratcliffe (2010) Biol. Lett. 7:233-236 on Bat brains|
|Sept 6||Living Jawless Vertebrates, cont.||Ch. 3|| Study Questions
Hagfish on sea floor
|Sept 11||Early Vertebrate Fossils||Ch. 3||Study Questions||Sansom et al. (2010) Nature 463:797-800 on Interpreting fossils|
|Sept 13||Chondrichthyans||Ch. 5|| Study Questions
Male Sand Tiger Shark Swimming
Whitetip Reef Sharks Mating
Leopard Shark Courtship
Lemon shark giving birth
|Sept 18|| Tree Quiz 1
Chondrichthyans, con't, Diversification of jaws and feeding
|Ch. 5|| Study Questions
Shark Feeding on Albatross
Whale Shark Feeding
Eagle Ray Feeding/Locomoting
Manta Ray Feeding
Jaw protrusion animations
Fish Suction Feeding
Jaw protrusion champion
|Myers et al. (2007) Science 315:1846-1850 on Effects of shark overfishing|
|Sept 20||Osteichthyan Origins and Living Actinopterygians||Ch. 6 (except pp. 125-134)|| Tree Quiz 1 Key
|Sept 25||Sarcopterygii and Evolution of Tetrapods
Exam 1 Review session: 5-7 pm in BPB131
|Ch. 6 (pp. 125-134); Ch. 9 (pp. 196-211)|| Study Questions
Lungfish vs. Bird
|Sept 27||EXAM 1 includes material through the origin of tetrapods (but not amphibian diversity)||---------|| Study Guide
Exam answer key posted outside Alejandro's office
|Oct 2||Amphibian Diversity||Ch. 10||Study Questions
|King et al. (2011) PNAS 108:21146-21151 on the Origin of tetrapod gaits|
|Oct 4||Amphibian Diversity||Ch. 10|| Study Questions
Salamander Pheromone Delivery
Salamander Sperm Transfer
|Oct 9||Amniote Origins and Diversity||Ch. 9 (pp. 211-218); Ch. 13|| Collections Tours Schedule
Frog vs. Snake
Lake Titicaca Frog
|Vredenburg et al. (2010) PNAS 107:9689-9694 on Amphibian extinctions|
|Oct 11||Desert Adaptations & Snakes||Ch. 13|| Study Questions
Blood Squirting in Horned Lizards
Snake Eating Crab
|Part II: Oct 16 - Dec 14, Dr. Kristiina Hurme|
|Oct 16|| Tree Quiz 2
|Ch. 12|| Study Questions
Evolution of shell (go to 4:39)
Box turtle vs Raccoon
Gopher tortoise burrows
|Schuyler et al. (2012) PLoS ONE 7(7):7e40884 on Sea turtles eating trash|
|Oct 18||Turtles, cont'd; Introduction to Archosaurs & Crocodilians||Ch. 16|| Tree Quiz 2 Key
Turtle hatchlings supercooling
Turtles Digging a Nest
Turtle Laying Eggs
Turtle Hatchlings Emerging
Turtle Hatchlings Heading to the Water
Alligator snapping turtle luring prey
Crocodile sprawling and upright locomotion
|Oct 23||Archosaurs: Crocodiles, cont'd; Pterosaurs and Other Mesosoic Diapsids||Ch. 15 & 16|| Study Questions
Female Crocodile Digging Out Hatchlings
Nile crocodile defending nest from monitor lizards
Caiman mother babysitting
Ichtyosaurs and Plesiosaurs
Ichthyosaurs and Plesiosaurs II
|Vergne et al. Zoology 114(2011):313-320 on Acoustic signals of baby black caimans|
|Oct 25|| Pterosaurs, cont'd; Dinosaurs
Exam 2 Review session: Monday, Oct. 29, 5-7 pm in BPB 131 - CANCELED DUE TO UNIVERSITY CLOSING
|Ch. 16|| Study Questions
Pterosaur Brain studies
|Oct 30||EXAM 2 - POSTPONED||---------|| Study Guide 2 for Dr. Hurme's part of the exam
|Nov 1||EXAM 2 includes all material since 1st exam||---------|
|Nov 6||Dinosaurs II||Ch. 16|| Study Questions
Allosaurus vs. Stegosaurus
Tyrannosaurus vs. Ankylosaurus
|Zelenitsky et al. Science 26 October 2012, Vol. 338 pp. 510-514 on Feathered Non-Avian Dinosaurs|
|Nov 8||Birds: Avian Origins||Ch. 16 (pp. 439-443)|| Study Questions
Wing-assisted Incline Running
|Nov 13||Birds: Diversity and Reproduction||Ch. 17|| Study Questions
Avian Tree of Life
|Taylor et al. PLoS ONE 2011, vol. 6(12) p. e26887 Tool use in New Caledonian crows|
|Nov 15||Birds: Feeding and Morphology||Ch. 17|| Study Questions
|Nov 27|| Tree Quiz 3
Bird: Morphology, cont'd.; Mammals: Origins and Radiation
|Ch. 18|| Study Questions
EXPLORE the mammalian tree of life (really cool!)
|Meachen and Samuels, PNAS 2012, vol. 109(11) p. 4191-6 Coyote evolution after megafaunal extinctions|
|Nov 29||Mammals: Mammal Diversity||Ch. 24|| Tree Quiz 3 Key
|Dec. 4|| Mammals: Diversity, Feeding and Reproduction
||Ch. 20|| Study Questions
Monkeys reject unequal pay
Monkey cooperation and fairness
|Brosnan and De Waal Nature 2003, vol. 425(6955) p. 297-99 Monkeys reject unequal pay|
|Dec 6||Mammals: Diversity, Feeding and Social Behavior||Ch. 21 and 25|| Study Questions
Placental birth (poor quality, go to 4:30)
Elephant Shrew - Sir David]
Mexican free-tailed bats
Sir David says BOO to a sloth!
Herbivores vs. Carnivores (African drum beat!!)
Meat-eaters (poor quality)
Sir David swims with manatees
Return to water (poor quality)
|Dec 14||FINAL EXAM 10:30 am-12:30 pm||---------|| Study Guide|
Note: You will be responsible for plotting groups, synapomorphies AND traits on the cumulative tree||