Biology of the Vertebrates Fall 2012

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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
Phone:(860) 486-0309
Office hours: Tuesdays 2-3 pm and by appointment


Exam 1 = 100 points
Exam 2 = 100 points
Final Exam = 150 points
#Research Reviews = 30 points
#Tree Quizzes = 15 points
#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.

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 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.

Tree Quizzes

On several of the research response days, we will incorporate additional questions about the phylogenetic tree of vertebrates into the written exercise. These will be worth a total of 15 points over the course of the semester. As with the research responses, you must be present to receive credit and no make-ups will be given. If you have a valid, documented reason for missing class on the day of a tree quiz, and have followed the policy on missed exams, then your quiz score will be prorated.

Collections Tours

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

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 Office of Student Services and Advocacy.

Other Absences
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.

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.

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?

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. 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.

Pdficon small.gif Exam 1 Study Guide
The answer key for exam 1 is posted outside of Alejandro's office.

Phylogenetic Tree Resources:
The Pdficon small.gif phylogenetic tree of vertebrates provides the backbone for this course.
Pdficon small.gif This phylogeny tutorial is designed to help students review their knowledge of trees.
Test your ability to interpret phylogenetic trees with this Pdficon small.gifTree Quiz.
Pdficon small.gif Tree Quiz Answers

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

Review Sessions:
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

Prehistoric rhino! 6 Dec 2012

New oldest dinosaur 4 Dec 2012

Diatryma: unequipped to be a carnivore? 23 Nov 2012

Turtles fossilised in sex embrace 19 June 2012

Chinese turtle passes WASTE urea through its MOUTH 11 October 2012

Bull sharks have strongest bite of all shark species 12 October 2012

Size matters for 'sex cheat' frogs 15 October 2012

Dolphin 'sponging' spans centuries 22 October 2012

Lampreys feed on whales

SNL lamprey skit If you were science advisor to the show, which line(s) would you change?

New species of Snub-nose Monkey found in Burma 30 August 2011

Pea-sized frog found in Borneo 30 August 2010
Pea-sized Frog.jpg

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

Urochordate heart beat
Hagfish defense
Predation by hagfish

McGuire and Ratcliffe (2010) Biol. Lett. 7:233-236 on Bat brains
Sept 6 Living Jawless Vertebrates, cont. Ch. 3 Study Questions
Hagfish Slime
Hagfish on sea floor
Hagfish feeding
Lamprey Spawning
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
Pdficon small.gif Sample 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) Pdficon small.gif Tree Quiz 1 Key
Study Questions

Paddlefish Feeding
Moray Eel Feeding (with Pharyngeal Jaw)
barreleye video
deep sea fish

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) --------- Pdficon small.gif 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
Caecilian Feeding
Salamander Pheromone Delivery
Salamander Sperm Transfer
Giant Salamander
Oct 9 Amniote Origins and Diversity Ch. 9 (pp. 211-218); Ch. 13 Collections Tours Schedule
Study Questions
Frog vs. Snake
Lake Titicaca Frog
Tail Autonomy
Vredenburg et al. (2010) PNAS 107:9689-9694 on Amphibian extinctions
Oct 11 Desert Adaptations & Snakes Ch. 13 Study Questions
Namib Chameleon
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 Pdficon small.gif Tree Quiz 2 Key
Study Questions
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
Alligator Courtship
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 Locomotion
Pterosaur Brain studies
Quadrupedal launching
Oct 30 EXAM 2 - POSTPONED --------- Pdficon small.gif 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
T-rex trying
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

Pheasants funny displays
Red-capped Manakin moonwalk
Common Cranes flying
Swallows power strokes
Hummingbird acrobatics
Pelicans feeding
Egret fishing, "what a clever bird"

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 Pdficon small.gif Tree Quiz 3 Key
Study Questions

Coelophysis Vs Cynodonts
Mammal origins (full episode)
A winning design (Intro+Platypus & Echidna shown in class)

Dec. 4 Mammals: Diversity, Feeding and Reproduction
Ch. 20 Study Questions
Monkeys reject unequal pay
Monkey cooperation and fairness
Marsupial birth
Water shrew
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]
Elephant shrew
Star-nosed mole
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)
Orangutan intelligence
Dec 14 FINAL EXAM 10:30 am-12:30 pm --------- Pdficon small.gif Study Guide
Pdficon small.gif Deuterostome tree

Note: You will be responsible for plotting groups, synapomorphies AND traits on the cumulative tree||