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James Madison University Departments of and

SYLLABUS - BIOLOGY/GEOLOGY 405 http://geollab.jmu.edu/Fichter/GeoBio405/index.html

SPRING, 2001

CREDIT HOURS: 3

BUILDING/ROOM: 209 Miller TIME: MWF 11:15-12:05

INSTRUCTOR: Lynn S. Fichter, Professor of Geology OFFICE: 233 Miller OFFICE PHONE: 6531 E-MAIL: [email protected] OFFICE HOURS: MW 10-11 TT 8-10; By appointment;

LABORATORY: The laboratory consists of learning the in a number of vertebrate and a and is done independently with the help of study guides.

FINAL EXAM: Friday, May 4, 10:30-12:30

TEXTS: k Benton, Michael J., 1997, , Chapman and Hall k Notebook of Lecture Illustrations - Copy Center k Handbook of the Vertebrate and Skeleton - Copy Center

LABORATORY VOUCHERS: This semester the university is assessing a charge for chemicals and other consumable items used in laboratory courses. Consequently, during the first two weeks of classes, each student in this course must obtain a paid “laboratory voucher” from the bookstore. Failure to obtain a voucher will lead to administrative withdrawal. L.S. Fichter, Spring, 2001 Syllabus 1 Bio/Geol 405 Vertebrate Paleontology

THE BREADTH OF VERTEBRATE PALEONTOLOGY

Vertebrate paleontology is a bastard science. It is wholly accepted by neither the geologists nor the zoologists. Yet, its proper study is dependent on knowledge and understanding of both. Even within the study of paleontology itself there is little contact between and vertebrate paleontologists, not to mention paleobotanists. One important reason is that the specialized training for each discipline begins early and diverges rapidly. The practicing vertebrate paleontologist, for example, is absolutely dependent on thorough and solid training in comparative , , , and vertebrate , not to mention geology subjects and statistics. Invertebrate paleontology, on the other , is more often used for dating rocks and is thus associated with and other geological subjects. Paleobotanists, naturally, associate with botany departments, far removed from geology and zoology. But one way or another, paleontology is an interdisciplinary science, drawing on specialized knowledge from many disciplines - jack of all trades, master of none. In this you do not require all the highly specialized knowledge a practicing vertebrate paleontologist needs. Instead as the semester proceeds I will introduce and develop whatever specific knowledge we need to understand the evolutionary debate in front of us at the moment. And, anyway, this class is a mixture of biology and geology majors and so what ever we talk about I usually have to explain biological concepts to the geologists and geological concepts to the biologists and in the process we all learn something new.

THE DEPTH OF VERTEBRATE PALEONTOLOGY

It used to be that many topics in evolutionary biology were pithy. That is, they were discussed in a few pages in a book, or there existed one or two papers on the subject. But not today. Nearly every interesting subject in paleontology and evolutionary biology has exploded in complexity. Where once there were a few pages of discussion, there now exist book-length expositions, often several, and a vast technical literature. There is hardly a group of , early or late, that is not rich in diversity, and absolutely fascinating. Just to survey all the major groups takes an entire semester, even without getting into their adaptations, lifestyles, and the interesting evolutionary problems they present. Where it was once possible to spend a leisurely class, or less, talking about everything important anyone had to say on a particular topic, these topics can now easily take many classes. The sum result is . . . one semester is not enough. I look back over old notes on certain topics and they comfortably took a class. When I revised my notes on these topics they easily expanded to several classes, before I panicked and struggled to get them down to only twice as much time as they used to take. But twice as much time is half as much time in a semester to talk about other subjects. L.S. Fichter, Spring, 2001 Syllabus 2 Bio/Geol 405 Vertebrate Paleontology

There is no easy resolution to this problem; it exists in every subject. But I am interested in understanding, not memorization or superficial surveys, . . . and understanding takes time. My resolution to this problem is to do both less, and more. The less is fewer groups, fewer processes, fewer issues discussed. The more is more understanding, in more depth, about the subjects we do discuss. Some groups will be mentioned only in passing, and some groups we explore in detail, like the bony , labrynthodont , and -like .

Atentative outline of the semester, based on the last time the course was taught, is at the back of the syllabus. But in broad outline it goes something like this. First, we begin with a discussion of principles of , systematics, and classification. Second, this is followed by a survey of vertebrate evolution. That is, who gave rise to whom, when, and the basic classification of the vertebrates. Older paleontology courses would consist only of this, but for us it is only the beginning. Third, we then utilize the phylogeny and classification as a skeleton upon which to hang arguments of evolutionary biology. There are two parts to the study of the evolutionary biology of the vertebrates. On the one hand, we use the phylogeny to explore the processes of functional , evolving systems, and biological adaptations to understand the evolution of the vertebrates. On the other hand, we examine the historical geology and of this planet in an attempt to understand the environmental conditions which existed in the past and influenced the evolution of the vertebrates. Finally, we correlate and integrate all the information to obtain a coherent picture of how both the earth and the vertebrate living on it got to their present state. By that time the semester will be long since over.

THE CURRENT STATE OF VERTEBRATE PALEONTOLOGY

One of the problems with being a scientist is that nothing you know can be taken for certain. In fact, being a scientist leads to the disconcerting possibility that everything you thought you knew will turn out to be wrong. This truism has shaken up all the sciences in this century, and no less vertebrate paleontology. Jarvik says,

"It is easy to see that (the) . . . more or less sophisticated trees found in even the most modern literature are erroneous in fundamental respects."

Indeed, animals formerly considered closely related are now viewed very suspiciously, and the traditional, thoroughly memorized, and well entrenched classifications are continuously being challenged and replaced by new and/or unfamiliar names. What is disconcerting about L.S. Fichter, Spring, 2001 Syllabus 3 Bio/Geol 405 Vertebrate Paleontology this is that the old, familiar we thought we knew and understood, have a tendency to be reclassified, rearranged, and reinterpreted in ways that violate everything we were originally taught. And there are continuous new finds which do not neatly fit in with already known organisms, leading to further doubt and confusion. Furthermore, a number of controversial ideas which seriously question our traditional beliefs about the biology of fossil vertebrates have been proposed, and vigorously argued - origins, warm blooded , and the origin of to name a few. To be perfectly honest I find some of this disconcerting, and I am torn between wanting to hang on to the old and familiar, and teach it as if nothing has changed, and feeling an obligation to face the new and unknown, and struggle to revise major portions of this course.

It is the second path I intend to follow. I realize that if I were to just make all the necessary changes, or not make them at all, you would not know the difference. Either you would learn the old names and theories, or the new, but since it is all equally unfamiliar it would probably be no big deal - except what you would learn would be outdated. But it is not as simple as that.

First, many of the new ideas are quite involved and complicated and it will probably take me more than once through the course to make the transition. Some subjects, which in the past we only knew enough about to have a few pages devoted to them, have expanded to having entire books (often several) devoted to them. Many of these books have relatively recent copyright dates on them. I try to keep up with these, but some lectures I may end up writing as I give them. Or I may suddenly understand something in a new way in the middle of a lecture, at which time my knowledge grows but the lecture may descend to chaos. I hope you hang in there with me in those cases; I will make it all right.

Second, our understanding of vertebrate evolution changes rapidly as new discoveries and studies are published. The discovery of one new fossil can change dramatically the way we look at a group - like the discovery of early amphibians with more than 5 fingers and , and the velociraptors. Likewise, several new books published recently have strongly influenced the way I look at some topics, and I plan to incorporate those ideas. What is gospel today is passe tomorrow.

Third, my job is not so much to teach vertebrate paleontology as to teach the science of evolutionary biology, and these major paradigm shifts are the essence of the scientific process and I need to explore them and you need to understand them. So a complicated subject keeps getting more complicated, but with many more possibilities. Share the adventure. L.S. Fichter, Spring, 2001 Syllabus 4 Bio/Geol 405 Vertebrate Paleontology

TESTING AND GRADING The final grade in this class is based on two criteria:

LABORATORY: It is not possible to talk about vertebrate evolution without reference to vertebrate skeletal anatomy. At times throughout the semester it is necessary for us to talk about bones, and compare the bones in one with bones in another. This can be boring, confusing, and frustrating unless you have some familiarity with those bones. Therefore, it is worth while to learn the skulls and of typical representatives. I don't want to belabor you with this too much, just enough to know the basics. See below for details.

LECTURE: Your lecture (and course) grade (assuming the laboratory is satisfactorily completed) is an average of all your scores on the items listed below. (Summaries of each category are provided below; more specific information provided later.)

5% Quiz # 1 - Vertebrate Classification and Systematics 5% Quiz # 2 - Vertebrate Phylogeny 5% Periodic Review Questions 16% Skeleton/Skull identification 22% Lecture Exam #1 22% Lecture Exam #2 22% Final Exam (not comprehensive) 100%

QUIZ #1 - THEORETICAL FOUNDATIONS

The quiz consists of questions drawn from the following concepts. This quiz occurs sometime within the third week of the semester - details to follow. A several day span will be scheduled for the quiz and you may take it anytime in that span. L Concepts in Evolutionary Biology. L Concepts in .

QUIZ #2 - PATTERNS OF VERTEBRATE EVOLUTION

The quiz consists of questions drawn from the following subjects. This quiz occurs sometime within the fifth week of the semester - details to follow. A several day span will be scheduled for the quiz and you may take it anytime in that span. L Memorize and reproduce an abbreviated classification of vertebrates. L Fill in whole or part the summary chart on the phylogeny of vertebrates discussed and explored in class. L.S. Fichter, Spring, 2001 Syllabus 5 Bio/Geol 405 Vertebrate Paleontology

L Given illustrations of representative members of each group found on the chart on the phylogeny of the vertebrates, classify the organism. L Discuss some aspect of a major geologic, environmental, climatic event associated with a specific and particular evolutionary transition.

PERIODIC REVIEW QUESTIONS

Scattered through the semester are a series of periodic review questions. The questions are designed primarily to get you to think about recent subject matter and clarify and come to understand some critical models, or facts, or strategies for solving problems of evolutionary biology. Also, during the grading I can let you know the standards to be striven for in answering the midterm and final questions. More information to follow.

THE LECTURE EXAMS AND FINAL

The subject matter this semester is intricate, diverse, and complex. In our attempts to unravel the evolutionary relationships among the vertebrates it is necessary to seek evidence and arguments from a wide diversity of disciplines; and to genuinely appreciate the problems and attempts to understand and solve them this evidence and these arguments need to be explored in some detail. At various points we need to discuss comparative invertebrate anatomy, physiology, vertebrate functional morphology, depositional systems, paleoclimatology, zoogeography, continental drift, evolutionary theory, structure of the and the meaning and basis of intelligence . . . and many other things, as well as the rather straight forward problems of vertebrate anatomy, classification, evolutionary relationships, and phylogeny.

To be tested in detail on all this material by traditional test methods would be overwhelming, and would defeat my purposes in teaching this class. My goals are not to force you into detailed knowledge of everything but rather to explore with you the diversity of this fascinating subject matter, the kinds of problems encountered, and the ways they are solved.

RULES AND PROCEDURES FOR MIDTERM AND FINAL

The two exams and final are take home, and must be taken according to the honor code of the University, and honor that must exist among the community of scientists. The exams consist of two parts, an essay portion, and an objective computer graded portion.

ESSAY PORTION OF TESTS: SPECIFIC PROCEDURES AND RULES: Ø All essay exam questions are available to you before the exam to allow you to prepare. L.S. Fichter, Spring, 2001 Syllabus 6 Bio/Geol 405 Vertebrate Paleontology

Ù You will not write answers to all the essay questions, but must be prepared to answer any of them. Ú You may bring with you to the exam one 3 x 5 inch index card for each test. with outlines (no illustrations or prose statements) of your answers to the questions These must be turned in with you answers. Û You will not know which questions to answer until just at the moment you are ready to take the exam. At the exam time I will give you a folded piece of paper, inside which are written the questions you are to answer. You open the paper when ready to take the exam. Ü Normally I try to give some choices of questions to answer so you are not completely stuck with questions you do not like or are not well prepared for. Ý Each exam is guided by the following rules. The rules are also written on the slip of paper containing the questions you are to answer.

RULES FOR ALL ESSAY EXAMS 1. You may take the exam any time in the several day period assigned. 2. You may not peek at the questions until just at the moment you are ready to take the exam. 3. If the question states information will be provided with the exam slip, that information is attached to the exam slip. 4. You must take the entire exam in one sitting, pit stops allowed. 5. You may have only the following with you: ( The exam paper ( Writing instruments ( Copies of any blank illustrations allowed by the questions. ( Refreshments for the duration ( One 3 x 5 inch index card with outlines of your answers.

GRADING EXAM ANSWERS: ( All grading is done on a 12 point scale (A+ = 12-11, A = 10.9-10, A- = 9.9-9, B+ = 8.9-8, etc.). ( Final grades are calculated by averaging exam questions for each exam, and multiplying them by the 22% for each exam. Because of the way the exams are done you may not all answer the same number of questions for each exam. so it is not possible ahead of time to say how much each question is worth.

OBJECTIVE, COMPUTER GRADED TESTS: This is the first time in this course I am experiment with an objective portion for the test. I will probably divide the grade 50/50 between the essay and objective portions, which means that the objective portion is equivalent to one of the essay questions. More information later. L.S. Fichter, Spring, 2001 Syllabus 7 Bio/Geol 405 Vertebrate Paleontology

LABORATORY THE LABORATORY CONSISTS OF TWO PARTS.

Smithsonian Field Trip - Attendance and a simple exercise (not handed in) is all that is required. The trip lasts all day, from early morning to evening (5 hours travel time). We spend time in the morning looking at the public displays of vertebrate fossils. The remainder of the afternoon is your own to visit whatever you wish (the Air and Space Museum--well worth the time, Museum of History and Technology, Art Museum, etc). We stop in Manassas for dinner on the way home. Failure to attend, except by express permis- sion of the Instructor, results in the loss of one final letter grade.

Study of the Vertebrate Skeleton You are asked to learn the following:

SKULLS SKELETONS TEETH You need to learn the skull of You need to learn You need to learn to recognize the following: the skeleton of one the teeth in the skull and lower of the following: of the following (list subject to change). : “ Canis, or “ Cat “ Mink “ “ “ “ Cat, or Dog Horse “ Rabbit, or “ “ Rabbit “ Hyena “ “ Squirrel : Skull of Either: “ “ “ Chelonia ( ) OR Beaver Groundhog “ (These are all largely “ Muskrat “ , OR “ “ “ the same and we have Cow examples of each, so “ Deer Mammal: Skull of: take your pick) “ Canis (Dog)

The study of vertebrate skeletons may seem complex at first, but unlike the study of invertebrate fossils which are continuously different from one group to another, knowledge of the skeleton is cumulative. In fact, the study of vertebrate skulls and skeletons gets easier with time since not only are the names carried through, the skull becomes progressively less complex up the evolutionary scale.

LABORATORY PROCEDURE

Procedure: The procedure for the laboratory study is as follows: L No formal schedule exists; each person works at their own pace, on their own time (although see schedule at end for time frames). The only exception is you need to L.S. Fichter, Spring, 2001 Syllabus 8 Bio/Geol 405 Vertebrate Paleontology

learn the vertebrate skeleton within the first week, and Amia within the first three weeks. This is so you are familiar with the basic bones and will not be lost in lecture. L For each skull, or skeleton, or the teeth sets to be studied a study guide is available in the notebook Handbook of the Vertebrate Skull and Skeleton. These vary from detailed descriptions to simple lists or illustrations of the bones. L You are encouraged in your study to develop a notebook of labeled sketches of the skulls and bones. Making sketches forces you to examine the specimens closely. Labeling the sketch helps to insure you know the osteology. Plus, such sketches are good for quick reference. Such sketches are for your own use; I will not collect, examine, grade, or do anything else with them.

Testing: L Each person studies the osteology of a given animal until they feel they know it. L When ready, you come with the skull or skeleton and show me that you know it by pointing out and naming each of the bones in the guide. ( If we agreed that you know that skull, move on to the next one. If not ;. . . try again

The grade for skeleton/skull identification is 16%. For this you must successfully complete the identification of the following (which must be identified in this order). L Skeleton L Amia L Reptile skull L Mammal skull L Mammal teeth The question on teeth is a question on the final exam. Of the remaining four, completing all four gives you an A for the 16%; 3 gives you a B; 2 gives you a C; 1 gives you a D.

REFERENCES AND READING

Because this subject is continuously evolving, specific readings have not been established for all lectures. The literature for vertebrate paleontology is quite voluminous, considering how specialized and esoteric the subject is. Books and important papers come out so fast I cannot begin to keep up with them.

Throughout the semester I try to provide suggested readings on the subjects we are covering. Such readings are not selected randomly or haphazardly, but are specifically chosen to do one or more of the following. ( Provide the best reference source for you to study or prepare answers to exam questions, corresponding to my particular lecture organization or emphasis. L.S. Fichter, Spring, 2001 Syllabus 9 Bio/Geol 405 Vertebrate Paleontology

( Introduce you to some of the wide variety of literature available in paleontology.

( Give a greater insight into the , depth, and variety of some of the subject matter...much more easily than can be accomplished in lecture.

The implication is that all of these readings will not require meticulous reading, although some might. You should at least pursue the suggested readings to discover what is available; what needs meticulous reading will then become clear enough. I provide all these readings in the classroom. It is a cardinal rule, therefore, That None of These Readings May Be Removed from the Laboratory under Any Circumstances for Any Period of Time. . . well, there are two exceptions: (1) IF there is a class in the room while you want to read you may take it into another room, BUT you must leave a note on the board--name, time, title of reading and return the reading immediately after use.

(2) If you want to xerox something you may remove it for the period of time just to do that; BUT leave a note on the board, and return it immediately! Since many people require the use of these readings, and some of the information necessary for exam preparation may be contained therein, the inconsiderate removal of any readings is considered cheating, and prosecuted as such. L.S. Fichter, Spring, 2001 Syllabus 10 Bio/Geol 405 Vertebrate Paleontology VERTEBRATE PALEONTOLOGY Biology/Geology 405 Tentative Spring, 2001 Semester Schedule (This schedule is based on the last time the course was taught and will give you an idea of the timing. It will probably undergo revision as the semester progresses)

Week 1 JANUARY W ...... Introduction F ...Classification, , Systematics Through Evolution of Evolutionary Thought Week 2 M ...... Microevolutionary Processes W ...... Macroevolutionary Processes (Effect and Pulse Hypotheses) F ...... Macroevolutionary Processes Finish Skeleton Identification Week 3 M ...... Taxonomy and Cladistics W ...... Survey of vertebrate evolution ...... (Origins; Jawless fish; Intro jawed fish; Acanthodians) F ...... Survey of Vertebrate Evolution ...... (Placoderms; Evol. Relationships among fishes; ) Week 4 M ...... Survey of Vertebrate Evolution ...... (; and Geologic History) W ...... Survey of Vertebrate Evolution ...... (Origin of Amphibians; Early Reptiles; Late Paleoenvironments) F ...... Survey of Vertebrate Evolution ...... (Late Paleozoic Paleoenvironments; Reptiles) Finish Amia Skull Week 5 FEBRUARY M ...... Survey of Vertebrate Evolution ...... (Late Paleozoic Paleoenvironments; Reptiles) W ...... The Origin of F ...... The Fractal Evolutionary Record ...... Thermodynamics and Evolution WEEK 6 M ...... Non-Equilibrium thermodynamics, and dissipative structures W ...... Positive and Negative Feedback and Adaptive Radiations F ...... Actinopterygian Evolution (through ) WEEK 7 M ...... Evolution (Holostei and Teleostei); Begin W ...... Comparing Actinopterygii and Sarcopterygii F ...... Sarcopterygii: Osmoregulation and Evolution

WEEK 8 L.S. Fichter, Spring, 2001 Syllabus 11 Bio/Geol 405 Vertebrate Paleontology M ...... Sarcoptergyii Evolution and the World W ...... Defining an Amphibian ...... Origin of Amphibian Anatomical Adaptations F ...... Preadptation MARCH SPRING BREAK ( ( ( ( ( ( ( ( ( ( Week 9 M ...... Preadaptation; Amphibian Origins: Scenarios and W ...... Two Phase Model, Mosaic Evolution, F ...... Evolutionary Trends in Labrynthodont Vertebrae and Skulls Finish Reptile Skull WEEK 10 M ...... Evolutionary Trends in Temnospondyl and Anthracosaur Amphibians W ...... Origin of the F ...... Osteological Definitions of Reptiles ...... Radiation of the Amniotes WEEK 11 M ...... : , , ...... The Anapsids Reptiles W ...... Defining Synapsids: & Evolution F ...... Begin Early Diaspsid Reptiles Finish Dog Skull WEEK 12 M ...... Initial Adaptive Radiations of the Diapsids ...... Archosauromorphs and Dinosaurs ...... Evolution of the Ankle and Posture in Archosauromorphs APRIL W ...... Dinosaurs F ...... Dinosaurs WEEK 13 M ...... Dinosaurs W ...... Biological Origins of mammals ...... Olson’s Origin of Mammals F ...... Olson’s Origin of Mammals ...... Dental Evolution and the Origin of Mammals WEEK 14 M ...... Dental Evolution and the Origin of Mammals W ...... in Mammals F ...... The Orders of Mammals Finish Mammal Teeth WEEK 15 M ...... Paleogeography, Climate and Mammal Evolution W ...... Paleogeography, Climate and Cenozoic Mammal Evolution

FINAL EXAM Friday, May 4, 10:30-12:30