Professor: Harvey E. Ballard, Jr., 406 Porter, (740) 593-4659
E-mail: ballardh@ohio.edu
Teaching Assistant: Nate Smucker, 400 Porter, (740) 593-1134
TA E-mail: ns218005@ohio.edu
Lectures: MWF, 10:10-11:00am, Porter 304
Labs: TTh, 3:10-5:00pm, Porter 408 (my laboratory)
Office hours: MW, 11:10noon-12:00noon; additionally by appointment.
Protocols to Some Important Molecular Systematic Approaches
Policies--Expectations, Lecture and lab attendance, Cheating, Weekly readings
Coursework and Grades--Everybody, Grad students, Laboratories, Exam review, Grading scale
Course Topics--Lecture and lab itinerary, Web notes
"La Policia son sus amigos" (A Final Word)
The course will explore molecular techniques currently used to hypothesize phylogenetic relationships and answer taxonomic, ecological and evolutionary questions at the population, species and lineage levels. Topic coverage will include widely used and some very new methods, and will focuse intensively on certain easily generated or broadly applicable DNA marker systems, specifically Inter-Simple Sequence Repeats (ISSRs), Amplified Fragment Length Polymorphisms (AFLPs) and microsatellites, for population-level questions; PCR-Restriction Fragment Length Polymorphisms (PCR-RFLPs) for species-level questions; and DNA sequencing for species- and higher level-questions. Although plants will figure heavily, the mitochondrial genome and widely used gene regions in it will be covered briefly, and studies of animal and fungal groups will also be reviewed. Marker generation, theoretical considerations and analytical algorithms are applicable to most organisms. This is a "methods" course, with lecture and lab material geared heavily toward preparing the student as a practitioner of "molecular systematic" approaches sensu lato.
Laboratory experience is an essential component of training in the course and is mandatory for everyone. In addition, graduate students will work to produce one of the following: (1) a mock (but complete) National Science Foundation Dissertation Improvement Grant proposal using data from the labs, from their own research, or from existing databases or published literature; (2) a review paper on a particular comparative molecular topic of their choice; (3) a manuscript polished as for submission to a scientific journal, using the data generated during our laboratory group project, including an appropriate review of relevant literature in the introduction and discussion; or (4) a 50-minute lecture on a comparative molecular topic.
While previous molecular biology experience is not necessary, given that all the protocols used in the laboratories are straightforward and simple to follow, a prior understanding of DNA structure, transcription and translation, and Mendelian genetics (such as concepts available from an evolution or genetics course) will be very useful to you. Exposure to plant systematics and population ecology would also be beneficial, in order for you to appreciate the broader context of applying molecular data to different kinds of questions.
Expectations: Following are reasonable expectations that I have of you. Note that most of these also apply to me!
Lecture and lab attendance: Attendance at lecture and lab is mandatory. I won't bother taking attendance; I will simply expect you to attend regularly unless you or someone in your family is dying.
Cheating: This includes but is not limited to using somebody else's answers on your own exams, not making a good-faith effort to participate actively in the lab research, and not relying primarily on your own data analysis, writing and background literature research for the graduate grant proposal. I encourage group effort in labs--working together to understand how to generate, analyze and interpret the meaning of molecular data. But expect to exert at least a reasonable amount of effort in trying everything in lab yourself, and if you're a graduate student, plan on working up the bulk of the grant proposal yourself. "Cheating" in any sense is not academically in your best interest.
Weekly readings : You will perform readings each week that include chapters from various books and journal articles across the diverse field of molecular ecology/systematics, and later even into molecular bases of organismal phenotypes, and other cool stuff.Every other week during the Friday 12:10-1:00pm class period, we will meet at the "Front Room" coffee shop in Baker Center instead of the lecture room, where we will discuss those readings, and additionally perhaps about the lab group project or other course-related issues.
For the weekly readings, I will link a PDF version to the appropriate day of the lecture itinerary, below. Considering some chapters or journal articles are quite long, it will be to your advantage to read them each week rather than let the assigned readings pile up, taking notes as you go. Each of the exams will include at least one question concerning each weekly reading.
Everybody: Everyone will take two exams (including the non-comprehensive final), each exam covering roughly one-half of the term's lecture material and assigned readings. Questions will be multiple-choice, matching, short answer, and short essay, and I will give you many options from which to choose, under various topics. You will answer sufficient numbers of questions to total 100 points. So, exam scores total 200 points possible. Everyone will also attend and participate in two 2-hour laboratories during most weeks, for which you will receive 100 points. After the first few weeks, we will usually meet as a group during the first lab meeting and as small groups independently to do additional work in the lab later in the week. Completion of the two exams and full participation in the laboratories fulfills undergraduate requirements for the course, bringing the total possible for undergraduates to 300 points.
Grad students: Graduate students must accomplish one additional feat beyond the two exams and laboratory practicum. They must complete one of the following: (1) a complete "mock" National Science Foundation Dissertation Improvement Grant proposal, including some application of molecular data using the knowledge and skills you have developed in the course, incorporating data generated in the course labs, their own data, or published data; (2) a 20-30 page (double-spaced) review paper on a topic of their choice; (3) a properly prepared journal article manuscript following the formatting details of a suitable journal, using data generated from the group lab project, and polished in all respects; or (4) a comprehensive 50-minute lecture on a topic of their choice. Any of these efforts represents the graduate student project, and is worth 100 points, bringing the total for graduate student course credit to 400 points. All students will participate in an "anonymous" peer review of other students' products, as part of the grading process, and to give students objective feedback. All grad students must commit to one of the four types of project, and provide me the subject or title, by the end of the third week; for lectures, we must also schedule the class period then. (Your choice of lecture might even be one of the topics I was prepared to give later in the term, rather than a topic you choose yourself; but you are responsible for compiling the information, organizing and presenting it in a coherent and well developed fashion).
For students working up a grant proposal--A grad student may use his/her own research data, published data (cited, of course), data generated in the laboratory, "fabricated" data, or a combination of these, as the focus for the grant proposal. It may develop any scientifically defensible research question and include any set of experimentally viable set of methodologies to accomplish it, but must include a complete and more or less realistic budget for the project. I will grade the grant proposal just as I would if I were sitting on the panel at NSF: for scientific merit of the question, defensible methodologies, implicit understanding of relevant (historical and recent) research literature, concern for current controversies or potential problems, terse clear writing, and a reasonable budget. You will be expected to follow the NSF format to the letter. I will be happy to help you along the way. I have developed Excel spreadsheets for painlessly calculating budgets for molecular markers and for travel and broad lab research expenses, which I'll share with you. The NSF Web URL for the Doctoral Dissertation Improvement Grant guidelines under the Biological Sciences Directorate follows: http://www.nsf.gov/pubsys/ods/getpub.cfm?nsf02173
For students preparing a review paper--The review paper should be arranged as an intelligent review of a topic covered by such "review" journals as Trends in Ecology and Evolution or Science. The abstract, body and literature cited should total 20-30 double-spaced pages (including any embedded figures). The paper should include coverage of key recent journal articles and review/text books, as well as pertinent classic works. Web resources are generally not admissible.
For students preparing a journal article manuscript--The manuscript should be arranged according to the Information for Contributors format of a well-known and suitable journal considering the data and scope. The data (or a subset of it) will come from the group lab project. The abstract, body and literature cited should total 20-30 double-spaced pages (including any embedded figures). The paper should include coverage of key recent journal articles and review/text books, as well as pertinent classic works. Web resources are generally not admissible.
For students preparing a lecture--The lecture must be comprehensive, well organized, and provide sufficient coverage of content to fill approximately 40 minutes, with the last 10 minutes devoted to leading discussion and answering questions. Powerpoint seminar-style is fine, but coherent "front of the room" delivery with slides or overheads is also fine. As with the review paper, the presentor must understand the topic reasonably well, be prepared to answer questions that may arise, and consult both recent and pertinent older works to provide a well-balanced and somewhat detailed overview of the topic (illustrative and illustrated examples or "case studies" are always appreciated).
Laboratories: Laboratories will consist of a series of hands-on activities giving you practical experience with various protocols to extract genomic DNA, perform PCR and access/visualize multi-locus markers and generate gene sequences for population-level genetic diversity and higher-level phylogenetic studies, respectively, and perform a diversity of analyses appropriate to particular data sets. I will also give you brief exposure to accessing data from GenBank and will encourage you to assemble data sets from previously published studies or public databases that interest you. If the lab student population is small (and the total lab fees from the group do not permit much actual data generation--molecular systematic studies are expensive!--we will attempt to generate data for a handful of samples but will devote more time to analysis and interpretation of results for a wide range of data sets. I will also distribute to you basic protocols for all the approaches we discuss or use, Excel budget spreadsheets with per-sample costs for diverse approaches that are valuable for budgeting in grant proposals, and I will introduce you to a range of software programs for different uses.
Exam review: I will hold a review session during the Thursday lab period in the week before each exam. I will also be available to everyone during office hours and by appointment throughout the term. I will hold the first exam during the Thursday lab period of Week 6, so that students have 2 hours to take the exam. The final exam takes place on Wednesday, 18 March, at 10:10 in Porter 304 (our usual class room).
| Undergrad
Pts |
Grad
Pts |
% | Letter
Grade |
| 276-300 | 368-400 | 92-100 | A |
| 270-275 | 360-367 | 90-91 | A- |
| 264-269 | 352-359 | 88-89 | B+ |
| 246-263 | 328-351 | 82-87 | B |
| 240-245 | 320-327 | 80-81 | B- |
| 234-239 | 312-319 | 78-79 | C+ |
| 216-233 | 288-311 | 72-77 | C |
| 210-215 | 280-287 | 70-71 | C- |
| 204-209 | 272-279 | 68-69 | D+ |
| 186-203 | 248-271 | 62-67 | D |
| 180-185 | 240-247 | 60-61 | D- |
| <180 | <240 | <60 | R.I.P. |
| 1 | Mon, 1/5 | Lecture | Intro to the course |
| Tue, 1/6 | Lab | NO LAB | Wed, 1/7 | Lecture | Morphology vs. molecules; Basics of molecular and evolutionary genetics |
| Thur, 1/8 | Lab | NO LAB | |
| Fri,1/9 | Lecture | Earlier methods: serology; amino acid sequencing and DNA:DNA hybridization | |
| 2 | Mon, 1/12 | Lecture | |
| Tue, 1/13 | Lab | Genomic DNA extraction & visualization | |
| Wed, 1/14 | Lecture | ||
| Thur, 1/15 | Lab | Genomic DNA extraction & visualization (cont.) | |
| Fri, 1/16 | Discussion | Front Room Coffeehouse, Baker Center | |
| 3 | Mon, 1/19 | Holiday | M. L. KING DAY |
| Tue, 1/20 | Lab | Microsatellites | |
| Wed, 1/21 | Lecture | ||
| Thur, 1/22 | Lab | Microsatellites (cont.) | |
| Fri, 1/23 | Lecture | Anonymous markers (RAPDs, ISSRs); AFLPs | |
| 4 | Mon, 1/26 | Lecture | |
| Tue, 1/27 | Lab | RAPDs, ISSRs | |
| Wed, 1/28 | Lecture | Distance methods of analysis | |
| Thur, 1/29 | Lab | AFLPs | |
| Fri, 1/30 | Discussion | Front Room Coffeehouse, Baker Center | |
| 5 | Mon, 2/2 | Lecture | |
| Tue, 2/3 | Lab | Genetic Diversity Analyses | |
| Wed, 2/4 | Lecture | ||
| Thur, 2/5 | Lab | Exam review | |
| Fri, 2/6 | Lecture | Studies in speciation and hybridization | |
| 6 | Mon, 2/9 | Lecture | Molecular cytogenetics; Single- vs. multi-copy DNA, gene families |
| Tue, 2/10 | Lab | Hybridization and Polyploidy Analyses | |
| Wed, 2/11 | Lecture | ||
| Thur, 2/12 | Lab | Exam 1: Weeks 1-5 | |
| Fri, 2/13 | Discussion | ||
| 7 | Mon, 2/16 | Lecture | Cladistic methods of analysis I: Fundamentals For your reading pleasure: Compleat Cladist |
| Tue, 2/17 | Lab | Sequence editing; parsimony analyses | |
| Wed, 2/18 | Lecture | Probabilistic methods of analysis | |
| Thur, 2/19 | Lab | Maximum likelihood and Bayesian analyses | |
| Fri, 2/20 | Lecture | Clade support statistics; Tests for non-random structure | |
| 8 | Mon, 2/23 | Lecture | Separate data sets vs. total evidence; Monophyletic constraints; Congruence tests |
| Tue, 2/24 | Lab | Clade support, monophyletic constraints, congruence tests | |
| Wed, 2/25 | Lecture | Rate heterogeneity, long branches and molecular clocks; Rates of diversification | |
| Thur, 2/26 | Lab | Rate and Diversification analyses | |
| Fri, 2/27 | Discussion | Front Room Coffeehouse, Baker Center | |
| 9 | Mon, 3/2 | Lecture |
Studies in morphological evolution and evolutionary radiations |
| Tue, 3/3 | Lab | Radiation analyses; research budgets | |
| We, 3/4 | Lecture | NO CLASS |
|
| Thur, 3/5 | Lab | Biogeographic analyses | |
| Fri, 3/6 | Lecture | Studies in biogeography | |
| 10 | Mon, 3/9 | Lecture | Ancient organisms--Studies of the algae (guest lecture by Dr. Morgan L. Vis) |
| Tue, 3/10 | Lab | Character mapping | |
| Wed, 3/11 | Lecture | Outgroup comparisons and hypothetical ancestors; Character mapping and biogeographic inference | |
| Thur, 3/12 | Lab | Exam review 2; Grad student non-lecture projects due | |
| Fri, 3/13 | Lecture | Topic TBA (guest lecture by Aliya Donnell) | |
| FINALS WK | Wed, 3/18, 10:10am | Exam | Exam 2: Weeks 6-10 |
Web notes: I will hotlink lecture notes, weekly readings, lab protocols and other lab activities to the appropriate days in the above table. These will be in Word or PDF format. You should access and print these out prior to the lectures and laboratories.
I encountered these signs with former grad student Ben Torke recently in Quito, Ecuador, during our month-long 1997 research expedition in the Andes to study violets. The signs, saying "the Police are your friends", blocked certain roads during festivals in which people choked the streets and engaged in fun and frolic (as well as rough-housing, looting and pickpocketing). Signs were flanked by police bearing automatic machine guns. Neither the signs nor the assault weapons instilled us with confidence in the message.
Contrary to the above, I am here to help you--to get through the course and enjoy the process. I want you to learn the material and appreciate it with the enthusiasm and wonder that I do! If you are having difficulties with the material itself, come see me as soon as you encounter problems, or call or e-mail me and set up a time to go over material at your and my earliest convenience. Waiting until the day before an exam is weeks too late! For simple, single questions, call or e-mail me; for complex questions or several questions, we'll schedule an appointment.
I am concerned that you have a worthwhile experience here at OU in spite of any personal or academic roadblocks you might have to face along the route, both during and beyond the Evolution course. Please feel free to meet with me to discuss PBIO courses, plant biology or evolution and systematics generally, academia, or personal issues impacting on your ability to negotiate this course or your degree program. Or just join me over a cup of coffee or tea to discuss the fate of the world! I may or may not have answers or experience for particular problems (although you might be surprised at the issues I've had to work through myself). Nevertheless, having a concerned "ear" available when you need it is always comforting, and can be very helpful.
I also utilize my contacts around the country and the world, in various institutions and agencies, to help set up employment and internship opportunities for undergraduate and graduate students. I keep abreast of graduate botany programs and various types of employment opportunities (academic and non-academic) in my areas of interest. I'm happy to write letters of recommendation and make phone calls or send letters on your behalf--if you are a decent student!
Written by Harvey Ballard; last revised 27 February, 2009.