ANT 3930 (7068) HONORS MOLECULAR
GENETICS AND EVOLUTION
Prof. Connie J. Mulligan
Class meets in B304 Turlington
Class time: Thursday,
periods 6-8 (12:50-3:50 pm), with a 15 min break
Office hours: Thurs, 10:30-12:30,
B119 Turlington Hall or by appointment in 409
Genetics Institute
Contact information:
Prof. Connie Mulligan
409 Genetics Institute,
Cancer and Genetics Research Complex
(352) 273-8092
http://www.clas.ufl.edu/users/mulligan/Webpage/index.html
Course summary: ANT3930 is an in-depth examination of the use of
molecular genetic data to address questions of human evolution and population genetics. The completion of the human genome sequence
has greatly facilitated the application of molecular genetic data to questions
of human evolution. Over the past ten
years, a wealth of genetic data has been generated on human populations
worldwide and new statistical methods have been developed to analyze these
data. These genetic data are currently
being used in a number of investigations, such as the reconstruction of past
migration events or the detection of admixture or gene flow in a population. Specific topics to be discussed include the
relationship of humans to non-human primates, emergence of anatomically modern
humans in Africa and migration out of Africa, Neanderthal genetics (did we
interbreed?), colonization of Europe and the
Course design:
This course is intended for advanced undergraduate students who have an
interest in human evolution as well as in molecular genetics. It is intended for students from all colleges
and departments – in the past, I have had students from anthropology,
chemistry, history, molecular genetics and microbiology, and zoology. A diverse audience makes for a more
interesting class since everyone has different backgrounds, different
perspectives and different interests to contribute to class discussions. Active participation is one of the strengths
of the class in this regard.
Course objectives and student goals: All students are expected to gain knowledge on the
molecular genetic basis for various theories of human evolution and subsequent
population movements. The class is
fairly intense and demanding because knowledge across a broad range of fields
is fundamental to an exploration of the molecular genetics of human evolution –
in fact, this course may be the most challenging course you have ever taken
with respect to developing expertise and familiarity with a wide range of
materials, techniques, publications, etc.
You are expected to do all of the required readings and to follow up
with additional readings if you do not understand a topic or concept. Additional readings are listed in the
textbook and can be found in the references in the journal articles;
furthermore, you should become familiar with searching PubMed for
supplementary, follow-up, or original readings.
Grading: Final grades will be determined by the following five
categories, each of which contributes 100 points to the final grade: 1) participation
(100 pts), 2) weekly summary/questions/comments (100 pts), 3) 2-4
homework exercises (25-50 pts each),
4) one oral presentations (100 pts total), and 5) one exam (100 pts). Possible points total 500. Grades will be based on the following point
percentages: 90-100%=A, 87-89%=B+, 80-86%=B, 77-79%=C+, 70-76%=C, 67-69%=D+,
60-66%=D, < 59%=E.
-
Participation is required of all students
and will be based on each student’s contribution of original comments,
questions, etc to the class. Students
are not graded on the brilliance of their statements, but on their willingness
to talk, a demonstration that the assigned material was read, and the
originality of their comments. Simply
showing up for class does not constitute participation. Remaining silent in class means that the
highest grade a student can receive is a B.
-
At the beginning of each class, a 1-paragraph summary and 2-3 questions or comments for each peer-reviewed
journal article assigned for that day’s class will be turned in. The summary/questions/comments are required
only for the peer-reviewed journal articles, not for the news-and-views type
articles (typically the titles that are in quotes in the course schedule below)
that are included in the course pack to provide background or summary
information. The
summary/questions/comments are intended to ensure that each student is prepared
to actively participate in class discussions.
-
There will be a
maximum of four homework exercises
involving the analysis of hypothetical or actual molecular data. The exercises are intended to give students
an opportunity to perform data analyses similar to those conducted in the
discussion papers and will be graded on effort and accuracy. Exercises must be turned in two weeks after
they are assigned. Students who miss the
class in which an exercise is assigned are expected to turn the exercise in on
time, i.e. two weeks after the missed class.
-
Each student will present one 15-20 min oral presentation based
on journal articles from the course packet.
The presentation must use MS Power Point. Regardless of whether a student is presenting
an article, all students will read all articles in the course packet and be
prepared to participate in class discussions of the articles. Students will sign up for articles for oral
presentation on the second day of class (only one student may sign up for each
article).
-
There will be one exam that will consist of short answer and
essay questions and questions similar to the homework exercises. Questions must be answered during the class
period without reference to books or notes of any kind. Calculators may
be used, but no cell phones, BlackBerry or similar devices will be allowed. Make-up exams will be scheduled only in
extenuating circumstances and will require a doctor’s note, police report, or
similar supporting documentation.
Useful
websites:
Although basic molecular
biological concepts will be reviewed, some knowledge of DNA structure, Mendelian genetics, and molecular biology is expected (such
as Intro Bio, BCS 2011). Useful
information is provided by several websites:
http://www.clas.ufl.edu/users/mulligan/Webpage/3930.2008/3930home.html – website for class
http://www.uflib.ufl.edu/ej/ - UF
database of available electronic journals (may only be available from a campus
computer)
http://www.ncbi.nlm.nih.gov/PubMed
- National Library of Medicine database of over 11 million journal articles
dating back to the 1960s
http://www.genome.gov/glossary.cfm
– NIH-maintained glossary of genetic terms
http://www.genomesonline.org/
- status of genome sequencing projects
http://www.genome.gov/LegislativeDatabase
- Database of federal and state laws focused on genetic issues, such as genetic
testing and counseling, insurance and employee discrimination, etc.
http://www.gene.ucl.ac.uk/hugo/
- Human Genome Organisation
http://www.stanford.edu/group/morrinst/hgdp.html
– Human Genome Diversity Project (dated, good for
historical perspective)
Class attendance policy: Because the class meets
only one time per week and because the class format is mainly discussion, it is
very difficult to make up missed classes by borrowing notes, etc. Therefore, students are strongly encouraged
to attend all classes and to arrive on time.
Computers are allowed in class for taking notes, but are not allowed
during exams. Class discussions/lectures
cannot be recorded in any manner without special permission. All cell phones must be turned off during
class.
Strategies for
success:
-
It is important to complete all the readings on time and it is best to
do the readings throughout the week. In
this way, you have time to think about and process the information during the
week and in between different readings.
Ideally, you would read some every night of the week. The amount of reading material is very
modest, particularly for an anthropology course. This is because it is expected that you will
re-read (gasp!) anything you do not understand the first time. I often re-read journal articles and find
myself discovering things that I completely missed on the first read. Or new items will come to light after having
read a different, but related article.
This is the intent of the readings – that they relate to each other and
increase your knowledge and expertise in an exponential way. During your reading, you should take copious
notes and these notes will form the basis of the summary + questions you must
turn in for every article.
-
You have two weeks to work on the exercises. These exercises are most likely completely
different from anything you’ve ever done and, thus, you may have lots of
questions about how to proceed. The
intent is that you will use the first week to start on the exercise and come to
class the next week (i.e. the week before the exercise is due) with any
questions you have about the exercise.
Do not wait until the second week to start the exercise. Also, I am always available by email to ask
questions about the exercises and often will be able to answer your question
immediately while you’re still working on the exercise.
-
For the oral presentation, it is a good idea to practice your entire
presentation without any stops the night before your scheduled presentation –
this ensures your talk is the correct length of time and develops good practice
for all public speaking.
-
Finally, you should review material throughout the course rather than
trying to cram everything in the night before the exam. Ask for help in taking notes, comprehending
the material, or preparing any of the written or oral assignments – I am
available during office hours, you can schedule an appointment outside of
office hours, and I am always available by email.
Copyright
information:
Lectures may not be tape-recorded without the prior express written permission
of Dr. Connie Mulligan. The contents of
the syllabus, lectures, lecture outlines, and handouts for this course are
copyrighted and intended for the private use of students registered in ANG
6461/ANT 4530. They therefore cannot
legally be reproduced, in part or in whole, by any commercial enterprise or for
any commercial purposes.
Accommodations for students
with disabilities: If you require accommodation due to a disability, please make an
appointment during my office hours so that we may discuss your needs. Students requesting classroom accommodation
must first register with the Dean of Students Office. The Dean of Students Office will provide
documentation to the student who must then provide this documentation to the
Instructor when requesting accommodation.
Academic honesty: As a result of completing
the registration form at the
An excellent website that
discusses plagiarism (it provides a definition and many useful examples) is http://www.csubak.edu/ssric/Modules/Other/plagiarism.htm. All students should read this material at
least once.
UF Counseling Services: On-campus services are
available for students having personal problems or lacking clear career and
academic goals. They include:
Course
schedule (readings and oral presentations are subject to change):
August 28 Introduction
Lecture – background
material
Video – The Gene Hunters (example of a study
conducted under the Human Genome Diversity Program)
September 4 The human genome
–
Human Evolutionary Genetics
(HEG), Chpts 1, 2 AND pp 88-89
–
Course packet
§
“Beyond Stones and Bones”, Newsweek, March 19, 2007
§
“Population geneticists move beyond the
single gene”, Science, June 22, 2007
§
“Working the (gene count) numbers: Finally,
a firm answer”, Science, May 25, 2007
§
“DNA study forces rethink of what it means
to be a gene”, Science, June 15, 2007
Lecture
–
Background material
–
How to read a scientific article
–
PubMed search
–
Discussion of oral presentations
Video – Gene Hunters
(continued)
Sign up for oral
presentation
September 11 Human genetic diversity
-
HEG – Chpts 3, 4
-
Course packet
§
“Human Genetic Variation”, Science, Dec 21,
2007
§
“James Watson’s genome sequenced at high
speed”, NatureNews, April 16, 2008
§
“International genome project launched”, NatureNews, Jan 22, 2008
§
Use of Y chromosome and mitochondrial DNA
population structure in tracing human migrations, Underhill and Kivisild, Annu Rev Genet, 2007,
41:539-564 (possible oral presentation).
§
DNA sequence from Cretaceous period bone fragments, Woodward et al.,
Science, 1994, 266:1229-1232 AND Technical comments, Science, 1995, 268:
1191-1194. (oral presentation)
September 18 Processes that shape genetic
diversity
-
HEG – Chpt 5
-
Course packet
§
Contrasting signatures of population growth
for mitochondrial DNA and Y chromosomes among human populations in
§
Rapid deployment of the five founding Amerind
mtDNA haplogroups via coastal land riverine
colonization, Fix, AJPA, 2005, 128:430-436. (oral presentation)
§
Global patterns of human mitochondrial DNA and Y-chromosome structure
are not influenced by higher migration rates of females versus males, Wilder et
al., Nature Genetics, 2004, 36:1122-1125
September
25 Making inferences
from diversity
-
HEG – Chpt 6
-
Course packet
§
“Are human brains still evolving?” AND Ongoing adaptive evolution of
ASPM, a brain size determinant in Homo
sapiens, Mekel-Bobrov et al., Science, 2005,
309:1730-1722 AND 2006 Comment AND 2006 Response to comment AND 2007 Comment. (oral
presentation)
§
“Genetic study
shakes up out of
October 2 Humans as apes
-
HEG – Chpt 7
-
Course packet
§
“Brain evolution studies go micro”
§
“Genomes throw
kinks in timing of chimp-human split”, Science, May 19, 2006
§
“Genomicists tackle the primate tree”, Science, April 13,
2007
§
“Relative differences: The myth of 1%”, Science, June 29, 2007
§
Implications of
natural selection in shaping 99.4% nonsynonymous DNA
identity between humans and chimpanzees: Enlarging genus Homo, Wildman
et al., 2003, Proc Natl Acad
Sci USA, 100:7181-7188 (oral presentation)
§
Mapping human genetic ancestry, Ebersberger et al., 2007, Mol Biol
Evol, 24:2266-2276 (oral presentation)
-
HEG – Chpt 8
-
Course packet
§
Global patterns of linkage disequilibrium at the CD4 locus and modern
human origins, Tishkoff et al, Science, 1996, 271:1380-1387 AND Technical
comment by Milford AND Response by Tishkoff et al. (possible oral presentation)
§
“Anthropologists cast doubt on human DNA evidence” AND “Were Cro-Magnons
too like us for DNA to tell?” AND Evidence for a genetic discontinuity between
Neandertals and 24,000-year-old anatomically modern Europeans, Caramelli et al., PNAS, 2003, 100:6593-6597. (oral
presentation)
§
“The dawn of Stone Age genomes” AND “No sex, please, we’re Neandertals”
AND Inconsistencies in Neanderthal genomic DNA sequences (Wall and Kim, 2007, PLoS Genetics, 2007, 3:1862-1866). (oral presentation)
§
Extra reading - No evidence of Neanderthal mtDNA
contribution to early modern humans, Serre et al.,
2004, PLoS Biology, 2:313-317
October 16 Global distribution of diversity
-
HEG – Chpt 9
-
Course packet
§
Ice ages and the
mitochondrial DNA chronology of human dispersals: A review, Forster, 2004, Phil
Trans R Soc Lond B, 359:255-264
§
Evidence for gradients of human genetic diversity within and among
continents, Serre and Paabo,
Genome Res, 2004, 14:1679-1685 (oral presentation)
§
“Did Early Human Go North or South?” AND Single, rapid coastal settlement
of Asia revealed by analysis of complete mitochondrial genomes, Macaulay et
al., Science, 2005, 308:1034-1036 (oral presentation)
-
HEG – Chpt 10
-
Course packet
§
DNAs from the European Neolithic, Barbujani and
Chikhi, Heredity, 2006, 1-2 AND Genetics and
the population history of Europe, Barbujani and Bertorelle, 2001, Proc Natl Acad Sci USA, 98:22-25. (oral presentation)
§
Y genetic data
support the Neolithic demic diffusion model, Chikhi et al., 2002, Proc Natl Acad Sci
§
“Prehistoric GM corn” AND Early allelic selection in maize as revealed by
ancient DNA, Jaenicke-Despres et al., Science, 2003,
302:1206-1208
-
Francis Collins, Director, NIH National Human Genome Research Institute
-
“Genomics, Medicine, and Society”
-
5:00-6:00pm, Health Professions, Nursing, Pharmacy Auditorium (http://campusmap.ufl.edu/?loc=0212&zoom=16)
-
Register at http://www.ufgi.ufl.edu/FL-Genetics-2008/symposium-registration.html
-
HEG – Chpt 11
-
Course packet
§
A three-stage
colonization model for the peopling of the
§
Gene flow across linguistic boundaries in Native North American
populations, Hunley and Long, PNAS, 2005,
102:1312-1317 (oral presentation)
§
DNA from pre-Clovis human coprolites in
-
HEG – Chpt 12
-
Course packet
§
“Y chromosome bears witness to story of the Jewish diaspora”
AND Jewish and Middle Eastern non-Jewish populations share a common pool of
Y-chromosome bi-allelic haplotypes, Hammer et al., PNAS, 2000, 97:6769-6774
(oral presentation)
§
Y chromosomes traveling south: The Cohen modal haplotype and the origins
of the Lemba – the “Black Jews of southern
-
HEG – Chpt 13
-
Course packet
§
“Are humans still evolving?”
§
“European skin turned pale only recently, gene suggests” AND “Ancient
DNA reveals Neanderthals with red hair, fair complexions” AND A melanocortin 1 receptor allele suggests varying
pigmentation among Neanderthals, Lalueza-Fox et al.
2007, ScienceExpress. (oral presentation)
§
Absence of the
lactase-persistence-associated allele in early Neolithic Europeans, Burger et
al., PNAS, 2007, 104:3736-3741 (oral presentation)
§
“Gene variant may influence how people learn from their mistakes” AND
Genetically determined differences in learning from errors, Klein et al. 2007,
Science, 318:1642-1645
-
HEG – Chpt 14
-
Course packet
§
“In genetic control of disease, does ‘race’ matter?”
§
To be handed out in class - New article on
effects of genetics and culture on identity and blood pressure – Gravlee and
Mulligan (possible oral presentation)
§
Ethics watch, Foster and Sharp, 2008, Nature
Reviews Genetics AND Genes ‘R Us, Lehrman, Nov 2007,
J Life Sci, 50-55 (oral presentation)
Review for exam
-
HEG – Chpt 15
-
Course packet
§
The coming paradigm shift in forensic
identification science, Saks and Koehler, 2005, Science, 309:8920895
Exam