Biology 280 – Molecular Ecology
Spring 2016
Meets:
Computer
Workshop:
11:40-12:55 am TTh
Room 228 Hills Building
Room 001 Marsh Life Science
12:00-3:00 pm Mondays
12:00-3:00 pm Wednesdays
Instructor:
C. William Kilpatrick
Office:
305 Marsh Life Science
Office Hours:
2:00 - 3:00 pm Tuesdays
10:00 - 11:00 am Wednesdays
1:00 - 2:00 pm Thursdays
Email:
C-William.Kilpatrick@uvm.edu
Course Description:
This is an upper level biology course designed to provide students
with exposure to the methods for examining molecular markers and how
these markers are used to address ecological and evolutionary questions.
Emphasis in this course will be placed on data analysis and inferences
from the data analysis. The course will start with a review of basic
genetics and the Castle-Hardy-Weinberg Equation. Various molecular
markers including allozymes and isozymes (protein electrophoresis),
restriction fragment (RFLP), DNA fingerprints (including RAPD & AFLP
markers), microsatellites (STR), single nucleotide polymorphisms (SNP)
and haplotypes (DNA sequencing) will be introduced but work with DNA
sequences and microsatellites will be emphasized. An overview of the
general methods, visualization of the resulting data, interpretation of data,
and strengths and limitations will be provided for each type of genetic
marker. The major topics covered in addition to genetic markers will
include Castle-Hardy-Weinberg equilibrium; genetic variability and genetic
differentiation; relatedness and parentage; indirect and direct estimates of
gene flow; estimation of effective population size; identification of
population growth or decline, lineage sorting and bottlenecks; and
detection of signatures of evolutionary events in population histories such
as inbreeding, selection and migration. To discuss these topics, various
other areas will be introduced including maximum likelihood, Bayesian
methods, coalescent theory and intraspecific phylogenetics and
phylogeography. In addition to class presentations, workbook exercises
will provide introduction and experience with methods of data analyses on
the topics listed above. These workbook exercises will require the use of
a number of computer packages and two weekly workshops in the
computer lab are scheduled. Knowledge and experience gained from
class presentations, computer workshops and workbook exercises will be
used to address questions on two take-home exams (mid-term and final).
Objectives:
1. Introduction to genetic markers including methods, visualizations,
interpretations and strengths and limitations.
2. Provide an intuitive grasp of relevant theory and analytical approaches
through lecture-style presentations, discussions, and primary journal
articles.
3. Obtain experience in using analytical methods to address ecological
and evolutionary questions through workbook exercises and takehome exams.
Grading:
Your grade in the course is determined by three components including
class participation, workbook exercises, and take-home exams. No
grading scale, simply those with the greatest number of accumulated
points will receive the highest grades. Graduate students should expect
additional problems for exercises, an additional workbook exercise, and
additional questions on take-home exams.
Exams: take-home (500 points each)
Mid-term
Final
Feb. 18
April 12
due March 22
due May 9 (10:30 am)
Workbook exercises: (10 exercises, 100 points each; Exercises need to
be handed in on the due date (first of the class meeting), as answers
to the exercise are often provided in the presentation.
1. Castle-Hardy-Weinberg Equilibrium
Part 1
Part 2
Part 3
2. Frequency Estimation and Genetic Variability
Part 1
Part 2
Part 3
due January 21
due January 28
due February 3
due February 1*-2
due February 9
due February 8*-9
Part 4
3. Relatedness and Parentage
4. Genetic Distance, F-statistics and
Indirect Estimation of Gene Flow
5. AMOVA
6. Population Assignment and Direct
Estimation of Gene Flow
7. Effective Population Size
8. Population History: Expansion, Equilibrium,
or Decline
9. Evolutionary History: Bottleneck or Selection
10. Intraspecific Phylogenetic and Phylogeography
due February 16
due March 1
due March 5
due March 22
due March 29
due April 5
due April 19
due April 26
due May 3
* Assignment will be due a the beginning of the Monday Computer
Workshop for students in that section
Class participation: (300 points)
Expect to be called on regularly to answer questions covered in assigned
readings and to have a short problem assigned at the close of class
meeting that will be due at the beginning of the next class meeting.
Text Books: Although there are now two relatively new text books in “Molecular
Ecology”, neither of these books provides the depth of coverage of most
topics that will be presented in this course. Both however, provide a
comprehensive introduction to the field and an overview of the topics
included.
BEEBEE, T., AND G. ROWE. 2008. An Introduction to Molecular Ecology.
Oxford University Press, New York, second edition, 400 pp.
FREELAND, J. R. 2005. Molecular Ecology. John Wiley and Sons, Ltd.,
West Sussex, England, 371 pp.
FREELAND, J. R., H. Kirk, and S. D. Petersen. 2011. Molecular Ecology.
John Wiley and Sons, Ltd., West Sussex, England, 484 pp.
The following represent a few additional books that might be helpful for
different topics covered in this course:
Population Genetics:
HARTL, D. L. 2000. A Primer of Population Genetics, 3rd edition, Sinauer
Associates, Sunderland, MA, 180 pp.
Molecular Evolution:
GRAUR, D., AND W.-H. LI. 2000. Fundamentals of Molecular Evolution.
Sinauer Associates, Sunderland, MA.
NEI, M., AND S. KUMAR. 2000. Molecular Evolution and Phylogenetics.
Oxfrord University Press, Oxford, 352 pp.
PAGE, R. D. M., AND E. C. HOLMES. 1998. Molecular Evolution: A
Phylogenetic Approach. Blackwell, Oxford.
Molecular Ecology:
AVISE, J. C. 1994. Molecular Markers, Natural History and Evolution.
Chapman and Hall, New York,
AVISE, J. C. 2000. Phylogeography: The History and Formation of
Species. Harvard University Press, Cambridge, MA.
AVISE, J. C., AND J. L. HAMRICK (eds.). 1996. Conservation Genetics: Case
Histories from Nature. Chapman and Hall, New York.
DESALLE, R., AND B. SCHIERWATER. 2003. Molecular Approaches to
Ecology and Evolution. Birkhauser, Boston, 364 pp.
FRANKHAM, R., J. D. BALLOU, AND D. A. BRISCOE. 2002. Introduction to
Conservation Genetics. Cambridge University Press, Cambridge.
HOELZEL, A. R. 2002. Molecular Genetic Analysis of Populations: A
Practical Approach. Oxford University Press, Oxford, 468 pp.
Lecture Schedule Molecular Ecology – Spring 2016
January 19
Introduction to Molecular Ecology, Review Basic Genetics,
and Castle-Hardy-Weinberg Equilibrium
January 21
Introduction to Population Genetics, Genotype and Allelic
Frequencies, Equilibrium Population Model, Review of
Castle-Hardy-Weinberg Equilibrium and Test of
Castle-Hardy-Weinberg Equilibrium, Exact Probability
January 26
Computer Packages for Testing CHW, Rejection of CHW,
and Introduction to Genetic Markers: Allelic Markers:
Allozymes and Microsatellites (STR)
January 28
Determination of Allele (Gene) and Genotypic Frequencies
and Introduction to Genetic Variation
February 2
Estimation of Genetic Variation, Genetic Markers:
Haplotypes: DNA Sequencing
February 4
Haplotypes: Selection of Genes, Sequence Alignment, and
Estimation of Haplotype Variation and Nucleotide
Diversity
February 9
Haplotype: RFLP and, Estimation of Haplotype Variation and
Nucleotide Diversity
February 11
Haplotype: Multilocus DNA Fingerprints, RAPDs, and
AFLPs, Estimation of Number Loci and Genetic
Variation, and Introduction to Maximum Likelihood
February 16
Maximum Likelihood, Linkage Equilibrium, and Introduction
to Relatedness
February 18
Relatedness Coefficients, Probability of Identity, Parentage
and Pedigree Analysis
February 23
Estimation to Genetic Similarity and Differentiation:
Multilocus Genotypic Data
February 25
Estimation of Genetic Distance (Haplotype Data) and
Introduction to F-statistics
March 1
Introduction to F-statistics
March 3
Indirect Estimation of Gene Flow, Historical and Current
Gene Flow Estimation,
March 15
Pitfalls of F- statistics and Other Approaches to Partitioning
Genetic Variation (AMOVA), Introduction to Bayesian
Analysis
March 17
Direct Estimation of Gene Flow: Population Assignment Test
and Detection of Migrants
March 22
Population Exclusion, Bayesian Clustering Methods:
Number of Populations
March 24
Introduction to Effective Population Size, Introduction to
Coalescent, Coalescent Methods
March 29
Effective Population Size, Estimation of Long-term and
Current Effective Population Size
March 31
Open
April 5
Estimation of Migration Rates and Coalescence Signatures
April 7
Population Size: Expanding, Stable or Declining, Mismatch
Distributions, Statistics Associated with Population
Expansion
April 12
Neutrality Test, Natural Selection, Adaptation and Neutral
Theory, Bottlenecks and Lineage Sorting
April 14
Evolutionary History: Inbreeding and Bottlenecks
April 19
Evolutionary History: Detection of Natural Selection
April 21
Landscape Genetics: Spatially Explicit Bayesian Clustering
Methods, SAMOVA & other approaches
April 26
Phylogeography: Intraspecific Phylogenies: Isolation by
Distance; Phenetic Methods: Neighbor-Joining Trees
Aprill 28
Phylogeography: Intraspecific Phylogenies: Minimal and
Median Spanning Networks and Maximum Parsimony
May 3
Phylogeography: Ecological Niche Modeling and Ecological
Genomics
Computer Workshop and Computer Programs
You will be expected to learn to use a lot of different computer programs in
this course, many of which are not particularly user friendly. These are not
programs that were developed for teaching labs but are the programs used by
researchers in the field of Molecular Ecology. To assist you with these computer
programs, a Computer Workshop will be held in the computer lab in room 001
Marsh Life Science to introduce you to these programs and assist you with
problems you may be encountering. Most of the programs we will be using are
“freeware” and you may download these programs on to your personal computer.
However, for the Computer Workshop you will need to use to computers in the
lab and have a 1 gigabyte or larger thumb drive on which I will be able to transfer
programs. You will need to have a thumb drive by the second computer
workshop (January 25 or 27). A few programs must be installed on computers
(will not run from a thumb drive), however, you may download may of these and
use them on your personal computer.
Computer Workshop Schedule:
Week 2
January 25-28
Excel, GenAlEx6 and GENEPOP
Week 3
February 1-3
GenAlEx6 and GENEPOP
Week 4
February 8-10
Clustal W, DnaSP, Arlequin (sequence data),
Mesquite
Week 5
February 15-17
Open
Week 6
February 22-24
GenAlEx6 (relatedness), GENEPOP, Cervus
Week 7
Feb. 29-March 2
GenAlEx6, GENEPOP, Arlequin, DnaSP
(FSTAT, GDA)
Week 9
March 14-16
GenAlEx6, Arlequin (AMOVA), GeneClass,
STRUCTURE
Week 10
March 21-23
GenAlEx6, GeneClass, STRUCTURE.
STRUCTURE HARVESTER,
Week 11
March 28-30
NeEstimator, ESTIM 1.2, MLNe,
TempoFs, Arlequin
Week 12
April 4-6
LAMARC, Arlequin, DnaSP, Kg test
Week 13
April 11-13
Arelequin, GenAlEx6, Bottleneck, BottleSim,
DetSel, DnaSP
Week 14
April 18-20
GenAlEx6, GENELAND, SAMOVA, Barrier
Week 15
April 25-27
MEGA, PHYLIP, PopART
Week 16
May 1-3
Open
Computer Programs: List of the PC programs that will likely be using during the
semester:
GenAlEx6 (ver 6.5) - http://biology-asset.anu.edu.au/GenAlEx/Download.html
GENEPOP (ver 4.5.1) - http://kimura.univ-msontp2.fr/~rousset/Genepop.htm
GENEPOP on the Web: http://genepop.curtin.edu.au/
DnaSP* (ver 5.0) - http://www.ub.edu/dnasp/DnaSP_OS.html
Clustal W - http://www.clustal.org/clustal2/
Mesquite – http://mesquiteproject.org
HP-RARE - http://www.montana.edu/kalinowski/Software/HPRare.htm
Cervus*(ver 3.0) - http://www.fieldgenetics.com/pages/aboutCervus_Using.jsp
GDA - http://hydrodictyon.eeb.uconn.edu/people/plewis/software.php
FSTATS (ver 2.9.3) - http://www2.unil.ch/popgen/softwares/fstat.htm
Arelequin (ver 3.5) –
http://CMPG.unige.ch/software/arlequin35/Arl35Downloads.html
WHICHRUN –
http:// bml.ucdavis.edu/research/research-programs/ecologyevolution conservation/salmon-research/salmon-genetics-software/
GeneClass (ver 2.0) –
http://www.montpellier.inra.fr/CBGP/software/GeneClass/index.html
STRUCTURE (ver 2.3.4) - http://pritchardlab.stanford.edu/structure.html
STRUCTURE HARVESTER – http://taylor0.biology.ucla.edu/structureHarvester/
LDNe - http://fish.washington.edu/xfer/LDNE/ replaced by NeEstimator –
http://www.molecularfisherieslaboratory.com.au/neestimator-software/
OneSAMP (online) - http://genomics.jun.alaska.edu/asp/Default.aspx [no longer
operating?]
Estim - ftp://isem.isem.univ-montp2.fr/pub/pc/estim [no longer available?]
MLNe – http://www.zsl.org/science/software/mine
TempoFs – http://folk.uio.no/ejorde/
LAMARC –
http://evolution.genetics.washington.edu/lamarc/lamarc-download.html
Kg Test - http://www.bioinformatics.org/kgtests/wiki/
Bottleneck - http://www.montpellier.inra.fr/CBGP/software/bottleneck/
Bottlesim – http://chkuo.name/software.html
DetSel - https://cran.r-project.org/web/packages/DetSel/index.html
GENELAND - http://cran.r-project.org/web/packages/Geneland/index.html
SAMOVA - http://cmpg.unibe.ch/software/samova/
Barrier (ver 2.2) – http://ecoanthropologie.mnhn.fr/software/barrier.html
PHYLIP - http://evolution.genetics.washington.edu/phylip.html
MEGA (ver 5 or 6) – http://www.megasoftware.net/mega.php
PopART – http://popart.otago.AC.NZ/downloads.shtml