Evolutionary Analysis
An examination of the mechanisms of evolution at single and multiple loci, including natural selection, genetic drift, and inbreeding. Reconstruction of the evolutionary history of both organisms and genes. Applications to human health and conservation biology. Optional fourth credit hour for laboratory includes an independent research component.

To do well in this course you will need to:

• Read before class. If you are pinched for time, at least look at the subject headings and any figures so that you will be prepared for lecture and discussion.
• Bring to class three typed questions inspired by the readings. These could be questions of clarification or interpretation, or ideas about how the approach could be extended. It will be best if your questions inspire discussion. Try to avoid questions that you could have easily answered, for example, by looking up a definition. It is ok to use scrap paper to print out your questions.
• Make sure to come see me if you are having difficulty. Population genetics and molecular evolution are challenging topics.

Back to the top of the page

---

SCHEDULE AT A GLANCE: Spring 2007

To see the assigment for a particular week,  click on the topic name.
Week	Topics
1	Definition and historical context
2	Mutation and Variation, Hardy-Weinberg equilibrium
3	Selection -- model and examples
4	Mutation-selection balance and migration
5	Inbreeding
6	Genetic drift
7	Neutral theory, and why sex?
8	Quantitative genetics
9	Speciation
10	Phylogeny reconstruction
11	Development and the fossil record
12	Human evolution
13	Special topics




Back to the top of the page





---

READING ASSIGNMENTS: Spring 2007

Date	Topic	Reading
Feb 6-8	Definition  Historical context	For historical background, read excerpt from Futuyma, on e-reserve   Quantitative trait distribution generated by alleles segregating at two loci example
Feb 13-15	Variation HW equil	For Tuesday, Mutation: 3rd edition text pages 109-114, 118-127; 4th edition text pages 146-147, 150-160   For Thursday, Variation in natural populations: 3rd edition text pp. 127-137. Note typo on page 129 (should say 52 + 16, not 52 * 16) 4th edition text pp. 160-166.
Feb 20-22	Selection	For Tuesday, read Evans et al. (2006) PNAS 103:18178-18183. I will send an email with instructions for discussion.   For Thursday, you don't have to bring 3 questions, but you have a problem set due. For support from the text, see pp. 152-165 (3rd edition, not box 5.5), or pp. 180-193 (4th edition, not box 6.5).   To do the 2nd part of the homework (now due Feb 27), you will need to download the software program Allele A1, which you can get from Jon Herron's website.   You will also need to download Tutorial 1 on Selection and Migration from the same website. There are some typos in the tutorial. For problem 2c, the Figure you want is 5.13, page 158 (3rd ed.) or 6.13, page 185 (4th ed). Also, the Y axis has been changed. You need to be aware that you are monitoring the increase in AdhF, rather than a decrease in AdhS, as the example states. Begin with a frequency of 0.35, and aim for a final frequency of about 0.95 after 50 generations. Please email me by Monday afternoon if this isn't clear.
Feb 27-Mar 1	Overdominance or heterozygote advantage Mutation-selection balance Migration	For Tuesday, hand in results from Allele A1 simulation on Adh (see above). Also calculate change in allele frequency and genotype frequency following one generation of eugenic sterilization (as we discussed in class.)   If you want support from the text for selection and dominance, see the figures and discussion in Box 5.7 (3rd ed.) or Box 6.7 (4th ed.).   Text to support mutation-selection balance can be found on pp. 185-191 (3rd ed.) and 213-218 (4th ed.). Text to support migration can be found on pp. 197-202 (3rd ed.) and 225-231 (4th ed.). You don't need to bring three questions to class for Thursday.
March 6-8	Inbreeding	For March 6, bring problem set #2, and questions from the inbreeding section of your text (pp. 236-245, 3rd edition (not box 6.6), pp. 264-272, 4th edition (not box 7.6)). March 6-13, genetic drift, covered on pp. 204-208, 210-217, and 221-223 of the 3rd edition, and 232-235, 238-245, and 249-251 of the 4th edition. March 8, population structure, especially Wright's F-statistics, which are not covered by your textbook. Make sure to get notes and the handout.
March 13-15	Genetic drift	March 13 discussion led by Cadran Cowansage, Jamie Enos, Stephanie Freese, Andrew Kwak, on: Backus, V. L., E. H. Bryant, C. R. Hughes, and L. M. Meffert. 1995. Effect of migration or inbreeding followed by selection on low-founder-number populations: implications for captive breeding programs. Conservation Biology 9(5): 1216-1224. March 15 First Exam
Mar 20-22	Neutral Theory Maintenance of Sex	March 20, neutral theory and molecular evidence for selection, see pp. 224-232 (3rd ed.), 251-260 (4th ed.) March 22 discussion led by Adrienne Angel, Eric Bergh, Alaina Clark, Richard Katz, Heather Nickerson, on: Corley, L. S., and A. J. Moore. 1999. Fitness of alternative modes of reproduction: developmental constraints and the evolutionary maintenance of sex. Proc. R. Soc. Lond. B 266: 471-476. For background on maintenance of sex, see pp 275-284 (3rd ed.), 303-312 (4th ed.)
April 3-5	Quantitative Genetics	April 3, genetic basis quantitative traits, and heritability. Find the Quantitative Genetics 1 reading on e-reserve. Read pp. 97-103, 111-115, and 131-133, and skim the rest. Please bring 3 questions to class on the required sections. April 5, QTL mapping, and selection on quantitative traits. For background, see pp. 317-319 and 294-299 (3rd ed) or pp. 347-349 and 325-328 (4th ed). You do not need to bring questions to class on this new material, but please review your notes and see if you have questions to ask at the beginning of class on the material we discussed Tuesday.
April 10	Speciation	Read and bring questions on: Schemske, D. W., and H. D. Bradshaw, Jr. 1999. Pollinator preference and the evolution of floral traits in monkeyflowers (Mimulus). Proc. Natl. Acad. Sci. (USA) 96:11910-11915.
April 17-19	Speciation Phylogeny reconstruction	April 17 discussion led by Lauren Bizzari, Charlotte Carrigan, Julia Germaine, Sean Prockter, Talia Savic, on: Roca, et al. 2001. Genetic evidence for two species of elephant in Africa. Science 293: 1473-1477. and Eggert, et al. 2002. The evolution and pylogeography of the African elephant inferred from mitochondrial DNA sequence and nuclear microsatellite markers. Proceedings of the Royal Society of London B 1993-2006. April 19 -- Don't read ahead, but later review speciation as necessary, Ch 15 (3rd ed.); Ch 16 (4th ed.). Also, don't read ahead, but later review phylogeny reconstruction as necessary, Ch. 14 (3rd ed.); Ch 4 (4th ed.). No work to hand in for April 19.
April 24-26	Phylogeny, cont. Second exam	April 24, Problem set 4 on phylogeny due in class. April 26, exam covers neutral theory/molecular evidence for selection, advantages/disadvantages of sex, quantitative genetics, speciation, and phylogeny reconstruction.
May 1-3	Development Fossil record	May 1, Bring questions and come prepared to discuss assigned reading: Knoll, A. H., and S. B. Carroll. 1999. Early animal evolution: Emerging views from comparative biology and geology. Science 284: 2129-2137. May 1, Review evo-devo as necessary, Ch 18 (3rd ed), Ch 19 (4th ed). May 3 discussion led by Leigh Audin, Annie Feutz, Carrie Lovejoy, Kristine Robin, on: Fondon, J. W. III, and H. R. Garner. 2004. Molecular origins of rapid and continuous morphological evolution. PNAS 101: 18058-18063.
May 8-10	Human evolution	May 8-10, review as necessary, Ch 19 (3rd ed.), Ch 20 (4th ed.) May 8 discussion led by Rachel Baird, Margaret Chute, Kim Cohen, Andrew Cox, Kathleen Nicholson, on: Stanford, C. B. 2006. Arboreal bipedalism in wild chimpanzees: implications for the evolution of hominid posture and locomotion. American Journal of Physical Anthropology 129:225-231. May 10 discussion led by Will Cantley, Sarah Clark, Derek Lederer, Liz Petit, on: Nesse "How is Darwinian medicine useful?" West J Med 2001 174:358-360 and MacCallum "Does Medicine without Evolution Make Sense?" PLoS Biology 2007 5(4):679-680   Powerpoint slides addressing geographic structure of human populations. (Shown in class.)

Back to the top of the page






---

LABORATORY SCHEDULE

Molecular and Quantitative Approaches to Orchid Conservation Genetics
Date	Lab	Work
Feb 6, 8	1	Expectations  Objectives and Schedule  DNA extraction  FYI, Do not print out.
Feb 13, 15	2	Overview of AFLP process  Digest and ligate DNA  On-line AFLP protocol  Manufacturer's AFLP protocol Do not print out.
Feb 20, 22	3	Preselective amplification for AFLP
Feb 27, Mar 1	4	Run out gel.   Selective amplification for AFLP
Mar 6, 8	5	Amplify microsatellites  Overview of microsatellites
Mar 13, 15	6	Run gels to look at microsatellite pcrs and look at AFLPs
Mar 20, 22	7	Re-try microsatellite pcr using positive control from Isotria medeoloides
Apr 3, 5	8	Run out microsatellite gel, and look at FAM AFLP results.  Familiarize yourself with GenAlEx. You can download the Molecular Ecology Notes overview from the GenAlEx website.  Play with this sample data file.  Review results from Isotria medeoloides AFLP data.
Apr 10, 12	9	Analyze microsat and/or AFLP data.  Re-do PCRs if warranted.  (Stone in DC)
Apr 17, 19	10	Obtain quantitative data on orchid phenotypes at the herbarium in Orono. (Lab will run late.)
Apr 24, 26	11	Analyze data.  Prepare presentations.  Download excel spreadsheets for Calopogon tuberosus, Corallorhiza maculata, Cypripedium acaule, Goodyera tesselata, Platanthera clavellata, P. hyperborea, P. psychodes, Pogonia ophioglossoides.  Download significance testing results for morphological variation among Maine populations.  Download the original spreadsheet giving names of counties and towns for each species. (Note that we substituted Goodyera tesselata for Goodyera repens, because we couldn't find the latter.)  Download box plots for traits that significantly differed among populations.   If you are preparing a poster on the morphological data, please feel free to email me with questions. The remainder of the species will be posted after the Thursday class enters their share of the data.
May 2, 4	12	Share posters with class. Talk about orchid morphological data.



Back to the top of the page