Bio 263 - Molecular Ecology

263 Molecular Ecology
One-half unit course for one semester. A survey of how molecular genetic tools are used to investigate ecological processes in natural populations of plant and animal species. Specific topics will include methods for sudying genetic variation at the protein and DNA levels, quantitative predictions from ecological and evolutionary theory, and application of molecualr genetic markers to research questions related to natural selection, gene flow, genetic drift, and non-random mating. Conferences will be student led and based on the primary literature. Prerequisites: Biology 101/102. Lecture-conference.

COURSE STAFF
The course is taught by Keith Karoly.

Keith's Office: B240; ext. 7846
Keith's Office Hours: by appointment
Send email to: kkaroly@reed.edu

WEB LINKS

Moodle for Moelcular Ecology We will be test-driving the Moodle "course management" system that Reed is adopting.
(Access to these pages is only available to studnets registered in the course).

Library Resources This page was developed by Linda Maddux (Reed's Science Librarian) with information and links to the library's resources that will be useful when researching topics in Molecular Ecology.

E-Reserves A direct link to the library's page where you can log on to download e-reserves (.pdf format) of articles for this course. Logging on requires a password.

Molecular
Ecology A direct link to the Reed library's electronic holdings for the journal Molecular Ecology.

ISSR Resource
Web site This site is maintained by Dr. Andrea Wolfe at Ohio State Univ. and provides information about the technique as well as methods for data analysis.

HOMEWORK When needed, images required for the homeowrk will be posted here:

Question 2, week 3

Question 2, week 4 tobacco chloroplast genome. Hold down this link and choose "Save to disk".

POPBIO: You will find that the program you used in Bio101 to study questions in populaiton genetics and ecology will be a very useful tool in helping you to understand the ecological and evolutionary dynamics of the processes we are discussing in Molecular Ecology.

This software was developed in the Biology Department at Reed College under the guidance of Robert Kaplan. The software is available free for your use and can be downloaded from the Biology Department's software web page. Click here or on the POPBIO icon to the left to download a copy of PopBio.

COURSE SCHEDULE: (Fall 2006)

The class meetsare from 1:10 to 2:30 PM, Tu & Th, in B215

Conference will take place during a portion of each Thursdays class

Date	Lecture	Conference see below for reading	Reading: unless otherwise noted, reading from Beebee TC and G Rowe. 2004. An introduction to molecular ecology. Oxford University Press, NY. (two-hour reserve in the Reed Library)
Aug 29 Aug 31	scope of molecular ecology genetic markers	no conference	Preface, Chapters 1 & 2., Appendix 1. Beebe and Rowe (2004) An Introduction to Molecular Ecology. you may also wish to consult your Bio 101/102 text : Purves et al. (2004) Life: the science of biology, 7th ed.
Sept 5 Sept 7	genetic markers selection vs. neutrality	morphological markers
Sept 12 Sept 14	allozymes allozymes	allozyme markers	Parker, PA, AA Snow, MD Schug. GC Booton, and PA Fuerst. 1998. What molecules can tell us about populations: choosing and using a molecular marker. Ecology 79: 361-382.
Sept 19 Sept 21	DNA-based markers DNA-based markers	comparing allozymes and DNA markers
Sept 26 Sept 28	DNA-based markers problems with DNA-based markers	problems with DNA-based markers
Oct 3 Oct 5	measuring identitiy measuring identitiy	Identity & paternity	Chapters 3 ., Appendix 2 . Beebe and Rowe (2004) An Introduction to Molecular Ecology.
Oct 10 Oct 12	mating systems & relatedness inbreeding coefficients	genetic variation & population structure
Oct 17 Oct 19	FALL BREAK
Oct 24 Oct 26	population structure population structure	inbreeding coefficients
Oct 31 Nov 2	migration rates migration rates	population structure and migration
Nov 7 Nov 9	phylogoegraphy phylogeography	phylogoegraphy
Nov 14 Nov 16	population size & genetic variation population size & genetic variation	genetic drift in natural populations
Nov 21 Nov 23	molecular genetics and adapatation NO CLASS (Thanksgiving)	NO CLASS (Thanksgiving)
Nov 28 Nov 30	Special Topics: TBA (Michael & Noah) Special Topic: TBA (Maggie & Ryan)	special topics
Dec 5	research proposals
Dec 13	FINAL EXAM (1 PM - 4 PM)

CONFERENCE SCHEDULE: (Fall 2006)

Conference will during our Thursday class (1:10 to 2:30 PM inB215)

You can download the boiler-plate for analyzing a paper by clicking on this link and choosing "SAVE TO DISK". The downloaded file will be an MS-Word document.

Date	Topic	Reading
Sept 7	morphological markers	Burlingame (1921) Variation and heredity in Lupinus. American Naturlaist 60: 427-448. Harding (1970) Genetics of Lupinus. II. the selective disadvantage of the pink flower color mutant in Lupinus nanus. Evolution 24:120-127.
Sept 14	allozyme markers	Hubby, JL, and RC Lewontin. 1966. A molecular approach to the study of genic heterozygosity in natural populations. I. The number of alleles at different loci in Drosophila pseudoobscura. Genetics 54: 577-594. Lewontin, RC. 1991. Twenty-Five Years Ago in GENETICS: Electrophoresis in the development of evolutionary genetics: milestone or millstone? Genetics 128: 657-662.
Sept 21	comparing allozymes and DNA markers	Esselman, EJ, L Jianqiang, DJ Crawford, JL Winduss, & AD Wolfe (1999) Clonal diversity in the rare Calamagrostis porteri ssp. insperata (Poaceae): comparative results for allozymes and random amplified polymorphic DNA (RAPD) and inter simple sequence repeat (ISSR) markers. Molecular Ecology 8: 443-451
Sept 28	problems with DNA-based markers	Saar, DE, NO Polans, PD Sorensen, and MR Duvall. 2001. Angiosperm DNA contamination by endophytic fungi: detection and methods of avoidance. Plant Molecular Biology Reporter 19(3) 249-260.
Oct 5	identity & paternity	Constable, JL, MV Ashley, J Goodall, & AE Pusey. 2001. Noninvasive paternity assignment in Gombe chimpanzees. Molecular Ecology 10: 1279-1300.
Oct 12	genetic variation & population structure	Stenström, A, BO Jonsson, IS Jónsdóttir, T Fagerström, & A Magnus. 2001. Genetic variation and clonal diversity in four clonal sedges (Carex) along the Arctic coast of Eurasia. Molecular Ecology 10(2): 497-513.
Oct 26	mating system	Schmidt-Adam, Young, & Murra (2000) Low outcrossing rates and shift in pollinators in New Zealand pohutukawa (Metrosideros excelsa; Myrtaceae). Am. J. Bot. 87: 1265-1271.
Nov 2	Library Resources	[theis week: library resources with Linda Maddux]
Nov 9	phylogoegraphy	Ehrich, D, VB Fedorov, NC Stenseth, CJ Krebs & A Kenney. 2000. Phylogeography and mitochondrial DNA (mtDNA) diversity in North American collared lemmings (Dicrostonyx groenlandicus). Molecular Ecology 9: 329-337.
Nov 16	Drift in natural populations	Waldick RC, Kraus SS, Brown M, and N White. 2002. Evaluating the effects of historic bottleneck events: an assessment of microsatellite variability in the endangered, North Atlantic right whale. Molecular Ecology 11 (11): 2241-2250.
Nov 23	NO CLASS (Thanksgiving)
Nov 28	Noah & Micahel	(Michael) Ernest, HB, MCT Penedo, BP May, M Syvanen & WM Boyce. 2000. Molecular tracking of mountain lions in the Yosemite Valley region in California: genetic analysis using microsatellites and faecal DNA. Molecular Ecology 9: 433-441. (Noah) Reichman , JR, LS Watrud , EH Lee, CA Burdick, MA Bollman, MJ Storm, GA King, & C Mallory-Smith. 2006. Establishment of transgenic herbicide-resistant creeping bentgrass (Agrostis stolonifera L.) in nonagronomic habitats. Molecular Ecology 15 (13): 4243-4256.
Nov 30	Maggie & Ryan	(Ryan) Hoglund, J, & L Shorey. 2003. Local genetic structure in a white-bearded manakin population. Molecular Ecology 12 (9): 2457-2463. (Maggie) Dearborn, DC, AD Anders, EA Schreiber, RMM Adams & UG Mueller. 2003. Inter-island movements and population differentiation in a pelagic seabird. . Molecular Ecology 12 (10): 2835-2843.

Maintained by the Reed College Biology Department
Last Modified 8/29/06
Questions/Comments to Keith.Karoly@directory.reed.edu

Moodle for Moelcular Ecology	We will be test-driving the Moodle "course management" system that Reed is adopting. (Access to these pages is only available to studnets registered in the course).
Library Resources	This page was developed by Linda Maddux (Reed's Science Librarian) with information and links to the library's resources that will be useful when researching topics in Molecular Ecology.
E-Reserves	A direct link to the library's page where you can log on to download e-reserves (.pdf format) of articles for this course. Logging on requires a password.
Molecular Ecology	A direct link to the Reed library's electronic holdings for the journal Molecular Ecology.
ISSR Resource Web site	This site is maintained by Dr. Andrea Wolfe at Ohio State Univ. and provides information about the technique as well as methods for data analysis.
HOMEWORK	When needed, images required for the homeowrk will be posted here: Question 2, week 3 Question 2, week 4 tobacco chloroplast genome. Hold down this link and choose "Save to disk".
	POPBIO: You will find that the program you used in Bio101 to study questions in populaiton genetics and ecology will be a very useful tool in helping you to understand the ecological and evolutionary dynamics of the processes we are discussing in Molecular Ecology. This software was developed in the Biology Department at Reed College under the guidance of Robert Kaplan. The software is available free for your use and can be downloaded from the Biology Department's software web page. Click here or on the POPBIO icon to the left to download a copy of PopBio.