FISH/BIOL 340 - Genetics and Molecular Ecology

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Course Description

Syllabus

Grading

Labs

Lab Project

Reading

Glossary of Terms

Links

Reading

Textbooks

The recommended textbook for this class is Russel (2003) Essential iGenetics (see below). If you have a genetics textbook or an extensive introductory text already, you may not need it, but it is highly recommended. I will provide page numbers for relevant reading in this book at the end of each lecture.

Russel P.J. (2003) Essential iGenetics. Benjamin Cummings (Pearson Education Inc.), San Francisco. ISBN: 0-8053-4697-X Excellent book on basic genetics and genetic analysis, with lots of very nice illustrations (you have seen some of them in my slides). Don't confuse this with other books in the iGenetics series. We are trying to get this ordered in the UW Bookstore, but you can also buy online from Amazon, Barnes&Noble and textbooks.com - note that if you buy this book second-hand, you won't have access to online material (e.g. animations). However, this is not absolutely necessary.

For background reading, I have put several books on reserve in the Odegaard Undergraduate Library. You can look up any terms you don't understand in these books, and read about more about the lecture material. These books are:

Beebee T & Rowe G (2007) Introduction to Molecular Ecology. Second Edition. Oxford University Press.

This is an excellent book, concentrating (as the title suggests) on the Molecular Ecology rather than basic genetics. This book covers much of what we talk about in class. It's relatively cheap ($ 42.75 oin Amazon) so it may be worth the investment. I'll probably use this one as the required textbook in years to come.

Hallerman E.M. (ed) (2003) Population Genetics: Principles and Applications for Fisheries Scientists. American Fisheries Society, Bethesda, Maryland.

Good book on population genetics. Some of the chapters are in the required readings. Available online from the American Fisheries Society, and relatively cheap if you are a member.

Freeman S & Herron JC (2004) Evolutionary Analysis. Prentice Hall.

A very good book to read up about the background of specific topics. Both authors are lecturers in the Department of Biology - this book is required text for their courses. If you are interested in evolutionary research, this is definitely the book to buy, and it also covers a lot of the class materials.

Required Readings

Book Chapters

Hallerman et al (2003) An Overview of Classical and Molecular Genetics.

Chapter from Hallerman, E.M. (ed) Population Genetics: Principles and Applications for Fisheries Scientists. American Fisheries Society, Bethesda, USA. - (Large file ~2MB). A good overview of Mendelian inheritance, the Hardy-Weinberg law and basic molecular biology.

Russel P.J. (2002) Population Genetics.

Chapter from the book below (iGenetics), providing a brief but exhaustive overview of population genetics. Big file (12MB).

Russel P.J. (2002) Molecular Evolution.

Chapter from the book below (iGenetics), providing a brief overview of some aspects of phylogenetic reconstruction. Big file (5MB).

Hauser L (2007) The Molecular Ecology of Dogfish Sharks

Recent review I wrote on the genetics of sharks in general and dogfish in particular. I won't ask anything specifically about this paper in the exam, but it describes some of the concepts we discussed in lecture and may therefore be useful reading material for exam preparation. It covers almost everything from phylogenetics to population genetics to parentage analysis, to an outlook on new genomic techniques

 

Labs

There are a few important papers for the lab:

Li ZZ, Gray AK, Love MS, Goto A, Asahida T, Gharrett AJ (2006) A key to selected rockfishes (Sebastes spp.) based on mitochondrial DNA restriction fragment analysis. Fishery Bulletin 104, 182-196.

Marko PB, Lee SC, Rice AM, et al. (2004) Mislabelling of a depleted reef fish. Nature 430, 309-310.

Trotta M, Schonhuth S, Pepe T, et al. (2005) Multiplex PCR method for use in real-time PCR for identification of fish fillets from grouper (Epinephelus and Mycteroperca species) and common substitute species. Journal Of Agricultural And Food Chemistry 53, 2039-2045.

 

Teletchea F, Maudet C, Hanni C (2005) Food and forensic molecular identification: update and challenges. Trends in Biotechnology 23, 359.

 

Woolfe M, Primrose S (2004) Food forensics: using DNA technology to combat misdescription and fraud. Trends in Biotechnology 22, 222.

Suggested Readings

Weekly scientific papers

For each week, we will provide a brief scientific paper, which is suggested reading to show you the applications of different methods (see Syllabus). The content of these papers is not on the exam per se, but I may use them as examples for material covered in lecture.

Week 1

Shivji MS, Chapman DD, Pikitch EK, Raymond PW (2005) Genetic profiling reveals illegal international trade in fins of the great white shark, Carcharodon carcharias. Conservation Genetics 6, 1035-1039. ( National Geographic Article on the paper).

Week 3

Russell AF, Hatchwell BJ (2001) Experimental evidence for kin-biased helping in a cooperatively breeding vertebrate. Proceedings Of The Royal Society Of London Series B-Biological Sciences 268, 2169-2174.

Week 4

Hoarau G, Boon E, Jongma DN, Ferber S, Palsson J, Van der Veer HW, Rijnsdorp AD, Stam WT, Olsen JL (2005) Low effective population size and evidence for inbreeding in an overexploited flatfish, plaice (Pleuronectes platessa L.). Proceedings Of The Royal Society B-Biological Sciences 272, 497-503.

Week 5

Zerjal T, Xue YL, Bertorelle G, Wells RS, Bao WD, Zhu SL, Qamar R, Ayub Q, Mohyuddin A, Fu SB, Li P, Yuldasheva N, Ruzibakiev R, Xu JJ, Shu QF, Du RF, Yang HM, Hurles ME, Robinson E, Gerelsaikhan T, Dashnyam B, Mehdi SQ, Tyler-Smith C (2003) The genetic legacy of the mongols. American Journal Of Human Genetics 72, 717-721.

Week 6

Seielstad MT, Minch E, Cavalli-Sforza LL (1998) Genetic evidence for a higher female migration rate in humans. Nature Genetics 20, 278-280.
Oota H, Settheetham-Ishida W, Tiwawech D, Ishida T, Stoneking M (2001) Human mtDNA and Y-chromosome variation is correlated with matrilocal versus patrilocal residence. Nature Genetics 29, 20-21.

Week 7

Shaw KL (2002) Conflict between nuclear and mitochondrial DNA phylogenies of a recent species radiation: What mtDNA reveals and conceals about modes of speciation in Hawaiian crickets. Proceedings Of The National Academy Of Sciences Of The United States Of America 99, 16122-16127.

Week 8

Devlin RH, D'Andrade M, Uh M, Biagi CA (2004) Population effects of growth hormone transgenic coho salmon depend on food availability and genotype by environment interactions. Proceedings Of The National Academy Of Sciences Of The United States Of America 101, 9303-9308.

Week 9

Boutet I, Meistertzheim AL, Tanguy A, Thebault MT, Moraga D (2005) Molecular characterization and expression of the gene encoding aspartate aminotransferase from the Pacific oyster Crassostrea gigas exposed to environmental stressors. Comparative Biochemistry And Physiology C-Toxicology & Pharmacology 140, 69-78.

Week 10

Walsh MR, Munch SB, Chiba S, Conover DO (2006) Maladaptive changes in multiple traits caused by fishing: impediments to population recovery. Ecology Letters 9, 142-148.

Another good source of information is Google and Google Scholar - it is amazing what you can find on the internet. However, be careful what you believe - generally, you should only trust academic (i.e. University, Colleges, Institutes) or peer-reviewed (e.g. journals) sites.