Bio 503 - Marine Molecular Ecology
Fall Semester 2007. 9 - 12 AM and 2 - 5 PM Wednesdays

This semseter-long course will introduce you to genetic tools - which ones are available, practical and useful for particular questions - and how these genetic analyses have been applied to a wide variety of ecological topics. We will focus on marine organiams and issues of dispersal, life histories, recruitment, habitat and mate choice, natural selection, the conservation of biodiversity, and speciation

INSTRUCTOR: Dr. Erik Sotka

OFFICE: 208 Grice Marine Laboratory

Syllabus & Schedule

Materials

-----------------------------------------------

SOFTWARE LINKS - freeware or shareware

Sequence traces - single
- 4Peaks MAC
- Chromas Lite PC
- FinchTV PC & MAC

Sequence traces - multiple alignment
- VectorNTI PC & MAC

Alignment
- BAli---Phy PC & MAC
- BioEdit (can also manipulate traces) PC
- ClustalX PC & MAC
- MaxAlign web-based
- Mesquite Project PC & MAC
- Se-Al MAC

Model of Evolution
- ModelTest-requires PAUP PC & MAC
- ModelTest Server (summarizes likelihood scores) web-based
- ModelTest-does NOT require PAUP PC & MAC
- ProtTest PC & MAC

Tree building / visualization
- FigTree PC & MAC
- HyPhy PC & MAC
- MEGA PC
- MrBayes PC & MAC
- PhyML PC & MAC & web-based
- PHYLIP PC & MAC
- TreeView PC & MAC
- TREE-PUZZLE -ML search PC & MAC
- Felsenstein's compilation of Phylogeny programs web-based

Population genetics / Statistics
- Arlequin 3.0 PC
- DnaSP PC
- GenePop web-based & PC
- GenAlEx MS Excel toolkit
- MEGA PC
- List of pop gen software PC

Genomics software
- Artemis PC & MAC
- eBiotools MAC

Miscellaneous
- Get unique haplotypes? COLLAPSE PC & Mac
- Calculate dN/dS? SNAP web-based
- PAST - PAleontological STatistics PC
- Formatting changes (NEXUS to FASTA, etc...)? web-based
- Formatting changes (usat data to 52 programs)? CREATE PC
- Sequence Manipulation Suite web-based
- NCBI Entrez web-based
- Int'l Genomics Consortium web-based
- Create new primers ? Primer3 web-based
- Create new primers from multiple alignment ? Primaclade web-based


Home


Discussion Articles

Week 1 :
Alter et al. (2007) DNA evidence for historic population size and past ecosystem impacts of gray whales Science 104:15162-15167


Week 2 :
Rose, Paynter and Hare (2006) Isolation by Distance in the Eastern Oyster Crassostrea virginica in Chesapeake Bay. Journal of Heredity 97:158-170
OPTIONAL readings Hellberg (2007) Footprints on water: the genetic wake of dispersal among reefs. Coral Reefs 26:463-473


Week 3 :
Portnoy et al. (2007) Genetic polyandry and sexual conflict in the sandbar shark, Carcharhinus plumbeus ,in the western North Atlantic and Gulf of Mexico Molecular Ecology 187-197


Week 4 (two required articles):
Levitan and Ferrell (2006) Selection on Gamete Recognition Proteins Depends on Sex, Density, and Genotype Frequency Science 267-269
Palumbi (1999) All males are not created equal: fertility differences depend on gamete recognition polymorphisms in sea urchins PNAS 96:12632-12637


Week 5 :
Quesada et al. (2007) Phylogenetic evidence for multiple sympatric ecological diversification in a marine snail Evolution 61:1600-1612


Week 6 (two required articles) :
Whitehead and Crawford (2006) Neutral and adaptive variation in gene expression PNAS 103: 5425-5430
Kammenga et al. (2007) Microarray challenges in ecology Trends in Ecology and Evolution 22:273-279


Week 7 :
Fallon (2007) Genetic data and the listing of species under the Endangered Species Act Conservation Biology 21:1186-1195