BISC 534 Advanced Seminar in Population Genetics of Marine Organisms

Fall Semester 2007

Course Overview: This seminar will explore mostly recent, primary scientific literature, bearing on broad themes in marine population genetics: the maintenance of genetic diversity, speciation, temporal variation, and hybridization. Assigned weekly readings comprise experimental or review papers, encompassing the history of at least one theme. Students are expected to participate vigorously in discussion.

Each student will be required to lead discussion of at least one set of weekly readings. The student presentation will be based on outside readings, to be assigned in consultation with the instructors, and should describe the state of the field prior to the work read; the questions addressed by the authors; their methods, data, and conclusions; a critique of the strengths and weaknesses of the work; what questions remain; and how these could be addressed.

By the week of October 15^th, students will identify a paper published within the previous year, about which they will write a detailed critique (three pages, single-spaced). A rough draft of the critique will be due the week of November 19 (Thanksgiving holiday week), with the final draft due at the last class.

Instructors: Suzanne Edmands, AHF 314, 0-5548, sedmands@usc.edu

Dennis Hedgecock, AHF 130, 1-2091, dhedge@usc.edu

Recommended Reference: Hedrick, P.W. 2006. Genetics of Populations, 3^rd edition. Jones and Bartlett, Sudbury Mass.

Grading: Letter grading

Location: AHF Conference Room

Students with Disabilities: Any student requesting academic accommodations based on a disability is required to register with the Office of Disability Services and Programs (DSP) each semester. A letter of verification for approved accommodations can be obtained from DSP. Be sure that the letter is delivered to the laboratory director as early in the semester as possible. DSP is located in STU 301 and is open 8:30-5:00, Monday through Friday. The telephone number for DSP is 213-740-0776.

Maintenance of Genetic Variation

Week 1: The evidence for balancing selection in heterogeneous environments

Hedrick, PW. 2006. Genetic polymorphism in heterogeneous environments: The age of genomics. Annual Review of Ecology Evolution and Systematics 37: 67-93. (updates earlier reviews of this topic in 1975 and 1986 and examines the evidence that balancing selection maintains diversity in natural populations)

Week 2: Labor Day

Week 3: Inferring Selection from the distribution of Fst

Lewontin, RC & J Krakauer. 1973. Distribution of gene frequency as a test of theory of selective neutrality of polymorphisms. Genetics 74: 175-195. (a highly cited paper whose core idea was devastatingly criticized in 1975 [see below] but has found new life in genome-wide association studies)

Nei, M & Maruyama, T. 1975. Lewontin-Krakauer Test for Neutral Genes – Comment. Genetics 80: 95-395.

Robertson, A. 1975. Lewontin-Krakauer Test For Neutral Genes – Comment. Genetics 80: 396-396.

Lewontin RC & J Krakauer. 1975. Testing Heterogeneity of F-values. Genetics 80: 397-398.

Week 4: Inferring Selection from the distribution of Fst – a marine and a Drosophila example

Karl, SA, & Avise, JC. 1992. Balancing selection at allozyme loci in oysters - implications from nuclear RFLPS. Science 256: 100-102. (an application of the L-K reasoning to oysters)

Taylor, MFJ, Shen, Y. & Kreitman, ME. 1995. A population genetic test of selection at the molecular-level. Science 270: :1497-1499. (positive evidence for the L-K reasoning)

Week 5: Inferring Selection from the distribution of Fst – Atlantic cod

Pogson, GH, Mesa, KA, & Boutilier, RG. 1995. Genetic population-structure and gene flow in the Atlantic cod Gadus morhua - a comparison of allozyme and nuclear RFLP loci. Genetics 139: 375-385. (another application of the L-K reasoning, this time to cod)

Nielsen, EE, Hansen, MM, & Meldrup, D. 2006. Evidence of microsatellite hitch-hiking selection in Atlantic cod (Gadus morhua L.): implications for inferring population structure in nonmodel organisms. Molecular Ecology 15: 3219-3229. (a more directed application of the L-K reasoning to cod)

Week 6: Inferring Selection from the distribution of Fst – Littorina

Johannesson, K., Johannesson, B, & Lundgren, U. 1995. Strong natural-selection causes microscale allozyme variation in a marine snail. Proceedings of the National Academy of Sciences of the United States of America 92: 2602-2606. (application of the L-K reasoning to intertidal snails)

Andrade SCS, & Solferini VN. 2007. Fine-scale genetic structure overrides macro-scale structure in a marine snail: nonrandom recruitment, demographic events or selection? Biological Journal of the Linnean Society 91: 23-36. (alternatives to selection in the case of intertidal snails)

Week 7: Lewontin & Krakauer revisited

Baer, CF. 1999. Among-locus variation in F_ST: Fish, allozymes and the Lewontin-Krakauer test revisited. Genetics 152: 653-659. (a meta-analysis of inter-locus variation in F_ST in fish)

Beaumont, MA. 2005. Adaptation and speciation: what can F_ST tell us? Trends in Ecology & Evolution 20: 435-440. (a thoughtful review of inter-locus variation in F_ST and methods for inferring selection)

Storz, JF. 2005. Using genome scans of DNA polymorphism to infer adaptive population divergence. Molecular Ecology 14: 671-688. (a definitive look at the power of whole genome scans)

Marine Speciation

Week 8: Genetic basis of postzygotic isolation

Coyne JA & HA Orr. 2004. The genetics of postzygotic isolation. Pp. 283-320 in JA Coyne & HA Orr, Speciation, Sinauer Associates, Sunderland, Mass. (how nearly everything we know about the genetics of postzygotic isolation concerns sex chromosomes and therefore does not apply to vast numbers of marine taxa)

Pennisi E. 2006. Two rapidly evolving genes spell trouble for hybrids. Science 314:1238-1239. (reviews candidate Dobzhansky-Muller incompatibilities – nearly all X-autosome conflicts with the exception of a nuc-mt conflict in Tigiropus)

Week 9: Speciation in marine microbes

Staley JT. 2006. The bacterial species dilemma and the genomic-phylogenetic species concept. Phil. Trans. R. Soc. B. 361:1899-1909. (bacterial speciation processes and species definitions)

Palenik B et al. 2007. The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation. PNAS 104(18):7705-7710. (role of local adaptation and horizontal gene transfer in species divergence)

Week 10: Prezygotic isolation and the role of gamete recognition in broadcast spawners

Levitan DR & DL Ferrell. 2006. Selection on gamete recognition proteins depends on sex, density, and genotype frequency. Science 312:267-269. (bindin in Strongylocentrotus)

Springer SA & BJ Crespi. 2007. Adaptive gamete-recognition divergence in a hybridizing Mytilus population. Evolution 61(4):772-783. (adaptive divergence of lysin – a possible case of reinforcement)

Temporal variation

Week 11: Temporal variation, genetic patchiness, and cohort analysis

Selkoe, KA, Gaines SD, Caselle, JE & Warner, RR. 2006. Current shifts and kin aggregation explain genetic patchiness in fish recruits. Ecology 87: 3082-3094. (the title says it all)

Gonzalez-Wanguemert, N, Perez-Ruza, FA-A, Canovas, F, Garcia-Charton, JA & Marcos, C. 2007. Temporal genetic variation in populations of Diplodus sargus from the SW Mediterranean Sea. Marine Ecology-Progress Series 334: 237-244. (not a highly fecund fish, yet…)

Week 12: Temporal variation and cohort analysis

Hedgecock D, Launey S, Pudovkin AI, Naciri, Y, Lapegue, S & Bonhomme, F. 2007. Small effective number of parents (N_b) inferred for a naturally spawned cohort of juvenile European flat oysters Ostrea edulis. Marine Biology 150: 1173-1182. (a surprise in Sophie’s Ph.D.)

Burford, MO & Larson, RJ. 2007. Genetic heterogeneity in a single year-class from a panmictic population of adult blue rockfish (Sebastes mystinus). Marine Biology 151: 451-465. (yet another recent example of kids not looking like adults)

Hybridization

Week 13: Genetic restoration

Tallmon DA, G Luikart & R Waples. 2004. The alluring simplicity and complex reality of genetic rescue. Trends Ecol. Evol. 19(9):489-496. (costs and benefits of introgression)

Hansen MM et al. 2006. Genetic restoration of a stocked brown trout Salmo trutta population using microsatellite DNA analysis of historical and contemporary samples. J. Appl. Ecol. 43:669-679. (marker-based identification of admixed individuals)

Weak 14: Controlled crosses

McClelland EK & KA Naish. 2007. What is the fitness outcome of crossing unrelated fish populations? A meta-analysis and an evaluation of future research directions. Cons. Genet 8:397-416. (generally beneficial effects in the F₁ and F₂)

Tymchuk WE, LF Sundstrom & RH Devlin. 2007. Growth and survival trade-offs and outbreeding depression in rainbow trout (Oncorhynchus mykiss). Evolution 61(5):1225-1237. (positive and negative effects in line crosses between wild and farmed populations)

Week 15: Hybrid taxa

Vollmer SV & SR Palumbi. 2002. Hybridization and the evolution of reef coral diversity. Science 296:2023-2025. (sterile and “immortal” F₁ hybrids)

Miller DJ & MJH Van Oppen. 2003. A ‘fair go’ for coral hybridization. Molec. Ecol. 12:805-807. (rebuttal to Vollmer & Palumbi)