The Topics Course

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First and second year students attend a four part, two year course during which faculty introduce students to core concepts in evolutionary biology.  This course appears in the university course catalog as BIO471-474.

BIO471
Population Ecology, Patterns of Diversity, and Basic Statistics (Jaenike)
This section of the course covers basic models of single-species population growth and regulation, the population dynamics of interspecific interactions (including competition and enemy-victim interactions), stability analysis, demography and life history variation, and patterns of species diversity.  Some basic statistics, including descriptive statistics vs. hypothesis testing, parametric vs. non-parametric statistics, and the visual presentation of data are also discussed.

Molecular Population Genetics (Presgraves)
A brief history of the neutral theory of molecular evolution, including derivation of several classical results.   Introductory coalescent theory and basic hypothesis testing using molecular population genetic data.  The interaction of natural selection and genetic linkage on patterns of DNA sequence polymorphism, divergence, and adaptation.

Select Topics in Evolutionary Ecology (Minckley)
Species concepts, particularly those other than the biological species concept, and how different species concepts influence research questions.  Theories of the evolutionary ecology of host specialization, cooperation, and community assembly.  The last lectures are on applied island biogeography.

BIO472
Mobile Elements and Eukaryotic Genomes (Eickbush)
A brief summary of the classes of mobile elements, how  these elements contribute to the large size of many genomes, and how they affect the functioning of genomes.  Analysis of what determines the accumulation or elimination of mobile elements from populations and species. Descriptions of what is known concerning the regulation of mobile elements with special emphasis on  the small RNA pathways.

Analysis of Quantitative Traits (Fry)
We spend two weeks exploring important but often neglected topics in the design, analysis and interpretation of experiments involving quantitative traits, including proper replication vs. pseudoreplication, computer intensive methods such as the bootstrap, and metaanalysis and publication bias.  The remaining three weeks focuses on the genetics of quantitative traits, including the effects of inbreeding, partitioning variation into its genetic and environmental components, the response to selection, and evolutionary quantitative genetics.

Intragenomic conflict (Larracuente)
Students get hands-on experience in genomic analysis with a focus on questions relating to intragenomic conflict. We discuss recent primary literature where authors use genomic techniques to study selfish genetic elements. Through workshops, students learn basic R and Perl programming and basic genome analysis techniques such as reference-based assembly methods, variant calling and population genomics analyses. We complete a short genomics project on the topic of intragenomic conflict and present the results on the final day of class.

BIO473
Evolution of Developmental Processes (Lambert)
Brief introduction to the position of evolutionary development in the two parent fields.  A primer on transcriptional regulation and early development in flies.  The evidence for the importance of regulatory change in the evolution of development, and counter-examples. Modularity in development and evolution.

BIO274
Introduction to Classical Population Genetics (Orr)
Topics covered include an introduction to probability theory, Hardy-Weinberg equilibrium, selection equations, genetic drift, mutation-selection equilibrium, probability of fixation, stationary distributions, and diffusion approximations.  Homework problem sets are assigned.

Levels of Selection, Selfish DNA, & Genetic Conflict (Werren)
We consider basic levels of selection theory and the consequences of selection at different levels (from gene to community) to evolution and adaptation.  We also cover the forms of genetic conflict (e.g. intragenomic,  nuclear-cytoplasmic, paternal-maternal genome, parent-offspring, sexual conflict) and how genetic conflict shapes biological processes.

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