Skim My review of the VEGAN R package to see an example of distance-based analysis of species composition.

Week 3: Model-based species composition analysis
Wang et al 2012, MVABUND paper

Week 4: Estimating population size
Skim Borchers et al. (the text) Chapter 3. Read for concepts. We'll talk a lot more about state (=process) and observation models at the end of the semester.
Borchers et al. Sections 6.1 - 6.3. Focus on the concepts used to define likelihoods, i.e. what is the process used to construct a model for the data. The likelihood in (6.8) is equivalent to the multinomial likelihood that I will focus on. That's because the multinomial provides a framework for lots of types of estimators.

Week 6: Heterogeneity
Background: Section 3.1, State and Observation models
Heterogeneity: Section 11.3

Week 6: Open populations - not in the book (Section 13.3 is a complicated example)
Copies of this chapter will be available when I get back to Ames
Pollock and Alpizar-Jara. 2005. Classical open-population capture-recapture models. Chapter 3 in Amstrup, McDonald and Manly, Handbook of Capture-Recapture Analysis
The first part of this chapter mirrors my presentation. There are lots of details in the second half of the chapter; skim those.