Schedule
Updated 9/5/2023
Classes 1-7: What is biodiversity? How do we quantify it?
1. August 24th Introductions. What does the word biodiversity mean to you?
- Reading: Syllabus
2. August 29th Class Cancelled Due to Hurricane Idalia. Rescheduled for August 31st Taxonomic Alpha, Beta, Gamma Diversity - Concepts
3. September 5th Phylogenetic and functional diversity - Concepts
- Reading: Comparing patterns of taxonomic, functional and phylogeneticdiversity in reef coral communities
- Only read the introduction. You can ignore the final two paragraphs of the introduction as well (i.e. you can stop once you hit the paragraph starting “Despite the importance of coral reefs”).
- Reading: Functional diversity (FD), species richness and community composition
- Only the introduction and the section on “Calculating FD” are required. The rest is optional.
- Questions
4. September 7th Taxonomic Alpha, Beta, Gamma Diversity - Practice
- Class Activity: Exploring taxonomic diversity. Bring computers.
- Before class install R (and RStudio is you want to use that) on your laptop.
- Files:
* R workbook
- rodent_controls.csv
- rodent_krats.csv
- R Packages to install: vegan
Weeks 8-13: Local-scale Biodiversity Patterns & Processes
7 September 12th Local Processes- Niches and Biotic and Environmental Filters
- Reading: Rethinking Community Assembly through the Lens of Coexistence Theory Read Section 1 (INTRODUCTION), Section 2 (CONTEMPORARY COEXISTENCE THEORY AND COMMUNITY ASSEMBLY), and the subsection of Section 3 titled “Trait-Phylogeny-Environment Relationships” (feel free to skip section 3.1, but read Sections 3.2, 3.2.1, 3.2.2, 3.2.3).
5 September 14th Activity: Exploring phylogenetic and functional diversity. Bring computers
- Same rodent files as last week plus:
- Mammal_supertree.tre
- rodent_wgts.csv
- R packages to install: picante, ape
9. September 19th Local Processes - The role of Stochasticity and History
8. September 21th Identifying Gaps in Knowledge
- Group Project Topic Development
- Topic-a-rama: Class Activity: (10/1) Group Project (Forming groups)
10. September 26th Local Taxonomic, Phylogenetic, and Functional Diversity
- Reading: Spatial mismatch and congruence between taxonomic, phylogenetic and functional diversity: the need for integrative conservation strategies in a changing world
- Questions
11. September 28th Group Project
- Structure of an Introduction
- Focus on 1st paragraph: Introducing your topic
- Activity: Finding the Gaps
- Watch this video
- Read the introduction from one of the following papers:
- Beta diversity patterns of bats in the Atlantic Forest: How does the scale of analysis affect the importance of spatial and environmental factors?
- Remote reefs and seamounts are the last refuges for marine predators across the Indo-Pacific
- Network structure of vertebrate scavenger assemblages at the global scale: drivers and ecosystem functioning implications
12. October 3rd Species Networks
- Readings: Two degrees of separation in complex food webs - only the first three paragraphs of the introduction
- Readings: Interaction strength promotes robustness against cascading effects in mutualisitic
13. October 5th Patterns of Abundance
- Readings: Species abundance distributions: moving beyond single prediction theories to integration within an ecological framework * Only the following sections are assigned: What is an SAD?, Why are SADs important?, Classical Theoretical Developments, Proliferation of models)
- Readings: Hyperdominance in the Amazonian Tree Flora
- Questions
- Class Activity: Group Projects
Classes 14-19 Regional-Scale Diversity Patterns & Processes
14. October 10th Regional Assembly - Dispersal
15. October 12th Regional Assembly - Environmental Heterogeneity
- Reading: The “Frankenpaper” - emailed to the class listserv
- Questions
- Class Activity: Group Projects
16. October 17th Habitat Fragmentation patterns
- Reading: Ongoing accumulation of plant diversity through habitat connectivity in a long-term experiment
- Questions
17. October 19th Group Project
- Discussion: The 2nd Paragraph - what is known
- Reading: TBD
- Group Projects
18. October 24th Core-Transient Species
19. October 26th Group Project Day
- Group Project Time
Classes 20-27 Global Biodiversity Patterns and Processes
20. October 31st: Biogeographic Processes: Biogeographic Regions
21. November 2nd Biogeographic Processes: Evolution
- Questions
- Group Project
22. November 7th Large-scale Patterns of Phylogenetic, Functional, and Species Diversity
23. November 9th Group Project Day
- Discussion: The Third Paragraph - what is missing
- Group Project Time
24. November 14th Endemism
25. November 16th Group Project Day
- No readings
26. November 29th Group Project Day
- 4th and 5th Paragraph discussions - why is there a gap in knowledge? and “Here we…”
- Group Project Time
27. November 30th Group Project Day
Class 28: Wrap-Up
28. December 5th: What have we learned? Wrapping up the Semester
- Readings: Look over the questions and topics on the schedule and reflect on what we have covered over the past semester
- Reading: Read over items of confusion from the very first paper of the semester
- Revisit The HillRisLambers model for community assembly. We’ll use it as our basis for creating our own model for biodiversity and revisiting our view of biodiversity.