This is the course website for UVic's BIOL 470-03 Advanced Ecology (aka 'Community and Ecosystem Ecology'), spring 2015. Here you will find the syllabus, PDF copies of the lecture and presentation slides (posted after class), readings and assignments. As a participant in this class, it is your responsibility to visit this website regularly to ensure that you have all o f the required information and materials for the class.
Classroom: CLE D125. Tutorials: CLE A108.
Classroom: CLE D125. Tutorials: CLE A108.
NEW: Tips on writing and revising your review paper.
NEW: R tutorials assignment 2 due Wednesday 25th March by 10:30am. Email your R script to [email protected] - see exampleanswer.r for an answer template. Details on the assignment are in the attached pdf, and make sure you download the updated NOAA CRED reef fish dataset (also attached below, "cred_diversity_assignment2.csv").
NEW: R tutorials assignment 2 due Wednesday 25th March by 10:30am. Email your R script to [email protected] - see exampleanswer.r for an answer template. Details on the assignment are in the attached pdf, and make sure you download the updated NOAA CRED reef fish dataset (also attached below, "cred_diversity_assignment2.csv").
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R tutorials Assignment 1 due Monday 2nd March at 2.30pm: Email your R script to [email protected] - see exampleanswer.r for an answer template. Details on the assignment are in the attached pdf, and make sure you download the updated NOAA CRED reef fish dataset (also attached below).
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Week 1 (January 6-9th) - Ecological Aims and Approaches
T: L - Course Introduction
W: L - What is ecology? Major areas of inquiry and approaches
Required reading:
Required readings:
T: L - Course Introduction
W: L - What is ecology? Major areas of inquiry and approaches
Required reading:
- Kingsland 'Defining ecology as a science' In: Foundations of Ecology - Classic Papers with Commentary. L.A. Real and J.H. Brown Eds.
Required readings:
- 1) Sagarin 2010 Observational approaches in ecology open new ground in a changing world
- 2) Lindenmayer and Likens 2011 Losing the culture of ecology
- 3) McGill 2013 The one true route to good science is..... Dynamic Ecology blog
- 4) Duffy 2013 The importance of diverse approaches in ecological research Dynamic Ecology blog
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definingscience.kingsland.1991.pdf | |
File Size: | 647 kb |
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sagarin_2010_frontiers_in_ecology_and_the_environment.pdf | |
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lindenmayerlikens2011.pdf | |
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Week 2 (January 12-16th) - Scale
M: Skills Tutorial 1 - Reading and critically evaluating papers: A major component of this course is reading, critiquing, and discussing the primary literature in the field of ecology. While you have probably already read many papers in the primary literature, it is likely that you could be doing so more effectively. We will discuss ways to achieve this in this tutorial, starting by reading the following two articles (you will have time to read these during the tutorial!):
W: D - The importance of scale in ecology
Required reading:
Required readings:
M: Skills Tutorial 1 - Reading and critically evaluating papers: A major component of this course is reading, critiquing, and discussing the primary literature in the field of ecology. While you have probably already read many papers in the primary literature, it is likely that you could be doing so more effectively. We will discuss ways to achieve this in this tutorial, starting by reading the following two articles (you will have time to read these during the tutorial!):
- 1) Little, J and R. Parker (2010) How to read a scientific paper
- 2) Collins, L How to read a scientific article
W: D - The importance of scale in ecology
Required reading:
- Levin (1992) 'The problem of pattern and scale in ecology' Ecology 73(6):1943-1967.
- McGill (2010) 'Matters of scale' Science 328: 575-576.
Required readings:
- Srivastava et al. (2004) 'Are natural microcosms useful model systems for ecology?' Trends in Ecology and Evolution (TREE) 19(7): 379-384.
- Carpenter (1996) 'Microcosm experiments have limited relevance for community and ecosystem ecology.' Ecology 77(3): 677-680.
470_spring2015_week2_scale.pdf | |
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srivastavaetal2004_tree.pdf | |
File Size: | 329 kb |
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levin1992_ecology.pdf | |
File Size: | 4647 kb |
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mcgill_scale.pdf | |
File Size: | 324 kb |
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carpenter1996_ecology.pdf | |
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Week 3 (January 19-23) - Biodiversity
M: Skills Tutorial 2 - How to moderate a discussion and give an effective presentation
T: L - Biodiversity: types, patterns, causes
Recommended Reading: Chapter 2 Mittelbach 2012 Community Ecology
Optional reading: I have posted Vellend et al. (2007) because it has a nice explanation of one of the biases that can arise in calculations of beta diversity, as well as Dornelas et al. (2014) because it is an interesting recent paper about global changes in alpha and beta diversity. These are solely for your interest!
W: D - Species diversity patterns - Led by Amanda & Marina
Required reading:
Required reading:
M: Skills Tutorial 2 - How to moderate a discussion and give an effective presentation
T: L - Biodiversity: types, patterns, causes
Recommended Reading: Chapter 2 Mittelbach 2012 Community Ecology
Optional reading: I have posted Vellend et al. (2007) because it has a nice explanation of one of the biases that can arise in calculations of beta diversity, as well as Dornelas et al. (2014) because it is an interesting recent paper about global changes in alpha and beta diversity. These are solely for your interest!
W: D - Species diversity patterns - Led by Amanda & Marina
Required reading:
- Classic: Hutchinson (1959) Homage to Santa Rosalia or why are there so many kinds of animals? American Naturalist.
- Recent: Mittelbach et al. (2007) Evolution and the latitudinal diversity gradient. Ecology Letters.
Required reading:
- Mouillet et al. (2014) Functional over-redundancy and high functional vulnerability in global fish faunas on tropical reefs. PNAS
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Week 4 (January 26-30th) - Diversity - Stability
M: Skills Tutorial 3 - Getting started in R
T: L - Diversity - stability
W: D - Diversity - stability - Led by Capri & Blake
Required reading:
Required reading:
M: Skills Tutorial 3 - Getting started in R
T: L - Diversity - stability
W: D - Diversity - stability - Led by Capri & Blake
Required reading:
- Classic: McCann (2000) The diversity-stability debate. Nature
- Recent: Rooney et al. (2006) Structural asymmetry and the stability of diverse food webs. Nature 442: 265-270.
Required reading:
- Schindler et al. (2010) Population diversity and the portfolio effect in an exploited species. Nature.
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Week 5 (February 2-6th) - Biodiversity - Ecosystem Function
M: Skills Tutorial 4 - Getting started in R - Part 2 Data Manipulation
T: L - Biodiversity - ecosystem function
Optional reading: Srivastava & Vellend (2005) Biodiversity-ecosystem function research: is it relevant to conservation? Annu. Rev. Evol. Evol. Syst.
W: D - Biodiversity - ecosystem function - Led by Dr. Baum
Required Reading:
Required Reading:
M: Skills Tutorial 4 - Getting started in R - Part 2 Data Manipulation
T: L - Biodiversity - ecosystem function
Optional reading: Srivastava & Vellend (2005) Biodiversity-ecosystem function research: is it relevant to conservation? Annu. Rev. Evol. Evol. Syst.
W: D - Biodiversity - ecosystem function - Led by Dr. Baum
Required Reading:
- Classic: Tilman et al. (1996) Nature
- Recent: Dewenter et al. (2007) PNAS Note: See Tuesday's lecture slides for the portion of the reading that you are responsible for presenting Wed. in class
- Huston (1997) Hidden treatments in ecological experiments: re-evaluating the ecosystem function of biodiversity. Oecologia 110:449-460.al
- Optional Reading:
Required Reading:
- Maestre et al. (2012). Plant Species Richness and Ecosystem Multifunctionality in Global Drylands. Science, 335(January), 214–218. doi:10.1126/science.1215442
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Week 6 (February 16-20th) - Species Interactions
M: Skills Tutorial 5 - Getting started in R - Part 3 Plotting
T: L - Predator-prey interactions
W: D - Predator-prey interactions - Led by Brynlee & Jessica
Required Reading:
Required Reading:
M: Skills Tutorial 5 - Getting started in R - Part 3 Plotting
T: L - Predator-prey interactions
W: D - Predator-prey interactions - Led by Brynlee & Jessica
Required Reading:
- Classic: MacArthur & Pianka (1966) On optimal use of a patchy environment. The American Naturalist 100(916): 603-609.
- Recent: Preisser et al. (2005) Scared to death? The effects of intimidation and consumption in predator-prey interactions. Ecology 86(2): 501-509.
Required Reading:
- DeCesare et a. (2009) Endangered, apparently: the role of apparent competition in endangered species conservation. Animal Conservation 13(2010): 353-362.
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Week 7 ( February 23-27th) - Trophic interactions
M: Skills Tutorial 6 - Diversity indices in R
T: L - Food chains and food webs, top down vs. bottom up control
W: D - Top down control and trophic cascades - Led by Gillian & Owen
Required Reading:
Required Reading:
M: Skills Tutorial 6 - Diversity indices in R
T: L - Food chains and food webs, top down vs. bottom up control
W: D - Top down control and trophic cascades - Led by Gillian & Owen
Required Reading:
- Classic: Hairston et al. 1960 Community structure, population control, and competition. American Naturalist.
- Recent: Estes et al. 2011 Trophic downgrading of planet earth. Science.
Required Reading:
- Prugh et al. 2009 The rise of the mesopredator. Bioscience
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Week 8 (March 2 - 6th) - Food webs and ecological networks
M: Skills Tutorial 7 - Diversity indices in R. **1st R assignment due**
T: L - Food webs and network models
W: D - Ecological networks - Led by Dr. Baum & Emily
Required Reading:
Required Reading:
M: Skills Tutorial 7 - Diversity indices in R. **1st R assignment due**
T: L - Food webs and network models
W: D - Ecological networks - Led by Dr. Baum & Emily
Required Reading:
- Classic: Paine (1966) Food web complexity and species diversity. The American Naturalist. 100(910): 65-75.
- Recent: Williams & Martinez (2000) Simple rules yield complex food webs. Nature
- Companion piece to the recent article: Wayt (2003) Virtual ecosystems. Conservation Magazine
Required Reading:
- Thompson et al. 2011. Food webs: reconciling the structure and function of biodiversity. Trends in Ecology and Evolution.
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Week 9 (March 9 - 13th) - Macroecology
M: Skills Tutorial 8 - Diversity indices in R
T: L - The macroecological approach and major patterns
W: D - Macroecology (foundation and a current example) - Led by Bryana and Hannah
Required Reading:
Required Reading:
M: Skills Tutorial 8 - Diversity indices in R
T: L - The macroecological approach and major patterns
W: D - Macroecology (foundation and a current example) - Led by Bryana and Hannah
Required Reading:
- Classic: Brown & Maurer 1989 Macroecology: the division of food and space among species on continents. Science
- Recent: Trøjelsgaard & Olesen. 2012. Macroecology of pollination networks. Global Ecology and Biogeography.
Required Reading:
- Beck et al. 2012. What's on the horizon for macroecology? Ecography.
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Week 10 (March 16 - 20th) - Resilience
M: Skills Tutorial 9 - How to write a review paper and how to evaluate a peer's review paper
T: L - Resilience Guest Lecture - Nancy Shackelford (PhD Candidate, School of Environmental Studies)
W: D - Led by Mary *Draft of review papers due in class to exchange for peer review*
Required Reading:
Required Reading:
M: Skills Tutorial 9 - How to write a review paper and how to evaluate a peer's review paper
T: L - Resilience Guest Lecture - Nancy Shackelford (PhD Candidate, School of Environmental Studies)
W: D - Led by Mary *Draft of review papers due in class to exchange for peer review*
Required Reading:
- Classic: Pimm 1984. The complexity and stability of ecosystems. Nature - the paper in which Pimm defines what is now known as 'engineering resilience'
- Recent: McClanahan 2012. Prioritizing key resilience indicators to support coral reef management in a changing climate. PLoS ONE.
Required Reading:
- Folke et al. 2004. Regime shifts, resilience, and biodiversity in ecosystem management. Annu. Rev. Ecol. Evol. Syst.
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Week 11 (March 23rd - 27th) - Ecological implications of climate change
M: Skills Tutorial 10 - Feedback on draft papers *Peer review of review paper due in tutorial*
T: L - Ecological implications of climate change
W: D - Led by Morgan and Landon **2nd R assignment due**
Required Reading:
Required Reading:
M: Skills Tutorial 10 - Feedback on draft papers *Peer review of review paper due in tutorial*
T: L - Ecological implications of climate change
W: D - Led by Morgan and Landon **2nd R assignment due**
Required Reading:
- Classic: Parmesan and Yohe. 2003. A globally coherent fingerprint of climate change impacts across natural systems. Nature.
- Recent: Cahill et al. 2012. How does climate change cause extinction? Proceedings of the Royal Society B
Required Reading:
- Dawson et al. 2011 Beyond predictions: biodiversity conservation in a changing climate. Science
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w11_climate_change.pdf | |
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Week 12 (March 30th - April 1st) - The future of ecology
M: Skills Tutorial 11 - How to be a professional ecologist (grad school, jobs outside of academia, advocacy)..... in other words, how to solve all your problems in 50 minutes :-)
T: L - How to be a professional ecologist (cont'd)
W: L - The future of ecology *Final review paper due to Dr. Baum by 4pm in Petch 116*
Required Reading:
M: Skills Tutorial 11 - How to be a professional ecologist (grad school, jobs outside of academia, advocacy)..... in other words, how to solve all your problems in 50 minutes :-)
T: L - How to be a professional ecologist (cont'd)
W: L - The future of ecology *Final review paper due to Dr. Baum by 4pm in Petch 116*
Required Reading:
- TBD
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