NRE 509: ECOLOGY: Science of Context and Interaction
Professors:
J. David Allan
Professor, School of Natural Resources and Environment
Dana 2066, ude.hcimu|nallad#ude.hcimu|nallad
William S. Currie
Associate Professor, School of Natural Resources and Environment
Dana 2532, ude.hcimu|eirrucw#ude.hcimu|eirrucw
Graduate Student Instructors for 2009:
Kyung Seo Park, SNRE PhD student
Office Hours: Wed. 2-4pm in 2544 DANA
ude.hcimu|krapoce#ude.hcimu|krapoce
Thomas Neeson, SNRE PhD student
Office Hours: Mon. 3-4pm
Tues. 10-11am
Wed. 1-2pm in 2544 DANA
ude.hcimu|noseen#ude.hcimu|noseen
Allie Schafer, SNRE MS student
Office Hours: Thurs. 11-1pm in 2536 DANA
ude.hcimu|hcseilla#ude.hcimu|hcseilla
Overview
The natural science core course provides a broad foundational treatment of concepts and processes that operate in ecological systems. It covers interactions among water, soils, the atmosphere, and basic life processes (respiration and photosynthesis) in terrestrial and aquatic ecosystems, including the principles of energy flow and the cycling of matter. It covers ecological principles such as population growth and regulation, trophic interactions, ecological networks, and community change. It covers evolution and natural selection. The course draws examples from some of the dominant habitats on earth, including rivers, lakes, wetlands, forests, deserts, and agricultural systems. Many of the principles and examples covered are designed to give students a foundation for the understanding or study of facets of global change.
Course Objectives
- To provide a common foundation in core natural sciences related to natural resources and the environment for all incoming MS students.
- To introduce quantitative and qualitative analysis of environmental systems to all MS students while developing a systems perspective and systems modeling skills.
- To foster knowledge-based critical thinking and the habit of cross-disciplinary interaction among students.
- To provide a transition to graduate school by expecting students to assimilate both basic and advanced information from diverse sources, including the primary scientific literature.
The Wiki
Do you wish the wiki worked differently? Have suggestions for new features or requests for pages?
Comments? Complements? Criticisms?
Lets talk about them:
Course calendar:
| Week | Monday lecture | Wednesday lecture | Computer lab |
|---|---|---|---|
| Sept 7 - 11 | No class | Core Themes and the (Eco)systems Approach (Currie) |
No lab this week |
| Sept 14 - 18 | A Brief History of Life on Planet Earth and the Origins of Life (Allan) |
Energy, Life, and Transformations (Currie) | Lab 0: Stella learning session |
| Sept 21 - 25 | Plant Physiology, Energetics, and Water Relations (Currie) |
Terrestrial Production, Decomposition, NPP, NEP, and C Storage (Currie) |
Lab 1: Terrestrial NPP and NEP (Week 1) |
| Sept 28 - Oct 2 | Climate, Glaciation, and Stability (Currie) | Vegetation Biomes (Currie) | Lab 1: Terrestrial NPP and NEP (Week 2) Lab 1 model due |
| Oct 5 - 9 | Natural Waters (Currie) | Nutrient Flows and Transformations from Terrestrial to Aquatic Ecosystems (Currie) |
Lab 2: Coastal wetland nutrient cycling (Week 1) Lab 1 analysis due |
| Oct 12 - 16 | Nutrient Cycling in Terrestrial Ecosystems (Currie) |
FIRST MIDTERM EXAM (In class) | No lab this week |
| Oct 19 - 23 | Fall study break - no class | Evolution by Natural Selection (Allan) | Lab 2: Coastal wetland nutrient cycling (Week 2) Lab 2 model due |
| Oct 26 - 30 | Population Growth (Allan) | Population Dynamics and Regulation (Allan) | Lab 3: Fish population regulation (Week 1) Lab 2 analysis due |
| Nov 2 - 6 | Species Interactions, Competitions, and Mutualisms (Allan) |
Consumer-Resource Interactions (Allan) | Lab 3: Fish population regulation (Week 2) Lab 3 model due |
| Nov 9 - 13 | Community Structure (Allan) | Lakes and Oceans (Allan) | Lab 4: Trophic interactions (Week 1) Lab 3 analysis due |
| Nov 16 - 18 | River Ecosystems (Allan) | Land Use/Land Cover Change (Currie) | Lab 4: Trophic interactions (Week 2) Lab 4 model due |
| Nov 23 - 25 | Human Systems: A Focus on Agriculture (Currie) |
SECOND MIDTERM EXAM Tuesday, Nov 24 5-7 pm (no class on Wednesday the 25th) |
Thanksgiving - No lab this week |
| Nov 30 - Dec 4 | Global Water (Allan) | Global Biodiversity (Allan) | Lab 5: Coupled human-natural systems (Week 1) Lab 4 analysis due |
| Dec 7 - 11 | The Biodiversity Crisis (Allan) | Global Systems (Currie) | Lab 5: Coupled human-natural systems (Week 2) Lab 5 model due |
| Dec 14 - 18 | Course Conclusion (Allan, Currie) | No class - study period | Lab 5 analysis due |
| Dec 21 | FINAL EXAM (Monday, Dec 21, 4-6 PM) | ||
Land Use/Land Cover Change
Lecture 20: November 23
Land use (the set of human actions within an area) and land cover (the physical material on a region's surface) are characteristics of a landscape that are critical for understanding landscape processes, conservation plans, and management options. These characteristics are highly variable with scale of focus, and by changing the resolution of your investigation you can get very different results. The correct resolution is a range where increased heterogeneity due to closer examination is no longer relevant to the research question. Differences in land cover (sometimes anthropomorphic, frequently not) create patches in a landscape separated by the matrix and populated by a subset of individuals from the species' meta-population. Patches, habitat fragmentation, and land use/land cover have changed through history and continue to change today causing challenges for conserving biodiversity.
Lecture 20
Global Water
Lecture 19: November 18
Only a small proportion of the Earth's water is free-flowing and fresh. This available fresh water flows through the hydrology cycle from the ocean to the atmosphere to the continents. Terrestrial water is is found on the surface, in soils and in the water table, and is affected by precipitation rates, soil characteristics, land cover, and ET Rates. Humans have had a significant impact on the terrestrial portion of the hydrology cycle due to urbanization's increased impervious surfaces, increasing runoff and dams, altering river flow.
Lecture 19
River Ecosystems
Lecture 18: November 16
The physical and biological processes in rivers are inextricably intertwined. Fluvial geomorphology is determined by the interplay between rivers and landscapes, specifically the bank's slope, volume of flowing water and substrate sediment type. These geomorphological characteristics in part dictate the ecological communities these rivers support including such invertebrate functional groups as grazers, scrapers, shredders, collector-gatherers and predators. These invertebrate communities depend on suspended organic material in the water column and vary considerably along different river reaches according to stream flow, nutrient availability and substrate type.
Lecture 18
Lake Ecosystems
Lecture 17: November 11
Lakes are formed in many ways, including glaciers, tectonics, and landslides. Once formed, lakes are characterized by seasonal turnovers of nutrients driven by temperature gradients. These temperature gradients are extremely important both ecologically and biogeochemically. Nitrogen and Phosphorus are two key elements in lake ecosystems - high influxes of these can cause eutrophication. According to Leibig's law of the minimum the mineral resource that is most scarce will be most limiting for growth in that ecosystem.
Lecture 17
Community Structure
Lecture 16: November 9
A community is the complex of species living together and interlinked through feeding relationships and other interactions that govern the flow of energy and cycling of nutrients. Food webs are a model for community structure and consist of trophic levels that can be regulated by resource availability (bottom up) or predation stress (top down).
Lecture 16
Consumer Resource Interactions
Lecture 15: November 4
Consumer-resource interactions are ubiquitous and are usually the driver of specialization. Fluctuations in prey and predator populations have a significant impact on the dynamics of the other and so are engaged in an evolutionary arms race to escape negative pressure from the other.
Lecture 15
Species Interactions: Two-Way Interactions, Mutualisms and Competition
Lecture 14: November 2
Mutualism, commensalism, predation and competition are the primary ways in which species interact in nature. Each interaction type can have huge consequences on an individual’s behavior, life-history traits, fitness and survivorship. Niche theory is a convenient way to partition an ecosystem and understand species interactions.
Lecture 14
Population Dynamics, Part Two
Lecture 13: October 28
Demographic characteristics of a population, such as age structure, are important determinants of population viability. Population sizes fluctuate in time and space and, depending on growth and loss rates, species will either persist or disappear.
Lecture 13
Population Growth and Regulation
Lecture 12: October 26
Population change is a balance of rates that increase of decrease population numbers including birth, immigration, death and emigration. Populations can’t grow exponentially forever; typically they reach a carrying capacity and feel the effects of negative feedbacks.
Lecture 12
"The Ecological Theater and the Evolutionary Play"
Lecture 11: October 21
Natural selection is the primary driver of evolution. Selection can be directional, stabilizing or disruptive but will always result in a change total gene frequencies in a population. Fitness – the number of viable offspring an individual produces – is a good metric for measuring the quality of life history traits and will impact the extent and pace of natural selection.
Lecture 11
Nutrient Cycling in Terrestrial Systems
Lecture 10: October 12
All nitrogen transformations require biology, and most notable of those transformations is nitrogen fixation from atmospheric nitrogen gas into biologically active forms. Soil weathering will dictate the amount of nitrogen that can be retained and kept for use by plants and microorganisms. Because nitrogen is generally a limiting resource many organisms have evolved ways to capture and sequester nitrogen as soon as it is available.
Lecture 10
Nutrient Flows from Terrestrial to Aquatic Systems
Lecture 9: October 7
The nitrogen cycle is critical for primary productivity and revolves around the processes of nitrification and denitrification. Most nitrogen transformations occur in the soil and are influenced by the presence or absence of oxygen.
Lecture 9
Biogeochemistry
Lecture 8: October 5
Water, as the universal solvent, is a critical molecule for life. In addition to the hydrogen and oxygen in water life generally requires C, N, P and S, along with the nutrients Ca, K, and Mg. pH is extremely important for biological processes and can be influenced by the carbonate complex cycling and human pollutants such as NOx and SO2.
Lecture 8
Vegetation Biomes
Lecture 7: September 30
Continents, Hadley cells and ocean currents influence global climate, which weathers rock, and creates soil. Soil characteristics vary with climate, extent of weathering and age. Climate and soils then dictate the type of vegetation present in every ecosystem around the world and because of the wide variety of climate conditions and soil types vegetation biomes are highly specialized and recognizable.
Lecture 7
Climate, Glaciation and Stability
Lecture 6: September 28
Global climate has fluctuated significantly over geological history. Temperature fluctuations have been marked by retreating and advancing glaciers, which are primarily responsible for carving the topography of the northern latitudes. Glacial periods have numerous causes within a complicated system of feedbacks including shifting plate tectonics, CO2 levels and Milankovich cycles.
Lecture 6
Terrestrial Production, Decomposition, NPP, NEP and C Storage
Lecture 5: September 23
Flows of carbon form the backbone of ecosystem functions. These fluxes move carbon between the atmosphere, plants and animals and soils in a ceaseless cycle. These fluxes are regulated by nutrient, water and oxygen availability, topography, disturbance regimes and successional patterns.
Lecture 5
Plant Physiology, Energetics and Water Relations
Lecture 4: September 21
Water and temperature are the major limiting factors of plant primary production. Plants have evolved three major physiological patterns to counter the effects of water scarcity and temperature fluctuations; they are referred to as C3, C4 and CAM. Each of these processes reflect important life-history tradeoffs made as plants expanded to different, challenging environments.
Lecture 4
Energy, Life and Transformations
Lecture 3: September 16
Life requires energy, and plants and animals have evolved many mechanisms for capturing, transforming and storing energy for all physiological processes. Reduction–Oxidation reactions – essentially electron flows – form the basis for most energy producing and transforming processes and these flows are characterized by surrounding conditions, especially the availability of oxygen.
Lecture 3
Life on Earth: A Brief History of Everything
Lecture 2: September 14
There is a single tree of life and understanding it is critical to our study of biodiversity, speciation and conservation. All extant taxa evolved from a single progenitor 6.5 billion years ago and ever since, life has been characterized by crisis and innovation driving the diversification we see today.
Lecture 2
Core Themes and the (Eco)System Approach
Lecture 1: September 9
Natural systems are intrinsically coupled to human systems. Natural landscapes and aquatic ecosystems are complex with many different scales of interactions. In the face of increasing human impacts on the earth and particularly climate change, studying, modeling and understanding these interactions is critical.
Lecture 1
Here are the test practice questions:
They've been sorted with the most recent posts first.
Review
review
Lecture 20 potential exam questions
lecture-20-potential-exam-questions
Lecture 19 Potential Exam Questions
lecture-18-potential-exam-questions
lecture 19 potential exam questions
lecture-19-potential-exam-questions
Lecture 18 Potential Exam Questions
lecture-8-potential-exam-questions
Lecture 18: Exam Questions
exam-questions
Lecture 17: Potential Exam Questions
chapter-17-potential-exam-questions
Lecture 17: Exam Questions
lecture-17-exam-questions
Lecture 16: Potential Exam Questions
lecture16
Lecture 15: Suggested Exam Questions
suggested-exam-questions
Lecture 15: Potential Exam Questions
lecture-14-exam-questions
Lecture 14: Suggested exam questions
suggested-exam-questions
Lecture 14: More suggested exam questions
more-suggested-exam-questions
Lecture 13: Suggested exam questions
suggested-exam-questions
Lecture 12: Suggested exam questions
suggested-exam-questions
Lecture 11: Potential Exam Questions
exam-questions
Lecture 11: Potential Exam Questions
lecture-11-exam-questions
Lecture 10: Potential Exam Questions
exam-question-lecture-9
Lecture 09: Nutrient flows Exam Questions
nutrient-flows-exam-questions
Lecture 08: Acid-Base Chemistry-Suggested Exam Questions
suggested-exam-questions
Here are all of the pages we've created with additional, outside information
They've been sorted with the most recent posts first.
IPCC Guidelines for Land Use, Land-Use Change, and Forestry
Monitoring Length/Time Scales and Techniques
The IPCC has published the following figure illustrating the range of temporal and spatial scales at which ecological processes occur and monitoring…
Lecture 11: Extra Info
The Man Who Wasn't Darwin
This is a piece on how Alfred Russel Wallace independently arrives at the same conclusion as Darwin's theory of natural selection - "On the Tendency of Varieties to depart…
The Water Cycle and Urbanization
Here are a few slides from a presentation detailing the effects of urbanization on the water cycle. For more information (or to see the whole presentation), please go to…
symbiosis: coral reefs
Coral Reefs are dominated by structure of coral, formed by diverse group of cnidarians that secrete calcium carbonate to make hard exoskeleton. Within this structure, coexist zooxanthellae, a…
Founder Effects vs. Bottleneck Effects
The Founder effect:
Genetic drift likely when a few individuals colonize an isolated island or patch of new habitat. The smaller the size population the less genetic diversity that will be present…
How to control fertile bison
November 20th's Wall Street Journal tells the story of conservationists attempts to control the population of non-native bison on Santa Catalina Island in Southern California, where the bison are a…
Lecture 19 - Extra Info: Dam Removal
Wisconsin Dam Removal Policy
For anyone with interest in Wisconsin's dam removal policy (as discussed in today's lecture), the link below will take you to the report written by the River Alliance…
Subsidies and Sustainable Agriculture in Africa
Reading #1 for Lecture 21
Dugger, C. W. Dec. 2, 2007. "Ending famine, simply by ignoring the experts." New York Times.
In her December 2, 2007 New York Times article, Celia Dugger dissects the…
The World is Prickly and Tastes Bad
“The World is Prickly and Tastes Bad” is a response to the ideas put forwards in the “The World is Green” hypothesis. Murdoch et al (1966) argued that just because there is an abundance of…
Colony Collapse Disorder follow-up
During lecture, Professor Allan highlighted colony collapse disorder (CCD) as an example of change in population dynamics. There is news that lends further insight into this phenomenon. In late…
Community Structure in the Great Lakes
In Professor Allan's lecture on community structure (Nov. 9th), we discussed how the concept of trophic cascades can be applied to lake plankton systems. Currently, there are significant changes…
Reading: Ecological Community Description
Ecological community description using the food web, species abundance, and body size
Cohen, Joel E., Thomas Jonsson, and Stephen R. Carpenter
This is a summary of this math-heavy reading for…
Reading: On the Origin of Ecological Structure
Reading: On the Origin of Ecological Structure
Scientists debate what dictates species composition in biological communities
-Alexander von Humbolt (1800s) - Essay on the Geography of Plants…
Rewilding North America
http://www.catsg.org/cheetah/05_library/5_3_publications/D/Donlan_2007_Restoring_Americas_big_wild_animals.pdf
Summary based on Donlan CJ. 2007. “Restoring America’s Big, Wild Animals.”…
Niche
Niche
Definitions
1904 Grinnell: a distributional unit that describes where an organism lives
1927 Elton: an organisms functional role in a community
1958 Hutchinson: a n-dimensional…
Lotka Volterra Model
Lotka-Volterra Model
Designed to predict oscillations in abundance of predator and prey populations
Rate of Change in Prey Population=Intrinsic growth rate of prey population - removal of prey by…
Predation and natural selection - guppy example
Shakuntala Makhijani
11/3/09
In the readings and material for the lecture on Wednesday, November 4, the concept of predation as a powerful mechanism for natural selection is discussed. I found and…
Vengeful Honey Guides
After Emily mentioned the price for not leaving the Honeyguide his fair share of honey, I couldn't stop laughing and had to go look this up for myself. With the help of Google I found that…
Lotka-Volterra Competition Simulation
For all of you interested in understanding a little bit more about the competition models we have seen, here is an interesting interactive website to look…
Climate Change and Population Dynamics of Invasive Species
Most invasive species are wimps, but some are Godzilla types.
— Professor David Allan
According to recent studies, poison ivy is one of those Godzilla types when it comes to rising CO2 levels….
Here are a few pages with helpful hints about working with the wiki:
They've been sorted with the most recent posts first.
Wiki FAQ
This is your course-notes site
Joining the site so you can post and edit:
You must get a free wikidot.com user account to join. Your username should have some semblance to your real name so that…
How to Add Photos to the Wiki
Frequently, a graph, figure or picture from the textbook or the lecture really sums up the concepts we're trying to post about. In that case, uploading it to the wiki would be extremely helpful,…
How To Edit Pages - Quickstart
If you are allowed to edit pages in this Site, simply click on edit button at the bottom of the page. This will open an editor.
To create a link to a new page, use syntax: new page name or…






















So what do you think? My goal was to design an interface that we could all use to more easily navigate to target pages of interest. The "Extra Info" tab is still a bit messy and I'd love other suggestions for organizing it - does most recent post first make sense? The syllabus isn't all that helpful - do you want it up or is it better just taken off? Is this layout easier? Do you have suggestions to make it better?
I'm going to need some help keeping all of these pages current. If you're so inclined send me an e-mail (cdonihue) and I'll show you how I made the site, or you can just look through the code.
Hope y'all don't mind the huge change and I especially hope we find it a bit easier to visit and post on. Good night!
Colin,
This is great! I'm glad someone took the initiative!!! Thanks, lauren cotter
These forum postings have some pretty good potential for dialogue. Start a new thread by typing in a "Post Title" or if you'd like to respond to an already existing thread click on the "reply" link under the latest posting.
Important note: once you've posted something you can't delete it (case in point: somewhere hiding in the wiki I have a bunch of very silly test posts back and forth to myself and I still can't figure out how to get rid of all of them).
You can put these dialogue boxes anywhere on the wiki though so be thinking of creative reasons for discussion - test questions, philosophical/existential debates, Stella rants etc. Let's try to keep this page focused on topics pertinent to the wiki as a whole - we can add as many others as you'd like everywhere else. All you have to do is write [[module Comments]] when editing a page.
I'm thinking of deleting that blank page in the Lecture 15 section—anyone know how?
I've had trouble figuring out how to delete pages too. The easiest way to remove it from the Lecture 15 section is to remove the tag (done). You can also "mark it as deleted" or some other such tagging, but it still floats around in the "list all pages" view. Not a big issue as there haven't been all that many that have been deleted but it could get messy. I think the only real way is for an admin to completely wipe it.
I deleted the tag though so it won't clutter the Lecture 15 section.