ECOL 592 Interdisciplinary Seminar

Past Offerings

Spring 2015

Foundations in Evolution

Colleen Webb

This semester we will be working through some fundamental and often classic papers in evolution. I believe that knowing about classic theory and experiments helps us to better understand the contemporary literature as well. How can we know where we are going if we do not know where we have been? The objective this semester is to help students build a broad and basic background in key areas of evolutionary research. I have collected a list of fundamental papers and divided them into eleven subject areas. We will cover at least one paper from each subject area, and enrolled students will be expected to lead discussion on at least one paper. There will be a number of important papers that we will not have time to read, but I hope that this discussion group will help you appreciate the value of a broad knowledge of the fundamental literature and that you will continue to read it. A secondary theme of the course will be techniques for management and leadership of discussions. Subject areas: Evolution of Populations, Systematics, Phylogenetics, Macroevolution, Natural Selection, Speciation, Hybridization, Molecular Evolution, Neutral Theory, Evolution and Development, and Scientific Method/Philosophy.

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Nature in the City

Liba Pejchar, Lindsay Ex

This seminar provides a unique opportunity to collaborate with the City of Fort Collins to design and sustain urban open space in our community. Students will be part of the innovative Nature in the City project (fcgov.com/natureinthecity), which is developing a 25-year vision for how all residents in the city will be able to access high-quality, natural experiences within a 10-minute walk from where they live and work. One of the key products for this effort is a set of design guidelines that will illustrate how nature can be incorporated into the urban environment. Students in this seminar will hail from diverse backgrounds to conduct the research and synthesis to propose design guidelines that are socially, ecologically, and economically sound. The format of the seminar will include a mix of learning opportunities and hands-on, interdisciplinary research leading to a product that will be used by developers, residents, business owners, and the City. Students who participate in this seminar will have the opportunity to shape the design of open space in the City of Fort Collins for the next 25-50 years.

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Ecological Diversity and Function

Colleen Webb, Clint Leach

The objective of this seminar will be to build a broad and basic background in key areas of diversity and function research in ecology. This is a central area of ecology, but the literature is vast. Through weekly paper discussions from a wide range of topics within this field, we hope to build a solid foundation that will provide a jumping-off point for students to continue to explore these areas. Topics that we plan to cover include: basics of diversity and how it is defined and quantified; the processes that structure diversity and the patterns they produce; the effect of diversity on ecosystem structure, function, and stability; traits-based perspectives on diversity. Time permitting, there may also be opportunities for students to select additional and/or more specific areas to explore, based on the interests of the class. Regular attendance is expected and students will be evaluated based on their participation.

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Women in science

Ruth Hufbauer

The goals of this course are to examine critically both how far women have come in science, as well as how far women have yet to go, to understand the benefits and challenges of being a woman scientist, and our inherent biases. We will also discuss what it means to be a feminist in different spheres and across different cultures. We will also touch on race, and LGBTQ issues, but the main focus for this course will be on women. We will read from the growing number of papers (especially data papers) in the literature evaluating the environment women experience in the work force in general, and in science in particular. We will also read from blogs, and engage on twitter. A different student, or students, will lead discussion each week, with the composition of the group of leaders chosen at random. Participation in all the meetings is expected, and both attendance and contributions to the discussions will be tallied. Listening and speaking with respect for others will be critical, and doing so mindfully will also be tallied. Leading discussion will account for 25% of the pass/fail grade, and participating will account for 75%.

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Spring 2014

Teaching Ecology to Undergraduate Students

Meena Balgopal, Sam Dunn, Aramati Casper

Issues of student learning, instructional strategies, curriculum development, and the construction of assessment tools in a college-level natural or physical science course will be discussed. Students will create a teaching portfolio by the end of the course similar to that required by the TILT post-secondary certificate program. The objectives of this course are for students to be able to: - Design curricula using the "universal design for learning" and "understanding by design" frameworks. -Synthesize how different instructional practices in a science course (lectures, laboratories, recitations) can promote critical thinking and inquiry skills. -Construct and evaluate meaningful assessment tools that reflect learning objectives for a college science course. -Write a college science teaching philosophy

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cancelled - Methods for Sampling Aquatic and Riparian Habitats

David Cooper, Erick Carlson

UNFORTUNATELY, THIS COURSE HAS BEEN CANCELLED. 1/16/14

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Terrestrial Ecosystem Sensitivity to Climate Change

Melinda Smith, Alan Knapp

The global scale of climate change means that all terrestrial ecosystems are, and will continue to be, impacted by alterations in temperature, precipitation and more frequent and severe periods of climatic extremes. Forecasting how any particular ecosystem will respond to predicted changes in climate requires knowing the magnitude of the change in the climate driver (e.g., change in precipitation or temperature), and the sensitivity of ecosystem processes to a given change in a climate parameter. However, we know much more about how climate drivers will change than we do about why ecosystems differ in their sensitivity to these forecast changes. With this seminar, students will explore the current state of knowledge of terrestrial ecosystem sensitivity to climate changes.

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Introduction to R

Ruth Hufbauer, Michael Koontz

R is an incredibly powerful tool for statistical analysis, data management, and visualization that has been increasingly used for ecological applications. It is open source, free, and available for all operating systems. Despite this availability, it is also considered a difficult language to learn�¢?? especially for those coming from a limited background in command line programming. This course aims to introduce users to R in an interactive, hands-on format. We will focus on topics that will be common to the needs of all ecologists such as structuring, summarizing, manipulating, and plotting data. Later portions of the course will devote time to more individual-specific needs of real data sets. Class sessions will be exercise-driven and the course will include guest lectures from graduate students who have had success using R in their research. Note: this is NOT a statistics course, though some help could be given to figure out the proper syntax for more complicated statistical analyses (e.g. generalized linear mixed models, multivariate analyses). It would be the student�¢??s responsibility to verify any results with a statistician! Expected learning outcomes: a basic command of the R language, a better sense of how to collect and enter data for future analysis, a head start on something directly applicable to your research, and tools for learning more about what R can offer your research.

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Interdisciplinary Water Research Seminar

LeRoy Poff, Jorge Ramirez

As global climate change and population growth increase demand for water resources, researchers and managers strive to maintain conditions that satisfy societal and ecological freshwater needs. Integrating physical, biologic, and social sciences is necessary to further understand feedbacks and linkages between physical response, biological requirements, and societal demand for freshwater. In this seminar, we focus on methods of interdisciplinary research and collaboration with regard to all aspects of the hydrologic cycle including the atmosphere, ecosystems and human dimensions of freshwater resources. The direction of this course will be largely determined by student interest with potential to explore connections between the atmosphere, projected changes in climate and water availability, freshwater management strategies, freshwater ecosystems, ecosystem services, public perception of freshwater resources, public outreach and education regarding water resources, and methods of integrating these topics across disciplines. In particular, we emphasize and encourage integration of research questions across disciplines to facilitate interdisciplinary collaboration. Current faculty of the Integrated Water, Atmosphere, Ecosystems Education and Research program (I-WATER), including LeRoy Poff (Biology), Jorge Ramirez (Civil and Environmental Engineering), Neil Grigg (Civil and Environmental Engineering), and Scott Denning (Atmospheric Sciences), will provide guidance and share experiences pertaining to case studies of interdisciplinary water resources research. Course content will be centered around student and faculty led discussions on current research projects, and reading and discussion of applicable literature. Students will be tasked with exploring an interdisciplinary collaboration with fellow students that involves their current research project and/or interests. Student groups will present a conceptual level research proposal and/or research findings in the latter part of the semester.

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Fall 2013

Natural Selection

Ruth Hufbauer

Natural selection is a fundamental but often misunderstood concept in ecology and evolutionary biology. We will start by reading from the publications that laid the foundation for current approaches to studying natural selection (i.e.Endler and Lande and Arnold). Then we will turn to more recent papers on selection, from field measurements, including demographic analyses, to genomic evidence of selection.

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Niche Models

Cameron Aldridge, Sunil Kumar, Barry Noon

This is a broad-ranging seminar course designed to expose students to the variety of quantitative and statistical techniques available to assess species-habitat relationships. Niche models are known by a variety of names including species distribution models, habitat relationship models, bioclimatic envelopes, and others. The concepts and application of these models are not new, although there are many new statistical algorithms to estimate niche relationships. They all rely on the concept of the niche�?�¢??the set of environmental conditions in which a species can survive and persist. They are particularly topical today because of concerns over the effects of climate change, energy development, and invasive species on the distribution and abundance of native species. Our goal is to expose students to a suite of different analytical approaches so as to give them a new tool set for future design of experiments and analyses of data. The course structure is one 50 minute period. The first portion of the class will consist of a brief introduction to a topic (~15 minutes). This is intended to cover some of the theoretical and conceptual foundations of a given statistical algorithm used for niche modeling, and provide an overview for a key paper we will read on the specific topic. The remainder of the class will be a discussion on the topic and the key paper(s), lead by that week�?�¢??s presenters (faulty or students). Students will lead one class presentation and discussion. Topics discussed in this course could include resource selection functions (RSFs), resource utilization functions (RUFs), occupancy models, Habitat Suitability Index (HSI) models, count-based models (Poisson and negative binomial regression), survival models, Ecological Niche Factor Analyses (ENFA), classification and regression tree (CART) models, Movement Models, Bayesian Belief Networks, Maximum Entropy Models, Model Assessment and Evaluation, and more.

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Population and Conservation Genomics

W. Chris Funk

Recent advances in next-generation sequencing and bioinformatics are revolutionizing population and conservation genetics. Population genomics is the study of numerous loci to understand the roles of evolutionary processes (genetic drift, gene flow, selection, and mutation) that shape variation across genomes and populations. Conservation genomics is the application of genomics to address questions important in conservation and management. This course will focus on the growing literature in these related fields. The course format will be student-led discussion of the literature, with the goal of understanding the promise, limitations, and most exciting opportunities for using genomic approaches to address basic evolutionary and ecological questions as well as applied questions in conservation and management.

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Sagebrush Steppe Vulnerability to Climate Change

Cynthia Brown, Cameron Aldridge, Jeff Morisette and Dennis Ojima

The 1 credit hour course will take a multidisciplinary approach to studying the vulnerability of sagebrush steppe ecosystems to the effects of climate change. We will first build a foundation of understanding of the sagebrush steppe ecosystem and climate predictions for region. Then, informed by land managers collaborating with us, students will work in small teams to develop portions of a vulnerability assessment. Two topics of particular interest are greater sage grouse (Centrocercus urophasianus) and cheatgrass (downy brome, Bromus tectorum) and how they will be affected by projected climate variation and directional change. Other topics are possible, especially if land manager needs indicate their importance. The course is one node of a distributed graduate seminar being led by Peter Adler at Utah State University, which was first taught in 2012 and has nodes across the country. Students will have the opportunity to participate in the Department of Interior "Vulnerability Assessment under Climate Change" (VA_CC) class in Jackson, WY October 9-11. The students who do will report back to the rest of the class and will earn one (1) additional academic credit hour for their work. All students should initially register for 1 credit and it will be determined before the drop/add period ends which students will take the 2 credit option.

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Evolutionary Concepts in Conservation

George Wittemyer, Dana Winkelman

We will explore topics regarding the importance of evolutionary concepts in species management, conservation and recovery efforts through discussion of key concepts and review of literature (both classic and current). The literature on human driven evolutionary change will be reviewed, and discussed in light of how conservation decisions potentially influence the trajectory of life history evolution.

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Spring 2013

science, diplomacy and international policy in a rapidly changing world

Gillian Bowser, Karelyn Cruz - Agricultural Development Advisor

What is the interplay between science and diplomacy in a world facing the greatest environmental challenge known? Here we will explore the nexus between science, policy and diplomacy in the context on managing species and ecosystem resources across international boundaries. The course will combine a series of lectures by U.S. State Department and USAID personnel (in person and online) on current treaty negotiations on species from tuna to migratory birds. Students can expect to learn how ecology interfaces with diplomacy and with several guest lectures by AAAS Fellows in Science and Diplomacy, they will also learn how PhD sciences work and interact in the diplomacy world. In addition, they will meet professional scientists and recent PhD graduates who have chosen to work in the science and diplomacy field. Text and reading materials will be from active negotiations and students will be expected to conduct analysis of actual UN treaties as writing assignments.

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IDL Programming: Processing and Visualizing Data

David Fanning, Michael Lefsky, Jamie Fuller

Interactive Data Language (IDL) is an interdisciplinary, cross-platform, high-level programming language used to organize, analyze, and visualize complex numerical data. It is similar to MatLab, but has its origins in the analysis and processing of image data. IDL's array-oriented structure and general ability to read any type of data file makes it perfect for working with remote sensing data. This class will cover the basics of IDL programming with the goal of writing IDL programs that can be added to ENVI, a remote sensing application written in the IDL language, to extend its functionality. Topics will include the basics of IDL programming (defining parameters and keywords, program structure, graphics and file output, error handling, memory management, and algorithm development), plus object-oriented programming concepts and interactive (widget) program development. There will be an emphasis on image processing and/or working with satellite data. It is assumed the student is familiar with some kind of programming language, but prior IDL programming experience is not required.

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Understanding and Managing for Resilient, Adaptable Social-Ecological Systems: Designing Sustainable Natural Resource Management Strategies for Systems Undergoing Change

Dennis Ojima, Shannon McNeeley

This course will explore the conceptual and analytical frameworks, methods, and tools used to understand social-ecological systems in the context of climate variability and change. We will do this by exploring a set of natural resource case studies, and we will develop research plans to implement research on vulnerable communities and their natural resource assets. The intent of this course is to provide an interdisciplinary, integrated framework to address natural resource issues with a resilience-science based approach to deal climate driven transitions on ecosystem services and a more adaptive and sustainable management pathway. In working group and class discussions we will participate in a creative interdisciplinary activity to further understand and to apply the principles of resilience science and social-ecological system interactions to develop a framework for studying changing social ecological conditions affecting the sustainability of natural resources. Goal: The course goal is to explore useful frameworks that enable integrated analysis of social-ecological systems for natural management, which incorporate social adaptation and resilience principles to deal with climate and land use changes.. Purpose: Development of analytical frameworks, methods, tools, and research approaches which will lead to resilient social-ecological systems. These will incorporate concepts which lead to understanding how to manage systems through transitional changes of ecosystem services and climate impacts.

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Fall 2012

Judicious Sentencing

Dan Brinkley, Tom Stohlgren

Even the biggest ideas in ecology are communicated by strings of relatively small, simple words. Clear packaging of ideas into word strings requires skill in designing sentences and paragraphs. This seminar will sharpen your ability to craft clear and graceful sentences and paragraphs. Each week we'll have a series of sentences (and later, paragraphs) for you to polish and share with other students. We'll discuss how the various revisions enhance clarity, and why. We'll try to learn from some of Limerick's Rules of Verbal Etiquette, including:

  • "When the passive-voice verb tries to drain the energy from your sentences, you must rescue the sentences and bring them back to life with active verbs."
  • "Words hate it when you ask them to convey unclear thoughts or not thoughts at all. The are very uncomfortable when readers ask them, 'What on earth are you trying to say?' and they have no answer to give."
  • "Weak subjects and verbs tremble and strain to hold up under the weight of important content. Kindness often requires their author to relieve them of this impossible task and replace them with strong subjects and strong verbs."
  • "When you ask a group of sentences to form a paragraph, they expect to arrive in the paragraph and find that they have a lot in common. They expect, moreover, to find that one sentence is in chargeÃ?¢?Ã?¦"

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Climate Science and Resource Management

Jeff Morisette, Dennis Ojima

Seminar series: The course objectives are twofold: (1) expose students to state-of-the-science research providing the best available climate science and synthesis to inform energy, land, and cultural resource management within the North Central Domain and (2) present collaborative opportunities between the students, lecturers, the North Central Climate Science Center Stakeholders, and University consortium for integrated vulnerability and adaptation research.

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Niche Models

Cameron Aldridge, Barry Noon, Sunil Kumar

This is a broad-ranging seminar course designed to expose students to the variety of quantitative and statistical techniques available to assess species-habitat relationships. Niche models are known by a variety of names including species distribution models, habitat relationship models, bioclimatic envelopes, and others. The concepts and application of these models are not new, although there are many new statistical algorithms to estimate niche relationships. They all rely on the concept of the niche - the set of environmental conditions in which a species can survive and persist. They are particularly topical today because of concerns over the effects of climate change, energy development, and invasive species on the distribution and abundance of native species. Our goal is to expose students to a suite of different analytical approaches so as to give them a new tool set for future design of experiments and analyses of data. The course structure is one 50 minute period. The first portion of the class will consist of a brief introduction to a topic (~15 minutes). This is intended to cover some of the theoretical and conceptual foundations of a given statistical algorithm used for niche modeling, and provide an overview for a key paper we will read on the specific topic. The remainder of the class will be a discussion on the topic and the key paper(s), lead by that week's presenters (faulty or students). Students will lead one class presentation and discussion. Topics discussed in this course could include resource selection functions (RSFs), resource utilization functions (RUFs), occupancy models, Habitat Suitability Index (HSI) models, count-based models (Poisson and negative binomial regression), survival models, Ecological Niche Factor Analyses (ENFA), classification and regression tree (CART) models, Movement Models, Bayesian Belief Networks, Maximum Entropy Models, Model Assessment and Evaluation, and more.

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On The Changing Arctic: The effects of climate change on the Arctic ecosystems

Joe von Fischer, Aki Koyama, Sam Dunn

Keywords: Climate Change, Biogeochemistry, Microbial Ecology, Plant-Soil-Microbe interactions, Permafrost, Hydrology, Plant Communities Description: The Arctic is warming at a faster rate than the rest of the planet. With this warming come changes in plant community composition, soil characteristics, permafrost, and microbial activity. What is uncertain is how the current paradigm will be affected by this change. This course seeks to review and synthesize current literature on the topic of Arctic warming, plant community shifts, permafrost hydrology, and microbial ecology in hopes of unifying threads of research from different sub disciplines of ecology. The structure of this course is guided discussion. Participants will take turns leading class and selecting papers to critically discuss and analyze. Through the course, the participants will co-author a comprehensive review on this subject.

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The political economy of technological innovation in agriculture and natural resources

Greg Graff

The innovation and adoption of new technologies, particularly in agriculture and natural resource industries, can be both beneficial and detrimental to large scale environmental sustainability. This seminar will guide students in the reading and discussion of classic and current academic analyses--drawing largely from the economics, policy, and ecology literatures. Topics to be considered will include the political influence of various economic, social, and environmental interests on government science and innovation policies, the impact of such policies on the innovation and adoption of new technologies, and evaluation of the impact of technologies on environmental sustainability.

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Current Topics in Acoustic Ecology and Engineering

George Wittemyer, Graeme Shannon

Natural ecosystems are being increasingly altered by human activities. Research has typically focused on the repercussions of physical impacts, but increasingly the preponderance and ramifications of acoustic alterations to ecosystems is recognized. This seminar will explore applied and evolutionary aspects of acoustic ecology as well as discuss approaches for characterizing acoustic processes. The goal of this seminar is to expose students to theory, approaches, and critical questions in the discipline of acoustic ecology. Class will be structured around discussion of key literature where the first portion of the class will consist of a brief introduction of the theoretical and conceptual foundations of a topic followed by discussion of the key paper(s) and topic, lead by that week's presenters (faulty or students). Students will lead one class presentation and discussion.

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Spring 2012

Examining Spatial Variability: Snowpack and Forest Properties

Steven Fassnacht

The objective of the course is to help students understand the concept of spatial variability by measuring snowpack and forest properties in the field. In group discussions, a spatial sampling strategy will be developed. Snow depth and other snowpack properties will be measured together with observations of the canopy, including density and tree mortality, where applicable. These field data will be collated and the students will work together to analyze the spatial variability. Grading will be based on the write-up for the proposed sampling and a brief report on the spatial variability. Assessment given as Pass/Fail.

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Current Human Dimensions Research

Esther Duke, Arren Allegretti

The Human Dimensions of Natural Resources Department will host a weekly research seminar series where faculty, advanced graduate students, and guests will present past or current research initiatives and future research ideas. Interaction with new research is of great importance to one�??�?�¢??s scholarly growth. These forums enable and encourage the formation of collaborations, peer feedback and suggestions, and the expansion of research knowledge. Focus: Human Dimensions of Natural Resources research emphasizes understanding the mutual interdependence of humans and their physical and social environments and attending to the needs and values of humans, human society and culture as it relates to the natural environment. The seminar presentations will be designed to inform and stimulate discussions on current and emerging HD research topics including such human-wildlife conflict, ecological economics, and coupled human-environment systems. Invited speakers will be encouraged to present their in-progress work since we want students and colleagues to learn about not just the findings but also the interdisciplinary research process. In addition this will give our speakers the opportunity to receive input from an interdisciplinary audience. HDNR Research Topic Examples: Climate Change Communication, Who Cares About Wildlife? Wildlife Values), Ecosystem Services, People and Places (Spatial Relationships),Emerging Zoonotic Disease, Sustainable Tourism, Nature and Child Development, Soundscapes and Natural Sounds, Protected Area Management, Indigenous and Local Ecological Knowledge, Open Space Management, Tourism Impacts,Human-Wildlife Conflict * This course is graded pass/fail. In order to receive ECOL 592 credit for the seminar, students attend at least 13 of the 15 seminars and write a 1-2 paragraph response paper on each seminar.

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Outreach in Ecology

Colleen Webb

The objective of this course is to help students understand the role of outreach in a research career and to engage in an outreach activity. We will address: What is outreach? Why should I engage in outreach? How do we balance outreach in a research career? The course will include discussion with guests who have special outreach expertise, engagement in a coordinated outreach activity and class presentation on the outreach experience. Outreach opportunities will be partnered with Poudre School District and the City of Fort Collins.

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Science at the Fringe

Dan Binkley, Tom Stohlgren

By definition, the frontiers of science are fraught with uncertainty; we can create more clever ideas than reality may endorse. How do we bring clarity to scientific thinking in ways that support creativity but retain skepticism? This seminar explores some aspects of classic logic, philosophy of science, and how scientific thinking has been harnessed (or not) in ecology.

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Foundations in Evolution

Colleen Webb

This semester we will be working through some fundamental and often classic papers in evolution. I believe that knowing about classic theory and experiments helps us to better understand the contemporary literature as well. How can we know where we are going if we do not know where we have been? The objective this semester is to help students build a broad and basic background in key areas of evolutionary research. I have collected a list of fundamental papers and divided them into eleven subject areas. We will cover at least one paper from each subject area, and enrolled students will be expected to lead discussion on at least one paper. There will be a number of important papers that we will not have time to read, but I hope that this discussion group will help you appreciate the value of a broad knowledge of the fundamental literature and that you will continue to read it. Subject areas: Evolution of Populations, Systematics, Phylogenetics, Macroevolution, Natural Selection, Speciation, Hybridization, Molecular Evolution, Neutral Theory, Evolution and Development, and Scientific Method/Philosophy.

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Current Research in Fire Ecology

Dr. Monique Rocca (GDPE, ESS), Dr. Chad Hoffman (FRS)

This course will cover current topics in the field of fire ecology, and will provide opportunities for students to interact with scientists and managers. Among other topics, we will discuss the interactions of climate change and fire, interactions between bark beetles and fire, Burned Area Emergency Response (BAER) treatments and effectiveness, challenges to modeling fire behavior, and wildland fire management. This course will operate on a two-week cycle. The first week, we will discuss peer-reviewed research articles. The following week will feature a presentation by a scientist and a chance to discuss his/her research as a group. Anyone with an interest in fire ecology is encouraged to sign up.

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Framing of ecosystem science and sustainability

Dennis Ojima

This course will explore the scope of ecosystem science as basis for transitioning toward sustainability. Fundamentals of ecosystem sciences will discussed in light of current transitions in social-ecological systems. Concepts related to coupled natural and human systems, ecosystem structure and function, thresholds, resilience, adaptive capacity, etc will be explored through examples and readings. Students will explore these concepts through discussion and leading discussion on specific topics related such as primary production and human appropriation of NPP; the effects of N loading and limits; water, ecosystem services and society; and others. Discussions will look at how society can reshape its relationship to ecosystem services in ways that can lead to sustainability. Additional product will be compiling a bibliography on these topics

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Fall 2011

Readings on Bayesian analysis of ecological models and data

Tom Hobbs

Students and faculty will discuss current literature applying Bayesian hierarchical models to research in ecology.

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Plant-insect interactions

Ruth Hufbauer, Andrew Norton, Paul Ode

We will cover classic and recent readings on the evolutionary ecology of interactions between plants and herbivorous insects

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Litter decomposition: re-considering paradigms and methods

M. Francesca Cotrufo

Litter decomposition is a fundamental process for the functioning of ecosystems and thus has been intensively studied for many decades. However, established paradigms and study methods have recently been questioned and even refuted. The course will discuss litter decomposition in light of the most novel and emerging findings, with the goal to define open questions, new paradigms and effective methods of study.

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Generation and analysis of microsatellite data

Mark P. Simmons

This semester we will start with secondary literature (reviews) and then move to the primary literature on generating and analyzing microsatellite (SSR) data for ecological and evolutionary studies.

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Spring 2011

Biotic influences on geomorphic process and form

Ellen Wohl

Geomorphologists have recently begun to explore whether there is a â??topographic signature of life,â?? or specific landscape features that reflect the activities of living organisms. We will read and discuss selected papers focusing on how plants and animals influence geomorphology, including hillslope and channel process and form. The seminar will meet for 50 minutes once a week. Participants will be expected to read the selected paper each week and participate in discussion of that paper and related issues, as well as choosing a paper and leading the discussion during one class meeting.

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Climate change effects on riparian ecosystems in western North America

Pat Shafroth, Lindsay Reynolds, Laura Perry

This course will explore potential direct and indirect effects of climate change on riparian ecosystems in western North America. We will discuss how predicted changes to temperature, atmospheric CO2, hydrologic regimes, human water demand and dam regulation might influence riparian ecosystems. We will also critique modeling approaches used to assess climate change effects on rivers and riparian systems. Class time each week will include short lectures and discussion of primary literature readings.

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Ecological Niche Models

Cameron Aldridge, Sunil Kumar

This is a broad-ranging seminar course designed to expose students to the variety of quantitative and statistical techniques available to assess species-habitat relationships. Ecological niche models are known by a variety of names including species distribution models, habitat relationship models, bioclimatic envelopes, and others. The concepts and application of these models are not new, although there are many new statistical algorithms and machine learning methods to estimate niche relationships. They all rely on the concept of the niche�¯�¿�½the set of environmental conditions in which a species can survive and persist. They are particularly topical today because of concerns over the effects of climate change and invasive species on the distribution and abundance of native species and ecosystems. Our goal is to expose students to a suite of different analytical approaches and their applications so as to give them a new tool set for future design of experiments and analyses of data. The course structure is one 50 minute period per week. The first portion of the class will consist of a brief introduction to a topic (~15 minutes). This is intended to cover some of the theoretical and conceptual foundations of a given statistical algorithm used for niche modeling, and provide an overview for a key paper we will read on the specific topic. The remainder of the class will be a discussion on the topic and the key paper lead by that week�¯�¿�½s presenters (instructor, students, or visiting speaker). Students will lead one class presentation and discussion. Topics discussed in this course could include resource selection functions (RSFs), resource utilization functions (RUFs), occupancy models, habitat suitability index (HSI) models, count-based models (Poisson and negative binomial regression), survival models, generalized linear models (GLMs) and generalized additive models (GAMs), classification and regression trees (CART), random forest, boosted regression trees, maximum entropy modeling (or Maxent), Ecological Niche Factor Analyses (ENFA), genetic algorithm for rule-set production (GARP), quantile regression, Bayesian belief networks, model assessment and evaluation, and more.

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Evolution of ecological limits

Angert, Amy

We will break the semester into 3 sections examining the very different spatial and temporal scales that have been used to address this topic: 1) niche evolution across habitat gradients, 2) the evolution of geographic ranges and 3) ecological controls on net diversification rates across clades. At the start of each section, we will have an in-depth review of basic theory and important past work on the topic. Subsequent weeks will focus on discussion of recent primary literature, with an emphasis on empirical tests in natural systems.

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Judicious Sentencing

Dan Binkley, Tom Stohlgren

Even the biggest ideas in ecology are communicated by strings of relatively small, simple words. Clear packaging of ideas into word strings requires skill in designing sentences and paragraphs. This seminar will sharpen your ability to craft clear and graceful sentences and paragraphs. Each week we'll have a series of sentences (and later, paragraphs) for you to polish and share with other students. We'll discuss how the various revisions enhance clarity, and why. We'll try to learn from some of Limerick's Rules of Verbal Etiquette, including: "When the passive-voice verb tries to drain the energy from your sentences, you must rescue the sentences and bring them back to life with active verbs." "Words hate it when you ask them to convey unclear thoughts or not thoughts at all. They are very uncomfortable when readers ask them, 'What on earth are you trying to say?' and they have no answer to give." "Weak subjects and verbs tremble and strain to hold up under the weight of important content. Kindness often requires their author to relieve them of this impossible task and replace them with strong subjects and strong verbs." "When you ask a group of sentences to form a paragraph, they expect to arrive in the paragraph and find that they have a lot in common. They expect, moreover, to find that one sentence is in charge..."

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Ecology in Extreme Environments

Diana Wall, Shane Kanatous

Upon first sight, Antarctica strikes the observer as barren, cold and lifeless. However, scientific research has shown the continent to have a rich marine life including penguins and seals, and uniquely structured terrestrial ecosystems. Antarctica has become a model for understanding the biology and role of species in ecosystems. What physiological adaptations allow marine and terrestrial organisms to survive? How will global changes affect the species and ecosystems and how does this inform our knowledge of other ecosystems? This upper division/graduate class will explore these questions and more through a series of 2 hr discussions and lectures of the current and classic Antarctic literature. Attendance is also required for 2 of 3 talks by Colorado Antarctic Scientists as part of the Antarctic lecture series held at the Public Library throughout the semester.

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Ecology, Gender, Equity and North-South Exchange: Social and Human Dimensions of Global Climate Change

Gillian Bowser, Osman Hamdan

This seminar will focus on topics like the impact of natural resource (mis)use in developed countries on climate change and resource use and availability in developing countries as well as the impact of terms of trade and unequal exchange. Students will explore the UN Framework Convention on Climate Change and how it relates to vulnerable populations. Students will do oral presentations for the majority of their grade. Class participation is required.

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Fall 2010

The Fringe of Knowledge: Science at the Frontiers of Ecology

Dan Binkley, Tom Stohlgren

Ecology is the science of integrating biology and environment into dynamic systems. As ecologists, we spend a great deal of time investing the details of biology and environments, but what about that "science" word? How can an understanding and appreciation of the philosophies and realities of Science strengthen our work in ecology, and leave us less prone to believe in unlikely stories? This seminar will use readings and discussions to hone our understanding of logic, philosophy, and what this has to do with high-quality science and ecology. If the seminar fills up, a second section may be opened (check back).

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Readings in Evolutionary Behavioral Ecology

Lisa Angeloni

This seminar will provide an introduction to the field Evolutionary Behavioral Ecology, through student-led discussions of readings from a new edited volume on the topic.

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Current Topics in Wildland Fire Ecology and Management

Dr. Monique Rocca

This one-credit seminar will be offered during the Fall 2010 semester within the Graduate Degree Program in Ecology and FRWS. This course will be organized and coordinated by the Student Association for Fire Ecology at CSU. Anyone with an interest in this topic is encouraged to register or participate, registration is not necessary for participation. This course will be offered in association with SAFE, though everyone is welcome to participate. Students taking the class for credit will be expected to read assigned papers and participate in class discussions/facilitation, and field trips (if offered). Performance will be evaluated based on participation and engagement. This course will be student-led and topics can change or evolve as the group's interest dictates. Students will share in course topic selection and discussion facilitation. Possible topics include: Global Climate Change: Implications for fire & carbon management Smoke Emissions /Air Quality Concerns / Smoke Modeling Recent changes in fire management policy : Historical context and future directions Overview of Decision Support Systems (strengths and weaknesses) Restoring Ecosystem Processes in fragmented landscapes Beetles/Drought mortality - Implications for fire behavior and management Guest speakers will be invited as available and applicable. A field trip may be offered to a recent fire in the area (Cow Creek Fire?) based on interest and scheduling availability.

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Pathways to adaptation to global change: Nexus among livelihoods, sustainable development, and ecosystem services

Dennis Ojima, Kathleen Galvin

Graduate Seminar: Adaptation strategies to climate change in human-environment systems need a more integrative approach which links livelihoods, ecosystem services, and sustainable development goals. The reading selected for this seminar will look at various frameworks being developed to cope with the challenges in development global change and to better assess how livelihoods are being affected and how ecosystem services need to be conserved as part of adaptation strategies.

Initial discussions will cover several key publications and the following discussions will look at various readings selected by the class.

The discussion group will consist of eight 2-hour discussion periods held during the semester. Schedule to be developed after our first meeting.

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Current topics in Microbial Biogeochemistry

Mary Stromberger, Joe von Fischer, Matt Wallenstein

Students will meet weekly to discuss current and classic papers at the interface of microbial ecology and biogeochemistry

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Readings in Quantitative Genetics

Kim Hoke, W. Chris Funk

In this course, we will discuss the book "Introduction to Quantitative Genetics" in the beginning part of the semester and read primary literature later in the course, mainly with a focus on genetics of outbred organisms and experimental design/analysis.

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Spring 2010

Landscape Genetics

Chris Funk, Melanie Murphy

Landscape genetics is the integration of landscape ecology and population genetics to address questions related to species' ecology, connectivity, population decline, patterns of genetic variation, and population dynamics. Implementation of landscape genetics requires a broad range of interdisciplinary skills and development of new analytical tools. The goal of the course is to build the skills necessary to perform robust landscape genetics analyses and to address current problems in landscape genetics. This course is a unique opportunity facilitated by the National Center for Ecological Analysis and Synthesis (NCEAS) as a Distributed Graduate Seminar (DGS). Sections of the course are being offered in the United States, Canada, Switzerland and France. The course will consist of lectures (given by sections leaders who are the expert on the topic), discussion of primary literature, hands-on exercises, and a project collaborating with an interdisciplinary students/faculty leaders across sections. Students can register for either 2 or 3 credits (project is required for 3 credits).

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Foundations in Evolution

Colleen Webb

This semester we will be working through some fundamental and often classic papers in evolution. I believe that knowing about classic theory and experiments helps us to better understand the contemporary literature as well. How can we know where we are going if we do not know where we have been? The objective this semester is to help students build a broad and basic background in key areas of evolutionary research. I have collected a list of fundamental papers and divided them into eleven subject areas. We will cover at least one paper from each subject area, and enrolled students will be expected to lead discussion on at least one paper. There will be a number of important papers that we will not have time to read, but I hope that this discussion group will help you appreciate the value of a broad knowledge of the fundamental literature and that you will continue to read it. Subject areas: Evolution of Populations, Systematics, Phylogenetics, Macroevolution, Natural Selection, Speciation, Hybridization, Molecular Evolution, Neutral Theory, Evolution and Development, and Scientific Method/Philosophy.

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Readings in Microbial Ecology and Biogeochemistry

Joe von Fischer

This reading and discussion seminar will explore ideas about how improved understanding of biogeochemical processes can come from studying microbial ecology.

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Assessing Socio-Ecological Values for Water Management

Melinda Laituri, LeRoy Poff

Within a research framework, how do we bridge and articulate the gap between social values and ecological values for water management within the context of climate change??? There is a rich literature that addresses the role of water governance focusing on water as a human right, the hydro-social cycle that links human use and water supply, and the role of ecosystem services and ecological values in water resource management. This literature needs to be explored to ascertain the contributions to balancing human needs with ecosystem services. This class will examine this body of knowledge to identify where there are overlaps and gaps in the research frameworks to better understand the role of water management/planning in the 21st C. Students will examine the following set of questions with the aim to: 1) develop a white paper that clarifies the complexity of this issue and 2) identify the growing literature that contributes to understanding those links: Ecological science: What are ecosystem services in rivers? How are they defined/measured? How do we distinguish between short-term measures and long-term sustainability? Social science: What does the public care about and how much are we willing to pay for it? How do we place EGS in a valuation context? How do we 'harmonize' this translation to reflect ecological science? How does the social-ecological interface get translated to management? Governance issues: What are the institutional linkages between science and policy and how can science inform policy to develop better arguments to incorporate the ecosystem perspective into human-focused environmental governance structures?

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Adapting for Sustainability

Dennis Ojima

The challenges we face today as a society are unheralded due to the pace at which human activities are affecting the climate, biogeochemical cycles, and biodiversity throughout the globe. The current pace of change to the earth system and to the climate will express itself over the coming decades, if not centuries. Finding the appropriate adaptation strategies under these changing conditions are necessary now. In addition, our ability to address challenges to sustainable development is increasingly being hindered due to growing consumption rates of natural resources, population growth, and environmental degradation. As we attempt to achieve our goals for sustainable development, we are faced with continuing changes in climate that we need to adapt to take advantage of emerging opportunities and off-set climate impacts. The course will consist of selected reading which will be presented as in lecture and discussed in panel discussions (led by students). Invited lectures will also be incorporated on key topics to provide expert insights on the science, policy, and societal issues. Lectures and discussions will cover recent thoughts on adapting to climate change and meeting goals of sustainable development. Class will meet once each week for two hours; day and time to be announced.

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Ecology and Evolution of Parasitism

Kate Huyvaert, David Eads

This is a seminar course exploring emerging ideas in disease ecology including ecoimmunology, life history variation and disease, individual fitness and population-level consequences of disease, and contemporary community and ecosystem-level issues in disease ecology. Complementary readings from the primary literature will be discussed. This course will meet once per week, first 8 weeks of the semester, meeting time to be determined at the first meeting

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Fall 2009

R for Evolutionary Analysis

Rachel Mueller

Group-led computer lab-based course in which we will work (as a group) through various uses of R in evolutionary analysis.

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Dendrochronology: Methods and Applications

Peter Brown, Carissa Aoki

Tree-ring data have proven critical for documenting and evaluating longer-term climatic and ecological dynamics. This course will combine lectures, readings, and hands-on application to look at the basics of tree-ring research methods, with an emphasis on reconstructing climate and forest and fire histories. Field sampling and data analysis for the course will have specific application to forest management and environmental education at the Shambhala Center, a Buddhist retreat north of Fort Collins. Articles for discussion will be selected to highlight current applications of tree-ring data.

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Wildlife - Habitat Relationships

Cameron Aldridge, Barry Noon

This is a broad-ranging seminar course designed to expose students to the variety of quantitative and statistical techniques available to assess wildlife-habitat relationships. Ultimately, the data one collects and the question you ask will somewhat dictate the analytical modeling approaches you will have available to you. In many cases however, there are multiple options for analyzing your data. Our goal is to expose students to a suite of different analytical approaches so as to give them a new tool set for future design of experiments and analyses of data. We will focus on key papers to discuss concepts and analyses. Students will present key concept papers and lead the associated discussion. While many of the modeling approaches we discuss will inherently have spatial or applications, we will also discuss non-spatial techniques. Topics discussed in this course could include resource selection functions (RSFs), resource utilization functions (RUFs), occupancy models, Habitat Suitability Index (HSI) models, count-based models (Poisson and negative binomial regression), survival models, Ecological Niche Factor Analyses (ENFA), Movement Models, Bayesian Belief Networks, and more.

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Disturbance Ecology of the Colorado Front Range Forests

Monique Rocca, Matt Diskin

The seminar will consist of two or three field trips to Colorado's Front Range forests to learn about different disturbance regimes. Field trips will be lead by local professors and researchers who will talk about their research. Two trips are currently planned: Rocky Mountain National Park: Jason Sibold, a professor in the Department of Anthropology, will lead a trip to discuss fire regimes and beetle disturbances in the high elevation forests of the Park. This will be a one day field trip leaving early in the morning on Friday, September 11. Hayman Fire: This field trip will consist of a two day excursion to the site of the Hayman Fire. Lee MacDonald, a professor in the Department of Forest, Rangeland, and Watershed Stewardship, will take a day to talk about the effects of fire and management practices on soils and hydrology. On the other day, Paula Fornwalt, an ecologist with the Rocky Mountain Research Station, will talk about understory vegetation in the burned area. We will depart around 8:30 on Friday, October 9 and return on Saturday, October 10. One additional trip is currently being planned for later in the semester. Details will follow soon.

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Spring 2009

Application of spectral analysis methods to data interpretation

Ellen Wohl, Dennis Harry

We will spend the first part of the semester discussing the basics of spectral analysis; different analysis methods, types of data that can be analyzed, and interpretation of analysis. We will spend the last third of the semester going over examples from the literature. We hope to draw on a braod range of examples that reflect participant interest; examples include time-series data and 1d (linear) and 2d spatial data.

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Biogeography and biogeochemistry of arctic and alpine ecosystems Part II

Heidi Steltzer, Matt Wallenstein, Jessica Ernakovich

This will be an interdisciplinary ecology seminar on the biogeography of plants and microbes in arctic and alpine ecosystems and its influence on biogeochemical cycles. The aim of the course will be to understand the similarities and differences among plant and microbial communities in arctic and alpine ecosystems; the physical and chemical processes that differentiate these systems; and the potential influence of biogeography on ecosystem response to climate change. This course is a continuation from the Fall semester. Students will continue to identify climate data sets from around the world to use in a comparative analysis of arctic and alpine environments, to complete a meta-analysis of the data, and to lead discussions on key articles.

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Molecular Ecology Seminar

Amy Angert, Chris Funk

This is a discussion group for graduate students enrolled in BZ481 Molecular Ecology. This course will provide a broad introduction to the use of molecular markers to address questions in ecology, evolution, behavior and conservation. We will begin by learning about genetic variation and basic population genetic principles, then we will delve into the applications of genetic markers for understanding relatedness, population and community structure, and conservation of biodiversity. Finally, we will discuss practical issues that arise when applying and interpreting molecular apporaches in ecology. The course is designed for graduate students and advance undergraduates. The format will be a combinaton of lecture and discussions.

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Current Topics in Tree Physiology

Mike Ryan, Bill Bauerle

Present background and discuss papers on current topics in Tree Physiology. Learn to use common tools in Tree Physiology: LiCor 6400, Leaf Water Potential, soil respiration.

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Global Change and the Developing World: Ecosystem and Societal Impacts, Adaptation and Mitigation

Julia Klein, Niall Hanan

This course will investigate the potential impacts of global change on climate, ecosystems and societies in the developing world where limited access to technological and financial solutions may reduce opportunities for mitigation and adaptation, and thus increase vulnerability. We will focus on how changes in rainfall, temperature and other climatic variables in Africa, Asia and South America will impact natural, pastoral and agricultural communities and landscapes, and lead to changes in productivity, cropping patterns, food security and economics. Students will analyze how climatic and anthropogenic change will likely influence land use, water resources, human health and equitability. The class will seek to develop an in-depth understanding of likely trends in ecological and social wellbeing in less developed countries, and contrast these to likely trends in more affluent regions of the world where resources are likely to be available to mitigate and adapt to changing conditions.

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Ecology and Equity in Africa and North America

Mike Coughenour, Gillian Bowser

This seminar course will examine linkages between environmental equity and ecosystem processes in Africa and North America. Environmental equity is concerned with the disproportionate distribution of environmental problems among subpopulations at local through global scales. Inequity arises when some subpopulations such as the poor or minorities are disproportionately exposed and vulnerable to environmental changes arising from global warming, pollution, and overuse of natural resources due to population growth. The poor in many parts of Africa and North America are closely tied to the land and natural resources for their livelihoods, so inequitable access to opportunities for generating wealth from natural resources can be both a cause and a consequence of poverty. This seminar course will interweave these issues through discussion and comparative analyses of impoverished peoples and the ecosystems they are a part of within a rural Africa and North America. It will also explore differences and similarities among subpopulations, such as minorities vs. majorities, and the poor vs. the affluent, in access to knowledge and participation in the ecological sciences.

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Multivariate Analysis for Community Ecology

Monique Rocca

In this course, students will learn popular techniques for analyzing multivariate ecological data, with an emphasis on ordination and classification of multivariate data characteristic of community ecology. Students will gain a conceptual understanding of multivariate analyses and interpretation, and will practice implementing these techniques on a dataset of their choice. By the end of the semester, students will be comfortable working with the Pcord software package and have the skills necessary to perform a multivariate analyses that will stand up to peer review. We will meet weekly as a group for informal lectures, at least for the first half of the semester. The second half of the semester will be more flexible in order to pursue topics of interest to the group and allow students time to work with their own data. As a final project, students will write a journal-style manuscript (which may lead to a thesis chapter or a publication).

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Fall 2008

Riparian Ecology in the Arid and Mountain West

David Cooper, Kurt Fausch, LeRoy Poff

Lessons Learned from the 1988 Yellowstone Fires

Bill Romme

Lessons Learned from the 1988 Yellowstone Fires

Evolution

Mark Simmons

Evolution

Judicious Sentencing

Dan Binkley, Tom Stohlgren

Judicious Sentencing

Journal Club: Gene Flow

John McKay, Chris Funk, Amy Angert

Journal Club: Gene Flow

Biogeography and Biogeochemistry of Arctic and Alpine Systems Part I

Matt Wallenstein, Heidi Steltzer, Jessica Ernakovich

Biogeography and Biogeochemistry of Arctic and Alpine Systems Part I

IPCC AR4: The State of Global Climate Change

Peter Brown

IPCC AR4: The State of Global Climate Change

Spring 2008

Treeline Ecology and Ecophysiology

Jonathan Coop

Dendrochronology: Methods and Applications

Peter Brown

Dendrochronology: Methods and Applications

Ecology in Extreme Environments

Diana Wall, Shane Kanatous

Ecology in Extreme Environments

Genes to Ecosystems

Alan Knapp, John McKay, Seth Munson

Genes to Ecosystems

Genetics of Small Populations

Mike Antolin, John McKay

Genetics of Small Populations

R for Ecologists: A Participatory Primer

Tom Hobbs

R for Ecologists: A Participatory Primer

Fall 2007

Exploring Ecological Data Sets

Tom Stohlgren

IPCC AR4: The State of Global Climate Change

Peter Brown

IPCC AR4: The State of Global Climate Change

Getting Control of Your Data

Jim Graham

Getting Control of Your Data

Neutral Theory in Ecology

Colleen Webb

Neutral Theory in Ecology

Advanced Topics in Soil Ecology

Matt Wallenstein

Advanced Topics in Soil Ecology

Science and Society in Search of Sustainable Development: 20 Years after the Bruntland Report

Dennis Ojima

Science and Society in Search of Sustainable Development: 20 Years after the Bruntland Report

Spring 2007

Watershed Processes in Subalpine Forest Ecosystems:Overview of Hydrological, Biogeochemical, and Ecological Research at the US Forest Service Fraser Experimental Forest

Chuck Rhoades, Kate Dwire, Rob Hubbard

Historical Conditions in Valley Bottoms of the Colorado Front Range

Ellen Wohl

Historical Conditions in Valley Bottoms of the Colorado Front Range

Inferring the Evolutionary History of Weedy and Invasive Species

John McKay

Inferring the Evolutionary History of Weedy and Invasive Species

Judicious Sentencing

Dan Binkley

Judicious Sentencing

Evolutionary Ecology of Parasitism

Mike Antolin, Liz Harp

Evolutionary Ecology of Parasitism

Fall 2006

Molecular Ecology

Michael Douglas, Marlis Douglas

On the Origin of Species: The Book and the Current Debate

Ruth Huffbauer

On the Origin of Species: The Book and the Current Debate

 

Current Offerings

Current ECOL 592 course descriptions available on the ECOL 592 page.