University of Michigan
Department of Ecology and Evolutionary Biology

Interrogating Data With Models (Aaron King)

Ecologists are frequently taught statistical recipes that can be used to analyze data, e.g., correlation, regression, analysis of variance. These classical methods have been designed with analytical tractability foremost in mind. The assumptions on which they depend are such that they typically afford only an oblique perspective on the specific ecological questions we wish to answer. This is a pity, since hard-won data are effectively squandered when we can ask only crude questions of them.

Advances in computational power over the last decades have brought more complex statistical procedures within the realm of the possible such that it is now possible to design statistical tests that directly answer the ecological questions we ask. This is evident from the fact that the ecological literature now abounds with references to likelihood, Bayesian inference, and information-based model selection.

In this course, students will have an opportunity to apply these approaches to questions they themselves find interesting. We will study a number of examples in which we have to

1. refine scientific questions into statistical questions by means of mathematical models
2. put these models to the test by bringing them into risky contact with data

Course work will consist of readings from several texts (see below) and from the primary literature, a number of computer labs, and a project. It is hoped that advanced graduate students will take this opportunity to view their data in new ways through the use of models.

Texts:

• Bolker (preprint) "Ecological Models and Data in R"
• Hilborn and Mangel (1997) "The Ecological Detective"
• Turchin (2003) "Complex Population Dynamics"
• Burnham and Anderson (2002) "Model Selection and Multimodel Inference", 2nd ed.

Prerequisites:

• A burning scientific question.
• Willingness to engage with others in thinking about ecological questions.
• Willingness to think and talk about the philosophy of science.
• Some numerical or statistical computing experience.
• Candidate standing.
• Calculus.

For more information, please contact the instructor at kingaa@umich.edu

Modeling and Programming for Ecology and Evolutionary Biology (Annette Ostling)

Increasingly, the ability to translate between qualitative hypotheses and their more exact expression in the form of mathematical equations is becoming an essential skill for all biologists.  Subsequently, the ability to program a computer is becoming another essential skill.  The analysis of these mathematical models, for the purposes of gaining fundamental insights into biological phenomena and testing predictions against data, very often requires the use of computation. The key goals of this course are to teach students how to 1) understand and develop basic mathematical models of ecological and evolutionary phenomena, and 2) analyze those mathematical models using a combination of "pencil and paper" and computational approaches.  This course will take an example-driven approach, teaching any mathematical concepts beyond calculus needed to understand example mathematical models in ecology and evolutionary biology, as well as assuming no prior knowledge of programming.  The course will primarily make use of the R software environment, a freely available resource, and will also introduce students to the use of campus clusters.  Some very basic data manipulation and statistics using R will be covered, but the focus of the course will be on mathematical modeling and using R to analyze mathematical models, rather than the statistical analysis of data.

For more information, please contact the instructor at aostling@umich.edu

This course introduces students to the field of evolution and development, with an emphasis on genetics as a unifying force. After reviewing fundamental principles in developmental and evolutionary biology, papers from the primary literature investigating the molecular mechanisms responsible for evolutionary change will be discussed. The course provides the opportunity to learn about the basic principles and latest discoveries in the burgeoning field of evolutionary developmental biology. This course will also integrate material presented in both EEB and MCDB courses, providing a bridge between disciplines and helping students to develop a more holistic view of biology. Finally, the format of the course explicitly emphasizes the development of critical thinking and written and oral communication skills. Also view a previous syllabus.

Molecular Ecology is an academic discipline that links research in ecology and evolution through the use of DNA markers. This class surveys the most important DNA markers and analytical methods currently used in Molecular Ecology. Topics include population structure, kinship, parentage, community phylogeny, phylogeography, microbial ecology and species discovery. This course explores key topics in molecular ecology through lectures, discussion of primary literature and analysis workshops. The topics include population structure, phylogeography, kinship and parentage analyses, species discovery, ancient DNA, microbial ecology and community phylogeny. Students will learn to evaluate the utility and limitations of different DNA markers, and they will be encouraged to evaluate the use of these markers in their own research areas. Students are expected to write a short paper that highlights use of DNA markers or genetic analyses in their own area of interest. Some background knowledge in evolution, genetics and statistics is required. Grading is based on class participation, quizzes, problem sets and presentations.

This course aims to give students an advanced and updated perspective of plant evolution on the following topics: phylogenetic concepts, a phylogeny of photosynthetic life, evolution of genomes in plants, evolution of development (molecular genetics, biochemistry, and physiology), and evolution of interaction of plants with their abiotic and biotic environment.

This course will focus on the ways environments shape the behavior and life histories of animals. Because environments pose constraints, behaviors have "better" and "worse" impacts on an organism's survival and reproduction. This course will consider hypothesis in five areas.

Ecology, systematic and identification of trees, shrubs, and vines are studies in weekly field trips to diverse Michigan ecosystems--including upland, wetland, and floodplain forests. Lectures focus on glacial landscape history, biogeography, and ecology of Michigan forests.

Lectures cover many aspects of the biology of lower vertebrates known as fishes, including evolution, physiology, functional morphology, phylogeny, bio geography, ecology, and reproduction. The systematic position of fish among vertebrates is discussed and exemplary assemblages exam.

Emphasis on living animals and evolution. Embryology, development, and molting; elementary physiology, ecology, genetics and behavior, and functional external and internal morphology; and geological history. Classification of adults and immatures.

This course covers ecological and evolutionary aspects of geography of populations, communities, and lineages. The course investigates the physical and biological processes shaping geographic patterns of species richness, community structure, and ecosystems over the earth and at regional and local scales, as well as the geographic structure of populations and species. Historical dimensions of these topics include dispersal and vicariance in relation to speciation, extinction, and earth history. The course assumes that students have a background in ecology and evolutionary biology. Class time will involve lectures and regular discussions. Assignments include three essay-based exercises and a term paper. The course text is Biogeography (3rd edition) by Lomolino, Riddle, and Brown (2006); readings also include papers from the current literature in biogeography, macroecology, and phylogeography, posted on the CTools web site. The goal of this course is to provide students with an understanding of how evolution proceeds through time in relation to geography. The course explores the limitation of distributions of organisms by barriers, including climate, effects on species formation and extinction, species abundance and richness, dispersal, and vicariance.

A greater focus on the microbial component of the biosphere is warranted, since "microbes run the world." If we are to build comprehensive and predictive models for ecosystems important to environmental and human health, we need a better understanding of how microbial communities assemble and operate. This course will cover the ecology of microbes by highlighting their interactions with each other and the environment, and will present the latest insights into their role in ecosystems ranging from thawing permafrost to the human gastrointestinal tract. Ecological and evolutionary concepts and tools used in microbial research, including novel "omics" techniques, will be introduced. The course also aims at uncovering how concepts developed in plant and animal ecology do and do not translate to the microbial world.

Principles of systematic botany, including training in the major groups of vascular plants in terms of their morphology, anatomy, cytology, ecology, and reproductive biology, as well as problems win numerical taxonomy, biosystematics, and botanical nomenclature. Laboratory includes plant specimens and visual aids.

The course introduces students to generic-level organization of 25 neo-tropical plant families. Families covered are (1) ecologically widespread and abundant in the neo-tropics or (2) of taxonomic or economic significance. Meetings include lectures on comparative morphology, anatomy, and ecological /economic significance of families and their included genera, and a laboratory during which students examine dried specimens. A field trip to Missouri Botanical Garden in Missouri is included. This course will introduce students to generic-level organization of 25 neo-tropical plant families. Families covered are 1) ecologically widespread and abundant in the neo-tropics or 2) of taxonomic or economic significance. Meetings include lectures on comparative morphology, anatomy, and ecological/economic significance of families and their included genera, and a laboratory during which students examine dried specimens.

Background and Goals: Mathematical models are the backbone of ecological theory; they form the basis for modern approaches to understanding, managing, and predicting the dynamics of ecological systems. This course provides an overview of the major classes of ecological models, with an emphasis on ecological dynamics. We will focus on principles guiding the formulation of models and on the mathematical techniques that can be used to analyze them. We will examine deterministic and stochastic models, structured and unstructured models, single- and multiple-species models. Because ecological systems are typically nonlinear, we cannot often "solve" model equations: we employ techniques of nonlinear analysis, stochastic analysis, and numerical analysis to obtain results. This course will introduce many of these techniques in the context of ecological theory.

An additional goal of the course is to develop students' skills in the use of mathematical software. We will make extensive use of Matlab and R for numerical computations and Mathematica for symbolic computation.

Audience: Applied math and advanced ecology students interested in the use of mathematical models and theoretical, statistical, and computational ecology.

The techniques introduced in the course will be useful to students from many disciplines, including chemical engineering, economics, natural resources, public health, and so on.

Prerequisites: To get the most out of the class, students should have a firm grasp of elementary linear algebra (e.g., MATH 214, 217, 417, or 419) and ordinary differential equations (e.g., MATH 214, 216, 256, 286, or 316), and have had some exposure to probability. Students without these prerequisites should consult the instructor before registering.

Topics: Dynamics of single-species populations;elementary bifurcation theory; optimal harvesting theory; branching process models; Markov chain models; dynamics of interacting populations (predation, competition, and mutualism); age-structured populations; mathematical epidemiology. Additional topics may be included according to students' interests.

Expectations: Attendance at and participation in lectures and labs is expected. Grades will be based on problem sets assigned from time to time.

Text: Mark Kot, Elements of Mathematical Ecology, Cambridge Univ. Press (2003). ISBN: 0521001501

The course describes the biological diversity of prokaryotic microorganisms, members of the Domain Bacteria and Domain Archaea, examining the evolutionary origins of microbial life, the metabolic roles extant prokaryotes carry out in maintaining the biosphere, their physiological adaptations to the environment and to environmental extremes, and modern phylogenetic approaches for their identification and evolutionary analysis.

This course covers basic concepts dealing with the ecology of plant-animal interactions and coevolution. Topics include such interactions as behavior, pollination, seed dispersal and predation, and various mutualisms. Readings are from the current literature.

Background in ecology and evolution is required. There are lectures and discussion. Grades are based on paper, oral presentations, and discussions.

Textbook: None. Readings from the current literature will be used.

GSI classEEB 475: Conservation Biology and Ecosystem Management 5 credits

Ecosystem Ecology is a lecture/discussion course that focuses on understanding the physical, chemical, and biological processes regulating the dynamics of terrestrial and aquatic ecosystems. We discuss classic and current topics in ecology that have built our understanding of ecosystem organization and function. The course integrates across disciplines of physiological, microbial, population, and community ecology to understand how and why ecosystems differ in composition, structure, and function, and how ecosystems change over time. Students are expected to have a solid background in biology and ecology. We also expect that students will be able to use general principles of mathematics, physics, chemistry, and biology as tools to understand ecological processes occurring at the ecosystem level.

The scope of the course includes examples from terrestrial, marine, and freshwater ecosystems.

Principles governing the phenomena of single and interacting populations are examined, from basic tenets to cutting-edge research questions. Population and community-level perspectives are integrated by drawing parallels between approaches and considering how to scale up from the phenomena of one or a few species to the structure and dynamics of whole communities.

The three classes commonly called fishes include more species of vertebrates than all other classes combined. Fishes also have a higher rate of endangerment than all other classes of vertebrates, due to human use of aquatic resources. Ecology of Fishes is a course for juniors and seniors that focuses on the dramatic interaction between fishes and their habitats. The course covers: physiological, behavioral, and numerical responses of fishes to biotic and abiotic factors; the relationship between environmental factors and fish energetics, growth, survival, behavior, and reproduction; adaptations of fish for survival under different environmental constraints in major habitat types; and the role of humans in fishery declines and fish conservation. The course can be taken as a stand-alone lecture for 3 credit hours (section 003) or as a lecture and lab for 4 credit hours (section 001). The lab uses field trips and lab experiments to elucidate the relationships between fishes and their habitats. At least five of the lab sections are typically completed on local lakes and streams.

Covers physiological, behavioral, and numerical responses of fishes to biotic and abiotic factors; the relationship between fish and the physical, chemical, and biological parameters of major habitat types; adaptations of fish for survival under different constraints.

Soils as central components of terrestrial ecosystems. Major emphasis is placed on physical, chemical, and biological properties and their relationships to plant growth and ecosystem processes. Understanding is developed using a combination of lectures, field- and lab-based exercises, and individual research. Students are expected to have a background in chemistry and biology. In particular, a working knowledge of chemical equilibria, ionic solution chemistry, pH, and oxidation-reduction reactions is highly recommended. Students without such background should consult with the instructor before enrolling. Also useful (although not required) are familiarity with biochemistry, plant physiology, microbiology, geology, and local flora. You will find it very helpful if you have had, or are currently enrolled in, Woody Plants (NRE 437).

This course examines processes and patterns of evolution at the molecular level, as well as methods of phylogenetic analysis using molecular characters, such as amino acid sequences, DNA sequences, and features of genome organization. These evolutionary topics and methods are key components in the developing field of bioinformatics. Textbook: Molecular Evolution: A Phylogenetic Approach, by R.D.M. Page and E.C. Holmes. Blackwell Science. Molecular Evolution and Phylogenetics, by M. Nei and S. Kumar. Oxford University Press. This course will examine processes and patterns of evolution at the molecular level, as well as methods of phylogenetic analysis using molecular characters, such as amino acid sequences, DNA sequences, and features of genome organization. These evolutionary topics and methods are key components in the developing field of bioinformatics.

This course is an introduction to the application of stable and radiogenic isotopes to Biogeochemistry, Environmental Science, Ecology and Paleo-ecology. The primary emphasis will be on the applications of light and "non-traditional" stable isotopes, with a smaller emphasis placed on the application of radiogenic isotopes. The course will begin with the theory, nomenclature and methods of isotope analysis. This will be followed by applications of: H and O isotopes in the atmosphere and in paleo-thermometry; C, N and S isotopes in plants, foodwebs, soils and oceans; "non-traditional" isotopes such as Fe, Ca and Hg in the growing range of Earth surface studies; and the application of radiogenic isotopes as fingerprints of contaminant and nutrient sources.

Advisory prerequisite: Permission of instructor

This course explores various topics in evolutionary biology, with an emphasis on conceptual principles and generalizations. Fundamental principles are discussed in relation to topics of active contemporary research and controversy. It includes lectures and discussion on major principles in population genetics, molecular and phenotypic evolution, speciation, evolutionary developmental biology, phylogenetics, and macroevolution. The course is broadly relevant to many other fields, from conservation biology to genomics. The course is not a replacement for other EEB courses (e.g., population genetics or molecular evolution). There will be readings from Futuyma plus about two papers or other readings per lecture. Grades will be based on one midterm exam and one final exam (during exam week). Textbook: Evolution, D.J. Futuyma. This course provides a foundation in evolutionary biology for students whose professional activities will require familiarity with this field. It includes lectures and discussion on major principles in population genetics molecular and phenotypic evolution, speciation, evolutionary developmental biology phylogenetics, and macroevolution. Fundamental principles are discussed in relation to topics of active contemporary research and controversy.

This course provides an in-depth examination of current theory and empirical research in community ecology. Topics include the mechanisms of species interactions, indirect effects, the influence of temporal and spatial heterogeneity, metacommunity ecology, and the consequences of community structure for ecosystem processes. It provides a venue for an in depth exploration of the literature in community ecology, and for critically evaluating theoretical and empirical advances in this area.

Consent: With permission of instructor.
Advisory prerequisites: 16 hours in Biology, Graduate standing and permission of instructor.
Repeatability: May not be repeated for credit.
Incoming graduate students are required to sign up for EEB 700 with the 700 advisor during the 1st week of fall term and EEB 730 in the winter term of the first year. Credits chosen are flexible.

Advisory prerequisite: Graduate standing and permission of instructor.
Repeatability: May be repeated for credit.
Consent: With permission of instructor.
A graduate seminar course providing opportunity to discuss current work and new developments in Ecology and Evolutionary Biology.

Advisory prerequisite: Graduate standing and permission of instructor. Appointment as Teaching Assistant in Biology.
Consent: With permission of instructor.
Seminars, demonstrations, and orientation for college teaching in biology. Available for all pre-candidate teaching assistants.

Advisory prerequisite: Election for dissertation work by doctoral student not yet admitted as a candidate. Graduate standing.
Consent: With permission of instructor.
Advisory prerequisites: Election for dissertation work by doctoral student not yet admitted as a candidate. Graduate standing.
Grading: Grading basis of 'S' or 'U'.
Repeatability: May be repeated for credit.
Election for dissertation work by doctoral student not yet admitted as a candidate.