Graduate Courses

The theory and practice of ecology, including the ecology of individuals, population dynamics and regulation, community structure, ecosystem function, and ecological interactions at broad spatial and temporal scales. Topics such as climate change, fisheries management, and infectious diseases are placed in an ecological context.

Prerequisite: MATH 112 or equivalent.

1 Yale College course credit(s)

Study of evolutionary novelties, their functional morphology, and their role in the diversity of life. Introduction to techniques used for studying the diversity of animal body plans. Evolutionary innovations that have allowed groups of organisms to increase their diversity.

0.5 Yale College course credit(s)

An overview of evolutionary biology as the discipline uniting all of the life sciences. Reading and discussion of scientific papers to explore the dynamic aspects of evolutionary biology. Principles of population genetics, paleontology, and systematics; application of evolutionary thinking in disciplines such as developmental biology, ecology, microbiology, molecular biology, and human medicine.

1 Yale College course credit(s)

Overview of the ecology and evolution of pathogens (bacteria, viruses, protozoa) and their impact on host populations. Topics include theoretical concepts, ecological and evolutionary dynamics, molecular biology, and epidemiology of ancient and emerging diseases. 

1 Yale College course credit(s)

A field-based introduction to ecological research, using experimental and descriptive approaches, comparative analysis, and modeling for field and small-group projects. Weekly field trips explore local lake, salt marsh, rocky intertidal, traprock ridge, and upland forest ecosystems. Includes one Saturday field trip and a three-day trip during the October recess. Concurrently with or after EEB 2220 or with permission of instructor.

1 Yale College course credit(s)

An introduction to the study of animal behavior from an evolutionary and ecological perspective. Topics include decision-making, group living and cooperation, sexual selection and mating behavior, signaling and communication. In addition to lectures, in-class discussions and activities, students engage in the material by design and implement their own research projects.

Prerequisite: BIOL 104, or permission of instructor.

Hands-on experience with the plant groups examined in the accompanying lectures. Local field trips.

To be taken concurrently with EEB 2246.

0.5 Yale College course credit(s)

Evolutionary history and diversity of terrestrial arthropods (body plan, phylogenetic relationships, fossil record); physiology and functional morphology (water relations, thermoregulation, energetics of flying and singing); reproduction (biology of reproduction, life cycles, metamorphosis, parental care); behavior (migration, communication, mating systems, evolution of sociality); ecology (parasitism, mutualism, predator-prey interactions, competition, plant-insect interactions).

To be taken concurrently with EEB 2251L.

1 Yale College course credit(s)

Comparative anatomy, dissections, identification, and classification of terrestrial arthropods; specimen collection; field trips.

Concurrently with or after EEB 2250.

0.5 Yale College course credit(s)

An overview of animal diversity that explores themes including animal phylogenetics (evolutionary relationships), comparative studies of evolutionary patterns across species, organism structure and function, and the interaction of organisms with their environments. Most animal lineages are marine invertebrates, so marine invertebrates are the focus of most of the course.

To be taken concurrently with EEB 2256L.

1 Yale College course credit(s)

The study of invertebrate anatomy and diversity in a laboratory and field setting. Activities will include will examine live animals and museum specimens, as well as local field trips. Some field trips will fall on weekends.

This lab must be taken concurrently with the lecture EEB 2255.

0.5 Yale College course credit(s)

A survey of fish diversity, including jawless vertebrates, chimaeras and sharks, lungfishes, and ray-finned fishes. Topics include the evolutionary origin of vertebrates, the fossil record of fishes, evolutionary diversification of major extant fish lineages, biogeography, ecology, and reproductive strategies of fishes

1 Yale College course credit(s)

Laboratory and field studies of fish diversity, form, function, behavior, and classification. The course primarily involves study of museum specimens and of living and fossil fishes. Concurrently with EEB 2264.

0.5 Yale College course credit(s)

An overview of avian biology and evolution, including the structure, function, behavior, and diversity of birds. The evolutionary origin of birds, avian phylogeny, anatomy, physiology, neurobiology, breeding systems, and biogeography.

Enrollment limited to 50.

1 Yale College course credit(s)

Laboratory and field studies of avian morphology, diversity, phylogeny, classification, identification, and behavior.

Enrollment limited to 12.

0.5 Yale College course credit(s)

Exploration of a range of coastal and pelagic ecosystems. Relationships between biological systems and the physical processes that control the movements of water and productivity of marine systems. Anthropogenic impacts on oceans, such as the effects of fishing and climate change. Includes three Friday field trips.

Enrollment limited to 15.

1 Yale College course credit(s)

The study of plant interactions with their environment, at the level of individuals, and of how plant-plant interactions mediate environmental interactions at the level of populations, communities, and ecosystems. Incorporation of empirical and theoretical perspectives, emphasizing the empirical origins of concepts in plant ecology and effective empirical tests of conceptual and mathematical predictions.

1 Yale College course credit(s)

Plant ecology is the study of plant interactions with their environment, at the level of individuals, and of how plant-plant interactions mediate environmental interactions at the level of populations, communities, and ecosystems. The course incorporates empirical and theoretical perspectives, emphasizing the empirical origins of concepts in plant ecology and effective empirical tests of conceptual and mathematical predictions. Students read the primary scientific literature extensively, both for content and to build familiarity with methodological standards and the scientific writing.

1 Yale College course credit(s).

This course covers core questions in community ecology related to species interactions, species coexistence theory, species-environment interactions, the consequences of biological diversity, spatial ecology, food webs, and eco-evolutionary interactions.  Lectures emphasize the theoretical and conceptual foundations of these topics and incorporate the empirical and experimental evidence supporting and confronting contemporary views.

Prerequisites: EEB 2220 or EVST 2200, or with permission of instructor.

1 Yale College course credit(s).

Genetic variation is the currency by which natural selection is translated into evolutionary change. In this course we dissect patterns of genetic variation using an evolutionary mindset to ultimately understand what shapes genetic variation in nature and the potential for species to adapt to new and changing environments. This class unites two foundational fields of evolutionary genetics; quantitative genetics (the study of the genetic basis of complex traits) and population genetics (the study of gene variant frequencies across time and space), with an ultimate goal of understanding evolutionary change in nature. Although this course is lecture based, there is much opportunity for hands-on learning. Students use real-life and simulated genetic data to map the genetic basis of traits and investigate the evolutionary forces responsible for shaping genetic variation in nature. We also discuss how quantitative and population genetics theory are applied to the modern genomic era, particularly in the context of detecting genomic signatures of adaptation. Lastly, we discuss the application of evolutionary genetics to human populations, including the usefulness and missteps of these applications for science and society.

Prerequisite: EEB 2225, Evolutionary Biology.

Ecosystem ecology asks how abiotic and biotic processes come together to shape the diversity in form and function across Earth’s ecosystems, from the flow of energy and materials through the environment, to how communities of organisms interact with their environment. This course examines the factors that influence ecosystem structure and function: the processes that shape how energy, water, carbon, and nutrients cycle through ecosystems, the role of disturbance on these processes, and feedbacks from human-induced global change.

Prerequisites: EEB 2220(link is external) or EVST 2220(link is external), or with permission of instructor.

1 Yale College course credit(s).

Introduction to the ways in which evolutionary science informs medical research and clinical practice. Diseases of civilization and their relation to humans’ evolutionary past; the evolution of human defense mechanisms; antibiotic resistance and virulence in pathogens; cancer as an evolutionary process. Students view course lectures on line; class time focuses on discussion of lecture topics and research papers.

Prerequisite: BIOL 101–01040.

1 Yale College course credit(s)

When thinking about microbes what comes to mind are usually diseases and unpleasant smells from the fridge or the basement. Nevertheless, microbes and the communities they form are key contributors to our wellbeing and the functioning of the planet. This course provides an introduction to microbial ecology, with an emphasis on how microbial systems differ from their macroscopic counterparts, including defining a microbial species; sampling/experimenting with microbes; principles of microbial growth, metabolism, and death; species interactions and community assembly in different environments; microbial community functions; elements of microbial evolution.

BIOL 1010, BIOL 1020, BIOL 1030, & BIOL 1040. General Ecology EEB 2220 and MCDB 2900 are encouraged but not required.

1 credit for Yale College students

The diversity and evolutionary history of living and extinct primates. Focus on major controversies in primate systematics and evolution, including the origins and relationships of several groups. Consideration of both morphological and molecular studies. Morphological diversity and adaptations explored through museum specimens and fossil casts.

Requires Permission of the Instructor

Recommended preparation: ANTH 1400.

I Yale College course credit(s).

This course introduces students to the theory behind evolutionary biology. The aim of the course is for the student to understand how evolution works, focusing on the quantitative and predictive theory that is the backbone of modern evolutionary thinking. The course covers three main areas: An introduction to population genetics, an introduction to quantitative genetics and the genotype-phenotype map, and an introduction to life-history evolution. To master this material and to put the concepts studied in class into practice, students work on weekly problem sets. Through the completion of the course assignments, students gain valuable quantitative and mathematical modeling skills.

Prerequisites: One of the following: EEB 2225, PHYS 1700/1710 or 1800/1810 or permission of the instructor.

Phylogenetic Biology is the study of the evolutionary relationships between organisms, and the use of evolutionary relationships to understand other aspects of organism biology. This course surveys phylogenetic methods, providing a detailed picture of the statistical, mathematical, and computational tools for building phylogenies and using them to study evolution. We also examine the application of these tools to particular problems in the literature and emerging areas of study.

Prerequisites: EEB 2225 and an organismal course.

1 Yale College course credit(s)

Topics to be announced. Graded Satisfactory/Unsatisfactory.

Topics to be announced. Graded Satisfactory/Unsatisfactory.

Graded Satisfactory/Unsatisfactory.

Requires Permission of the Instructor

This 5-week discussion seminar considers issues related to the responsible conduct of research. Topics addressed include: research misconduct, plagiarism, data acquisition and management, mentoring and collaboration, authorship and peer review, the use of animals and humans in scientific research, sexual harassment, diversity, and balancing professional and personal life.

This course takes place within EEB 6501: Advanced Topics. First-year students are required to register for both courses.

An introduction to the philosophy of biology, with application to specific current problems. The course focuses on two major strands of thinking seeking answers to two fundamental and to some extent complementary questions: “How do we know?” [epistemology] and “What things really exist in the world?” [ontology]. These two themes have the most important impact on the practice of science, as they pertain to the nature of the scientific enterprise and how it works [epistemology and philosophy of science], as well as what scientists consider part of reality [science-related ontology: unicorns and phlogiston, NO; atoms, electrons, YES; but what about species and genes? Do they have the same status as atoms?]. In each of these fields of philosophy we outline the main positions and discuss how they apply to past and current debates in biology—in particular, but not exclusively, evolutionary biology.

1 Yale College course credit(s)

Limnology, the study of the physical, chemical, and biological properties of inland waters, focuses on lakes where physical (light, temperature, and mixing) and chemical (dissolved elements and compounds) properties interact with the ecology and evolution of organisms. Topics include origins and morphology of inland waters; physical and chemical properties; diversity and interactions among the organisms found in lakes; historical perspectives; and understanding conservation and management in the context of global change. Frequent field trips to local freshwater ecosystems.

Research Rotation 

Research Rotation II 

Insects transmit pathogens that cause many emerging and re-emerging human and agriculture-related diseases. Many of these diseases, which are referred to as neglected tropical diseases (NTDs), have a dramatically negative impact on human health in the developing world. Furthermore, they cause indirect devastation by significantly reducing agricultural productivity and nutrient availability, exacerbating poverty and deepening disparities. This course introduces students to the biological interactions that occur between major groups of important disease vectors and the pathogens they transmit. Lectures cover current research trends that relate to the ecology and physiology of insect vectors. Course content focuses on how these aspects of vector biology relate to the development and implementation of innovative and effective disease-control strategies.

Prerequisite: full year of college/university-level biology, or permission of the instructor(s).

Plant ecology is the study of plant interactions with their environment, at the level of individuals, and of how plant-plant interactions mediate environmental interactions at the level of populations, communities, and ecosystems. The course incorporates empirical and theoretical perspectives, emphasizing the empirical origins of concepts in plant ecology and effective empirical tests of conceptual and mathematical predictions. Students read the primary scientific literature extensively, both for content and to build familiarity with methodological standards and the scientific writing.

n December 2022, nations worldwide committed to a new set of goals for biodiversity conservation. In the 15th Conference of the Parties of the Convention on Biological Diversity they agreed to a Global Biodiversity Framework that lays out ambitious goals and targets. Importantly, for the first time, the framework specifies biodiversity monitoring to support achieving these goals, setting up a more critical role than ever for relevant science to contribute to the success of the overall ambition. This course addresses the science for measuring progress and providing decision-support for meeting these commitments. Following an initial assessment of framework language, we evaluate for each of the goals and targets that address biodiversity threats the required evidence to support a robust and representative measurement at global scale. We discuss key scientific papers addressing the concepts, methods, and evidence supporting these measurements for ecosystems and species. We then critically evaluate how currently available data, methods, and tools can support the monitoring envisioned by the framework. We closely review the opportunities enabled by remote sensing and the new generation of model-supported indicators of biodiversity change they support. Finally, we discuss the potential of several new or emerging technologies and approaches such as camera traps, GPS tracking, community science, machine learning, and others to offer an improved foundation for monitoring planetary biodiversity change.

A seminar course discussing the philosophical roots of and empirical research in structuralism and macroevolution. We read selected papers in philosophy of evolutionary biology, comparative phylogenetic methods, macroevolutionary studies, and the role of natural history in evolutionary thought. Each topic is paired with readings on empirical research that involves similar issues. The course concludes with a short writing assignment that analyzes a contemporary question in macroevolution or structural/organismic research.

The field of evolutionary biology is increasingly drawing on genomic data, and the field of genomic biology is becoming more evolutionary as genomes are sequenced for a broader diversity of organisms. This course focuses on the evolution of genome sequence and function at macroevolutionary timescales, with an emphasis on building practical computational skills for genomic and phylogenetic comparative analyses. The focus is more on using phylogenies to understand genome evolution than on using genomes to build phylogenies.

This course will provide guidance and practice for graduate students in grant and manuscript writing in the fields of ecology and evolutionary biology. Students will produce one grant application (NSF GRFP/DDIG or similar) and one manuscript for publication (on a topic of their choice, to contribute to their thesis or other ongoing work). Application to course & instructor permission required: see Canvas site.

All living things exist in an era of unprecedented global-scale environmental change. Global change encompasses numerous, often interconnected phenomena that are currently impacting organisms. These include rising temperatures, ocean acidification, habitat loss and degradation, overexploitation, novel pathogens, and toxin exposure. This course focuses on global change from the perspective of the organisms themselves. Our goal as biologists is to understand the magnitude of the problem by addressing the following questions: (1) What are the principal ways in which organisms are being challenged due to human impact? (2) What mechanisms are there for organisms to adaptively respond to these challenges? and (3) What can we do to help organisms? To address these questions, we delve into the scientific literature on distinct topics related to global change, discussing one of these topics in each class meeting. Key papers from the literature are assigned to help guide discussion. This course is discussion-based and interactive; each week a student leads discussion along with the instructor. A secondary goal of the course is to help students improve their written communication abilities, either through a traditional term paper or something else, like a grant application or a dissertation chapter. Depending on the number of students and their goals, we might tackle a review paper together, with the goal of obtaining a peer-reviewed publication.

Prerequisites: introductory biology and evolution.

In this course we examine principles of the ecology of infectious disease in light of three pandemics: the 1918 influenza pandemic, the HIV/AIDS pandemic, and the COVID-19 pandemic. The course covers principles of zooneses, disease emergence, herd immunity, basic vaccinology, and other fundamental concepts. It also focuses on social and cultural factors that fomented these pandemics.

One of the most striking patterns of biodiversity is its uneven distribution across the tree of life. Theory suggests that this disparity in diversity reflects feedback between ecological and phenotypic evolution. Adaptive radiations, the rapid multiplication of species into distinct ecological niches, is a key example of this phenomenon. While studies about adaptive radiation have grown exponentially over the past decades, fundamental questions remain. For example, how does phenotypic diversification unfold during radiation? How do species interactions shape species richness in adaptive radiation? Do adaptive radiations play out in parallel across continental and island contexts, or are there repeatable differences among them? The goal of this course is to critically dissect the field of adaptive radiation. Specifically, we unpack its major features and identify unresolved lacunae. To do so, we delve into the scientific literature on distinct topics related to adaptive radiation. Key papers from the literature are assigned to help guide discussion. We begin with a brief survey of recent syntheses on adaptive radiation to refresh our understanding and, most importantly, identify key gaps in empirical knowledge. Then, we explore several studies focused on less-studied axes of adaptive radiation to catalyze our thinking.

Prerequisites: BIOL 103/104 (or equivalent) and EEB 5225 (or equivalent).

Behavior is the first line of defense against parasites and pathogens. Behavioral defenses allow organisms to minimize contact with infectious agents, and the concept of the “behavioral immune system” was developed to encompass a range of evolved behaviors that help minimize the fitness costs of infection. The COVID-19 pandemic has made the term “social distancing” a household term; however, distancing and many other avoidance strategies are employed by a wide range of organisms to combat infectious agents. In this seminar, we examine our current understanding of the behavioral immune system across the diversity of animals, including humans. Specifically, we explore: (1) the mechanisms of behavioral immunity; (2) the ecological, evolutionary, and epidemiological consequences of these behaviors; and (3) key costs of behavioral immunity that maintain intra- and interspecific variation. To do this, we discuss and synthesize the scientific literature on the behavioral immune system, drawing parallels to work on the physiological immune system. The first weeks of the course focus on instructor-selected papers, and subsequent weeks incorporate student-selected papers.

Nature-based climate solutions have gained increasing attention in the past decade as possible contributors to reducing our net carbon emissions to the atmosphere, without necessarily reducing gross emissions. Prominent nature-based solutions include forestation (reforestation, afforestation, plantation forestry), avoided deforestation, and soil carbon sequestration. This seminar includes weekly readings and discussion around themes in the management of ecosystem carbon storage.

This seminar is intended for Ph.D. students. It is open to master’s students and undergraduates by permission of the instructor only, based on a one- or two-paragraph description of interest in the course.

Organisms are routinely faced with many abiotic and biotic pressures that impact their survivorship, growth, and reproductive success. For example, a lizard’s ability to perform fitness-based tasks (like foraging or predator evasion) is limited by the thermal dependence of its performance, its hydric and metabolic economy, and its morphological dimensions. Yet, organisms are not exclusively at the whim and mercy of their surroundings. Of key importance is the preeminent role that organisms exert on their own selective environments and, correspondingly, on their evolution. This course considers the diverse ways in which organisms engineer their own evolutionary trajectories. Some of the topics we cover include niche construction, extended phenotypes, behavioral drive, the Bogert effect, and adaptive virulence (particularly in the context of the COVID-19 pandemic).

Open to upper-level undergraduates who have taken BIOL 1030, BIOL 1040, and EEB 2225 (or the equivalent).

TBA

Speciation and adaptation are two fundamental processes that generate the diversity of life seen on earth to date. This graduate-level seminar course will explore the evolutionary mechanisms responsible for these phenomena by delving into the primary literature to explore classic examples of adaptation and speciation using a genetics and genomics lens.

Topics and class time are chosen by the participants, and have included reading books and/or a series of papers on particular topics (e.g., homology; morphological phylogenetics; evolution of egg colors and exposed nesting in dinosaurs/birds; origin of snake ecology; conflicts between morphology and molecules; role of fossils in phylogenetic inference).