Graduate Program

Topics to be announced. Graded Satisfactory/Unsatisfactory.

Topics to be announced. Graded Satisfactory/Unsatisfactory.

Statistical and probabilistic analysis of biological problems, presented with a unified foundation in basic statistical theory. Problems are drawn from genetics, ecology, epidemiology, and bioinformatics.

An introduction to ecological and evolutionary principles underpinning efforts to conserve Earth’s biodiversity. Efforts to halt the rapid increase in disappearance of both plants and animals. Discussion of sociological and economic issues.

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.

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.

An overview of evolutionary biology as the discipline uniting all of the life sciences. Evolution explains the origin of life and Earth’s biodiversity, and how organisms acquire adaptations that improve survival and reproduction. This course uses reading and discussion of scientific papers to emphasize that evolutionary biology is a dynamic science, involving active research to better understand the mysteries of life. We discuss principles of population genetics, paleontology, and systematics; application of evolutionary thinking in disciplines such as developmental biology, ecology, microbiology, molecular biology, and human medicine.

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. 

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.

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.

Introduction to the major plant groups and their evolutionary relationships, with an emphasis on the diversification and global importance of flowering plants.

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

Evolutionary history and diversity of terrestrial arthropods (body plan, phylogenetic relations, fossil record); physiology and functional morphology (water relations, thermo-regulation, 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).

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).

A study of animal diversity, with a focus on the evolution of marine invertebrates. The course will draw extensively on the Invertebrate Zoology collections at the Peabody Museum. The lecture does not have to be taken concurrently with the lab.

A study of animal diversity, with a focus on the evolution of marine invertebrates. The course will draw extensively on the Invertebrate Zoology collections at the Peabody Museum. The lecture and lab must be taken concurrently.

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.

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.
 

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.

Functional genomics has opened the opportunity to assess the activity state of all genes in the genomes in a largely scalable way. Many cell types, tissues, and characters can readily be assessed across many species, leading to a new field of evolutionary or comparative functional genomics. At the same time this new field of data analysis can be used to address many deep issues in organismic evolution, like the evolution of cell types, the homology among cell types, etc. In this seminar we review the current state of published literature as it pertains to the evolutionary analysis of transcriptomes and epigenetic marks and their bearing on issues of cell and tissue evolution and homology.

An advanced treatment of ecology, including species interactions, species coexistence theory, species-environment interactions, the maintenance and consequences of biological diversity, spatial ecology, food webs, and eco-evolutionary interactions.

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.

Topics related to analyzing molecular genetic data to answer questions in evolution and ecology. Methods to detect selection in DNA sequences and other molecular data, and landscape genetics, overlaying genetic data on ecological maps from global imaging. Other topics will be determined by interests of participants.

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.

This is an advanced botany course, preferably for students that have taken EEB 246 in addition to BIO 104; otherwise permission must be obtained from the instructor. A keen interest in plants is a must.

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).

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.

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

Life history evolution studies how the phenotypic traits directly involved in reproductive success are shaped by evolution to solve ecological problems. Nowhere is the interplay between evolution and ecology more intimate.

Requires Permission of the Instructor

Biodiversity and the many functions it provides are changing worldwide. This sets up a critical need for a better understanding of mechanisms underpinning this change and the development of new information products to help monitoring and mitigation. New technologies, data, and methods, as well as conceptual advances these have inspired, now increasingly enable work addressing this challenge for species and communities at global scale.

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).

This 1-credit graduate seminar course examines various topics in the ecology and evolution of microbes, with an emphasis on prokaryotes (Eubacteria, Archaea) and single-celled eukaryotes (yeasts, protists). The goal of this course is for the students to develop a quantitative understanding of microbial community ecology, focusing on the mechanisms of community assembly, microbial biogeography, and the role of evolution in structuring microbial communities and endowing them with function. Microbial communities have many unique properties and differ in fundamental ways from those formed by macroscopic organisms. The course will examine these unique properties through readings of the primary literature, including both classic papers and cutting-edge advances in the field. The course will be quantitative in nature, and will explicitly discuss how mathematical models can allow us to understand ecological and evolutionary processes in microbial communities.

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.

An introduction to the ways evolving biological systems can be described, modeled, and analyzed by using a dynamical systems approach.  Concrete models will be explored with respect to field or laboratory observations.  Extensive use will be made of the software package Mathematica, but prior experience with the program is not required.

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 and diversity and adaptations explored through museum specimens and fossil casts.

Research Rotation Fall Semester

Research Rotation II Spring Semester

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).