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Phylogenetic Analysis Lab
This two-part lab from Barnard College helps students construct cladograms (also called phylogenetic trees) in order to understand the types of data, methods, and assumptions that are used to determine evolutionary relationships. The exercises, which can be used or adapted to enhance the study of evolution in an introductory biology course, ask students to construct cladograms for two different groups of organisms: fictitious organisms from the “family” Squirmidae, and real organisms from the kingdom Plantae. Discussion questions and learning objectives are included. Comprehensive background information helps students understand the major concepts behind cladistic methods, and procedures clearly explain how to construct cladograms for both the hypothetical and real groups of organisms. This lab uses two computer programs: Mesquite software for evolutionary biology, which is designed to help biologists analyze comparative data about organisms; and BioEdit, a biological sequence alignment editor used to examine plant protein sequences. Both software programs are free, and links to them are available in the “related resources” section of this resource. For the lab analysis of the kingdom Plantae, educators will need to purchase the seven live plant specimens noted in the lab instructions. Most live plant specimens can be obtained from Carolina Biological. (Barnard grows its own plants in a campus greenhouse. Educators might inquire whether similar plant resources exist at their own colleges or universities.) The majority of the exercises, with very few modifications, can also be performed without the Mesquite or BioEdit programs. Educators who prefer an alternative draft that does not require the use of any computer software can email Dr. Jessica Goldstein, director of Introductory Biology Labs, Department of Biology, Barnard College, at email@example.com.
Program Director: Paul E. Hertz, Ph.D.
Award Years: 1991, 1996, 2000, 2004, 2008
Summary: Barnard College is a private baccalaureate institution in New York City. Its HHMI-funded educational initiative, the Hughes Science Pipeline Project, is a multi-faceted program designed to enhance nearly every aspect of science education at Barnard College. Highlights include:
- The development of a four-year research-based curriculum in functional genomics focusing on the hornworm Manduca sexta, a model organism commonly used to study biological questions, especially in neuroscience. The curriculum, which encompasses animal behavior, genetics, molecular biology, and neurophysiology, was designed to spark student excitement in original scientific research from introductory to advanced levels.
- The creation of a variety of other new experiments and laboratory exercises focusing on genomics and bioinformatics. These laboratories are or will become available on the Barnard biology website.
- A program of research internships for undergraduates distributed among five science departments: biology, chemistry, environmental science, physics and astronomy, and psychology. Internships are available to rising sophomores, juniors, and seniors; all full-time faculty members are eligible to serve as mentors. Each Research Intern spends 10 weeks during the summer working with a Barnard faculty mentor to initiate a year-long research project, and then completes the project during the following academic year. All Research Interns present their work at an annual Student Research Symposium, and many also present their findings at off-campus scientific meetings and in scientific journals.
- The Supplemental Instruction (SI) program, which offers peer-led group study sessions to improve student study skills, provide a supportive, structured environment that will retain students who might otherwise be at risk of leaving the sciences, and provide students with peer mentors, who counsel SI participants about advanced science courses and strategies for completing requirements for postgraduate study.
- Other opportunities to enhance and extend science education, including the annual Distinguished Women in Science Lecture; summer classes in chemistry and mathematics for selected incoming students; a series of career panels and presentations throughout the academic year; and a practicum and research experience for undergraduate students in the Education Program.
- The use of technical consultants and training to help biology faculty members implement genomics curricula and to introduce new software, instruments, and research techniques into the curriculum.
- The Intercollegiate Partnership (ICP), a collaboration between Barnard College and LaGuardia Community College of the City University of New York, which seeks to facilitate the transfer of community college students to four-year colleges. The ICP focuses on students interested in the natural sciences. Each annual cycle of the ICP includes three phases: a residential summer program; the potential to enroll in classes at Barnard during the following academic year; and a final summer research experience.
- Science in the City, a curriculum project that integrates mathematics, health, reading, writing, poetry, and art to guide elementary school students in their scientific exploration of the plant life in their neighborhoods. In addition to providing a curricular product that has been distributed free of charge to local schools, the Science in the City project provided useful training for the undergraduates who developed it.