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Shaffer CD, Alvarez CJ, Bednarski AE, Dunbar D, Goodman AL, Reinke C, Rosenwald AG, Wolyniak MJ, Bailey C, Barnard D, Bazinet C, Beach DL, Bedard JEJ, Bhalla S, Braverman J, Burg M, Chandrasekaran V, Chung HM, Clase K, DeJong RJ, DiAngelo JR, Du C, Eckdahl TT, Eisler H, Emerson JA, Frary A, Frohlich D, Gosser Y, Govind S, Haberman A, Hark AT, Hauser C, Hoogewerf A, Hoopes LLM, Howell CE, Johnson D, Jones CJ, Kadlec L, Kaehler M, Silver Key SC, Kleinschmit A, Kokan NP, Kopp O, Kuleck G, Leatherman J, Lopilato J, MacKinnon C, Martinez-Cruzado JC, McNeil G, Mel S, Mistry H, Nagengast A, Overvoorde P, Paetkau DW, Parrish S, Peterson CN, Preuss M, Reed LK, Revie D, Robic S, Roecklein-Canfield J, Rubin MR, Saville K, Schroeder S, Sharif K, Shaw M, Skuse G, Smith CD, Smith MA, Smith ST, Spana E, Spratt M, Sreenivasan A, Stamm J, Szauter P, Thompson JS, Wawersik M, Youngblom J, Zhou L, Mardis ER, Buhler J, Leung W, Lopatto D, Elgin SCR. A course-based research experience: how benefits change with increased investment in instructional time. CBE Life Sci Educ 2014; 13:111-30. [PMID: 24591510 PMCID: PMC3940452 DOI: 10.1187/cbe-13-08-0152] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
There is widespread agreement that science, technology, engineering, and mathematics programs should provide undergraduates with research experience. Practical issues and limited resources, however, make this a challenge. We have developed a bioinformatics project that provides a course-based research experience for students at a diverse group of schools and offers the opportunity to tailor this experience to local curriculum and institution-specific student needs. We assessed both attitude and knowledge gains, looking for insights into how students respond given this wide range of curricular and institutional variables. While different approaches all appear to result in learning gains, we find that a significant investment of course time is required to enable students to show gains commensurate to a summer research experience. An alumni survey revealed that time spent on a research project is also a significant factor in the value former students assign to the experience one or more years later. We conclude: 1) implementation of a bioinformatics project within the biology curriculum provides a mechanism for successfully engaging large numbers of students in undergraduate research; 2) benefits to students are achievable at a wide variety of academic institutions; and 3) successful implementation of course-based research experiences requires significant investment of instructional time for students to gain full benefit.
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Affiliation(s)
- Christopher D. Shaffer
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
- Address correspondence to: Christopher D. Shaffer ()
| | - Consuelo J. Alvarez
- Department of Biological and Environmental Sciences, Longwood University, Farmville, VA 23909
| | | | - David Dunbar
- Science Department, Cabrini College, Radnor, PA 19087
| | - Anya L. Goodman
- Department of Chemistry and Biochemistry, California Polytechnic State University, San Luis Obispo, CA 93405
| | | | | | | | - Cheryl Bailey
- Department of Biochemistry, University of Nebraska–Lincoln, Lincoln, NE 68588
| | - Daron Barnard
- Biology Department, Worcester State University, Worcester, MA 01602
| | | | - Dale L. Beach
- Department of Biological and Environmental Sciences, Longwood University, Farmville, VA 23909
| | | | - Satish Bhalla
- Department of Computer Science & Engineering, Johnson C. Smith University, Charlotte, NC 28216
| | - John Braverman
- Department of Biology, Saint Joseph's University, Philadelphia, PA 19131
| | - Martin Burg
- Departments of Biomedical Sciences & Cell and Molecular Biology, Grand Valley State, Allendale, MI 49401
| | | | - Hui-Min Chung
- Department of Biology, University of West Florida, Pensacola, FL 32514
| | - Kari Clase
- Technology Leadership & Innovation Department, Purdue University, West Lafayette, IN 47907
| | | | | | - Chunguang Du
- Department of Biology & Molecular Biology, Montclair State University, Montclair, NJ 07043
| | - Todd T. Eckdahl
- Department of Biology, Missouri Western State University, St. Joseph, MO 64507
| | - Heather Eisler
- Department of Biology, University of the Cumberlands, Williamsburg, KY 40769
| | | | - Amy Frary
- Department of Biological Sciences, Mount Holyoke, South Hadley, MA 01075
| | - Donald Frohlich
- Biology Department, University of St. Thomas, Houston, TX 77006
| | | | - Shubha Govind
- Biology Department, City College of New York, New York, NY 10031
| | - Adam Haberman
- Biology Department, Oberlin College, Oberlin, OH 44074
| | - Amy T. Hark
- Biology Department, Muhlenberg College, Allentown, PA 18104
| | - Charles Hauser
- Department of Bioinformatics, St. Edwards University, Austin, TX 78704
| | | | | | - Carina E. Howell
- Department of Biological Sciences, Lock Haven University of Pennsylvania, Lock Haven, PA 17745
| | - Diana Johnson
- Department of Biological Sciences, George Washington University, Washington, DC 20052
| | | | - Lisa Kadlec
- Department of Biology, Wilkes University, Wilkes-Barre, PA 18701
| | | | | | - Adam Kleinschmit
- Department of Biology, Adams State University, Alamosa, CO 81101
| | - Nighat P. Kokan
- Department of Natural Sciences, Cardinal Stritch University, Milwaukee, WI 53217
| | - Olga Kopp
- Department of Biology, Utah Valley University, Orem, UT 84058
| | - Gary Kuleck
- Department of Biology, Loyola Marymount University, Los Angeles, CA 90045
| | - Judith Leatherman
- Department of Biological Sciences, University of Northern Colorado, Greeley, CO 80639
| | - Jane Lopilato
- Biology Department, Simmons College, Boston, MA 02115
| | - Christy MacKinnon
- Biology Department, University of the Incarnate Word, San Antonio, TX 78209
| | | | - Gerard McNeil
- Department of Biology, York College–City University of New York, Jamaica, NY 11451
| | - Stephanie Mel
- Division of Biological Sciences, University of California–San Diego, La Jolla, CA 92093
| | | | - Alexis Nagengast
- Departments of Chemistry and Biochemistry, Widener University, Chester, PA 19013
| | | | - Don W. Paetkau
- Department of Biology, Saint Mary's College, Notre Dame, IN 46556
| | - Susan Parrish
- Biology Department, McDaniel College, Westminster, MD 21157
| | | | - Mary Preuss
- Department of Biological Sciences, Webster University, Webster Groves, MO 63119
| | - Laura K. Reed
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35401
| | - Dennis Revie
- Department of Biology, California Lutheran University, Thousand Oaks, CA 91360
| | - Srebrenka Robic
- Department of Biology, Agnes Scott College, Decatur, GA 30030
| | | | - Michael R. Rubin
- Department of Biology, University of Puerto Rico at Cayey, Cayey, PR 00736
| | | | | | - Karim Sharif
- Department of Natural Sciences, LaGuardia Community College, Long Island City, NY 11101
| | - Mary Shaw
- Department of Biology, New Mexico Highlands University, Las Vegas, NM 87701
| | - Gary Skuse
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY 14623
| | | | - Mary A. Smith
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411
| | - Sheryl T. Smith
- Department of Biology, Arcadia University, Glenside, PA 19038
| | - Eric Spana
- Department of Biology, Duke University, Durham, NC 27708
| | - Mary Spratt
- Department of Biology, William Woods University, Fulton, MO 65251
| | - Aparna Sreenivasan
- Science and Environmental Policy, California State University–Monterey Bay, Seaside, CA 93955
| | - Joyce Stamm
- Department of Biology, University of Evansville, Evansville, IN 47722
| | - Paul Szauter
- Biology Department, University of New Mexico, Albuquerque, NM 87106
| | | | - Matthew Wawersik
- Department of Biology, College of William & Mary, Williamsburg, VA 23187
| | - James Youngblom
- Department of Biology, California State University–Stanislaus, Turlock, CA 95382
| | - Leming Zhou
- Department of Health Information Management, University of Pittsburgh, Pittsburgh, PA 15213
| | - Elaine R. Mardis
- Genome Institute, Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108
| | - Jeremy Buhler
- Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, MO 63130
| | - Wilson Leung
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - David Lopatto
- Department of Psychology, Grinnell College, Grinnell, IA 50112
| | - Sarah C. R. Elgin
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
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Gravel S, Zakharia F, Moreno-Estrada A, Byrnes JK, Muzzio M, Rodriguez-Flores JL, Kenny EE, Gignoux CR, Maples BK, Guiblet W, Dutil J, Via M, Sandoval K, Bedoya G, Oleksyk TK, Ruiz-Linares A, Burchard EG, Martinez-Cruzado JC, Bustamante CD. Reconstructing Native American migrations from whole-genome and whole-exome data. PLoS Genet 2013; 9:e1004023. [PMID: 24385924 PMCID: PMC3873240 DOI: 10.1371/journal.pgen.1004023] [Citation(s) in RCA: 133] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 10/29/2013] [Indexed: 12/12/2022] Open
Abstract
There is great scientific and popular interest in understanding the genetic history of populations in the Americas. We wish to understand when different regions of the continent were inhabited, where settlers came from, and how current inhabitants relate genetically to earlier populations. Recent studies unraveled parts of the genetic history of the continent using genotyping arrays and uniparental markers. The 1000 Genomes Project provides a unique opportunity for improving our understanding of population genetic history by providing over a hundred sequenced low coverage genomes and exomes from Colombian (CLM), Mexican-American (MXL), and Puerto Rican (PUR) populations. Here, we explore the genomic contributions of African, European, and especially Native American ancestry to these populations. Estimated Native American ancestry is in MXL, in CLM, and in PUR. Native American ancestry in PUR is most closely related to populations surrounding the Orinoco River basin, confirming the Southern America ancestry of the Taíno people of the Caribbean. We present new methods to estimate the allele frequencies in the Native American fraction of the populations, and model their distribution using a demographic model for three ancestral Native American populations. These ancestral populations likely split in close succession: the most likely scenario, based on a peopling of the Americas thousand years ago (kya), supports that the MXL Ancestors split kya, with a subsequent split of the ancestors to CLM and PUR kya. The model also features effective populations of in Mexico, in Colombia, and in Puerto Rico. Modeling Identity-by-descent (IBD) and ancestry tract length, we show that post-contact populations also differ markedly in their effective sizes and migration patterns, with Puerto Rico showing the smallest effective size and the earlier migration from Europe. Finally, we compare IBD and ancestry assignments to find evidence for relatedness among European founders to the three populations. Populations of the Americas have a rich and heterogeneous genetic and cultural heritage that draws from a diversity of pre-Columbian Native American, European, and African populations. Characterizing this diversity facilitates the development of medical genetics research in diverse populations and the transfer of medical knowledge across populations. It also represents an opportunity to better understand the peopling of the Americas, from the crossing of Beringia to the post-Columbian era. Here, we take advantage sequencing of individuals of Colombian (CLM), Mexican (MXL), and Puerto Rican (PUR) origin by the 1000 Genomes project to improve our demographic models for the peopling of the Americas. The divergence among African, European, and Native American ancestors to these populations enables us to infer the continent of origin at each locus in the sampled genomes. The resulting patterns of ancestry suggest complex post-Columbian migration histories, starting later in CLM than in MXL and PUR. Whereas European ancestral segments show evidence of relatedness, a demographic model of synonymous variation suggests that the Native American Ancestors to MXL, PUR, and CLM panels split within a few hundred years over 12 thousand years ago. Together with early archeological sites in South America, these results support rapid divergence during the initial peopling of the Americas.
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Affiliation(s)
- Simon Gravel
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- McGill University and Génome Québec Innovation Centre, Montréal, Québec, Canada
- * E-mail:
| | - Fouad Zakharia
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Andres Moreno-Estrada
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Jake K. Byrnes
- Department of Genetics, Stanford University, Stanford, California, United States of America
- Ancestry.com DNA LLC, San Francisco, California, United States of America
| | - Marina Muzzio
- Department of Genetics, Stanford University, Stanford, California, United States of America
- Laboratorio de Genética Molecular Poblacional, Instituto Multidisciplinario de Biología Celular (IMBICE). CCT- CONICET-La Plata, Argentina and Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, La Plata, Argentina
| | | | - Eimear E. Kenny
- Department of Genetics, Stanford University, Stanford, California, United States of America
- Department of Genetics and Genomic Sciences, The Charles Bronfman Institute for Personalized Medicine, Center for Statistical Genetics, and Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Christopher R. Gignoux
- Department of Bioengineering and Therapeutic Sciences and Medicine, Univeristy of California San Francisco, San Francisco, California, United States of America
| | - Brian K. Maples
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Wilfried Guiblet
- Department of Biology, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico
| | - Julie Dutil
- Department of Biochemistry, Ponce School of Medicine and Health Sciences, Ponce, Puerto Rico
| | - Marc Via
- Department of Bioengineering and Therapeutic Sciences and Medicine, Univeristy of California San Francisco, San Francisco, California, United States of America
- Department of Psychiatry and Clinical Psychobiology, University of Barcelona, Barcelona, Spain
| | - Karla Sandoval
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | | | | | - Taras K. Oleksyk
- Department of Biology, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico
| | - Andres Ruiz-Linares
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Esteban G. Burchard
- Department of Bioengineering and Therapeutic Sciences and Medicine, Univeristy of California San Francisco, San Francisco, California, United States of America
| | | | - Carlos D. Bustamante
- Department of Genetics, Stanford University, Stanford, California, United States of America
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