Stephen Schaeffer

Professor of Biology

507A Mueller
University Park, PA 16802
He/Him
sws4@psu.edu

Bio & Links
Publications

Research Summary

Population Genetics and Genomics of Chromosomal Rearrangements in Drosophila

Huck Affiliations

Bioinformatics and Genomics

Publication Tags

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Drosophila Genes Population Chromosomes Genomics Genome Mutation Gene Flow Gene Frequency Drosophila Pseudoobscura Population Genetics Sampling Gulf Of Mexico Genetic Recombination Phylogeny Inversion History Gene Order Hydrocarbons Chromosome Inversion Metagenomics Reproductive Isolation Pressure Linkage Disequilibrium Sex Ratio

Most Recent Publications

Evolution of Genome Organization

Stephen Schaeffer, Encyclopedia of Evolutionary Biology

Timing of Bownes stage five embryos in Drosophila pseudoobscura.

Dynisty Wright, Stephen Schaeffer, 2022, Drosophila Information Service on p. 15-18

The relevance of chromatin architecture to genome rearrangements in Drosophila

Dynisty Wright, Stephen W. Schaeffer, 2022, Philosophical Transactions of the Royal Society B: Biological Sciences

Broad geographic sampling reveals predictable, pervasive, and strong seasonal adaptation in Drosophila

Heather Machado, Alan Bergland, Ryan Taylor, Susanne Tilk, Emily Behrman, Kelly Dyer, Daniel Fabian, Thomas Flatt, Josefa Gonzalez, Talia Karasov, Bernard Kim, Iryna Kozeretska, Brian Lazzaro, Thomas Merritt, John Pool, Katherine O'Brien, Subhash Pajpurohit, Paula Roy, Stephen Schaeffer, Svitlana Serga, Paul Schmidt, Dmitri Petrov, 2021, eLife on p. e67577

Broad geographic sampling reveals the shared basis and environmental correlates of seasonal adaptation in drosophila

Heather E. Machado, Alan O. Bergland, Ryan Taylor, Susanne Tilk, Emily Behrman, Kelly Dyer, Daniel K. Fabian, Thomas Flatt, Josefa González, Talia L. Karasov, Bernard Kim, Iryna Kozeretska, Brian P. Lazzaro, Thomas J.S. Merritt, John E. Pool, Katherine O’brien, Subhash Rajpurohit, Paula R. Roy, Stephen W. Schaeffer, Svitlana Serga, Paul Schmidt, Dmitri A. Petrov, 2021, eLife

Drosophila Evolution over Space and Time (DEST): A New Population Genomics Resource

Martin Kapun, Joaquin C.B. Nunez, María Bogaerts-Márquez, Jesús Murga-Moreno, Margot Paris, Joseph Outten, Marta Coronado-Zamora, Courtney Tern, Omar Rota-Stabelli, Maria P. García Guerreiro, Sònia Casillas, Dorcas J. Orengo, Eva Puerma, Maaria Kankare, Lino Ometto, Volker Loeschcke, Banu S. Onder, Jessica K. Abbott, Stephen W. Schaeffer, Subhash Rajpurohit, Emily L. Behrman, Mads F. Schou, Thomas J.S. Merritt, Brian P. Lazzaro, Amanda Glaser-Schmitt, Eliza Argyridou, Fabian Staubach, Yun Wang, Eran Tauber, Svitlana V. Serga, Daniel K. Fabian, Kelly A. Dyer, Christopher W. Wheat, John Parsch, Sonja Grath, Marija Savic Veselinovic, Marina Stamenkovic-Radak, Mihailo Jelic, Antonio J. Buendía-Ruíz, Maria Josefa Gómez-Julián, Maria Luisa Espinosa-Jimenez, Francisco D. Gallardo-Jiménez, Aleksandra Patenkovic, Katarina Eric, Marija Tanaskovic, Anna Ullastres, Lain Guio, Miriam Merenciano, Sara Guirao-Rico, Vivien Horváth, Darren J. Obbard, Elena Pasyukova, Vladimir E. Alatortsev, Cristina P. Vieira, Jorge Vieira, Jorge Roberto Torres, Iryna Kozeretska, Oleksandr M. Maistrenko, Catherine Montchamp-Moreau, Dmitry V. Mukha, Heather E. Machado, Keric Lamb, Tânia Paulo, Leeban Yusuf, Antonio Barbadilla, Dmitri Petrov, Paul Schmidt, Josefa Gonzalez, Thomas Flatt, Alan O. Bergland, 2021, Molecular Biology and Evolution on p. 5782-5805

Extensive recombination suppression and epistatic selection causes chromosome-wide differentiation of a selfish sex chromosome in drosophila pseudoobscura

Zachary L. Fuller, Spencer A. Koury, Christopher J. Leonard, Randee E. Young, Kobe Ikegami, Jonathan Westlake, Stephen Richards, Stephen W. Schaeffer, Nitin Phadnis, 2020, Genetics on p. 205-226

How chromosomal rearrangements shape adaptation and speciation: Case studies in Drosophila pseudoobscura and its sibling species Drosophila persimilis

Zachary L. Fuller, Spencer A. Koury, Nitin Phadnis, Stephen W. Schaeffer, 2019, Molecular Ecology on p. 1283-1301

How chromosomal rearrangements shape adaptation and speciation: Case studies in Drosophila pseudoobscura and its sibling species Drosophila persimilis.

Z Fuller, S Koury, N Phadnis, Stephen Schaeffer, 2018, Molecular ecology

Muller “elements” in Drosophila: How the search for the genetic basis for speciation led to the birth of comparative genomics

Stephen W. Schaeffer, 2018, Genetics on p. 3-13

Most-Cited Papers

How chromosomal rearrangements shape adaptation and speciation: Case studies in Drosophila pseudoobscura and its sibling species Drosophila persimilis

Zachary L. Fuller, Spencer A. Koury, Nitin Phadnis, Stephen W. Schaeffer, 2019, Molecular Ecology on p. 1283-1301

Ancestral polymorphisms explain the role of chromosomal inversions in speciation

Zachary L. Fuller, Christopher J. Leonard, Randee E. Young, Stephen W. Schaeffer, Nitin Phadnis, 2018, PLoS Genetics

Genomics of natural populations: How differentially expressed genes shape the evolution of chromosomal inversions in Drosophila pseudoobscura

Zachary L. Fuller, Gwilym D. Haynes, Stephen Richards, Stephen W. Schaeffer, 2016, Genetics on p. 287-301

Broad geographic sampling reveals the shared basis and environmental correlates of seasonal adaptation in drosophila

Species distribution and population connectivity of deep-sea mussels at hydrocarbon seeps in the Gulf of Mexico

Baptiste Faure, Stephen W. Schaeffer, Charles R. Fisher, 2015, PLoS One on p. e0118460

Genomics of natural populations: Evolutionary forces that establish and maintain gene arrangements in Drosophila pseudoobscura

Zachary L. Fuller, Gwilym D. Haynes, Stephen Richards, Stephen W. Schaeffer, 2017, Molecular Ecology on p. 6539-6562

Restriction to large-scale gene flow vs. regional panmixia among cold seep Escarpia spp. (Polychaeta, Siboglinidae)

Dominique A. Cowart, Chunya Huang, Sophie Arnaud-Haond, Susan L. Carney, Charles R. Fisher, Stephen W. Schaeffer, 2013, Molecular Ecology on p. 4147-4162

Depth-dependent gene flow in Gulf of Mexico cold seep Lamellibrachia tubeworms (Annelida, Siboglinidae)

Dominique A. Cowart, Kenneth M. Halanych, Stephen W. Schaeffer, Charles R. Fisher, 2014, Journal of Aquatic Ecosystem Health on p. 139-154