Stephen Schaeffer

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Titles and Affiliations
Professor, Biology

Research Summary

Interested in the genomic processes that alter gene and chromosomal frequencies in natural populations of plants and animals. He is testing hypotheses about how chromosomal inversions arise, spread and are maintained in populations. He is also studying th

Research Keywords

Recent Publications

The relevance of chromatin architecture to genome rearrangements in Drosophila

Wright, D. & Schaeffer, S. W., Aug 1 2022, In: Philosophical Transactions of the Royal Society B: Biological Sciences. 377, 1856, 20210206.

Research output: Contribution to journalArticlepeer-review

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

Kapun, M., Nunez, J. C. B., Bogaerts-Márquez, M., Murga-Moreno, J., Paris, M., Outten, J., Coronado-Zamora, M., Tern, C., Rota-Stabelli, O., García Guerreiro, M. P., Casillas, S., Orengo, D. J., Puerma, E., Kankare, M., Ometto, L., Loeschcke, V., Onder, B. S., Abbott, J. K., Schaeffer, S. W., Rajpurohit, S., & 50 othersBehrman, E. L., Schou, M. F., Merritt, T. J. S., Lazzaro, B. P., Glaser-Schmitt, A., Argyridou, E., Staubach, F., Wang, Y., Tauber, E., Serga, S. V., Fabian, D. K., Dyer, K. A., Wheat, C. W., Parsch, J., Grath, S., Veselinovic, M. S., Stamenkovic-Radak, M., Jelic, M., Buendía-Ruíz, A. J., Gómez-Julián, M. J., Espinosa-Jimenez, M. L., Gallardo-Jiménez, F. D., Patenkovic, A., Eric, K., Tanaskovic, M., Ullastres, A., Guio, L., Merenciano, M., Guirao-Rico, S., Horváth, V., Obbard, D. J., Pasyukova, E., Alatortsev, V. E., Vieira, C. P., Vieira, J., Torres, J. R., Kozeretska, I., Maistrenko, O. M., Montchamp-Moreau, C., Mukha, D. V., Machado, H. E., Lamb, K., Paulo, T., Yusuf, L., Barbadilla, A., Petrov, D., Schmidt, P., Gonzalez, J., Flatt, T. & Bergland, A. O., 2021, In: Molecular biology and evolution. 38, 12, p. 5782-5805 24 p.

Research output: Contribution to journalArticlepeer-review

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

Machado, H. E., Bergland, A. O., Taylor, R., Tilk, S., Behrman, E., Dyer, K., Fabian, D. K., Flatt, T., González, J., Karasov, T. L., Kim, B., Kozeretska, I., Lazzaro, B. P., Merritt, T. J. S., Pool, J. E., O’brien, K., Rajpurohit, S., Roy, P. R., Schaeffer, S. W., Serga, S., & 2 othersSchmidt, P. & Petrov, D. A., Jun 2021, In: eLife. 10, e67577.

Research output: Contribution to journalArticlepeer-review

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

Fuller, Z. L., Koury, S. A., Leonard, C. J., Young, R. E., Ikegami, K., Westlake, J., Richards, S., Schaeffer, S. W. & Phadnis, N., Sep 2020, In: Genetics. 216, 1, p. 205-226 22 p.

Research output: Contribution to journalArticlepeer-review

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

Fuller, Z. L., Koury, S. A., Phadnis, N. & Schaeffer, S. W., Mar 2019, In: Molecular ecology. 28, 6, p. 1283-1301 19 p.

Research output: Contribution to journalArticlepeer-review

Ancestral polymorphisms explain the role of chromosomal inversions in speciation

Fuller, Z. L., Leonard, C. J., Young, R. E., Schaeffer, S. W. & Phadnis, N., Jul 2018, In: PLoS genetics. 14, 7, e1007526.

Research output: Contribution to journalArticlepeer-review

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

Schaeffer, S. W., Sep 2018, In: Genetics. 210, 1, p. 3-13 11 p.

Research output: Contribution to journalArticlepeer-review

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

Fuller, Z. L., Haynes, G. D., Richards, S. & Schaeffer, S. W., Dec 2017, In: Molecular ecology. 26, 23, p. 6539-6562 24 p.

Research output: Contribution to journalArticlepeer-review

Evolution of Single-Domain Globins in Hydrothermal Vent Scale-Worms

Projecto-Garcia, J., Le Port, A. S., Govindji, T., Jollivet, D., Schaeffer, S. W. & Hourdez, S., Dec 1 2017, In: Journal Of Molecular Evolution. 85, 5-6, p. 172-187 16 p.

Research output: Contribution to journalArticlepeer-review

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

Fuller, Z. L., Haynes, G. D., Richards, S. & Schaeffer, S. W., Sep 2016, In: Genetics. 204, 1, p. 287-301 15 p.

Research output: Contribution to journalArticlepeer-review

Investigation of population structure in Gulf of Mexico Seepiophila jonesi (Polychaeta, Siboglinidae) using cross-amplified microsatellite loci

Huang, C., Schaeffer, S. W., Fisher, C. R. & Cowart, D. A., 2016, In: PeerJ. 2016, 8, e2366.

Research output: Contribution to journalArticlepeer-review

Exemplar or matching: modeling DCJ problems with unequal content genome data

Yin, Z., Tang, J., Schaeffer, S. W. & Bader, D. A., Nov 1 2016, In: Journal of Combinatorial Optimization. 32, 4, p. 1165-1181 17 p.

Research output: Contribution to journalArticlepeer-review

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

Faure, B., Schaeffer, S. W. & Fisher, C. R., Apr 10 2015, In: PloS one. 10, 4, e0118460.

Research output: Contribution to journalArticlepeer-review

Selective forces acting during multi-domain protein evolution: the case of multi-domain globins

Projecto-Garcia, J., Jollivet, D., Mary, J., Lallier, F. H., Schaeffer, S. W. & Hourdez, S., Dec 25 2015, In: SpringerPlus. 4, 1, 354.

Research output: Contribution to journalArticlepeer-review

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

Cowart, D. A., Halanych, K. M., Schaeffer, S. W. & Fisher, C. R., Sep 2014, In: Hydrobiologia. 736, 1, p. 139-154 16 p.

Research output: Contribution to journalArticlepeer-review