Representative Publications
- Aquadro, C. F., A. L. Weaver, S. W. Schaeffer, and W. W.
Anderson,
1991 Molecular evolution of inversions in Drosophila pseudoobscura:
The amylase gene region. Proc. Natl. Acad. Sci. USA 88: 305-309.
- Schaeffer, S. W., and E. L. Miller, 1991 Nucleotide sequence
analysis
of Adh genes estimates the time of geographic isolation of the
Bogota
population of Drosophila pseudoobscura. Proc. Natl. Acad. Sci.
USA
88: 6097-6101.
- Anderson, W. W., J. Arnold, D. G. Baldwin, A. T. Beckenbach, C.
J.
Brown, S. H. Bryant, J. A. Coyne, L. G. Harshman, W. B. Heed, D. E.
Jeffrey,
L. B. Klaczko, B. C. Moore, J. M. Porter, J. R. Powell, T. Prout, S. W.
Schaeffer, J. C. Stephens, C. E. Taylor, M. E. Turner, G. O. Williams
and, J. A. Moore, 1991 Four decades of inversion polymorphism in Drosophila
pseudoobscura. Proc. Natl. Acad. Sci. USA, 88: 10367-10371.
- Schaeffer, S. W., and E. L. Miller, 1992 Molecular population
genetics of an electrophoretically monomorphic protein in the alcohol
dehydrogenase region of Drosophila pseudoobscura. Genetics 132:
163-178. Abstract
- Schaeffer, S. W., and E. L. Miller, 1992 Estimates of gene flow
in Drosophila pseudoobscura determined from nucleotide sequence
analysis
of the alcohol dehydrogenase region. Genetics 132: 471-480. Abstract
- Schaeffer, S. W., and E. L. Miller, 1993 Estimates of linkage
disequilibrium and the recombination parameter determined from
segregating nucleotide sites
in the alcohol dehydrogenase region of Drosophila pseudoobscura.
Genetics
135: 541-552.Abstract
- Walthour, C. S., and S. W. Schaeffer, 1994 Molecular population
genetics of sex determination genes: The transformer gene of Drosophila
melanogaster.
Genetics 136: 1367-1372. Abstract
- Schaeffer, S. W., 1994 Molecular population genetics in Drosophila
pseudoobscura: three future directions. In Non-neutral Evolution:
Theories
and Molecular Data. Editor: Brian Golding, Chapman &Hall, New York,
pp.
29-45.
- Schaeffer, S. W., 1995 Population genetics in Drosophila
pseudoobscura: A synthesis based on nucleotide sequence data for the
Adh gene. In Genetics of Natural Populations: The Continuing Importance
of Theodosius Dobzhansky. Editor: L. Levine, Columbia University Press,
NY, pp. 329-352.
- Richman, A. D., T.-H. Kao, S. W. Schaeffer, and M. K. Uyenoyama,
1995
S-allele sequence diversity in natural populations of Solanum
carolinense
(Horsenettle). Heredity 75: 405-415.Abstract
- Akashi, H., and S. W. Schaeffer, 1997 Natural selection and the
frequency distributions of "silent" polymorphism in Drosophila.
Genetics 146: 295-307.Abstract
- Schaeffer, S. W., 1997 Molecular population genetics of a
phenotypically monomorphic protein in Drosophila, pp. 133-148 in Progress
in Population Genetics and Human Evolution, edited by P. Donnelly,
and S. Tavaré. Springer, New York.
- Pritchard, J. K., and S. W. Schaeffer, 1997 Polymorphism
and
divergence at a Drosophila pseudogene locus. Genetics 147:199-208. Abstract
- Schaeffer, S. W. and M. Aguadé, 2000 Evidence for
balancing,
directional, and background selection in molecular evolution. In
Evolutionary Genetics: From Molecules to Morphology. Editors: R.
S. Singh and C.
B. Krimbas, Cambridge University Press, 1:124-142.
- Mullineaux, L. S., C. R. Fisher, C. H. Peterson, and S. W.
Schaeffer,
2000 Vestimentiferan tubeworm interactions at hydrothermal vents.
Oecologia 123: 275-284.
- Kovacevic, M. and S. W. Schaeffer, 2000 Molecular population
genetics
of X-linked genes in Drosophila pseudoobscura. Genetics
156:155-172.
- Schaeffer, S. W., C. S. Walthour, D. M. Toleno, A. T. Olek, and
E. L.
Miller 2001 Protein variation in ADH and ADH-RELATED in
Drosophila pseudoobscura:
Linkage disequilibrium between single nucleotide polymorphisms and
protein
alleles. Genetics 159: 673-687.
- Schaeffer, S. W., 2002 Molecular population genetics of sequence
length
diversity in the Adh region of Drosophila pseudoobscura.
Genet.
Res., Camb. 80: 163-175.
- Schaeffer, S. W., P. Goetting-Minesky, M. Kovacevic, J. Peoples,
J.
L. Graybill, J. M. Miller, K. Kim, J. G. Nelson and W. W. Anderson,
2003
Evolutionary genomics of inversions in Drosophila pseudoobscura:
Evidence
for epistasis. Proc. Natl. Acad. Sci. USA 100: 8319-8324.
- Schaeffer,
S. W., M. J. Bernhardt, and W. W. Anderson 2003 Evolutionary
rearrangement of the amylase genomic regions
between Drosophila
melanogaster and D. pseudoobscura. J.
Heredity 94: 464-471.
- Richards, S., Y. Liu, B. R. Bettencourt, P. Hradecky, S.
Letovsky, R. Nielsen, K. Thornton, M. A. Todd, R. Chen, R. P. Meisel,
O. Couronne, S. Hua, M. A. Smith, H. J. Bussemaker, M. F. V. Batenburg,
S. L. Howells, S. E. Scherer, E. Sodergren, B. B. Matthews, M. A.
Crosby, A. J. Schroeder, D. Ortiz-Barrientos, C. M. Rives, M. L.
Metzker, D. M. Muzny, G. Scott, D. Steffen, D. A. Wheeler, K. C.
Worley, P. Havlak, K. J. Durbin, A. Eagan, R. Gill, J. Hume, M. B.
Morgan, Y. Huang, L. Waldron, D. Verduzco, K. P. Blankenburg, H.
Robertson, I. Dubchak, M. A. F. Noor, W. W. Anderson, K. White, A. G.
Clark, S. W. Schaeffer, W. M. Gelbart, G. Weinstock and R. A. Gibbs,
2005 Comparative genome sequencing of Drosophila
pseudoobscura: Chromosomal, gene and cis-element
evolution. Genome Research 15: 1-18.
- Flores, J. F., S. L. Carney, B. N. Green, J. K. Freytag, S. W. Schaeffer, C. R. Fisher, and W. E. Royer 2005 Sulfide binding is mediated by zinc ions discovered in the crystal structure of a hydrothermal vent tubeworm hemoglobin. Proc.Natl. Acad. Sci. USA 102: 2713-2718.
- Schaeffer, S. W. and W. W. Anderson 2005 Mechanisms of genetic exchange within the chromosomal inversions of Drosophila pseudoobscura. Genetics 171: 1729-1739.
- Steglich, C. and S. W. Schaeffer 2006 The ornithine decarboxylase gene of Trypanosoma brucei: evidence for horizontal gene transfer from a vertebrate source. Infection, Genetics and Evolution 6: 205-219.
- Carney, S. L., M. I. Formica, H. Divatia, K. Nelson, C. R. Fisher, and S. W. Schaeffer 2006 Population structure of the mussel Bathymodiolus childressi from Gulf of Mexico hydrocarbon seeps. Deep Sea Research--Oceanographic Research Papers 53: 1061-1072.
- Susan L. Carney, Jason F. Flores, Kathryn M. Orobona, David A. Butterfield, Charles R. Fisher, and Stephen W. Schaeffer 2007 Environmental differences in hemoglobin gene expression in the hydrothermal vent tubeworm, Ridgeia piscesae. Comp. Biochem and Physiol Part B 146 (2007) 326–337.
- Meisel, R. P. and S. W. Schaeffer 2007 Meiotic transmission of Drosophila pseudoobscura chromosomal arrangements. PLoS one 2:e530.
- Drosophila 12 Genomes Consortium 2007 Evolution of genes and genomes on the Drosophila phylogeny. Nature 450: 203-218.
- M. A. F. Noor, D. A. Garfield, S. W. Schaeffer, and C. A. Machado 2007. Divergence between the Drosophila pseudoobscura and D. persimilis genome sequences in relation to their inversions. Genetics 177: 1417–1428 pdf
- Rosenbloom, K., J. Taylor, S. W. Schaeffer, J. Kent, D. Haussler, W. Miller 2007 Phylogenomic Resources at the UCSC Browser In: Phylogenomics (ed. W. J. Murphy) Methods in Molecular Biology Series, Humana Press, Totowa, NJ, USA
- Schaeffer, S. W., A. Bhutkar, B. F. McAllister, M. Matsuda, L. M. Matzkin, P. M. O' Grady, C. Rohde, V. L. S. Valente, M. Aguadé, W. W. Anderson, K. Edwards, A. C. L. Garcia, J. Goodman, J. Hartigan, E. Kataoka, R. T. Lapoint, E. R. Lozovsky, C. A. Machado, M. A. F. Noor, M. Papaceit, L. K. Reed, S. Richards, T. T. Rieger, S. M. Russo, H. Sato, C. Segarra, D. R. Smith, T. F. Smith, V. Strelets, Y. N. Tobari, Y. Tomimura, M. Wasserman, T. Watts, R. Wilson, K. Yoshida, T. A. Markow, W. M. Gelbart, and T. C. Kaufman 2008 Polytene Chromosomal Maps of 11 Drosophila species: The order of genomic scaffolds inferred from genetic and physical maps. Genetics 179: 1601-1655 pdf
- Bhutkar, A. J., S.W. Schaeffer, S. Russo, M. Xu, T. F. Smith, W. J. Gelbart 2008 Chromosomal rearrangement inferred from comparisons of twelve Drosophila genomes Genetics 179: 1657–1680. pdf
- Schaeffer, S. W. 2008 Selection in heterogeneous environments maintains the gene arrangement polymorphism of D. pseudoobscura. Evolution 62: 3082–3099 pdf