PSU Profiles
Last Name

Stephen Schaeffer

InstitutionEberly College of Science
Address507A Mueller Lab
University Park, PA 16802
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    Other Positions
    InstitutionHuck Institutes of the Life Sciences

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    Professor of Biology


    Bioinformatics and Genomics, Genetics


    B.S., West Virginia Wesleyan College, 1978
    M.S., West Virginia University, 1980
    Ph.D., University of Georgia, 1985


    Dr. Schaeffer's research focuses on the genomic processes that alter gene and chromosomal frequencies in natural populations of plants and animals.

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    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Fuller ZL, Haynes GD, Richards S, Schaeffer SW. Genomics of natural populations: Evolutionary forces that establish and maintain gene arrangements in Drosophila pseudoobscura. Mol Ecol. 2017 Dec; 26(23):6539-6562. PMID: 29055159.
      View in: PubMed
    2. Projecto-Garcia J, Le Port AS, Govindji T, Jollivet D, Schaeffer SW, Hourdez S. Evolution of Single-Domain Globins in Hydrothermal Vent Scale-Worms. J Mol Evol. 2017 Dec; 85(5-6):172-187. PMID: 29094190.
      View in: PubMed
    3. Huang C, Schaeffer SW, Fisher CR, Cowart DA. Investigation of population structure in Gulf of Mexico Seepiophila jonesi (Polychaeta, Siboglinidae) using cross-amplified microsatellite loci. PeerJ. 2016; 4:e2366. PMID: 27635334; PMCID: PMC5012325.
    4. Fuller ZL, Haynes GD, Richards S, Schaeffer SW. Genomics of Natural Populations: How Differentially Expressed Genes Shape the Evolution of Chromosomal Inversions in Drosophila pseudoobscura. Genetics. 2016 09; 204(1):287-301. PMID: 27401754; PMCID: PMC5012393.
    5. Faure B, Schaeffer SW, Fisher CR. Species distribution and population connectivity of deep-sea mussels at hydrocarbon seeps in the Gulf of Mexico. PLoS One. 2015; 10(4):e0118460. PMID: 25859657; PMCID: PMC4393317.
    6. Fuller ZL, Haynes GD, Zhu D, Batterton M, Chao H, Dugan S, Javaid M, Jayaseelan JC, Lee S, Li M, Ongeri F, Qi S, Han Y, Doddapaneni H, Richards S, Schaeffer SW. Evidence for stabilizing selection on codon usage in chromosomal rearrangements of Drosophila pseudoobscura. G3 (Bethesda). 2014 Oct 17; 4(12):2433-49. PMID: 25326424; PMCID: PMC4267939.
    7. Cowart DA, Huang C, Arnaud-Haond S, Carney SL, Fisher CR, Schaeffer SW. Restriction to large-scale gene flow vs. regional panmixia among cold seep Escarpia spp. (Polychaeta, Siboglinidae). Mol Ecol. 2013 Aug; 22(16):4147-4162. PMID: 23879204.
      View in: PubMed
    8. Wallace AG, Detweiler D, Schaeffer SW. Molecular population genetics of inversion breakpoint regions in Drosophila pseudoobscura. G3 (Bethesda). 2013 Jul 08; 3(7):1151-63. PMID: 23665879; PMCID: PMC3704243.
    9. Kang S, Tang J, Schaeffer SW, Bader DA. Rec-DCM-Eigen: reconstructing a less parsimonious but more accurate tree in shorter time. PLoS One. 2011; 6(8):e22483. PMID: 21887219; PMCID: PMC3160844.
    10. Wallace AG, Detweiler D, Schaeffer SW. Evolutionary history of the third chromosome gene arrangements of Drosophila pseudoobscura inferred from inversion breakpoints. Mol Biol Evol. 2011 Aug; 28(8):2219-29. PMID: 21339510.
      View in: PubMed
    11. Meisel RP, Hilldorfer BB, Koch JL, Lockton S, Schaeffer SW. Adaptive evolution of genes duplicated from the Drosophila pseudoobscura neo-X chromosome. Mol Biol Evol. 2010 Aug; 27(8):1963-78. PMID: 20351054; PMCID: PMC2915643.
    12. Projecto-Garcia J, Zorn N, Jollivet D, Schaeffer SW, Lallier FH, Hourdez S. Origin and evolution of the unique tetra-domain hemoglobin from the hydrothermal vent scale worm Branchipolynoe. Mol Biol Evol. 2010 Jan; 27(1):143-52. PMID: 19755665.
      View in: PubMed
    13. Schaeffer SW. Selection in heterogeneous environments maintains the gene arrangement polymorphism of Drosophila pseudoobscura. Evolution. 2008 Dec; 62(12):3082-99. PMID: 18764919.
      View in: PubMed
    14. Schaeffer SW, Bhutkar A, McAllister BF, Matsuda M, Matzkin LM, O'Grady PM, Rohde C, Valente VL, Aguadé M, Anderson WW, Edwards K, Garcia AC, Goodman J, Hartigan J, Kataoka E, Lapoint RT, Lozovsky ER, Machado CA, Noor MA, Papaceit M, Reed LK, Richards S, Rieger TT, Russo SM, Sato H, Segarra C, Smith DR, Smith TF, Strelets V, Tobari YN, Tomimura Y, Wasserman M, Watts T, Wilson R, Yoshida K, Markow TA, Gelbart WM, Kaufman TC. Polytene chromosomal maps of 11 Drosophila species: the order of genomic scaffolds inferred from genetic and physical maps. Genetics. 2008 Jul; 179(3):1601-55. PMID: 18622037; PMCID: PMC2475758.
    15. Bhutkar A, Schaeffer SW, Russo SM, Xu M, Smith TF, Gelbart WM. Chromosomal rearrangement inferred from comparisons of 12 Drosophila genomes. Genetics. 2008 Jul; 179(3):1657-80. PMID: 18622036; PMCID: PMC2475759.
    16. Rosenbloom K, Taylor J, Schaeffer S, Kent J, Haussler D, Miller W. Phylogenomic resources at the UCSC Genome Browser. Methods Mol Biol. 2008; 422:133-44. PMID: 18629665.
      View in: PubMed
    17. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 2007 Nov 08; 450(7167):203-18. PMID: 17994087.
      View in: PubMed
    18. Noor MA, Garfield DA, Schaeffer SW, Machado CA. Divergence between the Drosophila pseudoobscura and D. persimilis genome sequences in relation to chromosomal inversions. Genetics. 2007 Nov; 177(3):1417-28. PMID: 18039875; PMCID: PMC2147956.
    19. Meisel RP, Schaeffer SW. Meiotic transmission of Drosophila pseudoobscura chromosomal arrangements. PLoS One. 2007 Jun 13; 2(6):e530. PMID: 17565383; PMCID: PMC1885828.
    20. Carney SL, Flores JF, Orobona KM, Butterfield DA, Fisher CR, Schaeffer SW. Environmental differences in hemoglobin gene expression in the hydrothermal vent tubeworm, Ridgeia piscesae. Comp Biochem Physiol B Biochem Mol Biol. 2007 Mar; 146(3):326-37. PMID: 17240180.
      View in: PubMed
    21. Steglich C, Schaeffer SW. The ornithine decarboxylase gene of Trypanosoma brucei: Evidence for horizontal gene transfer from a vertebrate source. Infect Genet Evol. 2006 May; 6(3):205-19. PMID: 16344004.
      View in: PubMed
    22. Schaeffer SW, Anderson WW. Mechanisms of genetic exchange within the chromosomal inversions of Drosophila pseudoobscura. Genetics. 2005 Dec; 171(4):1729-39. PMID: 16143625; PMCID: PMC1456099.
    23. Flores JF, Fisher CR, Carney SL, Green BN, Freytag JK, Schaeffer SW, Royer WE. Sulfide binding is mediated by zinc ions discovered in the crystal structure of a hydrothermal vent tubeworm hemoglobin. Proc Natl Acad Sci U S A. 2005 Feb 22; 102(8):2713-8. PMID: 15710902; PMCID: PMC549462.
    24. Richards S, Liu Y, Bettencourt BR, Hradecky P, Letovsky S, Nielsen R, Thornton K, Hubisz MJ, Chen R, Meisel RP, Couronne O, Hua S, Smith MA, Zhang P, Liu J, Bussemaker HJ, van Batenburg MF, Howells SL, Scherer SE, Sodergren E, Matthews BB, Crosby MA, Schroeder AJ, Ortiz-Barrientos D, Rives CM, Metzker ML, Muzny DM, Scott G, Steffen D, Wheeler DA, Worley KC, Havlak P, Durbin KJ, Egan A, Gill R, Hume J, Morgan MB, Miner G, Hamilton C, Huang Y, Waldron L, Verduzco D, Clerc-Blankenburg KP, Dubchak I, Noor MA, Anderson W, White KP, Clark AG, Schaeffer SW, Gelbart W, Weinstock GM, Gibbs RA. Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution. Genome Res. 2005 Jan; 15(1):1-18. PMID: 15632085; PMCID: PMC540289.
    25. Schaeffer SW, Bernhardt MJ, Anderson WW. Evolutionary rearrangement of the amylase genomic regions between Drosophila melanogaster and Drosophila pseudoobscura. J Hered. 2003 Nov-Dec; 94(6):464-71. PMID: 14691313.
      View in: PubMed
    26. Schaeffer SW, Goetting-Minesky MP, Kovacevic M, Peoples JR, Graybill JL, Miller JM, Kim K, Nelson JG, Anderson WW. Evolutionary genomics of inversions in Drosophila pseudoobscura: evidence for epistasis. Proc Natl Acad Sci U S A. 2003 Jul 08; 100(14):8319-24. PMID: 12824467; PMCID: PMC166227.
    27. Schaeffer SW. Molecular population genetics of sequence length diversity in the Adh region of Drosophila pseudoobscura. Genet Res. 2002 Dec; 80(3):163-75. PMID: 12688655.
      View in: PubMed
    28. Schaeffer SW, Walthour CS, Toleno DM, Olek AT, Miller EL. Protein variation in Adh and Adh-related in Drosophila pseudoobscura. Linkage disequilibrium between single nucleotide polymorphisms and protein alleles. Genetics. 2001 Oct; 159(2):673-87. PMID: 11606543; PMCID: PMC1461836.
    29. Kovacevic M, Schaeffer SW. Molecular population genetics of X-linked genes in Drosophila pseudoobscura. Genetics. 2000 Sep; 156(1):155-72. PMID: 10978282; PMCID: PMC1461252.
    30. Mullineaux LS, Fisher CR, Peterson CH, Schaeffer SW. Tubeworm succession at hydrothermal vents: use of biogenic cues to reduce habitat selection error? Oecologia. 2000 May; 123(2):275-284. PMID: 28308732.
      View in: PubMed
    31. Pritchard JK, Schaeffer SW. Polymorphism and divergence at a Drosophila pseudogene locus. Genetics. 1997 Sep; 147(1):199-208. PMID: 9286680; PMCID: PMC1208104.
    32. Akashi H, Schaeffer SW. Natural selection and the frequency distributions of "silent" DNA polymorphism in Drosophila. Genetics. 1997 May; 146(1):295-307. PMID: 9136019; PMCID: PMC1207945.
    33. Richman AD, Kao TH, Schaeffer SW, Uyenoyama MK. S-allele sequence diversity in natural populations of Solanum carolinense (Horsenettle). Heredity (Edinb). 1995 Oct; 75 ( Pt 4):405-15. PMID: 7591834.
      View in: PubMed
    34. Walthour CS, Schaeffer SW. Molecular population genetics of sex determination genes: the transformer gene of Drosophila melanogaster. Genetics. 1994 Apr; 136(4):1367-72. PMID: 8013913; PMCID: PMC1205917.
    35. Schaeffer SW, Miller EL. Estimates of linkage disequilibrium and the recombination parameter determined from segregating nucleotide sites in the alcohol dehydrogenase region of Drosophila pseudoobscura. Genetics. 1993 Oct; 135(2):541-52. PMID: 8244013; PMCID: PMC1205654.
    36. Schaeffer SW, Miller EL. Estimates of gene flow in Drosophila pseudoobscura determined from nucleotide sequence analysis of the alcohol dehydrogenase region. Genetics. 1992 Oct; 132(2):471-80. PMID: 1427038; PMCID: PMC1205150.
    37. Schaeffer SW, Miller EL. Molecular population genetics of an electrophoretically monomorphic protein in the alcohol dehydrogenase region of Drosophila pseudoobscura. Genetics. 1992 Sep; 132(1):163-78. PMID: 1398051; PMCID: PMC1205114.
    38. Schaeffer SW, Miller EL. Nucleotide sequence analysis of Adh genes estimates the time of geographic isolation of the Bogota population of Drosophila pseudoobscura. Proc Natl Acad Sci U S A. 1991 Jul 15; 88(14):6097-101. PMID: 2068088; PMCID: PMC52029.
    39. Aquadro CF, Weaver AL, Schaeffer SW, Anderson WW. Molecular evolution of inversions in Drosophila pseudoobscura: the amylase gene region. Proc Natl Acad Sci U S A. 1991 Jan 01; 88(1):305-9. PMID: 1702542; PMCID: PMC50799.
    40. Schaeffer SW, Aquadro CF, Langley CH. Restriction-map variation in the Notch region of Drosophila melanogaster. Mol Biol Evol. 1988 Jan; 5(1):30-40. PMID: 2833676.
      View in: PubMed
    41. Schaeffer SW, Aquadro CF. Nucleotide sequence of the Adh gene region of Drosophila pseudoobscura: evolutionary change and evidence for an ancient gene duplication. Genetics. 1987 Sep; 117(1):61-73. PMID: 3666441; PMCID: PMC1203188.
    42. Schaeffer SW, Aquadro CF, Anderson WW. Restriction-map variation in the alcohol dehydrogenase region of Drosophila pseudoobscura. Mol Biol Evol. 1987 May; 4(3):254-65. PMID: 2833670.
      View in: PubMed
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