Stephen W. Schaeffer, B.S., M.S., Ph.D. - Publications

Biology Pennsylvania State University, State College, PA, United States 
Evolutionary Genetics and Genomics

55 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Berdan EL, Barton NH, Butlin R, Charlesworth B, Faria R, Fragata I, Gilbert KJ, Jay P, Kapun M, Lotterhos KE, Mérot C, Durmaz Mitchell E, Pascual M, Peichel CL, Rafajlović M, ... ... Schaeffer SW, et al. How chromosomal inversions reorient the evolutionary process. Journal of Evolutionary Biology. PMID 37942504 DOI: 10.1111/jeb.14242  0.576
2022 Wright D, Schaeffer SW. The relevance of chromatin architecture to genome rearrangements in . Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 377: 20210206. PMID 35694744 DOI: 10.1098/rstb.2021.0206  0.764
2021 Kapun M, Nunez JCB, Bogaerts-Márquez M, Murga-Moreno J, Paris M, Outten J, Coronado-Zamora M, Tern C, Rota-Stabelli O, García Guerreiro MP, Casillas S, Orengo DJ, Puerma E, Kankare M, Ometto L, ... ... Schaeffer SW, et al. Drosophila Evolution over Space and Time (DEST) - A New Population Genomics Resource. Molecular Biology and Evolution. PMID 34469576 DOI: 10.1093/molbev/msab259  0.569
2021 Machado HE, Bergland A, Taylor RW, Tilk S, Behrman E, Dyer K, Fabian DK, Flatt T, González J, Karasov TL, Kim BY, Kozeretska I, Lazzaro BP, Merritt T, Pool JE, ... ... Schaeffer SW, et al. Broad geographic sampling reveals the shared basis and environmental correlates of seasonal adaptation in Drosophila. Elife. 10. PMID 34155971 DOI: 10.7554/eLife.67577  0.547
2020 Fuller ZL, Koury SA, Leonard CJ, Young RE, Ikegami K, Westlake J, Richards S, Schaeffer SW, Phadnis N. Extensive Recombination Suppression and Epistatic Selection Causes Chromosome-Wide Differentiation of a Selfish Sex Chromosome in . Genetics. PMID 32732371 DOI: 10.1534/Genetics.120.303460  0.806
2018 Fuller ZL, Koury SA, Phadnis N, Schaeffer SW. How chromosomal rearrangements shape adaptation and speciation: Case studies in Drosophila pseudoobscura and its sibling species D. persimilis. Molecular Ecology. PMID 30402909 DOI: 10.1111/Mec.14923  0.798
2018 Schaeffer SW. Muller "Elements" in : How the Search for the Genetic Basis for Speciation Led to the Birth of Comparative Genomics. Genetics. 210: 3-13. PMID 30166445 DOI: 10.1534/genetics.118.301084  0.536
2018 Fuller ZL, Leonard CJ, Young RE, Schaeffer SW, Phadnis N. Ancestral polymorphisms explain the role of chromosomal inversions in speciation. Plos Genetics. 14: e1007526. PMID 30059505 DOI: 10.1371/Journal.Pgen.1007526  0.808
2017 Projecto-Garcia J, Le Port AS, Govindji T, Jollivet D, Schaeffer SW, Hourdez S. Evolution of Single-Domain Globins in Hydrothermal Vent Scale-Worms. Journal of Molecular Evolution. PMID 29094190 DOI: 10.1007/s00239-017-9815-7  0.362
2017 Fuller ZL, Haynes GD, Richards S, Schaeffer SW. Genomics of Natural Populations: Evolutionary Forces that Establish and Maintain Gene Arrangements in Drosophila pseudoobscura. Molecular Ecology. PMID 29055159 DOI: 10.1111/Mec.14381  0.833
2016 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. 4: e2366. PMID 27635334 DOI: 10.7717/Peerj.2366  0.786
2016 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. PMID 27401754 DOI: 10.1534/Genetics.116.191429  0.829
2015 Projecto-Garcia J, Jollivet D, Mary J, Lallier FH, Schaeffer SW, Hourdez S. Selective forces acting during multi-domain protein evolution: the case of multi-domain globins. Springerplus. 4: 354. PMID 26191481 DOI: 10.1186/s40064-015-1124-2  0.307
2015 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. 10: e0118460. PMID 25859657 DOI: 10.1371/Journal.Pone.0118460  0.386
2015 Yin Z, Tang J, Schaeffer SW, Bader DA. Exemplar or matching: modeling DCJ problems with unequal content genome data Journal of Combinatorial Optimization. DOI: 10.1007/S10878-015-9940-4  0.324
2014 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, et al. Evidence for stabilizing selection on codon usage in chromosomal rearrangements of Drosophila pseudoobscura. G3 (Bethesda, Md.). 4: 2433-49. PMID 25326424 DOI: 10.1534/G3.114.014860  0.807
2014 Cowart DA, Halanych KM, Schaeffer SW, Fisher CR. Depth-dependent gene flow in Gulf of Mexico cold seep Lamellibrachia tubeworms (Annelida, Siboglinidae) Hydrobiologia. 736: 139-154. DOI: 10.1007/S10750-014-1900-Y  0.337
2013 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). Molecular Ecology. 22: 4147-62. PMID 23879204 DOI: 10.1111/Mec.12379  0.773
2013 Wallace AG, Detweiler D, Schaeffer SW. Molecular population genetics of inversion breakpoint regions in Drosophila pseudoobscura. G3 (Bethesda, Md.). 3: 1151-63. PMID 23665879 DOI: 10.1534/G3.113.006122  0.71
2013 Cowart DA, Huang C, Schaeffer SW. Identification and amplification of microsatellite loci in deep-sea tubeworms of the genus Escarpia (Polychaeta, Siboglinidae) Conservation Genetics Resources. 5: 479-482. DOI: 10.1007/s12686-012-9832-1  0.391
2011 Kang S, Tang J, Schaeffer SW, Bader DA. Rec-DCM-Eigen: reconstructing a less parsimonious but more accurate tree in shorter time. Plos One. 6: e22483. PMID 21887219 DOI: 10.1371/Journal.Pone.0022483  0.346
2011 Wallace AG, Detweiler D, Schaeffer SW. Evolutionary history of the third chromosome gene arrangements of Drosophila pseudoobscura inferred from inversion breakpoints. Molecular Biology and Evolution. 28: 2219-29. PMID 21339510 DOI: 10.1093/Molbev/Msr039  0.753
2010 Meisel RP, Hilldorfer BB, Koch JL, Lockton S, Schaeffer SW. Adaptive evolution of genes duplicated from the Drosophila pseudoobscura neo-X chromosome. Molecular Biology and Evolution. 27: 1963-78. PMID 20351054 DOI: 10.1093/Molbev/Msq085  0.824
2010 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. Molecular Biology and Evolution. 27: 143-52. PMID 19755665 DOI: 10.1093/molbev/msp218  0.332
2010 Pia Miglietta M, Hourdez S, Cowart DA, Schaeffer SW, Fisher C. Species boundaries of Gulf of Mexico vestimentiferans (Polychaeta, Siboglinidae) inferred from mitochondrial genes Deep-Sea Research Part Ii: Topical Studies in Oceanography. 57: 1916-1925. DOI: 10.1016/J.Dsr2.2010.05.007  0.39
2010 McMullin ER, Nelson K, Fisher CR, Schaeffer SW. Population structure of two deep sea tubeworms, Lamellibrachia luymesi and Seepiophila jonesi, from the hydrocarbon seeps of the Gulf of Mexico Deep-Sea Research Part I: Oceanographic Research Papers. 57: 1499-1509. DOI: 10.1016/j.dsr.2010.07.012  0.763
2008 Schaeffer SW. Selection in heterogeneous environments maintains the gene arrangement polymorphism of Drosophila pseudoobscura. Evolution; International Journal of Organic Evolution. 62: 3082-99. PMID 18764919 DOI: 10.1111/j.1558-5646.2008.00504.x  0.532
2008 Rosenbloom K, Taylor J, Schaeffer S, Kent J, Haussler D, Miller W. Phylogenomic resources at the UCSC Genome Browser. Methods in Molecular Biology (Clifton, N.J.). 422: 133-44. PMID 18629665 DOI: 10.1007/978-1-59745-581-7_9  0.383
2008 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, et al. Polytene chromosomal maps of 11 Drosophila species: the order of genomic scaffolds inferred from genetic and physical maps. Genetics. 179: 1601-55. PMID 18622037 DOI: 10.1534/Genetics.107.086074  0.797
2008 Bhutkar A, Schaeffer SW, Russo SM, Xu M, Smith TF, Gelbart WM. Chromosomal rearrangement inferred from comparisons of 12 Drosophila genomes. Genetics. 179: 1657-80. PMID 18622036 DOI: 10.1534/Genetics.107.086108  0.53
2007 Noor MA, Garfield DA, Schaeffer SW, Machado CA. Divergence between the Drosophila pseudoobscura and D. persimilis genome sequences in relation to chromosomal inversions. Genetics. 177: 1417-28. PMID 18039875 DOI: 10.1534/Genetics.107.070672  0.568
2007 Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM, Singh ND, ... ... Schaeffer SW, et al. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 450: 203-18. PMID 17994087 DOI: 10.1038/Nature06341  0.767
2007 Meisel RP, Schaeffer SW. Meiotic transmission of Drosophila pseudoobscura chromosomal arrangements. Plos One. 2: e530. PMID 17565383 DOI: 10.1371/Journal.Pone.0000530  0.826
2007 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. Comparative Biochemistry and Physiology. Part B, Biochemistry & Molecular Biology. 146: 326-37. PMID 17240180 DOI: 10.1016/J.Cbpb.2006.11.002  0.637
2006 Steglich C, Schaeffer SW. The ornithine decarboxylase gene of Trypanosoma brucei: Evidence for horizontal gene transfer from a vertebrate source. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. 6: 205-19. PMID 16344004 DOI: 10.1016/j.meegid.2005.05.004  0.428
2006 Carney SL, Formica MI, Divatia H, Nelson K, Fisher CR, Schaeffer SW. Population structure of the mussel "Bathymodiolus" childressi from Gulf of Mexico hydrocarbon seeps Deep-Sea Research Part I: Oceanographic Research Papers. 53: 1061-1072. DOI: 10.1016/j.dsr.2006.03.002  0.563
2005 Schaeffer SW, Anderson WW. Mechanisms of genetic exchange within the chromosomal inversions of Drosophila pseudoobscura. Genetics. 171: 1729-39. PMID 16143625 DOI: 10.1534/genetics.105.041947  0.687
2005 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. Proceedings of the National Academy of Sciences of the United States of America. 102: 2713-8. PMID 15710902 DOI: 10.1073/Pnas.0407455102  0.551
2005 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, ... ... Schaeffer SW, et al. Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution. Genome Research. 15: 1-18. PMID 15632085 DOI: 10.1101/Gr.3059305  0.812
2003 Schaeffer SW, Bernhardt MJ, Anderson WW. Evolutionary rearrangement of the amylase genomic regions between Drosophila melanogaster and Drosophila pseudoobscura. The Journal of Heredity. 94: 464-71. PMID 14691313 DOI: 10.1093/jhered/esg094  0.638
2003 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. Proceedings of the National Academy of Sciences of the United States of America. 100: 8319-24. PMID 12824467 DOI: 10.1073/pnas.1432900100  0.737
2003 Mcmullin ER, Hourdez S, Schaeffer SW, Fisher CR. Phylogeny and biogeography of deep sea vestimentiferan tubeworms and their bacterial symbionts Symbiosis. 34: 1-41.  0.747
2002 Schaeffer SW. Molecular population genetics of sequence length diversity in the Adh region of Drosophila pseudoobscura. Genetical Research. 80: 163-75. PMID 12688655 DOI: 10.1017/S0016672302005955  0.432
2002 Carney SL, Peoples JR, Fisher CR, Schaeffer SW. AFLP analyses of genomic DNA reveal no differentiation between two phenotypes of the vestimentiferan tubeworm Ridgeia piscesae Cahiers De Biologie Marine. 43: 363-366.  0.586
2001 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. 159: 673-87. PMID 11606543  0.3
2000 Kovacevic M, Schaeffer SW. Molecular population genetics of X-linked genes in Drosophila pseudoobscura. Genetics. 156: 155-72. PMID 10978282  0.492
1997 Pritchard JK, Schaeffer SW. Polymorphism and divergence at a Drosophila pseudogene locus. Genetics. 147: 199-208. PMID 9286680  0.585
1995 Richman AD, Kao TH, Schaeffer SW, Uyenoyama MK. S-allele sequence diversity in natural populations of Solanum carolinense (Horsenettle). Heredity. 75: 405-15. PMID 7591834 DOI: 10.1038/Hdy.1995.153  0.406
1994 Walthour CS, Schaeffer SW. Molecular population genetics of sex determination genes: the transformer gene of Drosophila melanogaster. Genetics. 136: 1367-72. PMID 8013913  0.385
1992 Schaeffer SW, Miller EL. Estimates of gene flow in Drosophila pseudoobscura determined from nucleotide sequence analysis of the alcohol dehydrogenase region. Genetics. 132: 471-80. PMID 1427038  0.331
1991 Schaeffer SW, Miller EL. Nucleotide sequence analysis of Adh genes estimates the time of geographic isolation of the Bogota population of Drosophila pseudoobscura. Proceedings of the National Academy of Sciences of the United States of America. 88: 6097-101. PMID 2068088 DOI: 10.1073/Pnas.88.14.6097  0.437
1991 Aquadro CF, Weaver AL, Schaeffer SW, Anderson WW. Molecular evolution of inversions in Drosophila pseudoobscura: the amylase gene region. Proceedings of the National Academy of Sciences of the United States of America. 88: 305-9. PMID 1702542 DOI: 10.1073/Pnas.88.1.305  0.783
1988 Schaeffer SW, Aquadro CF, Langley CH. Restriction-map variation in the Notch region of Drosophila melanogaster. Molecular Biology and Evolution. 5: 30-40. PMID 2833676 DOI: 10.1093/Oxfordjournals.Molbev.A040475  0.763
1987 Schaeffer SW, Aquadro CF. Nucleotide sequence of the Adh gene region of Drosophila pseudoobscura: evolutionary change and evidence for an ancient gene duplication. Genetics. 117: 61-73. PMID 3666441  0.614
1987 Schaeffer SW, Aquadro CF, Anderson WW. Restriction-map variation in the alcohol dehydrogenase region of Drosophila pseudoobscura. Molecular Biology and Evolution. 4: 254-65. PMID 2833670 DOI: 10.1093/Oxfordjournals.Molbev.A040438  0.712
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