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Items: 46

1.

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

Fuller ZL, Koury SA, Phadnis N, Schaeffer SW.

Mol Ecol. 2019 Mar;28(6):1283-1301. doi: 10.1111/mec.14923. Epub 2018 Dec 10.

2.
3.

Ancestral polymorphisms explain the role of chromosomal inversions in speciation.

Fuller ZL, Leonard CJ, Young RE, Schaeffer SW, Phadnis N.

PLoS Genet. 2018 Jul 30;14(7):e1007526. doi: 10.1371/journal.pgen.1007526. eCollection 2018 Jul.

4.

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

Projecto-Garcia J, Le Port AS, Govindji T, Jollivet D, Schaeffer SW, Hourdez S.

J Mol Evol. 2017 Dec;85(5-6):172-187. doi: 10.1007/s00239-017-9815-7. Epub 2017 Nov 1.

PMID:
29094190
5.

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

Fuller ZL, Haynes GD, Richards S, Schaeffer SW.

Mol Ecol. 2017 Dec;26(23):6539-6562. doi: 10.1111/mec.14381. Epub 2017 Nov 15.

PMID:
29055159
6.

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

Huang C, Schaeffer SW, Fisher CR, Cowart DA.

PeerJ. 2016 Aug 23;4:e2366. doi: 10.7717/peerj.2366. eCollection 2016.

7.

Genomics of Natural Populations: How Differentially Expressed Genes Shape the Evolution of Chromosomal Inversions in Drosophila pseudoobscura.

Fuller ZL, Haynes GD, Richards S, Schaeffer SW.

Genetics. 2016 Sep;204(1):287-301. doi: 10.1534/genetics.116.191429. Epub 2016 Jul 8.

8.

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

Projecto-Garcia J, Jollivet D, Mary J, Lallier FH, Schaeffer SW, Hourdez S.

Springerplus. 2015 Jul 16;4:354. doi: 10.1186/s40064-015-1124-2. eCollection 2015.

9.

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

Faure B, Schaeffer SW, Fisher CR.

PLoS One. 2015 Apr 10;10(4):e0118460. doi: 10.1371/journal.pone.0118460. eCollection 2015.

10.

Evidence for stabilizing selection on codon usage in chromosomal rearrangements of Drosophila pseudoobscura.

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.

G3 (Bethesda). 2014 Oct 17;4(12):2433-49. doi: 10.1534/g3.114.014860.

11.

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

Cowart DA, Huang C, Arnaud-Haond S, Carney SL, Fisher CR, Schaeffer SW.

Mol Ecol. 2013 Aug;22(16):4147-4162. doi: 10.1111/mec.12379. Epub 2013 Jul 23.

PMID:
23879204
12.

Molecular population genetics of inversion breakpoint regions in Drosophila pseudoobscura.

Wallace AG, Detweiler D, Schaeffer SW.

G3 (Bethesda). 2013 Jul 8;3(7):1151-63. doi: 10.1534/g3.113.006122.

13.

Rec-DCM-Eigen: reconstructing a less parsimonious but more accurate tree in shorter time.

Kang S, Tang J, Schaeffer SW, Bader DA.

PLoS One. 2011;6(8):e22483. doi: 10.1371/journal.pone.0022483. Epub 2011 Aug 24.

14.

Evolutionary history of the third chromosome gene arrangements of Drosophila pseudoobscura inferred from inversion breakpoints.

Wallace AG, Detweiler D, Schaeffer SW.

Mol Biol Evol. 2011 Aug;28(8):2219-29. doi: 10.1093/molbev/msr039. Epub 2011 Feb 21.

PMID:
21339510
15.

Adaptive evolution of genes duplicated from the Drosophila pseudoobscura neo-X chromosome.

Meisel RP, Hilldorfer BB, Koch JL, Lockton S, Schaeffer SW.

Mol Biol Evol. 2010 Aug;27(8):1963-78. doi: 10.1093/molbev/msq085. Epub 2010 Mar 29.

16.

Origin and evolution of the unique tetra-domain hemoglobin from the hydrothermal vent scale worm Branchipolynoe.

Projecto-Garcia J, Zorn N, Jollivet D, Schaeffer SW, Lallier FH, Hourdez S.

Mol Biol Evol. 2010 Jan;27(1):143-52. doi: 10.1093/molbev/msp218.

PMID:
19755665
17.

Selection in heterogeneous environments maintains the gene arrangement polymorphism of Drosophila pseudoobscura.

Schaeffer SW.

Evolution. 2008 Dec;62(12):3082-99. doi: 10.1111/j.1558-5646.2008.00504.x. Epub 2008 Sep 1.

PMID:
18764919
18.

Polytene chromosomal maps of 11 Drosophila species: the order of genomic scaffolds inferred from genetic and physical maps.

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.

Genetics. 2008 Jul;179(3):1601-55. doi: 10.1534/genetics.107.086074. Epub 2008 Jul 13.

19.

Chromosomal rearrangement inferred from comparisons of 12 Drosophila genomes.

Bhutkar A, Schaeffer SW, Russo SM, Xu M, Smith TF, Gelbart WM.

Genetics. 2008 Jul;179(3):1657-80. doi: 10.1534/genetics.107.086108. Epub 2008 Jul 13.

20.
21.

Evolution of genes and genomes on the Drosophila phylogeny.

Drosophila 12 Genomes Consortium, 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, Abad JP, Abt DN, Adryan B, Aguade M, Akashi H, Anderson WW, Aquadro CF, Ardell DH, Arguello R, Artieri CG, Barbash DA, Barker D, Barsanti P, Batterham P, Batzoglou S, Begun D, Bhutkar A, Blanco E, Bosak SA, Bradley RK, Brand AD, Brent MR, Brooks AN, Brown RH, Butlin RK, Caggese C, Calvi BR, Bernardo de Carvalho A, Caspi A, Castrezana S, Celniker SE, Chang JL, Chapple C, Chatterji S, Chinwalla A, Civetta A, Clifton SW, Comeron JM, Costello JC, Coyne JA, Daub J, David RG, Delcher AL, Delehaunty K, Do CB, Ebling H, Edwards K, Eickbush T, Evans JD, Filipski A, Findeiss S, Freyhult E, Fulton L, Fulton R, Garcia AC, Gardiner A, Garfield DA, Garvin BE, Gibson G, Gilbert D, Gnerre S, Godfrey J, Good R, Gotea V, Gravely B, Greenberg AJ, Griffiths-Jones S, Gross S, Guigo R, Gustafson EA, Haerty W, Hahn MW, Halligan DL, Halpern AL, Halter GM, Han MV, Heger A, Hillier L, Hinrichs AS, Holmes I, Hoskins RA, Hubisz MJ, Hultmark D, Huntley MA, Jaffe DB, Jagadeeshan S, Jeck WR, Johnson J, Jones CD, Jordan WC, Karpen GH, Kataoka E, Keightley PD, Kheradpour P, Kirkness EF, Koerich LB, Kristiansen K, Kudrna D, Kulathinal RJ, Kumar S, Kwok R, Lander E, Langley CH, Lapoint R, Lazzaro BP, Lee SJ, Levesque L, Li R, Lin CF, Lin MF, Lindblad-Toh K, Llopart A, Long M, Low L, Lozovsky E, Lu J, Luo M, Machado CA, Makalowski W, Marzo M, Matsuda M, Matzkin L, McAllister B, McBride CS, McKernan B, McKernan K, Mendez-Lago M, Minx P, Mollenhauer MU, Montooth K, Mount SM, Mu X, Myers E, Negre B, Newfeld S, Nielsen R, Noor MA, O'Grady P, Pachter L, Papaceit M, Parisi MJ, Parisi M, Parts L, Pedersen JS, Pesole G, Phillippy AM, Ponting CP, Pop M, Porcelli D, Powell JR, Prohaska S, Pruitt K, Puig M, Quesneville H, Ram KR, Rand D, Rasmussen MD, Reed LK, Reenan R, Reily A, Remington KA, Rieger TT, Ritchie MG, Robin C, Rogers YH, Rohde C, Rozas J, Rubenfield MJ, Ruiz A, Russo S, Salzberg SL, Sanchez-Gracia A, Saranga DJ, Sato H, Schaeffer SW, Schatz MC, Schlenke T, Schwartz R, Segarra C, Singh RS, Sirot L, Sirota M, Sisneros NB, Smith CD, Smith TF, Spieth J, Stage DE, Stark A, Stephan W, Strausberg RL, Strempel S, Sturgill D, Sutton G, Sutton GG, Tao W, Teichmann S, Tobari YN, Tomimura Y, Tsolas JM, Valente VL, Venter E, Venter JC, Vicario S, Vieira FG, Vilella AJ, Villasante A, Walenz B, Wang J, Wasserman M, Watts T, Wilson D, Wilson RK, Wing RA, Wolfner MF, Wong A, Wong GK, Wu CI, Wu G, Yamamoto D, Yang HP, Yang SP, Yorke JA, Yoshida K, Zdobnov E, Zhang P, Zhang Y, Zimin AV, Baldwin J, Abdouelleil A, Abdulkadir J, Abebe A, Abera B, Abreu J, Acer SC, Aftuck L, Alexander A, An P, Anderson E, Anderson S, Arachi H, Azer M, Bachantsang P, Barry A, Bayul T, Berlin A, Bessette D, Bloom T, Blye J, Boguslavskiy L, Bonnet C, Boukhgalter B, Bourzgui I, Brown A, Cahill P, Channer S, Cheshatsang Y, Chuda L, Citroen M, Collymore A, Cooke P, Costello M, D'Aco K, Daza R, De Haan G, DeGray S, DeMaso C, Dhargay N, Dooley K, Dooley E, Doricent M, Dorje P, Dorjee K, Dupes A, Elong R, Falk J, Farina A, Faro S, Ferguson D, Fisher S, Foley CD, Franke A, Friedrich D, Gadbois L, Gearin G, Gearin CR, Giannoukos G, Goode T, Graham J, Grandbois E, Grewal S, Gyaltsen K, Hafez N, Hagos B, Hall J, Henson C, Hollinger A, Honan T, Huard MD, Hughes L, Hurhula B, Husby ME, Kamat A, Kanga B, Kashin S, Khazanovich D, Kisner P, Lance K, Lara M, Lee W, Lennon N, Letendre F, LeVine R, Lipovsky A, Liu X, Liu J, Liu S, Lokyitsang T, Lokyitsang Y, Lubonja R, Lui A, MacDonald P, Magnisalis V, Maru K, Matthews C, McCusker W, McDonough S, Mehta T, Meldrim J, Meneus L, Mihai O, Mihalev A, Mihova T, Mittelman R, Mlenga V, Montmayeur A, Mulrain L, Navidi A, Naylor J, Negash T, Nguyen T, Nguyen N, Nicol R, Norbu C, Norbu N, Novod N, O'Neill B, Osman S, Markiewicz E, Oyono OL, Patti C, Phunkhang P, Pierre F, Priest M, Raghuraman S, Rege F, Reyes R, Rise C, Rogov P, Ross K, Ryan E, Settipalli S, Shea T, Sherpa N, Shi L, Shih D, Sparrow T, Spaulding J, Stalker J, Stange-Thomann N, Stavropoulos S, Stone C, Strader C, Tesfaye S, Thomson T, Thoulutsang Y, Thoulutsang D, Topham K, Topping I, Tsamla T, Vassiliev H, Vo A, Wangchuk T, Wangdi T, Weiand M, Wilkinson J, Wilson A, Yadav S, Young G, Yu Q, Zembek L, Zhong D, Zimmer A, Zwirko Z, Jaffe DB, Alvarez P, Brockman W, Butler J, Chin C, Gnerre S, Grabherr M, Kleber M, Mauceli E, MacCallum I.

Nature. 2007 Nov 8;450(7167):203-18.

PMID:
17994087
22.

Meiotic transmission of Drosophila pseudoobscura chromosomal arrangements.

Meisel RP, Schaeffer SW.

PLoS One. 2007 Jun 13;2(6):e530.

23.

Environmental differences in hemoglobin gene expression in the hydrothermal vent tubeworm, Ridgeia piscesae.

Carney SL, Flores JF, Orobona KM, Butterfield DA, Fisher CR, Schaeffer SW.

Comp Biochem Physiol B Biochem Mol Biol. 2007 Mar;146(3):326-37. Epub 2006 Nov 17.

PMID:
17240180
24.

The ornithine decarboxylase gene of Trypanosoma brucei: Evidence for horizontal gene transfer from a vertebrate source.

Steglich C, Schaeffer SW.

Infect Genet Evol. 2006 May;6(3):205-19. Epub 2005 Dec 15.

PMID:
16344004
25.

Mechanisms of genetic exchange within the chromosomal inversions of Drosophila pseudoobscura.

Schaeffer SW, Anderson WW.

Genetics. 2005 Dec;171(4):1729-39. Epub 2005 Sep 2.

26.

Sulfide binding is mediated by zinc ions discovered in the crystal structure of a hydrothermal vent tubeworm hemoglobin.

Flores JF, Fisher CR, Carney SL, Green BN, Freytag JK, Schaeffer SW, Royer WE Jr.

Proc Natl Acad Sci U S A. 2005 Feb 22;102(8):2713-8. Epub 2005 Feb 14.

27.

Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution.

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.

Genome Res. 2005 Jan;15(1):1-18.

28.

Evolutionary rearrangement of the amylase genomic regions between Drosophila melanogaster and Drosophila pseudoobscura.

Schaeffer SW, Bernhardt MJ, Anderson WW.

J Hered. 2003 Nov-Dec;94(6):464-71.

PMID:
14691313
29.

Evolutionary genomics of inversions in Drosophila pseudoobscura: evidence for epistasis.

Schaeffer SW, Goetting-Minesky MP, Kovacevic M, Peoples JR, Graybill JL, Miller JM, Kim K, Nelson JG, Anderson WW.

Proc Natl Acad Sci U S A. 2003 Jul 8;100(14):8319-24. Epub 2003 Jun 24.

30.
31.
32.

Molecular population genetics of X-linked genes in Drosophila pseudoobscura.

Kovacevic M, Schaeffer SW.

Genetics. 2000 Sep;156(1):155-72.

33.

Tubeworm succession at hydrothermal vents: use of biogenic cues to reduce habitat selection error?

Mullineaux LS, Fisher CR, Peterson CH, Schaeffer SW.

Oecologia. 2000 May;123(2):275-284. doi: 10.1007/s004420051014.

PMID:
28308732
34.

Polymorphism and divergence at a Drosophila pseudogene locus.

Pritchard JK, Schaeffer SW.

Genetics. 1997 Sep;147(1):199-208.

35.
36.

S-allele sequence diversity in natural populations of Solanum carolinense (Horsenettle).

Richman AD, Kao TH, Schaeffer SW, Uyenoyama MK.

Heredity (Edinb). 1995 Oct;75 ( Pt 4):405-15.

PMID:
7591834
37.
41.
42.

Molecular evolution of inversions in Drosophila pseudoobscura: the amylase gene region.

Aquadro CF, Weaver AL, Schaeffer SW, Anderson WW.

Proc Natl Acad Sci U S A. 1991 Jan 1;88(1):305-9.

43.

Restriction-map variation in the Notch region of Drosophila melanogaster.

Schaeffer SW, Aquadro CF, Langley CH.

Mol Biol Evol. 1988 Jan;5(1):30-40.

PMID:
2833676
45.

Restriction-map variation in the alcohol dehydrogenase region of Drosophila pseudoobscura.

Schaeffer SW, Aquadro CF, Anderson WW.

Mol Biol Evol. 1987 May;4(3):254-65.

PMID:
2833670
46.

A comprehensive package for DNA sequence analysis in FORTRAN IV for the PDP-11.

Arnold J, Eckenrode VK, Lemke K, Phillips GJ, Schaeffer SW.

Nucleic Acids Res. 1986 Jan 10;14(1):239-54.

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