Stephen W Schaeffer

Stephen W Schaeffer

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Stephen W Schaeffer

Stephen W Schaeffer

Publications by authors named "Stephen W Schaeffer"

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

Mol Ecol 2019 03 10;28(6):1283-1301. Epub 2018 Dec 10.

Department of Biology, 208 Erwin W. Mueller Laboratory, The Pennsylvania State University, University Park, Pennsylvania.

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http://doi.wiley.com/10.1111/mec.14923
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http://dx.doi.org/10.1111/mec.14923DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6475473PMC
March 2019

Muller "Elements" in : How the Search for the Genetic Basis for Speciation Led to the Birth of Comparative Genomics.

Genetics 2018 09;210(1):3-13

Department of Biology, The Pennsylvania State University, State College, Pennsylvania 16802-5301

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http://dx.doi.org/10.1534/genetics.118.301084DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6116959PMC
September 2018

Ancestral polymorphisms explain the role of chromosomal inversions in speciation.

PLoS Genet 2018 07 30;14(7):e1007526. Epub 2018 Jul 30.

Department of Biology, University of Utah, Salt Lake City, UT, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1007526DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6085072PMC
July 2018

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

Mol Ecol 2017 Dec 15;26(23):6539-6562. Epub 2017 Nov 15.

Department of Biology, 208 Erwin W. Mueller Laboratory, The Pennsylvania State University, University Park, PA, USA.

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http://dx.doi.org/10.1111/mec.14381DOI Listing
December 2017

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

Genetics 2016 09 8;204(1):287-301. Epub 2016 Jul 8.

Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802-5301.

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http://dx.doi.org/10.1534/genetics.116.191429DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5012393PMC
September 2016

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

PeerJ 2016 23;4:e2366. Epub 2016 Aug 23.

Department of Biology, Pennsylvania State University, University Park, PA, United States; Current affiliation: Department of Animal Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States.

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http://dx.doi.org/10.7717/peerj.2366DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5012325PMC
September 2016

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

PLoS One 2015 10;10(4):e0118460. Epub 2015 Apr 10.

Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0118460PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4393317PMC
April 2016

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

Springerplus 2015 16;4:354. Epub 2015 Jul 16.

CNRS UMR 7144, Station Biologique de Roscoff, Places Georges Teissier, 29680 Roscoff, France ; Laboratoire Adaptation et Diversité en Milieu Marin, UPMC Université Paris 06, Place Georges Teissier, 29680 Roscoff Cedex, France.

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http://dx.doi.org/10.1186/s40064-015-1124-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4503718PMC
July 2015

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

Mol Ecol 2013 Aug 23;22(16):4147-4162. Epub 2013 Jul 23.

Department of Biology, The Pennsylvania State University, 208 Erwin W. Mueller Laboratory, University Park, PA, 16802, USA.

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http://dx.doi.org/10.1111/mec.12379DOI Listing
August 2013

Molecular population genetics of inversion breakpoint regions in Drosophila pseudoobscura.

G3 (Bethesda) 2013 Jul 8;3(7):1151-63. Epub 2013 Jul 8.

Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802-5301, USA.

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http://dx.doi.org/10.1534/g3.113.006122DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3704243PMC
July 2013

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

PLoS One 2011 24;6(8):e22483. Epub 2011 Aug 24.

School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0022483PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3160844PMC
January 2012

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

Mol Biol Evol 2011 Aug 21;28(8):2219-29. Epub 2011 Feb 21.

Department of Biology, The Pennsylvania State University, Mueller Laboratory, PA, USA.

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http://dx.doi.org/10.1093/molbev/msr039DOI Listing
August 2011

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

Mol Biol Evol 2010 Aug 29;27(8):1963-78. Epub 2010 Mar 29.

Intercollege Graduate Program in Genetics, The Pennsylvania State University, PA, USA.

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http://dx.doi.org/10.1093/molbev/msq085DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2915643PMC
August 2010

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

Evolution 2008 Dec 1;62(12):3082-99. Epub 2008 Sep 1.

Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.

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http://dx.doi.org/10.1111/j.1558-5646.2008.00504.xDOI Listing
December 2008

Chromosomal rearrangement inferred from comparisons of 12 Drosophila genomes.

Genetics 2008 Jul 13;179(3):1657-80. Epub 2008 Jul 13.

Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA.

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http://dx.doi.org/10.1534/genetics.107.086108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2475759PMC
July 2008

Evolution of genes and genomes on the Drosophila phylogeny.

Authors:
Andrew G Clark Michael B Eisen Douglas R Smith Casey M Bergman Brian Oliver Therese A Markow Thomas C Kaufman Manolis Kellis William Gelbart Venky N Iyer Daniel A Pollard Timothy B Sackton Amanda M Larracuente Nadia D Singh Jose P Abad Dawn N Abt Boris Adryan Montserrat Aguade Hiroshi Akashi Wyatt W Anderson Charles F Aquadro David H Ardell Roman Arguello Carlo G Artieri Daniel A Barbash Daniel Barker Paolo Barsanti Phil Batterham Serafim Batzoglou Dave Begun Arjun Bhutkar Enrico Blanco Stephanie A Bosak Robert K Bradley Adrianne D Brand Michael R Brent Angela N Brooks Randall H Brown Roger K Butlin Corrado Caggese Brian R Calvi A Bernardo de Carvalho Anat Caspi Sergio Castrezana Susan E Celniker Jean L Chang Charles Chapple Sourav Chatterji Asif Chinwalla Alberto Civetta Sandra W Clifton Josep M Comeron James C Costello Jerry A Coyne Jennifer Daub Robert G David Arthur L Delcher Kim Delehaunty Chuong B Do Heather Ebling Kevin Edwards Thomas Eickbush Jay D Evans Alan Filipski Sven Findeiss Eva Freyhult Lucinda Fulton Robert Fulton Ana C L Garcia Anastasia Gardiner David A Garfield Barry E Garvin Greg Gibson Don Gilbert Sante Gnerre Jennifer Godfrey Robert Good Valer Gotea Brenton Gravely Anthony J Greenberg Sam Griffiths-Jones Samuel Gross Roderic Guigo Erik A Gustafson Wilfried Haerty Matthew W Hahn Daniel L Halligan Aaron L Halpern Gillian M Halter Mira V Han Andreas Heger LaDeana Hillier Angie S Hinrichs Ian Holmes Roger A Hoskins Melissa J Hubisz Dan Hultmark Melanie A Huntley David B Jaffe Santosh Jagadeeshan William R Jeck Justin Johnson Corbin D Jones William C Jordan Gary H Karpen Eiko Kataoka Peter D Keightley Pouya Kheradpour Ewen F Kirkness Leonardo B Koerich Karsten Kristiansen Dave Kudrna Rob J Kulathinal Sudhir Kumar Roberta Kwok Eric Lander Charles H Langley Richard Lapoint Brian P Lazzaro So-Jeong Lee Lisa Levesque Ruiqiang Li Chiao-Feng Lin Michael F Lin Kerstin Lindblad-Toh Ana Llopart Manyuan Long Lloyd Low Elena Lozovsky Jian Lu Meizhong Luo Carlos A Machado Wojciech Makalowski Mar Marzo Muneo Matsuda Luciano Matzkin Bryant McAllister Carolyn S McBride Brendan McKernan Kevin McKernan Maria Mendez-Lago Patrick Minx Michael U Mollenhauer Kristi Montooth Stephen M Mount Xu Mu Eugene Myers Barbara Negre Stuart Newfeld Rasmus Nielsen Mohamed A F Noor Patrick O'Grady Lior Pachter Montserrat Papaceit Matthew J Parisi Michael Parisi Leopold Parts Jakob S Pedersen Graziano Pesole Adam M Phillippy Chris P Ponting Mihai Pop Damiano Porcelli Jeffrey R Powell Sonja Prohaska Kim Pruitt Marta Puig Hadi Quesneville Kristipati Ravi Ram David Rand Matthew D Rasmussen Laura K Reed Robert Reenan Amy Reily Karin A Remington Tania T Rieger Michael G Ritchie Charles Robin Yu-Hui Rogers Claudia Rohde Julio Rozas Marc J Rubenfield Alfredo Ruiz Susan Russo Steven L Salzberg Alejandro Sanchez-Gracia David J Saranga Hajime Sato Stephen W Schaeffer Michael C Schatz Todd Schlenke Russell Schwartz Carmen Segarra Rama S Singh Laura Sirot Marina Sirota Nicholas B Sisneros Chris D Smith Temple F Smith John Spieth Deborah E Stage Alexander Stark Wolfgang Stephan Robert L Strausberg Sebastian Strempel David Sturgill Granger Sutton Granger G Sutton Wei Tao Sarah Teichmann Yoshiko N Tobari Yoshihiko Tomimura Jason M Tsolas Vera L S Valente Eli Venter J Craig Venter Saverio Vicario Filipe G Vieira Albert J Vilella Alfredo Villasante Brian Walenz Jun Wang Marvin Wasserman Thomas Watts Derek Wilson Richard K Wilson Rod A Wing Mariana F Wolfner Alex Wong Gane Ka-Shu Wong Chung-I Wu Gabriel Wu Daisuke Yamamoto Hsiao-Pei Yang Shiaw-Pyng Yang James A Yorke Kiyohito Yoshida Evgeny Zdobnov Peili Zhang Yu Zhang Aleksey V Zimin Jennifer Baldwin Amr Abdouelleil Jamal Abdulkadir Adal Abebe Brikti Abera Justin Abreu St Christophe Acer Lynne Aftuck Allen Alexander Peter An Erica Anderson Scott Anderson Harindra Arachi Marc Azer Pasang Bachantsang Andrew Barry Tashi Bayul Aaron Berlin Daniel Bessette Toby Bloom Jason Blye Leonid Boguslavskiy Claude Bonnet Boris Boukhgalter Imane Bourzgui Adam Brown Patrick Cahill Sheridon Channer Yama Cheshatsang Lisa Chuda Mieke Citroen Alville Collymore Patrick Cooke Maura Costello Katie D'Aco Riza Daza Georgius De Haan Stuart DeGray Christina DeMaso Norbu Dhargay Kimberly Dooley Erin Dooley Missole Doricent Passang Dorje Kunsang Dorjee Alan Dupes Richard Elong Jill Falk Abderrahim Farina Susan Faro Diallo Ferguson Sheila Fisher Chelsea D Foley Alicia Franke Dennis Friedrich Loryn Gadbois Gary Gearin Christina R Gearin Georgia Giannoukos Tina Goode Joseph Graham Edward Grandbois Sharleen Grewal Kunsang Gyaltsen Nabil Hafez Birhane Hagos Jennifer Hall Charlotte Henson Andrew Hollinger Tracey Honan Monika D Huard Leanne Hughes Brian Hurhula M Erii Husby Asha Kamat Ben Kanga Seva Kashin Dmitry Khazanovich Peter Kisner Krista Lance Marcia Lara William Lee Niall Lennon Frances Letendre Rosie LeVine Alex Lipovsky Xiaohong Liu Jinlei Liu Shangtao Liu Tashi Lokyitsang Yeshi Lokyitsang Rakela Lubonja Annie Lui Pen MacDonald Vasilia Magnisalis Kebede Maru Charles Matthews William McCusker Susan McDonough Teena Mehta James Meldrim Louis Meneus Oana Mihai Atanas Mihalev Tanya Mihova Rachel Mittelman Valentine Mlenga Anna Montmayeur Leonidas Mulrain Adam Navidi Jerome Naylor Tamrat Negash Thu Nguyen Nga Nguyen Robert Nicol Choe Norbu Nyima Norbu Nathaniel Novod Barry O'Neill Sahal Osman Eva Markiewicz Otero L Oyono Christopher Patti Pema Phunkhang Fritz Pierre Margaret Priest Sujaa Raghuraman Filip Rege Rebecca Reyes Cecil Rise Peter Rogov Keenan Ross Elizabeth Ryan Sampath Settipalli Terry Shea Ngawang Sherpa Lu Shi Diana Shih Todd Sparrow Jessica Spaulding John Stalker Nicole Stange-Thomann Sharon Stavropoulos Catherine Stone Christopher Strader Senait Tesfaye Talene Thomson Yama Thoulutsang Dawa Thoulutsang Kerri Topham Ira Topping Tsamla Tsamla Helen Vassiliev Andy Vo Tsering Wangchuk Tsering Wangdi Michael Weiand Jane Wilkinson Adam Wilson Shailendra Yadav Geneva Young Qing Yu Lisa Zembek Danni Zhong Andrew Zimmer Zac Zwirko David B Jaffe Pablo Alvarez Will Brockman Jonathan Butler CheeWhye Chin Sante Gnerre Manfred Grabherr Michael Kleber Evan Mauceli Iain MacCallum

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

Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA.

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http://dx.doi.org/10.1038/nature06341DOI Listing
November 2007

Meiotic transmission of Drosophila pseudoobscura chromosomal arrangements.

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

Intercollege Graduate Program in Genetics, Institute of Molecular Evolutionary Genetics, and Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0000530PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1885828PMC
June 2007

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

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

Department of Biology, The Pennsylvania State University, University Park, PA 16802-5301, USA.

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http://dx.doi.org/10.1016/j.cbpb.2006.11.002DOI Listing
March 2007

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

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

Department of Biology, Slippery Rock University, Slippery Rock, PA 16057, USA.

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http://dx.doi.org/10.1016/j.meegid.2005.05.004DOI Listing
May 2006

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

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

Department of Biology and Institute of Molecular Evolutionary Genetics, Pennsylvania State University, 208 Erwin W. Mueller Laboratories, University Park, PA 16802-5301, USA.

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http://dx.doi.org/10.1534/genetics.105.041947DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1456099PMC
December 2005

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

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

Department of Biology and Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park, PA 16802-5301, USA.

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http://dx.doi.org/10.1073/pnas.1432900100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC166227PMC
July 2003

Molecular population genetics of sequence length diversity in the Adh region of Drosophila pseudoobscura.

Genet Res 2002 Dec;80(3):163-75

Department of Biology, and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University, University Park, PA 16802-5301, USA.

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http://dx.doi.org/10.1017/s0016672302005955DOI Listing
December 2002