Evolution of genes and genomes on the Drosophila phylogeny

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. AndersonCharles 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, La Deana 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 Wade 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, Pablo Alvarez, Will Brockman, Jonathan Butler, Cheewhye Chin, Manfred Grabherr, Michael Kleber, Evan Mauceli, Iain MacCallum

Research output: Contribution to journalArticle

1240 Citations (Scopus)

Abstract

Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.

Original languageEnglish (US)
Pages (from-to)203-218
Number of pages16
JournalNature
Volume450
Issue number7167
DOIs
StatePublished - Nov 8 2007

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Phylogeny
Drosophila
Genome
Genes
Untranslated RNA
Inborn Genetic Diseases
Neurobiology
Nucleic Acid Regulatory Sequences
Genetic Models
Ecology
Drosophila melanogaster
Cell Biology
Animal Models
Research
Proteins

All Science Journal Classification (ASJC) codes

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Clark, A. G., Eisen, M. B., Smith, D. R., Bergman, C. M., Oliver, B., Markow, T. A., ... MacCallum, I. (2007). Evolution of genes and genomes on the Drosophila phylogeny. Nature, 450(7167), 203-218. https://doi.org/10.1038/nature06341
Clark, Andrew G. ; Eisen, Michael B. ; Smith, Douglas R. ; Bergman, Casey M. ; Oliver, Brian ; Markow, Therese A. ; Kaufman, Thomas C. ; Kellis, Manolis ; Gelbart, William ; Iyer, Venky N. ; Pollard, Daniel A. ; Sackton, Timothy B. ; Larracuente, Amanda M. ; Singh, Nadia D. ; Abad, Jose P. ; Abt, Dawn N. ; Adryan, Boris ; Aguade, Montserrat ; Akashi, Hiroshi ; Anderson, Wyatt W. ; Aquadro, Charles F. ; Ardell, David H. ; Arguello, Roman ; Artieri, Carlo G. ; Barbash, Daniel A. ; Barker, Daniel ; Barsanti, Paolo ; Batterham, Phil ; Batzoglou, Serafim ; Begun, Dave ; Bhutkar, Arjun ; Blanco, Enrico ; Bosak, Stephanie A. ; Bradley, Robert K. ; Brand, Adrianne D. ; Brent, Michael R. ; Brooks, Angela N. ; Brown, Randall H. ; Butlin, Roger K. ; Caggese, Corrado ; Calvi, Brian R. ; Bernardo De Carvalho, A. ; Caspi, Anat ; Castrezana, Sergio ; Celniker, Susan E. ; Chang, Jean L. ; Chapple, Charles ; Chatterji, Sourav ; Chinwalla, Asif ; Civetta, Alberto ; Clifton, Sandra W. ; Comeron, Josep M. ; Costello, James C. ; Coyne, Jerry A. ; Daub, Jennifer ; David, Robert G. ; Delcher, Arthur L. ; Delehaunty, Kim ; Do, Chuong B. ; Ebling, Heather ; Edwards, Kevin ; Eickbush, Thomas ; Evans, Jay D. ; Filipski, Alan ; Findeiß, Sven ; Freyhult, Eva ; Fulton, Lucinda ; Fulton, Robert ; Garcia, Ana C.L. ; Gardiner, Anastasia ; Garfield, David A. ; Garvin, Barry E. ; Gibson, Greg ; Gilbert, Don ; Gnerre, Sante ; Godfrey, Jennifer ; Good, Robert ; Gotea, Valer ; Gravely, Brenton ; Greenberg, Anthony J. ; Griffiths-Jones, Sam ; Gross, Samuel ; Guigo, Roderic ; Gustafson, Erik A. ; Haerty, Wilfried ; Hahn, Matthew W. ; Halligan, Daniel L. ; Halpern, Aaron L. ; Halter, Gillian M. ; Han, Mira V. ; Heger, Andreas ; Hillier, La Deana ; Hinrichs, Angie S. ; Holmes, Ian ; Hoskins, Roger A. ; Hubisz, Melissa J. ; Hultmark, Dan ; Huntley, Melanie A. ; Jaffe, David B. ; Jagadeeshan, Santosh ; Jeck, William R. ; Johnson, Justin ; Jones, Corbin D. ; Jordan, William C. ; Karpen, Gary H. ; Kataoka, Eiko ; Keightley, Peter D. ; Kheradpour, Pouya ; Kirkness, Ewen F. ; Koerich, Leonardo B. ; Kristiansen, Karsten ; Kudrna, Dave ; Kulathinal, Rob J. ; Kumar, Sudhir ; Kwok, Roberta ; Lander, Eric ; Langley, Charles H. ; Lapoint, Richard ; Lazzaro, Brian P. ; Lee, So Jeong ; Levesque, Lisa ; Li, Ruiqiang ; Lin, Chiao Feng ; Lin, Michael F. ; Lindblad-Toh, Kerstin ; Llopart, Ana ; Long, Manyuan ; Low, Lloyd ; Lozovsky, Elena ; Lu, Jian ; Luo, Meizhong ; Machado, Carlos A. ; Makalowski, Wojciech ; Marzo, Mar ; Matsuda, Muneo ; Matzkin, Luciano ; McAllister, Bryant ; McBride, Carolyn S. ; McKernan, Brendan ; McKernan, Kevin ; Mendez-Lago, Maria ; Minx, Patrick ; Mollenhauer, Michael U. ; Montooth, Kristi ; Mount, Stephen M. ; Mu, Xu ; Myers, Eugene ; Negre, Barbara ; Newfeld, Stuart ; Nielsen, Rasmus ; Noor, Mohamed A.F. ; O'Grady, Patrick ; Pachter, Lior ; Papaceit, Montserrat ; Parisi, Matthew J. ; Parisi, Michael ; Parts, Leopold ; Pedersen, Jakob S. ; Pesole, Graziano ; Phillippy, Adam M. ; Ponting, Chris P. ; Pop, Mihai ; Porcelli, Damiano ; Powell, Jeffrey R. ; Prohaska, Sonja ; Pruitt, Kim ; Puig, Marta ; Quesneville, Hadi ; Ravi Ram, Kristipati ; Rand, David ; Rasmussen, Matthew D. ; Reed, Laura K. ; Reenan, Robert ; Reily, Amy ; Remington, Karin A. ; Rieger, Tania T. ; Ritchie, Michael G. ; Robin, Charles ; Rogers, Yu Hui ; Rohde, Claudia ; Rozas, Julio ; Rubenfield, Marc J. ; Ruiz, Alfredo ; Russo, Susan ; Salzberg, Steven L. ; Sanchez-Gracia, Alejandro ; Saranga, David J. ; Sato, Hajime ; Schaeffer, Stephen Wade ; Schatz, Michael C. ; Schlenke, Todd ; Schwartz, Russell ; Segarra, Carmen ; Singh, Rama S. ; Sirot, Laura ; Sirota, Marina ; Sisneros, Nicholas B. ; Smith, Chris D. ; Smith, Temple F. ; Spieth, John ; Stage, Deborah E. ; Stark, Alexander ; Stephan, Wolfgang ; Strausberg, Robert L. ; Strempel, Sebastian ; Sturgill, David ; Sutton, Granger ; Sutton, Granger G. ; Tao, Wei ; Teichmann, Sarah ; Tobari, Yoshiko N. ; Tomimura, Yoshihiko ; Tsolas, Jason M. ; Valente, Vera L.S. ; Venter, Eli ; Craig Venter, J. ; Vicario, Saverio ; Vieira, Filipe G. ; Vilella, Albert J. ; Villasante, Alfredo ; Walenz, Brian ; Wang, Jun ; Wasserman, Marvin ; Watts, Thomas ; Wilson, Derek ; Wilson, Richard K. ; Wing, Rod A. ; Wolfner, Mariana F. ; Wong, Alex ; Ka-Shu Wong, Gane ; Wu, Chung I. ; Wu, Gabriel ; Yamamoto, Daisuke ; Yang, Hsiao Pei ; Yang, Shiaw Pyng ; Yorke, James A. ; Yoshida, Kiyohito ; Zdobnov, Evgeny ; Zhang, Peili ; Zhang, Yu ; Zimin, Aleksey V. ; Baldwin, Jennifer ; Abdouelleil, Amr ; Abdulkadir, Jamal ; Abebe, Adal ; Abera, Brikti ; Abreu, Justin ; Christophe Acer, St ; Aftuck, Lynne ; Alexander, Allen ; An, Peter ; Anderson, Erica ; Anderson, Scott ; Arachi, Harindra ; Azer, Marc ; Bachantsang, Pasang ; Barry, Andrew ; Bayul, Tashi ; Berlin, Aaron ; Bessette, Daniel ; Bloom, Toby ; Blye, Jason ; Boguslavskiy, Leonid ; Bonnet, Claude ; Boukhgalter, Boris ; Bourzgui, Imane ; Brown, Adam ; Cahill, Patrick ; Channer, Sheridon ; Cheshatsang, Yama ; Chuda, Lisa ; Citroen, Mieke ; Collymore, Alville ; Cooke, Patrick ; Costello, Maura ; D'Aco, Katie ; Daza, Riza ; De Haan, Georgius ; Degray, Stuart ; Demaso, Christina ; Dhargay, Norbu ; Dooley, Kimberly ; Dooley, Erin ; Doricent, Missole ; Dorje, Passang ; Dorjee, Kunsang ; Dupes, Alan ; Elong, Richard ; Falk, Jill ; Farina, Abderrahim ; Faro, Susan ; Ferguson, Diallo ; Fisher, Sheila ; Foley, Chelsea D. ; Franke, Alicia ; Friedrich, Dennis ; Gadbois, Loryn ; Gearin, Gary ; Gearin, Christina R. ; Giannoukos, Georgia ; Goode, Tina ; Graham, Joseph ; Grandbois, Edward ; Grewal, Sharleen ; Gyaltsen, Kunsang ; Hafez, Nabil ; Hagos, Birhane ; Hall, Jennifer ; Henson, Charlotte ; Hollinger, Andrew ; Honan, Tracey ; Huard, Monika D. ; Hughes, Leanne ; Hurhula, Brian ; Erii Husby, M. ; Kamat, Asha ; Kanga, Ben ; Kashin, Seva ; Khazanovich, Dmitry ; Kisner, Peter ; Lance, Krista ; Lara, Marcia ; Lee, William ; Lennon, Niall ; Letendre, Frances ; Levine, Rosie ; Lipovsky, Alex ; Liu, Xiaohong ; Liu, Jinlei ; Liu, Shangtao ; Lokyitsang, Tashi ; Lokyitsang, Yeshi ; Lubonja, Rakela ; Lui, Annie ; MacDonald, Pen ; Magnisalis, Vasilia ; Maru, Kebede ; Matthews, Charles ; McCusker, William ; McDonough, Susan ; Mehta, Teena ; Meldrim, James ; Meneus, Louis ; Mihai, Oana ; Mihalev, Atanas ; Mihova, Tanya ; Mittelman, Rachel ; Mlenga, Valentine ; Montmayeur, Anna ; Mulrain, Leonidas ; Navidi, Adam ; Naylor, Jerome ; Negash, Tamrat ; Nguyen, Thu ; Nguyen, Nga ; Nicol, Robert ; Norbu, Choe ; Norbu, Nyima ; Novod, Nathaniel ; O'Neill, Barry ; Osman, Sahal ; Markiewicz, Eva ; Oyono, Otero L. ; Patti, Christopher ; Phunkhang, Pema ; Pierre, Fritz ; Priest, Margaret ; Raghuraman, Sujaa ; Rege, Filip ; Reyes, Rebecca ; Rise, Cecil ; Rogov, Peter ; Ross, Keenan ; Ryan, Elizabeth ; Settipalli, Sampath ; Shea, Terry ; Sherpa, Ngawang ; Shi, Lu ; Shih, Diana ; Sparrow, Todd ; Spaulding, Jessica ; Stalker, John ; Stange-Thomann, Nicole ; Stavropoulos, Sharon ; Stone, Catherine ; Strader, Christopher ; Tesfaye, Senait ; Thomson, Talene ; Thoulutsang, Yama ; Thoulutsang, Dawa ; Topham, Kerri ; Topping, Ira ; Tsamla, Tsamla ; Vassiliev, Helen ; Vo, Andy ; Wangchuk, Tsering ; Wangdi, Tsering ; Weiand, Michael ; Wilkinson, Jane ; Wilson, Adam ; Yadav, Shailendra ; Young, Geneva ; Yu, Qing ; Zembek, Lisa ; Zhong, Danni ; Zimmer, Andrew ; Zwirko, Zac ; Alvarez, Pablo ; Brockman, Will ; Butler, Jonathan ; Chin, Cheewhye ; Grabherr, Manfred ; Kleber, Michael ; Mauceli, Evan ; MacCallum, Iain. / Evolution of genes and genomes on the Drosophila phylogeny. In: Nature. 2007 ; Vol. 450, No. 7167. pp. 203-218.
@article{3456dbafb9824e13beb82b0764067462,
title = "Evolution of genes and genomes on the Drosophila phylogeny",
abstract = "Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.",
author = "Clark, {Andrew G.} and Eisen, {Michael B.} and Smith, {Douglas R.} and Bergman, {Casey M.} and Brian Oliver and Markow, {Therese A.} and Kaufman, {Thomas C.} and Manolis Kellis and William Gelbart and Iyer, {Venky N.} and Pollard, {Daniel A.} and Sackton, {Timothy B.} and Larracuente, {Amanda M.} and Singh, {Nadia D.} and Abad, {Jose P.} and Abt, {Dawn N.} and Boris Adryan and Montserrat Aguade and Hiroshi Akashi and Anderson, {Wyatt W.} and Aquadro, {Charles F.} and Ardell, {David H.} and Roman Arguello and Artieri, {Carlo G.} and Barbash, {Daniel A.} and Daniel Barker and Paolo Barsanti and Phil Batterham and Serafim Batzoglou and Dave Begun and Arjun Bhutkar and Enrico Blanco and Bosak, {Stephanie A.} and Bradley, {Robert K.} and Brand, {Adrianne D.} and Brent, {Michael R.} and Brooks, {Angela N.} and Brown, {Randall H.} and Butlin, {Roger K.} and Corrado Caggese and Calvi, {Brian R.} and {Bernardo De Carvalho}, A. and Anat Caspi and Sergio Castrezana and Celniker, {Susan E.} and Chang, {Jean L.} and Charles Chapple and Sourav Chatterji and Asif Chinwalla and Alberto Civetta and Clifton, {Sandra W.} and Comeron, {Josep M.} and Costello, {James C.} and Coyne, {Jerry A.} and Jennifer Daub and David, {Robert G.} and Delcher, {Arthur L.} and Kim Delehaunty and Do, {Chuong B.} and Heather Ebling and Kevin Edwards and Thomas Eickbush and Evans, {Jay D.} and Alan Filipski and Sven Findei{\ss} and Eva Freyhult and Lucinda Fulton and Robert Fulton and Garcia, {Ana C.L.} and Anastasia Gardiner and Garfield, {David A.} and Garvin, {Barry E.} and Greg Gibson and Don Gilbert and Sante Gnerre and Jennifer Godfrey and Robert Good and Valer Gotea and Brenton Gravely and Greenberg, {Anthony J.} and Sam Griffiths-Jones and Samuel Gross and Roderic Guigo and Gustafson, {Erik A.} and Wilfried Haerty and Hahn, {Matthew W.} and Halligan, {Daniel L.} and Halpern, {Aaron L.} and Halter, {Gillian M.} and Han, {Mira V.} and Andreas Heger and Hillier, {La Deana} and Hinrichs, {Angie S.} and Ian Holmes and Hoskins, {Roger A.} and Hubisz, {Melissa J.} and Dan Hultmark and Huntley, {Melanie A.} and Jaffe, {David B.} and Santosh Jagadeeshan and Jeck, {William R.} and Justin Johnson and Jones, {Corbin D.} and Jordan, {William C.} and Karpen, {Gary H.} and Eiko Kataoka and Keightley, {Peter D.} and Pouya Kheradpour and Kirkness, {Ewen F.} and Koerich, {Leonardo B.} and Karsten Kristiansen and Dave Kudrna and Kulathinal, {Rob J.} and Sudhir Kumar and Roberta Kwok and Eric Lander and Langley, {Charles H.} and Richard Lapoint and Lazzaro, {Brian P.} and Lee, {So Jeong} and Lisa Levesque and Ruiqiang Li and Lin, {Chiao Feng} and Lin, {Michael F.} and Kerstin Lindblad-Toh and Ana Llopart and Manyuan Long and Lloyd Low and Elena Lozovsky and Jian Lu and Meizhong Luo and Machado, {Carlos A.} and Wojciech Makalowski and Mar Marzo and Muneo Matsuda and Luciano Matzkin and Bryant McAllister and McBride, {Carolyn S.} and Brendan McKernan and Kevin McKernan and Maria Mendez-Lago and Patrick Minx and Mollenhauer, {Michael U.} and Kristi Montooth and Mount, {Stephen M.} and Xu Mu and Eugene Myers and Barbara Negre and Stuart Newfeld and Rasmus Nielsen and Noor, {Mohamed A.F.} and Patrick O'Grady and Lior Pachter and Montserrat Papaceit and Parisi, {Matthew J.} and Michael Parisi and Leopold Parts and Pedersen, {Jakob S.} and Graziano Pesole and Phillippy, {Adam M.} and Ponting, {Chris P.} and Mihai Pop and Damiano Porcelli and Powell, {Jeffrey R.} and Sonja Prohaska and Kim Pruitt and Marta Puig and Hadi Quesneville and {Ravi Ram}, Kristipati and David Rand and Rasmussen, {Matthew D.} and Reed, {Laura K.} and Robert Reenan and Amy Reily and Remington, {Karin A.} and Rieger, {Tania T.} and Ritchie, {Michael G.} and Charles Robin and Rogers, {Yu Hui} and Claudia Rohde and Julio Rozas and Rubenfield, {Marc J.} and Alfredo Ruiz and Susan Russo and Salzberg, {Steven L.} and Alejandro Sanchez-Gracia and Saranga, {David J.} and Hajime Sato and Schaeffer, {Stephen Wade} and Schatz, {Michael C.} and Todd Schlenke and Russell Schwartz and Carmen Segarra and Singh, {Rama S.} and Laura Sirot and Marina Sirota and Sisneros, {Nicholas B.} and Smith, {Chris D.} and Smith, {Temple F.} and John Spieth and Stage, {Deborah E.} and Alexander Stark and Wolfgang Stephan and Strausberg, {Robert L.} and Sebastian Strempel and David Sturgill and Granger Sutton and Sutton, {Granger G.} and Wei Tao and Sarah Teichmann and Tobari, {Yoshiko N.} and Yoshihiko Tomimura and Tsolas, {Jason M.} and Valente, {Vera L.S.} and Eli Venter and {Craig Venter}, J. and Saverio Vicario and Vieira, {Filipe G.} and Vilella, {Albert J.} and Alfredo Villasante and Brian Walenz and Jun Wang and Marvin Wasserman and Thomas Watts and Derek Wilson and Wilson, {Richard K.} and Wing, {Rod A.} and Wolfner, {Mariana F.} and Alex Wong and {Ka-Shu Wong}, Gane and Wu, {Chung I.} and Gabriel Wu and Daisuke Yamamoto and Yang, {Hsiao Pei} and Yang, {Shiaw Pyng} and Yorke, {James A.} and Kiyohito Yoshida and Evgeny Zdobnov and Peili Zhang and Yu Zhang and Zimin, {Aleksey V.} and Jennifer Baldwin and Amr Abdouelleil and Jamal Abdulkadir and Adal Abebe and Brikti Abera and Justin Abreu and {Christophe Acer}, St and Lynne Aftuck and Allen Alexander and Peter An and Erica Anderson and Scott Anderson and Harindra Arachi and Marc Azer and Pasang Bachantsang and Andrew Barry and Tashi Bayul and Aaron Berlin and Daniel Bessette and Toby Bloom and Jason Blye and Leonid Boguslavskiy and Claude Bonnet and Boris Boukhgalter and Imane Bourzgui and Adam Brown and Patrick Cahill and Sheridon Channer and Yama Cheshatsang and Lisa Chuda and Mieke Citroen and Alville Collymore and Patrick Cooke and Maura Costello and Katie D'Aco and Riza Daza and {De Haan}, Georgius and Stuart Degray and Christina Demaso and Norbu Dhargay and Kimberly Dooley and Erin Dooley and Missole Doricent and Passang Dorje and Kunsang Dorjee and Alan Dupes and Richard Elong and Jill Falk and Abderrahim Farina and Susan Faro and Diallo Ferguson and Sheila Fisher and Foley, {Chelsea D.} and Alicia Franke and Dennis Friedrich and Loryn Gadbois and Gary Gearin and Gearin, {Christina R.} and Georgia Giannoukos and Tina Goode and Joseph Graham and Edward Grandbois and Sharleen Grewal and Kunsang Gyaltsen and Nabil Hafez and Birhane Hagos and Jennifer Hall and Charlotte Henson and Andrew Hollinger and Tracey Honan and Huard, {Monika D.} and Leanne Hughes and Brian Hurhula and {Erii Husby}, M. and Asha Kamat and Ben Kanga and Seva Kashin and Dmitry Khazanovich and Peter Kisner and Krista Lance and Marcia Lara and William Lee and Niall Lennon and Frances Letendre and Rosie Levine and Alex Lipovsky and Xiaohong Liu and Jinlei Liu and Shangtao Liu and Tashi Lokyitsang and Yeshi Lokyitsang and Rakela Lubonja and Annie Lui and Pen MacDonald and Vasilia Magnisalis and Kebede Maru and Charles Matthews and William McCusker and Susan McDonough and Teena Mehta and James Meldrim and Louis Meneus and Oana Mihai and Atanas Mihalev and Tanya Mihova and Rachel Mittelman and Valentine Mlenga and Anna Montmayeur and Leonidas Mulrain and Adam Navidi and Jerome Naylor and Tamrat Negash and Thu Nguyen and Nga Nguyen and Robert Nicol and Choe Norbu and Nyima Norbu and Nathaniel Novod and Barry O'Neill and Sahal Osman and Eva Markiewicz and Oyono, {Otero L.} and Christopher Patti and Pema Phunkhang and Fritz Pierre and Margaret Priest and Sujaa Raghuraman and Filip Rege and Rebecca Reyes and Cecil Rise and Peter Rogov and Keenan Ross and Elizabeth Ryan and Sampath Settipalli and Terry Shea and Ngawang Sherpa and Lu Shi and Diana Shih and Todd Sparrow and Jessica Spaulding and John Stalker and Nicole Stange-Thomann and Sharon Stavropoulos and Catherine Stone and Christopher Strader and Senait Tesfaye and Talene Thomson and Yama Thoulutsang and Dawa Thoulutsang and Kerri Topham and Ira Topping and Tsamla Tsamla and Helen Vassiliev and Andy Vo and Tsering Wangchuk and Tsering Wangdi and Michael Weiand and Jane Wilkinson and Adam Wilson and Shailendra Yadav and Geneva Young and Qing Yu and Lisa Zembek and Danni Zhong and Andrew Zimmer and Zac Zwirko and Pablo Alvarez and Will Brockman and Jonathan Butler and Cheewhye Chin and Manfred Grabherr and Michael Kleber and Evan Mauceli and Iain MacCallum",
year = "2007",
month = "11",
day = "8",
doi = "10.1038/nature06341",
language = "English (US)",
volume = "450",
pages = "203--218",
journal = "Nature",
issn = "0028-0836",
publisher = "Nature Publishing Group",
number = "7167",

}

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, ACL, 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, LD, 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, MAF, 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, Ravi Ram, K, 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, VLS, Venter, E, Craig Venter, J, 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, Ka-Shu Wong, G, 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, Christophe Acer, S, 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, Erii Husby, M, 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, Alvarez, P, Brockman, W, Butler, J, Chin, C, Grabherr, M, Kleber, M, Mauceli, E & MacCallum, I 2007, 'Evolution of genes and genomes on the Drosophila phylogeny', Nature, vol. 450, no. 7167, pp. 203-218. https://doi.org/10.1038/nature06341

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

In: Nature, Vol. 450, No. 7167, 08.11.2007, p. 203-218.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Evolution of genes and genomes on the Drosophila phylogeny

AU - Clark, Andrew G.

AU - Eisen, Michael B.

AU - Smith, Douglas R.

AU - Bergman, Casey M.

AU - Oliver, Brian

AU - Markow, Therese A.

AU - Kaufman, Thomas C.

AU - Kellis, Manolis

AU - Gelbart, William

AU - Iyer, Venky N.

AU - Pollard, Daniel A.

AU - Sackton, Timothy B.

AU - Larracuente, Amanda M.

AU - Singh, Nadia D.

AU - Abad, Jose P.

AU - Abt, Dawn N.

AU - Adryan, Boris

AU - Aguade, Montserrat

AU - Akashi, Hiroshi

AU - Anderson, Wyatt W.

AU - Aquadro, Charles F.

AU - Ardell, David H.

AU - Arguello, Roman

AU - Artieri, Carlo G.

AU - Barbash, Daniel A.

AU - Barker, Daniel

AU - Barsanti, Paolo

AU - Batterham, Phil

AU - Batzoglou, Serafim

AU - Begun, Dave

AU - Bhutkar, Arjun

AU - Blanco, Enrico

AU - Bosak, Stephanie A.

AU - Bradley, Robert K.

AU - Brand, Adrianne D.

AU - Brent, Michael R.

AU - Brooks, Angela N.

AU - Brown, Randall H.

AU - Butlin, Roger K.

AU - Caggese, Corrado

AU - Calvi, Brian R.

AU - Bernardo De Carvalho, A.

AU - Caspi, Anat

AU - Castrezana, Sergio

AU - Celniker, Susan E.

AU - Chang, Jean L.

AU - Chapple, Charles

AU - Chatterji, Sourav

AU - Chinwalla, Asif

AU - Civetta, Alberto

AU - Clifton, Sandra W.

AU - Comeron, Josep M.

AU - Costello, James C.

AU - Coyne, Jerry A.

AU - Daub, Jennifer

AU - David, Robert G.

AU - Delcher, Arthur L.

AU - Delehaunty, Kim

AU - Do, Chuong B.

AU - Ebling, Heather

AU - Edwards, Kevin

AU - Eickbush, Thomas

AU - Evans, Jay D.

AU - Filipski, Alan

AU - Findeiß, Sven

AU - Freyhult, Eva

AU - Fulton, Lucinda

AU - Fulton, Robert

AU - Garcia, Ana C.L.

AU - Gardiner, Anastasia

AU - Garfield, David A.

AU - Garvin, Barry E.

AU - Gibson, Greg

AU - Gilbert, Don

AU - Gnerre, Sante

AU - Godfrey, Jennifer

AU - Good, Robert

AU - Gotea, Valer

AU - Gravely, Brenton

AU - Greenberg, Anthony J.

AU - Griffiths-Jones, Sam

AU - Gross, Samuel

AU - Guigo, Roderic

AU - Gustafson, Erik A.

AU - Haerty, Wilfried

AU - Hahn, Matthew W.

AU - Halligan, Daniel L.

AU - Halpern, Aaron L.

AU - Halter, Gillian M.

AU - Han, Mira V.

AU - Heger, Andreas

AU - Hillier, La Deana

AU - Hinrichs, Angie S.

AU - Holmes, Ian

AU - Hoskins, Roger A.

AU - Hubisz, Melissa J.

AU - Hultmark, Dan

AU - Huntley, Melanie A.

AU - Jaffe, David B.

AU - Jagadeeshan, Santosh

AU - Jeck, William R.

AU - Johnson, Justin

AU - Jones, Corbin D.

AU - Jordan, William C.

AU - Karpen, Gary H.

AU - Kataoka, Eiko

AU - Keightley, Peter D.

AU - Kheradpour, Pouya

AU - Kirkness, Ewen F.

AU - Koerich, Leonardo B.

AU - Kristiansen, Karsten

AU - Kudrna, Dave

AU - Kulathinal, Rob J.

AU - Kumar, Sudhir

AU - Kwok, Roberta

AU - Lander, Eric

AU - Langley, Charles H.

AU - Lapoint, Richard

AU - Lazzaro, Brian P.

AU - Lee, So Jeong

AU - Levesque, Lisa

AU - Li, Ruiqiang

AU - Lin, Chiao Feng

AU - Lin, Michael F.

AU - Lindblad-Toh, Kerstin

AU - Llopart, Ana

AU - Long, Manyuan

AU - Low, Lloyd

AU - Lozovsky, Elena

AU - Lu, Jian

AU - Luo, Meizhong

AU - Machado, Carlos A.

AU - Makalowski, Wojciech

AU - Marzo, Mar

AU - Matsuda, Muneo

AU - Matzkin, Luciano

AU - McAllister, Bryant

AU - McBride, Carolyn S.

AU - McKernan, Brendan

AU - McKernan, Kevin

AU - Mendez-Lago, Maria

AU - Minx, Patrick

AU - Mollenhauer, Michael U.

AU - Montooth, Kristi

AU - Mount, Stephen M.

AU - Mu, Xu

AU - Myers, Eugene

AU - Negre, Barbara

AU - Newfeld, Stuart

AU - Nielsen, Rasmus

AU - Noor, Mohamed A.F.

AU - O'Grady, Patrick

AU - Pachter, Lior

AU - Papaceit, Montserrat

AU - Parisi, Matthew J.

AU - Parisi, Michael

AU - Parts, Leopold

AU - Pedersen, Jakob S.

AU - Pesole, Graziano

AU - Phillippy, Adam M.

AU - Ponting, Chris P.

AU - Pop, Mihai

AU - Porcelli, Damiano

AU - Powell, Jeffrey R.

AU - Prohaska, Sonja

AU - Pruitt, Kim

AU - Puig, Marta

AU - Quesneville, Hadi

AU - Ravi Ram, Kristipati

AU - Rand, David

AU - Rasmussen, Matthew D.

AU - Reed, Laura K.

AU - Reenan, Robert

AU - Reily, Amy

AU - Remington, Karin A.

AU - Rieger, Tania T.

AU - Ritchie, Michael G.

AU - Robin, Charles

AU - Rogers, Yu Hui

AU - Rohde, Claudia

AU - Rozas, Julio

AU - Rubenfield, Marc J.

AU - Ruiz, Alfredo

AU - Russo, Susan

AU - Salzberg, Steven L.

AU - Sanchez-Gracia, Alejandro

AU - Saranga, David J.

AU - Sato, Hajime

AU - Schaeffer, Stephen Wade

AU - Schatz, Michael C.

AU - Schlenke, Todd

AU - Schwartz, Russell

AU - Segarra, Carmen

AU - Singh, Rama S.

AU - Sirot, Laura

AU - Sirota, Marina

AU - Sisneros, Nicholas B.

AU - Smith, Chris D.

AU - Smith, Temple F.

AU - Spieth, John

AU - Stage, Deborah E.

AU - Stark, Alexander

AU - Stephan, Wolfgang

AU - Strausberg, Robert L.

AU - Strempel, Sebastian

AU - Sturgill, David

AU - Sutton, Granger

AU - Sutton, Granger G.

AU - Tao, Wei

AU - Teichmann, Sarah

AU - Tobari, Yoshiko N.

AU - Tomimura, Yoshihiko

AU - Tsolas, Jason M.

AU - Valente, Vera L.S.

AU - Venter, Eli

AU - Craig Venter, J.

AU - Vicario, Saverio

AU - Vieira, Filipe G.

AU - Vilella, Albert J.

AU - Villasante, Alfredo

AU - Walenz, Brian

AU - Wang, Jun

AU - Wasserman, Marvin

AU - Watts, Thomas

AU - Wilson, Derek

AU - Wilson, Richard K.

AU - Wing, Rod A.

AU - Wolfner, Mariana F.

AU - Wong, Alex

AU - Ka-Shu Wong, Gane

AU - Wu, Chung I.

AU - Wu, Gabriel

AU - Yamamoto, Daisuke

AU - Yang, Hsiao Pei

AU - Yang, Shiaw Pyng

AU - Yorke, James A.

AU - Yoshida, Kiyohito

AU - Zdobnov, Evgeny

AU - Zhang, Peili

AU - Zhang, Yu

AU - Zimin, Aleksey V.

AU - Baldwin, Jennifer

AU - Abdouelleil, Amr

AU - Abdulkadir, Jamal

AU - Abebe, Adal

AU - Abera, Brikti

AU - Abreu, Justin

AU - Christophe Acer, St

AU - Aftuck, Lynne

AU - Alexander, Allen

AU - An, Peter

AU - Anderson, Erica

AU - Anderson, Scott

AU - Arachi, Harindra

AU - Azer, Marc

AU - Bachantsang, Pasang

AU - Barry, Andrew

AU - Bayul, Tashi

AU - Berlin, Aaron

AU - Bessette, Daniel

AU - Bloom, Toby

AU - Blye, Jason

AU - Boguslavskiy, Leonid

AU - Bonnet, Claude

AU - Boukhgalter, Boris

AU - Bourzgui, Imane

AU - Brown, Adam

AU - Cahill, Patrick

AU - Channer, Sheridon

AU - Cheshatsang, Yama

AU - Chuda, Lisa

AU - Citroen, Mieke

AU - Collymore, Alville

AU - Cooke, Patrick

AU - Costello, Maura

AU - D'Aco, Katie

AU - Daza, Riza

AU - De Haan, Georgius

AU - Degray, Stuart

AU - Demaso, Christina

AU - Dhargay, Norbu

AU - Dooley, Kimberly

AU - Dooley, Erin

AU - Doricent, Missole

AU - Dorje, Passang

AU - Dorjee, Kunsang

AU - Dupes, Alan

AU - Elong, Richard

AU - Falk, Jill

AU - Farina, Abderrahim

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AU - Gadbois, Loryn

AU - Gearin, Gary

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AU - Giannoukos, Georgia

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AU - Grandbois, Edward

AU - Grewal, Sharleen

AU - Gyaltsen, Kunsang

AU - Hafez, Nabil

AU - Hagos, Birhane

AU - Hall, Jennifer

AU - Henson, Charlotte

AU - Hollinger, Andrew

AU - Honan, Tracey

AU - Huard, Monika D.

AU - Hughes, Leanne

AU - Hurhula, Brian

AU - Erii Husby, M.

AU - Kamat, Asha

AU - Kanga, Ben

AU - Kashin, Seva

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AU - Kisner, Peter

AU - Lance, Krista

AU - Lara, Marcia

AU - Lee, William

AU - Lennon, Niall

AU - Letendre, Frances

AU - Levine, Rosie

AU - Lipovsky, Alex

AU - Liu, Xiaohong

AU - Liu, Jinlei

AU - Liu, Shangtao

AU - Lokyitsang, Tashi

AU - Lokyitsang, Yeshi

AU - Lubonja, Rakela

AU - Lui, Annie

AU - MacDonald, Pen

AU - Magnisalis, Vasilia

AU - Maru, Kebede

AU - Matthews, Charles

AU - McCusker, William

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AU - Mehta, Teena

AU - Meldrim, James

AU - Meneus, Louis

AU - Mihai, Oana

AU - Mihalev, Atanas

AU - Mihova, Tanya

AU - Mittelman, Rachel

AU - Mlenga, Valentine

AU - Montmayeur, Anna

AU - Mulrain, Leonidas

AU - Navidi, Adam

AU - Naylor, Jerome

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AU - Nguyen, Nga

AU - Nicol, Robert

AU - Norbu, Choe

AU - Norbu, Nyima

AU - Novod, Nathaniel

AU - O'Neill, Barry

AU - Osman, Sahal

AU - Markiewicz, Eva

AU - Oyono, Otero L.

AU - Patti, Christopher

AU - Phunkhang, Pema

AU - Pierre, Fritz

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AU - Raghuraman, Sujaa

AU - Rege, Filip

AU - Reyes, Rebecca

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AU - Rogov, Peter

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AU - Ryan, Elizabeth

AU - Settipalli, Sampath

AU - Shea, Terry

AU - Sherpa, Ngawang

AU - Shi, Lu

AU - Shih, Diana

AU - Sparrow, Todd

AU - Spaulding, Jessica

AU - Stalker, John

AU - Stange-Thomann, Nicole

AU - Stavropoulos, Sharon

AU - Stone, Catherine

AU - Strader, Christopher

AU - Tesfaye, Senait

AU - Thomson, Talene

AU - Thoulutsang, Yama

AU - Thoulutsang, Dawa

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AU - Wilson, Adam

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AU - Young, Geneva

AU - Yu, Qing

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AU - Grabherr, Manfred

AU - Kleber, Michael

AU - Mauceli, Evan

AU - MacCallum, Iain

PY - 2007/11/8

Y1 - 2007/11/8

N2 - Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.

AB - Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.

UR - http://www.scopus.com/inward/record.url?scp=47149117454&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=47149117454&partnerID=8YFLogxK

U2 - 10.1038/nature06341

DO - 10.1038/nature06341

M3 - Article

C2 - 17994087

AN - SCOPUS:47149117454

VL - 450

SP - 203

EP - 218

JO - Nature

JF - Nature

SN - 0028-0836

IS - 7167

ER -

Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA et al. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 2007 Nov 8;450(7167):203-218. https://doi.org/10.1038/nature06341