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. 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; La Deana Hillier; Angie S. Hinrichs; Ian Holmes; Roger A. Hoskins; Melissa J. Hubisz; Dan Hultmark; Melanie A. Huntley; David B. Jaffe; Santosh Jagadeeshan; Marta Puig Font; Alfredo Ruiz Panadero

doi:10.1038/nature06341

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, Marta Puig Font, Alfredo Ruiz Panadero

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Resum

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. ©2007 Nature Publishing Group.

Idioma original	Anglès
Pàgines (de-a)	203-218
Revista	Nature
Volum	450
DOIs	https://doi.org/10.1038/nature06341
Estat de la publicació	Publicada - 8 de nov. 2007

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10.1038/nature06341

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https://www.scopus.com/pages/publications/47149117454

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Clark, A. G., Eisen, M. B., Smith, D. R., Bergman, C. M., Oliver, B., Markow, T. A., Kaufman, T. C., Kellis, M., Gelbart, W., Iyer, V. N., Pollard, D. A., Sackton, T. B., Larracuente, A. M., Singh, N. D., Abad, J. P., Abt, D. N., Adryan, B., Aguade, M., Akashi, H., ... Ruiz Panadero, A. (2007). Evolution of genes and genomes on the Drosophila phylogeny. Nature, 450, 203-218. https://doi.org/10.1038/nature06341

@article{9efd6108c5034c6db6b929b2b745cf06,

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. {\textcopyright}2007 Nature Publishing Group.",

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 \{Puig Font\}, Marta and \{Ruiz Panadero\}, Alfredo",

year = "2007",

month = nov,

day = "8",

doi = "10.1038/nature06341",

language = "English",

volume = "450",

pages = "203--218",

}

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, Puig Font, M & Ruiz Panadero, A 2007, 'Evolution of genes and genomes on the Drosophila phylogeny', Nature, vol. 450, pàg. 203-218. https://doi.org/10.1038/nature06341

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 - Puig Font, Marta

AU - Ruiz Panadero, Alfredo

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. ©2007 Nature Publishing Group.

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. ©2007 Nature Publishing Group.

UR - https://www.scopus.com/pages/publications/47149117454

U2 - 10.1038/nature06341

DO - 10.1038/nature06341

M3 - Article

SN - 0028-0836

VL - 450

SP - 203

EP - 218

JO - Nature

JF - Nature

ER -

Evolution of genes and genomes on the Drosophila phylogeny

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