Journal ArticleDOI
The origin of new genes: glimpses from the young and old
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TLDR
The study of ancient genes has highlighted the antiquity and general importance of some mechanisms of gene origination, and recent observations of young genes at early stages in their evolution have unveiled unexpected molecular and evolutionary processes.Abstract:
Genome data have revealed great variation in the numbers of genes in different organisms, which indicates that there is a fundamental process of genome evolution: the origin of new genes. However, there has been little opportunity to explore how genes with new functions originate and evolve. The study of ancient genes has highlighted the antiquity and general importance of some mechanisms of gene origination, and recent observations of young genes at early stages in their evolution have unveiled unexpected molecular and evolutionary processes.read more
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Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
LaDeana W. Hillier,Webb Miller,Ewan Birney,Wesley C. Warren,Ross C. Hardison,Chris P. Ponting,Peer Bork,David W. Burt,Martien A. M. Groenen,Mary E. Delany,Jerry B. Dodgson,Asif T. Chinwalla,Paul F. Cliften,Sandra W. Clifton,Kimberly D. Delehaunty,Catrina Fronick,Robert S. Fulton,Tina Graves,Colin Kremitzki,Dan Layman,Vincent Magrini,John Douglas Mcpherson,Tracie L. Miner,Patrick Minx,William E. Nash,Michael N. Nhan,Joanne O. Nelson,Lachlan G. Oddy,Craig Pohl,Jennifer Randall-Maher,Scott M. Smith,John W. Wallis,Shiaw Pyng Yang,Michael N Romanov,Catherine M. Rondelli,Bob Paton,Jacqueline Smith,David Morrice,Laura M. Daniels,Helen G. Tempest,Lindsay Robertson,Julio S. Masabanda,Darren K. Griffin,Alain Vignal,Valerie Fillon,Lina Jacobbson,Susanne Kerje,Leif Andersson,Richard P. M. A. Crooijmans,Jan Aerts,Jan J. van der Poel,Hans Ellegren,Randolph B. Caldwell,Simon J. Hubbard,Darren Grafham,Andrzej M. Kierzek,Stuart McLaren,Ian M. Overton,Hiroshi Arakawa,Kevin J. Beattie,Yuri Bezzubov,Paul E. Boardman,James K. Bonfield,Michael D. R. Croning,Robert L. Davies,Matthew D. Francis,Sean Humphray,Carol Scott,Ruth Taylor,Cheryll Tickle,William Brown,Jane Rogers,Jean-Marie Buerstedde,Stuart A. Wilson,Lisa Stubbs,Ivan Ovcharenko,Laurie Gordon,Susan Lucas,Marcia M. Miller,Hidetoshi Inoko,Takashi Shiina,James C. Kaufman,Jan Salomonsen,Karsten Skjoedt,Gane Ka-Shu Wong,Jun Wang,Bin Liu,Jian Wang,Jun Yu,Huanming Yang,Mikhail Nefedov,Maxim Koriabine,Pieter J. deJong,Leo Goodstadt,Caleb Webber,Nicholas J. Dickens,Ivica Letunic,Mikita Suyama,David Torrents,Christian von Mering,Evgeny M. Zdobnov,Kateryna D. Makova,Anton Nekrutenko,Laura Elnitski,Pallavi Eswara,David C. King,Shan Yang,Svitlana Tyekucheva,Anusha Radakrishnan,Robert S. Harris,Francesca Chiaromonte,James Taylor,Jianbin He,Monique Rijnkels,Sam Griffiths-Jones,Abel Ureta-Vidal,Michael M. Hoffman,Jessica Severin,Stephen M. J. Searle,Andy Law,David Speed,D. Waddington,Ze Cheng,Eray Tüzün,Evan E. Eichler,Zhirong Bao,Paul Flicek,David Shteynberg,Michael R. Brent,Jacqueline M. Bye,Elizabeth J. Huckle,Sourav Chatterji,Colin N. Dewey,Lior Pachter,Andrei Kouranov,Zissimos Mourelatos,Artemis G. Hatzigeorgiou,Andrew H. Paterson,Robert Ivarie,Mikael Brandström,Erik Axelsson,Niclas Backström,Sofia Berlin,Matthew T. Webster,Olivier Pourquié,Alexandre Reymond,Catherine Ucla,Stylianos E. Antonarakis,Manyuan Long,J. J. Emerson,Esther Betrán,Isabelle Dupanloup,Henrik Kaessmann,Angie S. Hinrichs,Gill Bejerano,Terrence S. Furey,Rachel A. Harte,Brian J. Raney,Adam Siepel,W. James Kent,David Haussler,Eduardo Eyras,Robert Castelo,Josep F. Abril,Sergi Castellano,Francisco Camara,Genís Parra,Roderic Guigó,Guillaume Bourque,Glenn Tesler,Pavel A. Pevzner,Arian F.A. Smit,Lucinda Fulton,Elaine R. Mardis,Richard K. Wilson +174 more
TL;DR: A draft genome sequence of the red jungle fowl, Gallus gallus, provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes.
Journal ArticleDOI
Sea Anemone Genome Reveals Ancestral Eumetazoan Gene Repertoire and Genomic Organization
Nicholas H. Putnam,Mansi Srivastava,Uffe Hellsten,Bill Dirks,Jarrod Chapman,Asaf Salamov,Astrid Terry,Harris Shapiro,Erika Lindquist,Vladimir V. Kapitonov,Jerzy Jurka,Grigory Genikhovich,Igor V. Grigoriev,Susan Lucas,Robert Steele,John R. Finnerty,Ulrich Technau,Mark Q. Martindale,Daniel S. Rokhsar,Daniel S. Rokhsar +19 more
TL;DR: A comparative analysis of the draft genome of an emerging cnidarian model, the starlet sea anemone Nematostella vectensis, suggests that gene “inventions” along the lineage leading to animals were likely already well integrated with preexisting eukaryotic genes in the eumetazoan progenitor.
Journal ArticleDOI
The evolution of gene duplications: classifying and distinguishing between models.
TL;DR: A comprehensive classification of the models that are relevant to all stages of the evolution of gene duplications is presented, each of which predicts a unique combination of evolutionary dynamics and functional properties.
Journal ArticleDOI
DNA Transposons and the Evolution of Eukaryotic Genomes
TL;DR: This review focuses on DNA-mediated or class 2 transposons and emphasizes how this class of elements is distinguished from other types of mobile elements in terms of their structure, amplification dynamics, and genomic effect.
Journal ArticleDOI
The locus of evolution: evo devo and the genetics of adaptation
Hopi E. Hoekstra,Jerry A. Coyne +1 more
TL;DR: There is no theoretical or empirical basis for the evo devo contention that adaptations involving morphology evolve by genetic mechanisms different from those involving physiology and other traits, and substantial data on the genetic basis of adaptation from both genome-wide surveys and single-locus studies are examined.
References
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Journal ArticleDOI
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TL;DR: The results of an international collaboration to produce and make freely available a draft sequence of the human genome are reported and an initial analysis is presented, describing some of the insights that can be gleaned from the sequence.
Journal ArticleDOI
The sequence of the human genome.
J. Craig Venter,Mark Raymond Adams,Eugene W. Myers,Peter W. Li,Richard J. Mural,Granger G. Sutton,Hamilton O. Smith,Mark Yandell,Cheryl A. Evans,Robert A. Holt,Jeannine D. Gocayne,Peter Amanatides,Richard M. Ballew,Daniel H. Huson,Jennifer R. Wortman,Qing Zhang,Chinnappa D. Kodira,Xiangqun H. Zheng,Lin Chen,Marian P. Skupski,Gangadharan Subramanian,Paul Thomas,Jinghui Zhang,George L. Gabor Miklos,Catherine R. Nelson,Samuel Broder,Andrew G. Clark,J. H. Nadeau,Victor A. McKusick,Norton D. Zinder,Arnold J. Levine,Richard J. Roberts,M. I. Simon,Carolyn W. Slayman,Michael W. Hunkapiller,Randall Bolanos,Arthur L. Delcher,Ian M. Dew,Daniel Fasulo,Michael Flanigan,Liliana Florea,Aaron L. Halpern,Sridhar Hannenhalli,Saul A. Kravitz,Samuel Levy,Clark M. Mobarry,Knut Reinert,Karin A. Remington,Jane Abu-Threideh,Ellen M. Beasley,Kendra Biddick,Vivien Bonazzi,Rhonda Brandon,Michele Cargill,Ishwar Chandramouliswaran,Rosane Charlab,Kabir Chaturvedi,Zuoming Deng,Valentina Di Francesco,Patrick Dunn,Karen Eilbeck,Carlos Evangelista,Andrei Gabrielian,Weiniu Gan,Wangmao Ge,Fangcheng Gong,Zhiping Gu,Ping Guan,Thomas J. Heiman,Maureen E. Higgins,Rui-Ru Ji,Zhaoxi Ke,Karen A. Ketchum,Zhongwu Lai,Yiding Lei,Zhenya Li,Jiayin Li,Yong Liang,Xiaoying Lin,Fu Lu,Gennady V. Merkulov,Natalia Milshina,Helen M. Moore,Ashwinikumar K Naik,Vaibhav A. Narayan,Beena Neelam,Deborah Nusskern,Douglas B. Rusch,Steven L. Salzberg,Wei Shao,Bixiong Chris Shue,Jingtao Sun,Zhen Yuan Wang,Aihui Wang,Xin Wang,Jian Wang,Ming-Hui Wei,Ron Wides,Chunlin Xiao,Chunhua Yan,Alison Yao,Jane Ye,Ming Zhan,Weiqing Zhang,Hongyu Zhang,Qi Zhao,Liansheng Zheng,Fei Zhong,Wenyan Zhong,Shiaoping C. Zhu,Shaying Zhao,Dennis A. Gilbert,Suzanna Baumhueter,Gene Spier,Christine Carter,Anibal Cravchik,Trevor Woodage,Feroze Ali,Huijin An,Aderonke Awe,Danita Baldwin,Holly Baden,Mary Barnstead,Ian Barrow,Karen Beeson,Dana A. Busam,Amy Carver,Ming Lai Cheng,Liz Curry,Steve Danaher,Lionel Davenport,Raymond Desilets,Susanne Dietz,Kristina Dodson,Lisa Doup,Steven Ferriera,Neha Garg,Andres Gluecksmann,Brit J. Hart,Jason Haynes,Charles Haynes,Cheryl Heiner,Suzanne Hladun,Damon Hostin,Jarrett Houck,Timothy Howland,Chinyere Ibegwam,Jeffery Johnson,Francis Kalush,Lesley Kline,Shashi Koduru,Amy Love,Felecia Mann,David May,Steven McCawley,Tina C. McIntosh,Ivy McMullen,Mee Moy,Linda Moy,Brian Murphy,Keith Nelson,Cynthia Pfannkoch,Eric Pratts,Vinita Puri,Hina Qureshi,Matthew Reardon,Robert Rodriguez,Yu-Hui Rogers,Deanna Romblad,Bob Ruhfel,Richard T. Scott,Cynthia Sitter,Michelle Smallwood,Erin Stewart,Renee Strong,Ellen Suh,Reginald Thomas,Ni Ni Tint,Sukyee Tse,Claire Vech,Gary Wang,Jeremy Wetter,Sherita Williams,Monica Williams,Sandra Windsor,Emily Winn-Deen,Keriellen Wolfe,Jayshree Zaveri,Karena Zaveri,Josep F. Abril,Roderic Guigó,Michael J. Campbell,Kimmen Sjölander,Brian Karlak,Anish Kejariwal,Huaiyu Mi,Betty Lazareva,Thomas Hatton,Apurva Narechania,Karen Diemer,Anushya Muruganujan,Nan Guo,Shinji Sato,Vineet Bafna,Sorin Istrail,Ross Lippert,Russell Schwartz,Brian P. Walenz,Shibu Yooseph,David Allen,Anand Basu,James Baxendale,Louis Blick,Marcelo Caminha,John Carnes-Stine,Parris Caulk,Yen-Hui Chiang,My Coyne,Carl Dahlke,Anne Deslattes Mays,Maria Dombroski,Michael Donnelly,Dale Ely,Shiva Esparham,Carl Fosler,Harold Gire,Stephen Glanowski,Kenneth Glasser,Anna Glodek,Mark Gorokhov,Ken Graham,Barry Gropman,Michael Harris,Jeremy Heil,Scott Henderson,Jeffrey Hoover,Donald Jennings,Catherine Jordan,James Jordan,John Kasha,Leonid Kagan,Cheryl L. Kraft,Alexander Levitsky,Mark Lewis,Xiangjun Liu,John Lopez,Daniel Ma,William H. Majoros,Joe McDaniel,Sean C. Murphy,Matthew Newman,Trung Hieu Nguyen,Ngoc Nguyen,Marc Nodell,Sue Pan,Jim Peck,Marshall Peterson,William Rowe,Robert Sanders,John Scott,Michael Simpson,Thomas J. Smith,Arlan Sprague,Timothy B. Stockwell,Russell Turner,Eli Venter,Mei Wang,Meiyuan Wen,David Wu,Mitchell Wu,Ashley Xia,Ali Zandieh,Xiaohong Zhu +272 more
TL;DR: Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems are indicated.
Book
The Neutral Theory of Molecular Evolution
TL;DR: The neutral theory as discussed by the authors states that the great majority of evolutionary changes at the molecular level are caused not by Darwinian selection but by random drift of selectively neutral mutants, which has caused controversy ever since.
Journal ArticleDOI
Initial sequencing and comparative analysis of the mouse genome.
Robert H. Waterston,Kerstin Lindblad-Toh,Ewan Birney,Jane Rogers,Josep F. Abril,Pankaj K. Agarwal,Richa Agarwala,Rachel Ainscough,Marina Alexandersson,Peter An,Stylianos E. Antonarakis,John Attwood,Robert Baertsch,J Bailey,K F Barlow,Stephan Beck,Eric Berry,Bruce W. Birren,Toby Bloom,Peer Bork,Marc Botcherby,Nicolas Bray,Michael R. Brent,Daniel G. Brown,Daniel G. Brown,Stephen D. Brown,Carol J. Bult,John Burton,Jonathan Butler,R. D. Campbell,Piero Carninci,Simon Cawley,Francesca Chiaromonte,Asif T. Chinwalla,Deanna M. Church,Michele Clamp,C M Clee,Francis S. Collins,Lisa Cook,Richard R. Copley,Alan Coulson,Olivier Couronne,James Cuff,Val Curwen,Tim Cutts,Mark J. Daly,Robert David,Joy Davies,Kimberly D. Delehaunty,Justin Deri,Emmanouil T. Dermitzakis,Colin N. Dewey,Nicholas J. Dickens,Mark Diekhans,Sheila Dodge,Inna Dubchak,Diane M. Dunn,Sean R. Eddy,Laura Elnitski,Richard D. Emes,Pallavi Eswara,Eduardo Eyras,Adam Felsenfeld,Ginger A. Fewell,Paul Flicek,Karen Foley,Wayne N. Frankel,Lucinda Fulton,Robert S. Fulton,Terrence S. Furey,Diane Gage,Richard A. Gibbs,Gustavo Glusman,Sante Gnerre,Nick Goldman,Leo Goodstadt,Darren Grafham,Tina Graves,Eric D. Green,Simon G. Gregory,Roderic Guigó,Mark S. Guyer,Ross C. Hardison,David Haussler,Yoshihide Hayashizaki,Deana W. LaHillier,Angela S. Hinrichs,Wratko Hlavina,Timothy Holzer,Fan Hsu,Axin Hua,Tim Hubbard,Adrienne Hunt,Ian J. Jackson,David B. Jaffe,L. Steven Johnson,Matthew Jones,Thomas A. Jones,A Joy,Michael Kamal,Elinor K. Karlsson,Donna Karolchik,Arkadiusz Kasprzyk,Jun Kawai,Evan Keibler,Cristyn Kells,W. James Kent,Andrew Kirby,Diana L. Kolbe,Ian F Korf,Raju Kucherlapati,Edward J. Kulbokas,David Kulp,Tom Landers,J. P. Leger,Steven Leonard,Ivica Letunic,Rosie Levine,Jia Li,Ming Li,Christine Lloyd,Susan Lucas,Bin Ma,Donna Maglott,Elaine R. Mardis,Lucy Matthews,Evan Mauceli,John Mayer,Megan McCarthy,W. Richard McCombie,Stuart McLaren,Kirsten McLay,John Douglas Mcpherson,James Meldrim,Beverley Meredith,Jill P. Mesirov,Webb Miller,Tracie L. Miner,Emmanuel Mongin,Kate Montgomery,Michael J. Morgan,Richard Mott,James C. Mullikin,Donna M. Muzny,William E. Nash,Joanne O. Nelson,Michael N. Nhan,Robert Nicol,Zemin Ning,Chad Nusbaum,Michael J. O’Connor,Yasushi Okazaki,Karen Oliver,Emma Overton-Larty,Lior Pachter,Genís Parra,Kymberlie H. Pepin,Jane Peterson,Pavel A. Pevzner,Robert W. Plumb,Craig Pohl,Alex Poliakov,Tracy C. Ponce,Chris P. Ponting,Simon C. Potter,Michael A. Quail,Alexandre Reymond,Bruce A. Roe,Krishna M. Roskin,Edward M. Rubin,Alistair G. Rust,Ralph Santos,Victor Sapojnikov,Brian Schultz,Jörg Schultz,Matthias S. Schwartz,Scott Schwartz,Carol Scott,Steven Seaman,Steve Searle,Ted Sharpe,Andrew Sheridan,Ratna Shownkeen,Sarah Sims,Jonathan Singer,Guy Slater,Arian F.A. Smit,Douglas Smith,Brian Spencer,Arne Stabenau,Nicole Stange-Thomann,Charles W. Sugnet,Mikita Suyama,Glenn Tesler,Johanna Thompson,David Torrents,Evanne Trevaskis,John Tromp,Catherine Ucla,Abel Ureta-Vidal,Jade P. Vinson,Andrew von Niederhausern,Claire M. Wade,Melanie M. Wall,R. J. Weber,Robert B. Weiss,Michael C. Wendl,Anthony P. West,Kris A. Wetterstrand,Raymond Wheeler,Simon Whelan,Jamey Wierzbowski,David Willey,Sophie Williams,Richard K. Wilson,Eitan E. Winter,Kim C. Worley,Dudley Wyman,Shan Yang,Shiaw Pyng Yang,Evgeny M. Zdobnov,Michael C. Zody,Eric S. Lander +222 more
TL;DR: The results of an international collaboration to produce a high-quality draft sequence of the mouse genome are reported and an initial comparative analysis of the Mouse and human genomes is presented, describing some of the insights that can be gleaned from the two sequences.