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.

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@article{Clark2007EvolutionOG, title={Evolution of genes and genomes on the Drosophila phylogeny.}, author={Andrew G Clark and Michael B Eisen and Douglas R Smith and Casey M Bergman and Brian Oliver and Therese A Markow and Thomas C Kaufman and Manolis Kellis and William Gelbart and Venky N Iyer and Daniel A Pollard and Timothy B Sackton and Amanda M Larracuente and Nadia D Singh and Jose P Abad and Dawn N Abt and Boris Adryan and Montserrat Aguade and Hiroshi Akashi and Wyatt W Anderson and Charles F Aquadro and David H Ardell and Roman Arguello and Carlo G Artieri and Daniel A Barbash and Daniel Barker and Paolo Barsanti and Phil Batterham and Serafim Batzoglou and Dave Begun and Arjun Bhutkar and Enrico Blanco and Stephanie A Bosak and Robert K Bradley and Adrianne D Brand and Michael R Brent and Angela N Brooks and Randall H Brown and Roger K Butlin and Corrado Caggese and Brian R Calvi and A Bernardo de Carvalho and Anat Caspi and Sergio Castrezana and Susan E Celniker and Jean L Chang and Charles Chapple and Sourav Chatterji and Asif Chinwalla and Alberto Civetta and Sandra W Clifton and Josep M Comeron and James C Costello and Jerry A Coyne and Jennifer Daub and Robert G David and Arthur L Delcher and Kim Delehaunty and Chuong B Do and Heather Ebling and Kevin Edwards and Thomas Eickbush and Jay D Evans and Alan Filipski and Sven Findeiss and Eva Freyhult and Lucinda Fulton and Robert Fulton and Ana C L Garcia and Anastasia Gardiner and David A Garfield and Barry E Garvin and Greg Gibson and Don Gilbert and Sante Gnerre and Jennifer Godfrey and Robert Good and Valer Gotea and Brenton Gravely and Anthony J Greenberg and Sam Griffiths-Jones and Samuel Gross and Roderic Guigo and Erik A Gustafson and Wilfried Haerty and Matthew W Hahn and Daniel L Halligan and Aaron L Halpern and Gillian M Halter and Mira V Han and Andreas Heger and LaDeana Hillier and Angie S Hinrichs and Ian Holmes and Roger A Hoskins and Melissa J Hubisz and Dan Hultmark and Melanie A Huntley and David B Jaffe and Santosh Jagadeeshan and William R Jeck and Justin Johnson and Corbin D Jones and William C Jordan and Gary H Karpen and Eiko Kataoka and Peter D Keightley and Pouya Kheradpour and Ewen F Kirkness and Leonardo B Koerich and Karsten Kristiansen and Dave Kudrna and Rob J Kulathinal and Sudhir Kumar and Roberta Kwok and Eric Lander and Charles H Langley and Richard Lapoint and Brian P Lazzaro and So-Jeong Lee and Lisa Levesque and Ruiqiang Li and Chiao-Feng Lin and Michael F Lin and Kerstin Lindblad-Toh and Ana Llopart and Manyuan Long and Lloyd Low and Elena Lozovsky and Jian Lu and Meizhong Luo and Carlos A Machado and Wojciech Makalowski and Mar Marzo and Muneo Matsuda and Luciano Matzkin and Bryant McAllister and Carolyn S McBride and Brendan McKernan and Kevin McKernan and Maria Mendez-Lago and Patrick Minx and Michael U Mollenhauer and Kristi Montooth and Stephen M Mount and Xu Mu and Eugene Myers and Barbara Negre and Stuart Newfeld and Rasmus Nielsen and Mohamed A F Noor and Patrick O'Grady and Lior Pachter and Montserrat Papaceit and Matthew J Parisi and Michael Parisi and Leopold Parts and Jakob S Pedersen and Graziano Pesole and Adam M Phillippy and Chris P Ponting and Mihai Pop and Damiano Porcelli and Jeffrey R Powell and Sonja Prohaska and Kim Pruitt and Marta Puig and Hadi Quesneville and Kristipati Ravi Ram and David Rand and Matthew D Rasmussen and Laura K Reed and Robert Reenan and Amy Reily and Karin A Remington and Tania T Rieger and Michael G Ritchie and Charles Robin and Yu-Hui Rogers and Claudia Rohde and Julio Rozas and Marc J Rubenfield and Alfredo Ruiz and Susan Russo and Steven L Salzberg and Alejandro Sanchez-Gracia and David J Saranga and Hajime Sato and Stephen W Schaeffer and Michael C Schatz and Todd Schlenke and Russell Schwartz and Carmen Segarra and Rama S Singh and Laura Sirot and Marina Sirota and Nicholas B Sisneros and Chris D Smith and Temple F Smith and John Spieth and Deborah E Stage and Alexander Stark and Wolfgang Stephan and Robert L Strausberg and Sebastian Strempel and David Sturgill and Granger Sutton and Granger G Sutton and Wei Tao and Sarah Teichmann and Yoshiko N Tobari and Yoshihiko Tomimura and Jason M Tsolas and Vera L S Valente and Eli Venter and J Craig Venter and Saverio Vicario and Filipe G Vieira and Albert J Vilella and Alfredo Villasante and Brian Walenz and Jun Wang and Marvin Wasserman and Thomas Watts and Derek Wilson and Richard K Wilson and Rod A Wing and Mariana F Wolfner and Alex Wong and Gane Ka-Shu Wong and Chung-I Wu and Gabriel Wu and Daisuke Yamamoto and Hsiao-Pei Yang and Shiaw-Pyng Yang and James A Yorke and Kiyohito Yoshida and Evgeny Zdobnov and Peili Zhang and Yu Zhang and Aleksey V Zimin and Jennifer Baldwin and Amr Abdouelleil and Jamal Abdulkadir and Adal Abebe and Brikti Abera and Justin Abreu and St Christophe Acer 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 Georgius De Haan 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 Chelsea D Foley and Alicia Franke and Dennis Friedrich and Loryn Gadbois and Gary Gearin and Christina R Gearin 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 Monika D Huard and Leanne Hughes and Brian Hurhula and M Erii Husby 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 Otero L Oyono 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}, journal={Nature}, year={2007}, volume={450 7167}, pages={203-18} }