Journal ArticleDOI
Molecular phylogenetics and the origins of placental mammals
William J. Murphy,Eduardo Eizirik,Eduardo Eizirik,Warren E. Johnson,Ya-Ping Zhang,Oliver A. Ryder,Stephen J. O'Brien +6 more
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TLDR
The potential weaknesses of limited character and taxon sampling are addressed in a comprehensive molecular phylogenetic analysis of 64 species sampled across all extant orders of placental mammals, providing new insight into the pattern of the early placental mammal radiation.Abstract:
The precise hierarchy of ancient divergence events that led to the present assemblage of modern placental mammals has been an area of controversy among morphologists, palaeontologists and molecular evolutionists. Here we address the potential weaknesses of limited character and taxon sampling in a comprehensive molecular phylogenetic analysis of 64 species sampled across all extant orders of placental mammals. We examined sequence variation in 18 homologous gene segments (including nearly 10,000 base pairs) that were selected for maximal phylogenetic informativeness in resolving the hierarchy of early mammalian divergence. Phylogenetic analyses identify four primary superordinal clades: (I) Afrotheria (elephants, manatees, hyraxes, tenrecs, aardvark and elephant shrews); (II) Xenarthra (sloths, anteaters and armadillos); (III) Glires (rodents and lagomorphs), as a sister taxon to primates, flying lemurs and tree shrews; and (IV) the remaining orders of placental mammals (cetaceans, artiodactyls, perissodactyls, carnivores, pangolins, bats and core insectivores). Our results provide new insight into the pattern of the early placental mammal radiation.read more
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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.
Journal ArticleDOI
International Union of Pharmacology. XXVII. Classification of Cannabinoid Receptors
Allyn C. Howlett,Francis Barth,Tom I. Bonner,Guy A. Cabral,Pierre Casellas,William A. Devane,Christian C. Felder,Miles Herkenham,Ken Mackie,Billy R. Martin,Raphael Mechoulam,Roger G. Pertwee +11 more
TL;DR: It is considered premature to rename cannabinoid receptors after an endogenous agonist as is recommended by the International Union of Pharmacology Committee on Receptor Nomenclature and Drug Classification, because pharmacological evidence for the existence of additional types of cannabinoid receptor is emerging and other kinds of supporting evidence are still lacking.
Journal ArticleDOI
An Approximately Unbiased Test of Phylogenetic Tree Selection
TL;DR: It is shown that the AU test is less biased than other methods in typical cases of tree selection, as well as in the analysis of mammalian mitochondrial protein sequences.
Journal ArticleDOI
Genome sequence, comparative analysis and haplotype structure of the domestic dog
Kerstin Lindblad-Toh,Claire M. Wade,Claire M. Wade,Tarjei S. Mikkelsen,Tarjei S. Mikkelsen,Elinor K. Karlsson,Elinor K. Karlsson,David B. Jaffe,Michael Kamal,Michele Clamp,Jean L. Chang,Edward J. Kulbokas,Michael C. Zody,Evan Mauceli,Xiaohui Xie,Matthew Breen,Robert K. Wayne,Elaine A. Ostrander,Chris P. Ponting,Francis Galibert,Douglas Smith,Pieter J. deJong,Ewen F. Kirkness,Pablo Alvarez,Tara Biagi,William Brockman,Jonathan Butler,Chee-Wye Chin,April Cook,James Cuff,Mark J. Daly,Mark J. Daly,David DeCaprio,Sante Gnerre,Manfred Grabherr,Manolis Kellis,Michael Kleber,Carolyne Bardeleben,Leo Goodstadt,Andreas Heger,Christophe Hitte,Lisa Kim,Klaus-Peter Koepfli,Heidi G. Parker,John P. Pollinger,Stephen M. J. Searle,Nathan B. Sutter,Rachael Thomas,Caleb Webber,Jennifer Baldwin,Jennifer Baldwin,Adal Abebe,Amr Abouelleil,Lynne Aftuck,Mostafa Ait-zahra,Tyler Aldredge,Nicole R. Allen,Peter An,Scott Anderson,Claudel Antoine,Harindra Arachchi,Ali Aslam,Laura Ayotte,Pasang Bachantsang,Andrew Barry,Tashi Bayul,Mostafa Benamara,Aaron M. Berlin,Daniel Bessette,Berta Blitshteyn,Toby Bloom,Jason Blye,Leonid Boguslavskiy,Claude Bonnet,Boris Boukhgalter,Adam Brown,Patrick Cahill,Nadia Calixte,Jody Camarata,Yama Cheshatsang,Jeffrey Chu,Mieke Citroen,Alville Collymore,Patrick Cooke,Tenzin Dawoe,Riza M. Daza,Karin Decktor,Stuart DeGray,Norbu Dhargay,Kimberly Dooley,Kathleen Dooley,Passang Dorje,Kunsang Dorjee,Lester Dorris,Noah Duffey,Alan Dupes,Osebhajajeme Egbiremolen,Richard Elong,Jill Falk,Abderrahim Farina,Susan Faro,Diallo Ferguson,Patricia Ferreira,Sheila A. Fisher,Michael Fitzgerald,Karen Foley,Chelsea D. Foley,Alicia Franke,Dennis C. Friedrich,Diane Gage,Manuel Garber,Gary Gearin,Georgia Giannoukos,Tina Goode,Audra Goyette,Joseph Graham,Edward Grandbois,Kunsang Gyaltsen,Nabil Hafez,Daniel S. Hagopian,Birhane Hagos,Jennifer Ruth Sadler Hall,Claire M. Healy,Ryan Hegarty,Tracey Honan,Andrea Horn,Nathan Houde,Leanne Hughes,Leigh Anne Hunnicutt,M. Husby,Benjamin Jester,Charlien Jones,Asha Kamat,Ben Kanga,Cristyn Kells,Dmitry Khazanovich,Alix Chinh Kieu,Peter Kisner,Mayank Kumar,Krista Lance,Thomas E. Landers,Marcia Lara,William H. Lee,Jean-Pierre Leger,Niall J. Lennon,Lisa Leuper,Sarah LeVine,Jinlei Liu,Xiaohong Liu,Yeshi Lokyitsang,Tashi Lokyitsang,Annie Lui,Jan Macdonald,John E. Major,Richard Marabella,Kebede Maru,Charles Matthews,Susan McDonough,Teena Mehta,James Meldrim,Alexandre Melnikov,Louis Meneus,Atanas Mihalev,Tanya Mihova,Karen Hughes Miller,Rachel Mittelman,Valentine Mlenga,Leonidas Mulrain,Glen Munson,Adam Navidi,Jerome Naylor,Tuyen T. Nguyen,Nga Nguyen,Cindy Nguyen,Thu Nguyen,Robert Nicol,Nyima Norbu,Choe Norbu,Nathaniel Novod,Tenchoe Nyima,Peter Olandt,Barry O'Neill,Keith O'Neill,Sahal Osman,Lucien Oyono,Christopher Patti,Danielle Perrin,Pema Phunkhang,Fritz Pierre,Margaret Priest,Anthony Rachupka,Sujaa Raghuraman,Rayale Rameau,Verneda Ray,Christina Raymond,Filip Rege,Cecil Rise,Julie Rogers,Peter Rogov,Julie Sahalie,Sampath Settipalli,Ted Sharpe,Terrance Shea,Mechele Sheehan,Ngawang Sherpa,Jianying Shi,Diana M. Shih,Jessie Sloan,Cherylyn Smith,Todd Sparrow,John Stalker,Nicole Stange-Thomann,Sharon Stavropoulos,Catherine Stone,Sabrina M. Stone,Sean M. Sykes,Pierre Tchuinga,Pema Tenzing,Senait Tesfaye,Dawa Thoulutsang,Yama Thoulutsang,Kerri Topham,Ira Topping,Tsamla Tsamla,Helen Vassiliev,Vijay Venkataraman,Andy Vo,Tsering Wangchuk,Tsering Wangdi,Michael Weiand,Jane E. Wilkinson,Adam Wilson,Shailendra Yadav,Shuli Yang,Xiaoping Yang,Geneva Young,Qing Yu,Joanne Zainoun,Lisa Zembek,Andrew Zimmer,Eric S. Lander,Eric S. Lander +241 more
TL;DR: A high-quality draft genome sequence of the domestic dog is reported, together with a dense map of single nucleotide polymorphisms (SNPs) across breeds, to shed light on the structure and evolution of genomes and genes.
References
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The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.
TL;DR: ClUSTAL X is a new windows interface for the widely-used progressive multiple sequence alignment program CLUSTAL W, providing an integrated system for performing multiple sequence and profile alignments and analysing the results.
Journal ArticleDOI
Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea
Hirohisa Kishino,Masami Hasegawa +1 more
TL;DR: A new method for estimating the variance of the difference between log likelihood of different tree topologies is developed by expressing it explicitly in order to evaluate the maximum likelihood branching order among Hominoidea.
Journal ArticleDOI
Quartet Puzzling: A Quartet Maximum-Likelihood Method for Reconstructing Tree Topologies
TL;DR: A versatile method, quartet puzzling, is introduced to reconstruct the topology (branching pattern) of a phylogenetic tree based on DNA or amino acid sequence data and outperforms neighbor joining in some cases with high transition/transversion bias.