Polytene Chromosomal Maps of 11 Drosophila Species: The Order of Genomic Scaffolds Inferred From Genetic and Physical Maps
Stephen W. Schaeffer,Arjun Bhutkar,Arjun Bhutkar,Bryant F. McAllister,Muneo Matsuda,Luciano M. Matzkin,Patrick M. O’Grady,Claudia Rohde,Vera L. S. Valente,Montserrat Aguadé,Wyatt W. Anderson,Kevin A. Edwards,Ana Cristina Lauer Garcia,Josh Goodman,James Hartigan,Eiko Kataoka,Richard T. Lapoint,Elena R. Lozovsky,Carlos A. Machado,Mohamed A. F. Noor,Montserrat Papaceit,Laura K. Reed,Stephen Richards,Tania Tassinari Rieger,Susan M. Russo,Hajime Sato,Carmen Segarra,Douglas Smith,Temple F. Smith,Victor B. Strelets,Yoshiko N. Tobari,Yoshihiko Tomimura,Marvin Wasserman,Thomas D. Watts,Robert L. Wilson,Kiyohito Yoshida,Therese A. Markow,William M. Gelbart,William M. Gelbart,Thomas C. Kaufman +39 more
TLDR
The sequencing of the 12 genomes of members of the genus Drosophila was taken as an opportunity to reevaluate the genetic and physical maps for 11 of the species, in part to aid in the mapping of assembled scaffolds.Abstract:
The sequencing of the 12 genomes of members of the genus Drosophila was taken as an opportunity to reevaluate the genetic and physical maps for 11 of the species, in part to aid in the mapping of assembled scaffolds Here, we present an overview of the importance of cytogenetic maps to Drosophila biology and to the concepts of chromosomal evolution Physical and genetic markers were used to anchor the genome assembly scaffolds to the polytene chromosomal maps for each species In addition, a computational approach was used to anchor smaller scaffolds on the basis of the analysis of syntenic blocks We present the chromosomal map data from each of the 11 sequenced non-Drosophila melanogaster species as a series of sections Each section reviews the history of the polytene chromosome maps for each species, presents the new polytene chromosome maps, and anchors the genomic scaffolds to the cytological maps using genetic and physical markers The mapping data agree with Muller's idea that the majority of Drosophila genes are syntenic Despite the conservation of genes within homologous chromosome arms across species, the karyotypes of these species have changed through the fusion of chromosomal arms followed by subsequent rearrangement eventsread more
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Ancient protostome origin of chemosensory ionotropic glutamate receptors and the evolution of insect taste and olfaction
Vincent Croset,Raphael Rytz,Scott F. Cummins,Aidan Budd,David Brawand,Henrik Kaessmann,Toby J. Gibson,Richard Benton +7 more
TL;DR: It is shown that IRs are expressed in olfactory organs across Protostomia—a major branch of the animal kingdom that encompasses arthropods, nematodes, and molluscs—indicating that they represent an ancestral protostome chemosensory receptor family.
Journal ArticleDOI
Highly evolvable malaria vectors: The genomes of 16 Anopheles mosquitoes
Daniel E. Neafsey,Robert M. Waterhouse,Mohammad Reza Abai,Sergey Aganezov,Max A. Alekseyev,James E. Allen,James Amon,Bruno Arcà,Peter Arensburger,Gleb N. Artemov,Lauren A. Assour,Hamidreza Basseri,Aaron M. Berlin,Bruce W. Birren,Stéphanie Blandin,Stéphanie Blandin,Andrew I. Brockman,Thomas R. Burkot,Austin Burt,Clara S. Chan,Cedric Chauve,Joanna C. Chiu,Mikkel B. Christensen,Carlo Costantini,Victoria L.M. Davidson,Elena Deligianni,Tania Dottorini,Vicky Dritsou,Stacey Gabriel,Wamdaogo M. Guelbeogo,Andrew Brantley Hall,Mira V. Han,Thaung Hlaing,Daniel S.T. Hughes,Daniel S.T. Hughes,Adam M. Jenkins,Xiaofang Jiang,Irwin Jungreis,Evdoxia G. Kakani,Evdoxia G. Kakani,Maryam Kamali,Petri Kemppainen,Ryan C. Kennedy,Ioannis K. Kirmitzoglou,Ioannis K. Kirmitzoglou,Lizette L. Koekemoer,Njoroge Laban,Nicholas Langridge,Mara K. N. Lawniczak,Manolis Lirakis,Neil F. Lobo,Ernesto Lowy,Robert M. MacCallum,Chunhong Mao,Gareth Maslen,Charles Mbogo,Jenny McCarthy,Kristin Michel,Sara N. Mitchell,Wendy Moore,Katherine A. Murphy,Anastasia N. Naumenko,Tony Nolan,Eva Maria Novoa,Samantha M. O’Loughlin,Chioma Oringanje,Mohammad Ali Oshaghi,Nazzy Pakpour,Philippos Aris Papathanos,Philippos Aris Papathanos,Ashley Peery,Michael Povelones,Anil Prakash,David P. Price,Ashok Rajaraman,Lisa J. Reimer,David C. Rinker,Antonis Rokas,Tanya L. Russell,N’Fale Sagnon,Maria V. Sharakhova,Terrance Shea,Felipe A. Simão,Felipe A. Simão,Frédéric Simard,Michel A. Slotman,Pradya Somboon,V. N. Stegniy,Claudio J. Struchiner,Claudio J. Struchiner,Gregg W.C. Thomas,Marta Tojo,Pantelis Topalis,Jose M. C. Tubio,Maria F. Unger,John Vontas,Catherine Walton,Craig S. Wilding,Judith H. Willis,Yi-Chieh Wu,Yi-Chieh Wu,Guiyun Yan,Evgeny M. Zdobnov,Evgeny M. Zdobnov,Xiaofan Zhou,Flaminia Catteruccia,Flaminia Catteruccia,George K. Christophides,Frank H. Collins,Robert S. Cornman,Andrea Crisanti,Andrea Crisanti,Martin J. Donnelly,Martin J. Donnelly,Scott J. Emrich,Michael C. Fontaine,Michael C. Fontaine,William M. Gelbart,Matthew W. Hahn,Immo A. Hansen,Paul I. Howell,Fotis C. Kafatos,Manolis Kellis,Daniel Lawson,Christos Louis,Shirley Luckhart,Marc A. T. Muskavitch,Marc A. T. Muskavitch,José M. C. Ribeiro,Michael A. Riehle,Igor V. Sharakhov,Zhijian Tu,Laurence J. Zwiebel,Nora J. Besansky +133 more
TL;DR: The authors investigated the genomic basis of vectorial capacity and explore new avenues for vector control, sequenced the genomes of 16 anopheline mosquito species from diverse locations spanning ~100 million years of evolution Comparative analyses show faster rates of gene gain and loss, elevated gene shuffling on the X chromosome, and more intron losses, relative to Drosophila.
Highly evolvable malaria vectors: The genomes of 16 Anopheles mosquitoes
Robert M. Waterhouse,Clara S. Chan,Irwin Jungreis,Eva Maria Novoa Pardo,Yi-Chieh Wu,Manolis Kellis +5 more
Journal ArticleDOI
The genomics of speciation in Drosophila: diversity, divergence, and introgression estimated using low-coverage genome sequencing.
TL;DR: It is concluded that chromosomal rearrangements have been vital to the ongoing persistence of these species despite recent hybridization and serves as a proof-of-principle on how whole genome sequencing can be applied to formulate and test hypotheses about species formation in lesser-known non-model systems.
Journal ArticleDOI
Chromosomal Rearrangement Inferred From Comparisons of 12 Drosophila Genomes
TL;DR: The results provide estimated chromosomal evolution rates across this set of species on the basis of whole-genome synteny analysis, which are found to be higher than those previously reported.
References
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Stephen F. Altschul,Thomas L. Madden,Alejandro A. Schäffer,Jinghui Zhang,Zheng Zhang,Webb Miller,David J. Lipman +6 more
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TL;DR: This is the first attempt since 1925 to publish a comprehensive account of the biology and genetics of Drosophila and it aims to collate the dauntingly large literature on the subject and to make more accessible the private language ot the Dosophilist.
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Evolution of genes and genomes on the Drosophila phylogeny.
Andrew G. Clark,Michael B. Eisen,Michael B. Eisen,Douglas Smith,Casey M. Bergman,Brian Oliver,Therese A. Markow,Thomas C. Kaufman,Manolis Kellis,Manolis Kellis,William M. Gelbart,Venky N. Iyer,Daniel A. Pollard,Timothy B. Sackton,Amanda M. Larracuente,Nadia D. Singh,José P. Abad,Dawn N. Abt,Boris Adryan,Montserrat Aguadé,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,Arjun Bhutkar,Enrico Blanco,Stephanie Bosak,Robert K. Bradley,Adrianne Brand,Michael R. Brent,Angela N. Brooks,Randall H. Brown,Roger K. Butlin,Corrado Caggese,Brian R. Calvi,A. Bernardo Carvalho,Anat Caspi,Sergio Castrezana,Susan E. Celniker,Jean L. Chang,Charles Chapple,Sourav Chatterji,Sourav Chatterji,Asif T. Chinwalla,Alberto Civetta,Sandra W. Clifton,Josep M. Comeron,James C. Costello,Jerry A. Coyne,Jennifer Daub,Robert David,Arthur L. Delcher,Kim D. 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Langley,Richard T. Lapoint,Brian P. Lazzaro,So Jeong Lee,Lisa Levesque,Ruiqiang Li,Ruiqiang Li,Chiao-Feng Lin,Michael F. Lin,Michael F. Lin,Kerstin Lindblad-Toh,Ana Llopart,Manyuan Long,Lloyd Low,Elena R. Lozovsky,Jian Lu,Meizhong Luo,Carlos A. Machado,Wojciech Makalowski,Mar Marzo,Muneo Matsuda,Luciano M. Matzkin,Bryant F. McAllister,Carolyn S. McBride,Brendan McKernan,Kevin McKernan,Maria Mendez-Lago,Patrick Minx,Michael U. Mollenhauer,Kristi L. Montooth,Stephen M. Mount,Xu Mu,Eugene W. Myers,Bárbara Negre,Stuart J. Newfeld,Rasmus Nielsen,Mohamed A. F. Noor,Patrick M. O’Grady,Lior Pachter,Montserrat Papaceit,Matthew J. Parisi,Michael Parisi,Leopold Parts,Jakob Skou Pedersen,Jakob Skou Pedersen,Graziano Pesole,Adam M. Phillippy,Chris P. Ponting,Mihai Pop,Damiano Porcelli,Jeffrey R. Powell,Sonja J. Prohaska,Kim D. Pruitt,Marta Sabariego Puig,Hadi Quesneville,Kristipati Ravi Ram,David M. Rand,Matthew D. Rasmussen,Laura K. Reed,Robert A. Reenan,Amy Denise Reily,Karin A. Remington,Tania Tassinari Rieger,Michael G. Ritchie,Charles Robin,Yu-Hui Rogers,Claudia Rohde,Julio Rozas,Marc Rubenfield,Alfredo Ruiz,Susan M. Russo,Steven L. Salzberg,Alejandro Sánchez-Gracia,Alejandro Sánchez-Gracia,David J. Saranga,Hajime Sato,Stephen W. Schaeffer,Michael C. Schatz,Todd A. Schlenke,Russell Schwartz,Carmen Segarra,Rama S. Singh,Laura K. Sirot,Marina Sirota,Nicholas Sisneros,Christopher D. Smith,Christopher D. Smith,Temple F. Smith,John Spieth,Deborah E. Stage,Alexander Stark,Alexander Stark,Wolfgang Stephan,Robert L. Strausberg,Sebastian Strempel,David Sturgill,Granger G. Sutton,Granger G. Sutton,Wei Tao,Sarah A. 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 P. Walenz,Jun Wang,Jun Wang,Marvin Wasserman,Thomas D. Watts,Derek Wilson,Richard K. Wilson,Rod A. Wing,Mariana F. Wolfner,Alex Wong,Gane Ka-Shu Wong,Gane Ka-Shu Wong,Chung-I Wu,Gabriel C. Wu,Daisuke Yamamoto,Hsiao Pei Yang,Shiaw Pyng Yang,James A. Yorke,Kiyohito Yoshida,Evgeny M. 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 M. 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 M. Daza,Georgius De Haan,Stuart DeGray,Christina Demaso,Norbu Dhargay,Kimberly Dooley,Erin E. 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 C. 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 L. 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 J. 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 P. 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,William Brockman,Jonathan Butler,Cheewhye Chin,Manfred Grabherr,Michael Kleber,Evan Mauceli,Iain MacCallum +429 more
TL;DR: 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.
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Drosophila: A Laboratory Handbook
TL;DR: This manual covers three approaches to the field: analysis of neural development, recording and imaging activities in the nervous system, and analysis of behavior.
Book
Progress and Prospects in Evolutionary Biology: The Drosophila Model
TL;DR: 1. Introduction and Overview 2. Population Genetics - Genes 3. population Genetics - Inversions 4. Evolution 5. Laboratory Studies 6. Speciation
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Evolution of genes and genomes on the Drosophila phylogeny.
Andrew G. Clark,Michael B. Eisen,Michael B. Eisen,Douglas Smith,Casey M. Bergman,Brian Oliver,Therese A. Markow,Thomas C. Kaufman,Manolis Kellis,Manolis Kellis,William M. Gelbart,Venky N. Iyer,Daniel A. Pollard,Timothy B. Sackton,Amanda M. Larracuente,Nadia D. Singh,José P. Abad,Dawn N. Abt,Boris Adryan,Montserrat Aguadé,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,Arjun Bhutkar,Enrico Blanco,Stephanie Bosak,Robert K. Bradley,Adrianne Brand,Michael R. Brent,Angela N. Brooks,Randall H. Brown,Roger K. Butlin,Corrado Caggese,Brian R. Calvi,A. Bernardo Carvalho,Anat Caspi,Sergio Castrezana,Susan E. Celniker,Jean L. Chang,Charles Chapple,Sourav Chatterji,Sourav Chatterji,Asif T. Chinwalla,Alberto Civetta,Sandra W. Clifton,Josep M. Comeron,James C. Costello,Jerry A. Coyne,Jennifer Daub,Robert David,Arthur L. Delcher,Kim D. Delehaunty,Chuong B. Do,Heather Ebling,Kevin A. Edwards,Thomas H. Eickbush,Jay D. Evans,Alan Filipski,Sven Findeiß,Sven Findeiß,Eva Freyhult,Lucinda Fulton,Robert S. Fulton,Ana Cristina Lauer Garcia,Anastasia Gardiner,David A. Garfield,Barry E. Garvin,Greg Gibson,Don Gilbert,Sante Gnerre,Jennifer Godfrey,Robert T. Good,Valer Gotea,Brenton Gravely,Anthony J. Greenberg,Sam Griffiths-Jones,Sam Griffiths-Jones,Samuel R. Gross,Roderic Guigó,Erik Gustafson,Wilfried Haerty,Matthew W. Hahn,Daniel L. Halligan,Aaron L. Halpern,Gillian M. Halter,Mira V. Han,Andreas Heger,LaDeana W. 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,Gary H. Karpen,Eiko Kataoka,Peter D. Keightley,Pouya Kheradpour,Ewen F. Kirkness,Leonardo Koerich,Karsten Kristiansen,Dave Kudrna,Rob J. Kulathinal,Sudhir Kumar,Roberta Kwok,Eric S. Lander,Charles H. Langley,Richard T. Lapoint,Brian P. Lazzaro,So Jeong Lee,Lisa Levesque,Ruiqiang Li,Ruiqiang Li,Chiao-Feng Lin,Michael F. Lin,Michael F. Lin,Kerstin Lindblad-Toh,Ana Llopart,Manyuan Long,Lloyd Low,Elena R. Lozovsky,Jian Lu,Meizhong Luo,Carlos A. Machado,Wojciech Makalowski,Mar Marzo,Muneo Matsuda,Luciano M. Matzkin,Bryant F. McAllister,Carolyn S. McBride,Brendan McKernan,Kevin McKernan,Maria Mendez-Lago,Patrick Minx,Michael U. Mollenhauer,Kristi L. Montooth,Stephen M. Mount,Xu Mu,Eugene W. Myers,Bárbara Negre,Stuart J. Newfeld,Rasmus Nielsen,Mohamed A. F. Noor,Patrick M. O’Grady,Lior Pachter,Montserrat Papaceit,Matthew J. Parisi,Michael Parisi,Leopold Parts,Jakob Skou Pedersen,Jakob Skou Pedersen,Graziano Pesole,Adam M. Phillippy,Chris P. Ponting,Mihai Pop,Damiano Porcelli,Jeffrey R. Powell,Sonja J. Prohaska,Kim D. Pruitt,Marta Sabariego Puig,Hadi Quesneville,Kristipati Ravi Ram,David M. Rand,Matthew D. Rasmussen,Laura K. Reed,Robert A. Reenan,Amy Denise Reily,Karin A. Remington,Tania Tassinari Rieger,Michael G. Ritchie,Charles Robin,Yu-Hui Rogers,Claudia Rohde,Julio Rozas,Marc Rubenfield,Alfredo Ruiz,Susan M. Russo,Steven L. Salzberg,Alejandro Sánchez-Gracia,Alejandro Sánchez-Gracia,David J. Saranga,Hajime Sato,Stephen W. Schaeffer,Michael C. Schatz,Todd A. Schlenke,Russell Schwartz,Carmen Segarra,Rama S. Singh,Laura K. Sirot,Marina Sirota,Nicholas Sisneros,Christopher D. Smith,Christopher D. Smith,Temple F. Smith,John Spieth,Deborah E. Stage,Alexander Stark,Alexander Stark,Wolfgang Stephan,Robert L. Strausberg,Sebastian Strempel,David Sturgill,Granger G. Sutton,Granger G. Sutton,Wei Tao,Sarah A. 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 P. Walenz,Jun Wang,Jun Wang,Marvin Wasserman,Thomas D. Watts,Derek Wilson,Richard K. Wilson,Rod A. Wing,Mariana F. Wolfner,Alex Wong,Gane Ka-Shu Wong,Gane Ka-Shu Wong,Chung-I Wu,Gabriel C. Wu,Daisuke Yamamoto,Hsiao Pei Yang,Shiaw Pyng Yang,James A. Yorke,Kiyohito Yoshida,Evgeny M. 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 M. 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 M. Daza,Georgius De Haan,Stuart DeGray,Christina Demaso,Norbu Dhargay,Kimberly Dooley,Erin E. Dooley,Missole Doricent,Passang Dorje,Kunsang Dorjee,Alan Dupes,Richard Elong,Jill Falk,Abderrahim Farina,Susan Faro,Diallo Ferguson,Sheila Fisher,Chelsea D. 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