Genome 10K: a proposition to Obtain Whole Genome Sequence For 10,000 Vertebrate Species




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Appendix 3: Technological issues


(To be provided)

Authors:


Coordinators: David Haussler, Stephen J. O’Brien, Oliver Ryder

Mammals Group Members: Scott Baker, James Estes, Jennifer Graves, Alexander Graphodatsky, Kris Helgen, *Warren Johnson, Harris Lewin, Gordon Luikart, *William Murphy, Steve O’Brien, Oliver Ryder, Mark Springer, Emma Teeling, Terrie Williams, Nathan Wolfe, YaPing Zhang

Birds Group Members: *Keith Barker, Joel Cracraft, Scott Edwards, Olivier Hanotte, *Fred Sheldon

Amphibians and Reptiles Group Members: *Andrew Crawford, Matthew LeBreton, Paolo Martelli, *Jim McGuire, *Robert Murphy, Brad Shaffer, *Barry Sinervo

Fishes Group Members: Fred Allendorf, Giacomo Bernardi, Guillamo Orti, David Rawson, *Byrappa Venkatesh, Robert Vrijenhoek, Robert Ward, *Ed Wiley

General Policy Group Members: Scott Baker, *Adam Felsenfeld, Eric Green, *Robert Hanner, *Olivier Hanotte, David Haussler, Paul Hebert, Steve O'Brien, Oliver Ryder, Hector Seuanez, YaPing Zhang

Analysis Group Members: *Michele Clamp, Mark Diekhans, David Haussler, Bailey Kessing, David Kingsley, *Webb Miller, Ngan Nguyen, Brian Pike, Stephan Schuster, Josh Stuart, Steve Turner

*Chairs


References:


44. Hackett, S.J., R.T. Kimball, S. Reddy, R.C.K. Bowie, E.L. Braun, M.J. Braun, J.L. Chojnowski, W.A. Cox, K.-L. Han, J. Harshman, C.J. Huddleston, B.D. Marks, K.J. Miglia, W.S. Moore, F.H. Sheldon, D.W. Steadman, C.C. Witt, and T. Yuri. A phylogenetic study of birds reveals their evolutionary history. Science 320: 1763- 1768.

Please chairs proof these numbers; they are the meat of the White paper

Add column for coalescence date time for each group also chairs??

Table 1: Vertebrate taxa [41]


Group

Orders

Families

Genera

Species

Mammals

29/29

100%

139/153

91%

552/1231

45%

1107/5417

20%

Birds

27/27

100%

179/205

87%

1537/2172

71%

4819/9723

50%

Amphibians

3/3

100%

45/61

74%

144/510

28%

394/6260

6%

Reptiles

3/4

75%

46/69

67%

360/1066

34%

816/8442

10%

Fishes

60/62

97%

382/515

74%

1270/4494

28%

2667/27977

10%

Extant of the current Genome 10K collection is tabulated as (number of species in collection) / (total number of species) and percentage with similar summaries for genera, families and orders. The total numbers are computed using the NCBI taxonomy (www. ncbi.nlm.nih.gov), but substituted the Wilson and Reeder [42] tree for the mammals and the Howard and Moore [43] tree for birds.



Table 2: List of collections and participating institutions (Fill this in)


Institutions

Steward(s)

Web address

Academy of Natural Sciences, Philadelphia

NEED TABLE OF SAMPLES




American Museum of Natural History

Joel Cracraft

http://research.amnh.org/ornithology/personnel/jlc.htm

Australian National University

NEED TABLE OF SAMPLES




Australian National Wildlife Collection, Canberra

Leo Joseph

http://www.csiro.au/places/ANWC.html

Bell Museum of Natural History, University of Minnesota

Keith Barker

http://www.bellmuseum.org/

Biodiversity Research Institute, University of Kansas

Edward Wiley

http://www.nhm.ku.edu/fishes/

Burke Museum, University of Washington

NEED TABLE OF SAMPLES




Círculo Herpetológico de Panamá

NEED TABLE OF SAMPLES




CSIRO Marine and Atmospheric Research

Robert Ward

http://www.cmar.csiro.au/anfc/

CTR for Reproduction of Endangered Species-San Diego Zoo

Oliver Ryder

http://www.sandiegozoo.org/conservation/about/administrators/oliver_ryder_ph.d/

The Frozen Ark

Olivier Hanotte

http://www.frozenark.org

Hong Kong Zoological Gardens

Paolo Martelli

http://www.lcsd.gov.hk/parks/hkzbg/en/index.php

Institute of Cytology and Genetics, Russian Academy, Siberian Branch

Alexander Graphodatsky

http://www.bionet.nsc.ru/indexEngl.html

Institute of Molecular and Cell Biology, Singapore

NEED TABLE OF SAMPLES




Kunming Institute of Zoology, Chinese Academy of Sciences

NEED TABLE OF SAMPLES




LIRANS Institute, University of Bedfordshire, UK,

David Rawson

http://www.beds.ac.uk/research/lirans/personnel/rawson_d

Louisiana State University Museum of Zoology

NEED TABLE OF SAMPLES




LSU Museum of Natural Science

Fred Sheldon

http://appl003.lsu.edu/natsci/lmns.nsf/$Content/Sheldon?OpenDocument

Marine Mammal Institute, Oregon State University

Scott Baker

http://mmi.oregonstate.edu/

Monterey Bay Aquarium Research Institute

NEED TABLE OF SAMPLES




Museum of Comparative Zoology, Harvard*

NEED TABLE OF SAMPLES




Museum of Vertebrate Zoology (MVZ)

NEED TABLE OF SAMPLES




Museum of Vertebrate Zoology, UC Berkeley

NEED TABLE OF SAMPLES




Museum Victoria, Australia

NEED TABLE OF SAMPLES




National Cancer Institute Lab of Genomic Diversity

Stephen O’Brien

http://home.ncifcrf.gov/ccr/lgd/

Natural History Museum of Los Angeles County

NEED TABLE OF SAMPLES




Royal Ontario Museum (ROM)

Robert Murphy

http://labs.eeb.utoronto.ca/murphy/

Smithsonian Institution, National Museum of Natural History

NEED TABLE OF SAMPLES




Smithsonian Tropical Research Institute

Andrew Crawford

http://www.stri.org/

Swedish Museum of Natural History

NEED TABLE OF SAMPLES




Texas A&M University

William Murphy

http://gene.tamu.edu/faculty_pages/faculty_MurphyW.php

The Field Museum, Chicago

NEED TABLE OF SAMPLES




UCLA, Institute of the Environment

Matthew LeBreton

http://www.ioe.ucla.edu/ctr/staff/LeBreton_Matthew.html

University College-Dublin

NEED TABLE OF SAMPLES




University of California, Riverside

NEED TABLE OF SAMPLES




University of California, Santa Cruz

NEED TABLE OF SAMPLES




University of Montana

NEED TABLE OF SAMPLES




University of Nebraska, Lincoln

Guillermo Orti

http://golab.unl.edu/index.html

University of Nevada, Las Vegas

NEED TABLE OF SAMPLES




University of Sheffield

Terence Burke

http://www.shef.ac.uk/molecol/terry-burke

Zoological Museum of Copenhagen, Denmark

NEED TABLE OF SAMPLES






Figure legends (need these) (Fill in references)


Legend(s) here

Figure 1: A phylogenetic view of the vertebrate subclass




Figure 2: The mammalian radiations




Figure 3: The birds of the world




Figure 4: The reptiles of today




Figure 5: The amphibians’ phylogeny


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