Table Of ContentMETHODS IN ENZYMOLOGY
EDITORS-IN-CHIEF
John N. Abelson Melvin I. Simon
DIVISIONOFBIOLOGY
CALIFORNIAINSTITUTEOFTECHNOLOGY
PASADENA,CALIFORNIA
FOUNDINGEDITORS
Sidney P. Colowick and Nathan O. Kaplan
Contributors to Volume 395
Articlenumbersareinparenthesesandfollowingthenamesofcontributors.
Affiliationslistedarecurrent.
Andrew J. Alverson (20), Section of Timothy W. Chumley (20), Section of
Integrative Biology, The University Integrative Biology, The University
of Texas at Austin, Austin, Texas of Texas at Austin, Austin, Texas
78712-0253 78712-0253
Olaf Bininda-Evans (38), Lehrstuhl fu¨r Andres Collazo (27), Department of
Tierzucht, Technical University of Cell and Molecular Biology, House
Munich, 85354 Freising-Weihenstephan, Ear Institute, Los Angeles, California
Germany 90057
Aure´lieBonin(10),Laboratoired’Ecolo- Luca Comai (30), Department of Bio-
gie Alpine (LECA), Universite´ Joseph logy, University of Washington, Seattle,
Fourier, F-38041 Grenoble Cedex 9, Washington98195
France
James A. Cotton (36), Department
Jeffrey L. Boore (19, 20), Evolutionary of Zoology, The Natural History
Genomics Department, Department of Museum, London SW7 5BD, United
EnergyJointGenomeInstitute&Lawr- Kingdom
ence, Berkeley National Lab, Walnut
Liying Cui (20), Department of Biology,
Creek,California94598
Huck Institutes of Life Science, The
Volker Brendel (22), Department of PennsylvaniaStateUniversity,University
Genetics, Iowa State University, Devel- Park,Pennsylvania16802
opment and Cell Biology, Ames, Iowa
Claude W. dePamphilis (20), Depart-
50011-3260
ment of Biology, Huck Institutes of
OlivierBricaud(27),DepartmentofCell LifeScience,ThePennsylvaniaStateUni-
and Molecular Biology, House Ear versity, University Park, Pennsylvania
Institute,LosAngeles,California90057 16802
Belinda S. W. Chang (34), Department Rob DeSalle (8, 25), Department
of Zoology, University of Toronto, ofInvertebrateZoology,AmericanMu-
Toronto,OntarioM5S3G5,Canada seum of Natural History, New York,
NewYork10024
Z. Jeffrey Chen (29, 30), Molecular
Genetics/MS2474, Department of Soil Kalpana Desai (27), Department of
andCropSciences,TexasA&MUniver- CellandMolecularBiology,HouseEar
sity,CollegeStation,Texas77843-2474 Institute,LosAngeles,California90057
MengChen(30),DepartmentofSoiland R. W. Doerge (30), Department of
Crop Sciences, Texas A&M University, Statistics, Purdue University, West
CollegeStation,Texas77843-2474 Lafayette,Indiana47907
ix
x contributors to volume 395
Qunfeng Dong (22), Department of T. Ryan Gregory (25), Department of
Genetics, Development and Cell Entomology, The Natural History Mu-
Biology, Iowa State University, Ames, seum, London SW7 5BD, United
Iowa50011-3260 Kingdom
Keith Earley (29), Biology Department, Rene´ Groben(18),AlfredWegenerInsti-
Washington University, Saint Louis, tute,D-27570Bremerhaven,Germany
Missouri63130
Martin Grube (4), Institute of Plant
Lori S. Eggert (6), Genetics Program, Sciences,Karl-Franzens-UniversityGraz,
Department of Systematic Biology, Na- 8010Graz,Austria
tional Museum of Natural History,
Smithsonian Institution, Washington, Luigi Guarino (17), Secretariat of the
DC20008-0551 PacificCommunity(SPC),Suva,Fiji
Dmitry A. Filatov (23), School of Rosemarie C. Haberle (20), Section of
Biosciences, University of Birmingham, Integrative Biology, The University
BirminghamB152TT,UnitedKingdom of Texas at Austin, Austin, Texas
78712-0253
Robert C. Fleischer (6), Genetics
Program, Department of Systematic Sallie J. Herman (20), Department of
Biology, National Museum of Nat- Biological Sciences, Central Washing-
ural History, Smithsonian Institution, ton University, Ellensburg, Washington
Washington,DC20008-0551 98923
H. Matthew Fourcade (20), Evolution- MichaelJ.Holland(28),Departmentof
ary Genomics Department, Department Biochemistry and Molecular Medicine,
of Energy Joint Genome Institute & UniversityofCalifornia,SchoolofMedi-
Lawrence, Walnut Creek, California cine,Davis,California95616
94598
Scott A. Jackson (24), Department of
Jeffrey O. French (33), Department of Agronomy, Purdue University, West
BiologicalSciences,CokerLifeSciences, Lafayette,Indiana47907
UniversityofSouthCarolina,Columbia,
Robert K. Jansen (20), Section of Inte-
SouthCarolina29208
grative Biology, The University of
Elizabeth A. Friar (1), Rancho Santa Texas at Austin and Institute of Cel-
Ana Botanic Garden, Claremont, Cali- lular and Molecular Biology, Austin,
fornia91711 Texas78712-0253
TravisC.Glenn(13,33),SavannahRiver Andy Jarvis (17), International Center
Ecology Laboratory, Savannah River for Tropical Agriculture (CIAT); Inter-
Site, Aiken, South Carolina 29803; De- national Plant Genetic Resources Insti-
partment of Biological Sciences, Coker tute(IPGRI),AA6713Cali,Colombia
LifeSciences,UniversityofSouthCaro-
lina,Columbia,SouthCarolina29208 Uwe John (2), Alfred Wegener Institute,
D-27570Bremerhaven,Germany
Kenneth J. Graham (28), Department of
Biochemistry and Molecular Medicine, L.SpencerJohnston(25),Departmentof
UniversityofCalifornia,SchoolofMed- Entomology, Texas A&M University,
icine,Davis,California95616 CollegeStation,Texas77843-2474
contributors to volume395 xi
Loren W. Knapp (33), Department of J. Robert Macey (19), Evolutionary
BiologicalSciences,CokerLifeSciences, Genomics Department, Department
UniversityofSouthCarolina,Columbia, of Energy Joint Genome Institute &
SouthCarolina29208 Lawrence, Berkeley National Lab,
WalnutCreek,California94598
RogerT.Koide(5),DepartmentofHorti-
culture, The Pennsylvania State Univer- Jesu´s E. Maldonado (6), Genetics
sity,UniversityPark,Pennsylvania16802 Program, Department of Systematic
Biology, National Museum of Na-
Elena M. Kramer (32), Department of
tural History, Smithsonian Institution,
Organismic and Evolutionary, Bio-
Washington,DC20008-0551
logy, Harvard University, Cambridge,
Massachusetts02138 Sarh Matthews (37), Arnold Arboretum
of Harvard University, Cambridge,
Lori Kroiss (22), Department of
Massachusetts02138
PlantPathology,BuckhoutLaboratory,
UniversityPark,Pennsylvania16802 Mikhail V. Matz (34), Whitney Labo-
ratory, University of Florida, St.
Jennifer V. Kuehl (20), Evolutionary
Augustine,Florida32080
Genomics Department, Department
of Energy Joint Genome Institute & Chikelu Mba (12), Plant Breeding
Lawrence, Walnut Creek, California Unit,JointFAO/IAEA,Agricultureand
94598 BiotechnologyLaboratory,International
Atomic Energy Agency, Laboratories,
DavidN.Kuhn(15),DepartmentofBio-
A-2444Seibersdorf,Austria
logical Sciences, Florida International
University,Miami,Florida33199 Andrew G. McCubbin (21), School
of Biological Sciences, Washington
Richard J. Lawrence (29), Biology
State University, Pullman, Washington
Department, Washington University,
99164-4236
SaintLouis,Missouri63130
Joel R. McNeal (20), Department
Hyeon-Se Lee (30), Department of of Biology, Huck Institutes of Life
Soil and Crop Sciences, Texas A&M
Science, The Pennsylvania State Uni-
University, College Station, Texas
versity, University Park, Pennsylvania
77843-2474
16802
JinsukJ.Lee(30),DepartmentofSoiland Mo´nicaMedina(19),EvolutionaryGeno-
Crop Sciences, Texas A&M University, micsDepartment,DepartmentofEnergy
CollegeStation,Texas77843-2474 Joint Genome Institute & Lawrence,
Berkeley National Lab, Walnut Creek,
James Leebens-Mack (20), Department
California94598
of Biology, Huck Institutes of Life
Science, The Pennsylvania State Uni- Linda Medlin (2, 16, 18), Alfred Wege-
versity, University Park, Pennsylvania ner Institute, D-27570 Bremerhaven,
16802 Germany
Michelle S. Lewis (29), Biology Depart- Tamra C. Mendelson (11), Department
ment, Washington University, Saint of Biology, University of Maryland,
Louis,Missouri63130 CollegePark,Maryland20742
xii contributors to volume 395
KatjaMetfies(16),AlfredWegenerInsti- SheetalRao(30),DepartmentofSoiland
tute,D-27570Bremerhaven,Germany Crop Sciences, Texas A&M University,
CollegeStation,Texas77843-2474
Bernard M. E. Moret (35), Department
of Computer Sciences, University of Linda A. Raubeson (20), Department of
NewMexico,Albuquerque,NewMexico Biological Sciences, Central Washington
87131 University,Ellensburg,Washington98923
Connie J. Mulligan (7), Department of JessicaL.Ray(26),DepartmentofPhar-
Anthropology, University of Florida, macy,FacultyofMedicine,Universityof
Gainesville,Florida32611 Tromso,N9037Tromso,Norway
Kaare M. Nielsen (3, 26), Department LetitiaReichart(14),SchoolofBiologi-
of Pharmacy, Faculty of Medicine, cal Sciences, Washington, State Univer-
University of Tromso; Norwegian Insti- sity,Pullman,Washington99164-4236
tute of Gene Ecology, N9037 Tromso,
EricH.Roalson(21),SchoolofBiologi-
Norway
cal Sciences, Washington State Univer-
LiseNordga˚rd(3),NorwegianInstituteof sity,Pullman,Washington99164-4236
GeneEcology,9294Tromso,Norway
Roger H. Sawyer (33), Department of
Frederick D. Oakley (22), Department BiologicalSciences,CokerLifeSciences,
of Genetics, Development and Cell UniversityofSouthCarolina,Columbia,
Biology, Iowa State University, Ames, SouthCarolina29208
Iowa50011-3260
Nancy A. Schable (13), Savannah River
Rhiannon Peery (20), Department of Ecology Laboratory, Savannah River
Biological Sciences, Central Washing- Site,Aiken,SouthCarolina29803
ton University, Ellensburg, Washington
RaymondJ.Schnell(15),USDepartment
98923
ofAgriculture,AgricultureResearchSer-
CraigS.Pikaard(29),BiologyDepartment, vice, Subtropical Horticulture Research
Washington University, Saint Louis, Station,Miami,Florida33158
Missouri63130
KerryL.Shaw(11),DepartmentofBiol-
J.ChrisPires(24),DepartmentofAgron- ogy, University of Maryland, College
omy, University of Wisconsin Madison, Park,Maryland20742
Madison,Wisconsin53706
JackSullivan(39),DepartmentofBiolo-
David D. Pollock (40), Department of gical Sciences; The Initiative for Bio-
Biological Sciences, Biological Compu- informatics and Evolutionary Studies,
tation and Visualization Center, Louisi- University of Idaho, Moscow, Idaho
ana State University, Baton Rouge, 83844-3051
Louisiana70803
PierreTaberlet(10),Laboratoired’Eco-
Franc¸ois Pompanon (10), Laboratoire logieAlpine(LECA),Universite´Joseph
d’Ecologie Alpine (LECA), Universite´ Fourier, F-38041 Grenoble Cedex 9,
Joseph Fourier, F-38041 Grenoble, France
Cedex9,France
JohnW.Taylor(31),PlantandMicrobial
Sasha Preuss (29), Biology Department, BiologyDepartment,UniversityofCali-
Washington University, Saint Louis, fornia, Berkeley, Berkeley, California
Missouri63130 94720
contributors to volume395 xiii
Lu Tian (30), Department of Soil and Zhengyuan O. Wang (40), Department
Crop Sciences, Texas A&M University, of BiologicalSciences, Biological Com-
CollegeStation,Texas77843-2474 putation and Visualization Center,
Louisiana State University, Baton
Joe Tohme (12, 17), Agrobiodiversity and
Rouge,Louisiana70803
BiotechnologyProject,InternationalCen-
ter for Tropical Agriculture (CIAT), TandyWarnow(35),TheDepartmentof
AA6713Cali,Columbia Computer Sciences, The University of
TexasatAustin,Austin,Texas78712
Jeffrey P. Townsend (31), Plant and
Microbial Biology Department, Univer- Michael S. Webster (14), School of
sity of California, Berkeley, Berkeley, Biological Sciences, Washington State
California94720 University, Pullman, Washington
99164-4236
TerjeTraavik(3),DepartmentofMedical
Biology,FacultyofMedicine,University Edward N. Wei (30), Department of
ofTromso;NorwegianInstituteofGene Soil and Crop Sciences, Texas A&M
Ecology,N9037Tromso,Norway University, College Station, Texas
77843-2474
Juan A. Ugalde (34), Whitney Lab-
oratory, University of Florida, St. Andrea D. Wolfe (9), Department
Augustine,Florida32080 of Evolution, Ecology, and Organismal
Biology, The Ohio State University,
Klaus Valentin (2), Alfred Wegener In-
Columbus,Ohio43210-1293
stitute,D-27570Bremerhaven,Germany
Stacia K. Wyman (20), Department of
Jason G. Walling (24), Department of
Computer Sciences, The University of
Agronomy, Purdue University, West
TexasatAustin,Austin,Texas78712-0253
Lafayette,Indiana47907
Sam Yeaman (17), International Center
Bing-Bing Wang (22), Iowa State Uni-
for Tropical Agriculture (CIAT); Inter-
versity, Department of Genetics, Devel-
nationalPlantGeneticsResourcesInsti-
opment and Cell Biology, Ames, Iowa
tute(IPGRI),AA6713Cali,Colombia
50011-3260
Jianlin Wang (30), Department of Soil
andCropSciences,TexasA&MUniver-
sity,CollegeStation,Texas77843-2474
Preface
Volume395ofMethodsinEnzymology,‘‘MolecularEvolution:Producingthe
BiochemicalData,’’PartB,reflectsthesignificantincreaseinthekindsofdata
available to researchers in the biological sciences as well as new and refined
methodsforanalyzingtheseandtraditionaldatatypessincethepublicationof
Part A, Volume 224 in 1993. These advances range from a refined ability to
extractDNAsamplesfromawidevarietyofenvironmentalsourcestoextrac-
tionofcompletegenomes.Additionally,ourtoolboxforstudyingmacromole-
culesusingfunctionalandphylogeneticanalyseshasexpandedsignificantly,to
includetranscriptandmicroarrayprofiling,applicationofconfocalmicroscopy
tounderstandingmorphology,andmorerefineddetectionandanalysesofgene
familyparalogs.
In this book we have brought together a wide range of methodologies for
studyingmolecularevolution.Thefirstsectionaddressesthreedifferentaspects
ofexploringbiologicaldiversity,namely,howwegathermacromoleculartem-
plates(Chapters1--8),howdifferentkindsofmolecularmarkersaredeveloped
(Chapters 9--19), and how we explore genomes (Chapters 20--26). Sections II
and III each address aspects of analysis of macromolecular data, partitioned
into analyses of function (Chapters 27--35), such as gene expression studies,
and phylogenetic analyses (Chapters 36--41), exploring various methods for
understandingmolecularevolutioninaphylogeneticcontext.
By no means do we expect that the coverage of this volume is exhaustive.
The breadth of application of new markers and analyses is beyond any
one volume. We have not been able to address some techniques here that
have recently come into common usage, particularly the application of
Bayesian inference methodologies to phylogenetic analyses. Recent reviews
oftheapplicationofthistechniqueareavailableintheliterature,particularly,
Huelsenbeck,J.P.,Larget,B.,Miller,R.E.,andRonquist,F., 2002,Potential
applications and pitfalls of Bayesian inference of phylogeny, Systematic
Biology51,673--688.
We wish to thank all of the authors for their valuable contributions to this
volume. We also wish to thank Cindy Minor and Noelle Gracy at Elsevier/
Academic Press for all of their help in preparing this volume and Mel Simon
andTomWhitefortheirhelpfulcommentsontheorganizationofthevolume.
Elizabeth A. Zimmer
Eric H. Roalson
xv
METHODS IN ENZYMOLOGY
VolumeI.PreparationandAssayofEnzymes
EditedbySidneyP.ColowickandNathanO.Kaplan
VolumeII.PreparationandAssayofEnzymes
EditedbySidneyP.ColowickandNathanO.Kaplan
VolumeIII.PreparationandAssayofSubstrates
EditedbySidneyP.ColowickandNathanO.Kaplan
VolumeIV.SpecialTechniquesfortheEnzymologist
EditedbySidneyP.ColowickandNathanO.Kaplan
VolumeV.PreparationandAssayofEnzymes
EditedbySidneyP.ColowickandNathanO.Kaplan
VolumeVI.PreparationandAssayofEnzymes(Continued)
PreparationandAssayofSubstrates
SpecialTechniques
EditedbySidneyP.ColowickandNathanO.Kaplan
VolumeVII.CumulativeSubjectIndex
EditedbySidneyP.ColowickandNathanO.Kaplan
VolumeVIII.ComplexCarbohydrates
EditedbyElizabethF.NeufeldandVictorGinsburg
VolumeIX.CarbohydrateMetabolism
EditedbyWillisA.Wood
VolumeX.OxidationandPhosphorylation
EditedbyRonaldW.EstabrookandMaynardE.Pullman
VolumeXI.EnzymeStructure
EditedbyC.H.W.Hirs
VolumeXII.NucleicAcids(PartsAandB)
EditedbyLawrenceGrossmanandKivieMoldave
VolumeXIII.CitricAcidCycle
EditedbyJ.M.Lowenstein
VolumeXIV.Lipids
EditedbyJ.M.Lowenstein
VolumeXV.SteroidsandTerpenoids
EditedbyRaymondB.Clayton
xvii
xviii methods in enzymology
VolumeXVI.FastReactions
EditedbyKennethKustin
VolumeXVII.MetabolismofAminoAcidsandAmines(PartsAandB)
EditedbyHerbertTaborandCeliaWhiteTabor
VolumeXVIII.VitaminsandCoenzymes(PartsA,B,andC)
EditedbyDonaldB.McCormickandLemuelD.Wright
VolumeXIX.ProteolyticEnzymes
EditedbyGertrudeE.PerlmannandLaszloLorand
VolumeXX.NucleicAcidsandProteinSynthesis(PartC)
EditedbyKivieMoldaveandLawrenceGrossman
VolumeXXI.NucleicAcids(PartD)
EditedbyLawrenceGrossmanandKivieMoldave
VolumeXXII.EnzymePurificationandRelatedTechniques
EditedbyWilliamB.Jakoby
VolumeXXIII.Photosynthesis(PartA)
EditedbyAnthonySanPietro
VolumeXXIV.PhotosynthesisandNitrogenFixation(PartB)
EditedbyAnthonySanPietro
VolumeXXV.EnzymeStructure(PartB)
EditedbyC.H.W.HirsandSergeN.Timasheff
VolumeXXVI.EnzymeStructure(PartC)
EditedbyC.H.W.HirsandSergeN.Timasheff
VolumeXXVII.EnzymeStructure(PartD)
EditedbyC.H.W.HirsandSergeN.Timasheff
VolumeXXVIII.ComplexCarbohydrates(PartB)
EditedbyVictorGinsburg
VolumeXXIX.NucleicAcidsandProteinSynthesis(PartE)
EditedbyLawrenceGrossmanandKivieMoldave
VolumeXXX.NucleicAcidsandProteinSynthesis(PartF)
EditedbyKivieMoldaveandLawrenceGrossman
VolumeXXXI.Biomembranes(PartA)
EditedbySidneyFleischerandLesterPacker
VolumeXXXII.Biomembranes(PartB)
EditedbySidneyFleischerandLesterPacker
VolumeXXXIII.CumulativeSubjectIndexVolumesI-XXX
EditedbyMarthaG.DennisandEdwardA.Dennis
VolumeXXXIV.AffinityTechniques(EnzymePurification:PartB)
EditedbyWilliamB.JakobyandMeirWilchek
methodsin enzymology xix
VolumeXXXV.Lipids(PartB)
EditedbyJohnM.Lowenstein
VolumeXXXVI.HormoneAction(PartA:SteroidHormones)
EditedbyBertW.O’MalleyandJoelG.Hardman
VolumeXXXVII.HormoneAction(PartB:PeptideHormones)
EditedbyBertW.O’MalleyandJoelG.Hardman
VolumeXXXVIII.HormoneAction(PartC:CyclicNucleotides)
EditedbyJoelG.HardmanandBertW.O’Malley
VolumeXXXIX.HormoneAction(PartD:IsolatedCells,Tissues,
andOrganSystems)
EditedbyJoelG.HardmanandBertW.O’Malley
VolumeXL.HormoneAction(PartE:NuclearStructureandFunction)
EditedbyBertW.O’MalleyandJoelG.Hardman
VolumeXLI.CarbohydrateMetabolism(PartB)
EditedbyW.A.Wood
VolumeXLII.CarbohydrateMetabolism(PartC)
EditedbyW.A.Wood
VolumeXLIII.Antibiotics
EditedbyJohnH.Hash
VolumeXLIV.ImmobilizedEnzymes
EditedbyKlausMosbach
VolumeXLV.ProteolyticEnzymes(PartB)
EditedbyLaszloLorand
VolumeXLVI.AffinityLabeling
EditedbyWilliamB.JakobyandMeirWilchek
VolumeXLVII.EnzymeStructure(PartE)
EditedbyC.H.W.HirsandSergeN.Timasheff
VolumeXLVIII.EnzymeStructure(PartF)
EditedbyC.H.W.HirsandSergeN.Timasheff
VolumeXLIX.EnzymeStructure(PartG)
EditedbyC.H.W.HirsandSergeN.Timasheff
VolumeL.ComplexCarbohydrates(PartC)
EditedbyVictorGinsburg
VolumeLI.PurineandPyrimidineNucleotideMetabolism
EditedbyPatriciaA.HoffeeandMaryEllenJones
VolumeLII.Biomembranes(PartC:BiologicalOxidations)
EditedbySidneyFleischerandLesterPacker
VolumeLIII.Biomembranes(PartD:BiologicalOxidations)
EditedbySidneyFleischerandLesterPacker
