Evolution of the Human Genome I: The Genome and Genes PDF
Preview Evolution of the Human Genome I: The Genome and Genes
Evolutionary Studies Naruya Saitou Editor Evolution of the Human Genome I The Genome and Genes Evolutionary Studies Serieseditor NaruyaSaitou,NationalInstituteofGenetics,Mishima,Japan Moreinformationaboutthisseriesathttp://www.springer.com/series/15220 Naruya Saitou Editor Evolution of the Human Genome I The Genome and Genes Editor NaruyaSaitou DivisionofPopulationGenetics NationalInstituteofGenetics Mishima,Japan ISSN2509-484X ISSN2509-4858 (electronic) EvolutionaryStudies ISBN978-4-431-56601-4 ISBN978-4-431-56603-8 (eBook) https://doi.org/10.1007/978-4-431-56603-8 LibraryofCongressControlNumber:2017961845 ©SpringerJapanKK2017 Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpart of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation,broadcasting,reproductiononmicrofilmsorinanyotherphysicalway,andtransmissionor informationstorageandretrieval,electronicadaptation,computersoftware,orbysimilarordissimilar methodologynowknownorhereafterdeveloped. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publicationdoesnotimply,evenintheabsenceofaspecificstatement,thatsuchnamesareexempt fromtherelevantprotectivelawsandregulationsandthereforefreeforgeneraluse. Thepublisher,theauthorsandtheeditorsaresafetoassumethattheadviceandinformationinthisbook arebelievedtobetrueandaccurateatthedateofpublication.Neitherthepublishernortheauthorsorthe editorsgiveawarranty,expressorimplied,withrespecttothematerialcontainedhereinorforanyerrors oromissionsthatmayhavebeenmade.Thepublisherremainsneutralwithregardtojurisdictionalclaims inpublishedmapsandinstitutionalaffiliations. Printedonacid-freepaper ThisSpringerimprintispublishedbySpringerNature TheregisteredcompanyisSpringerJapanKK The registered company address is: Shiroyama Trust Tower, 4-3-1 Toranomon, Minato-ku, Tokyo 105-6005,Japan Preface ThisbookisthefirstvolumeoftheEvolutionoftheHumanGenomeandisalsothe firstbookoftheEvolutionaryStudiesSpringerSeries.Iamtheserieseditorandthe editor of this present book. In the fall of 2011, I was asked by Dr. Daisuke Hoshiyama, who was an editor at Springer Japan at that time, to publish a book by Springer written in English. I thus planned one book titled Evolution of the HumanGenomeandaskedmorethan30peopletocontributetothebook.Because ofitslargesize,itwassuggestedtomethatIsplitthebookintotwovolumes:one dedicatedtothediversityofgenesinthehumangenome,andtheotherdedicatedto thediversityofmodernhumans.AfterDr.HoshiyamaleftSpringerJapanin2012, Mr.KaoruHashimotohandledthisbookuntil2014andthenDr.YasutakaOkazaki subsequently took charge of the book. While some authors needed time to finish theirchapters,IwasaskedtostartanewSpringerseries.IproposedEvolutionary StudiesanditwasacceptedbySpringerin2015(seriesURL¼http://www.springer. com/series/15220). Thus, this book became the first book under the new series. I thankMs.AikoHiraguchiatSpringerforoverseeingtheseriesandDr.Okazakifor directlytakingthisbookthroughthepublicationprocess. The book consists of two parts. Part I is “Overview of the Human Genome”, which includes seven chapters. Chapter 1, which I have written, is a brief look at human evolution and the human genome, and is also an introduction to the book. Chapter2byDanGraurisabout“rubbish”DNAwhichconsistsofthemajorpartof the human genome. Chapter 3 by Satoshi Oota is on GC content heterogeneity of thehumangenome.ContentsofChaps.2and3alsoapplytonon-humanvertebrate genomes.ProteinandRNAcodinggenesofthehumangenomearesummarizedin Chap.4byTadashiImanishi.TakashiKitanodescribesduplicatedgenesinChap.5, andrecombinationsarediscussedbyLudovicaMontanucciandJaumeBertranpetit in Chap. 6, with special reference to linkage disequilibria (LD). Part I ends with Chap. 7, in which copy number variations (CNVs) and microsatellite DNA poly- morphismarediscussedbyNaokoTakezaki. Part II of this book, “The Human Genome Viewed Through Genes” contains eight chapters with a wide variety of topics covering various gene systems. Yoko v vi Preface Satta,YukakoKatsura,andMineyoIwasediscussgenesonXandYchromosomes inChap.8,andTimothyA.JinamdiscussesHLAgenesfromthepointofviewof humanpopulationstudiesinChap.9.ShojiKawamuraandAmandaMelingivean extensivereviewofopsingenesinprimatesingeneralinChap.10.Genesinvolved in morphological phenotypes are discussed in Chap. 11 by Ryosuke Kimura, and transcriptionfactorgenesare extensivelydiscussedbyMahokoTakahashiandSo NakagawainChap.12.IturoInouefocusesonthegeneticsofdiabetesinChap.13, andthenheandHirotoNakaokareviewdisease-relatedgenesinChap.14.Thelast chapterofthisbook,Chap.15,isnotonthegenomeofhumansbutofmicrobesin humans. Genomes of these human superorganisms are amply discussed by ChaochunWeiandBenJia. Although not comprehensive, this book covers a wide variety of genes and genetic systems regarding the human genome. I hope readers will grasp the huge diversityofgenesandDNAsequencesinthehumangenome. Finally,astheeditorofthebook,IwouldliketodedicateittothelateDr.Allan Wilson,apioneerofhumanmolecularevolutionarystudies,whodiedin1991atthe ageof56. Mishima,Japan NaruyaSaitou Contents PartI OverviewoftheHumanGenome 1 HumanEvolutionandHumanGenomeataGlance. . . . . . . . . . . . 3 NaruyaSaitou 2 RubbishDNA:TheFunctionlessFractionofthe HumanGenome. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19 DanGraur 3 GCContentHeterogeneity. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61 SatoshiOota 4 Protein-CodingandNoncodingRNAGenes. . . . . . . . . . . . . . . . . . 93 TadashiImanishi 5 DuplicatedGenes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117 TakashiKitano 6 Recombination. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131 LudovicaMontanucciandJaumeBertranpetit 7 CNVsandMicrosatelliteDNAPolymorphism. . . . . . . . . . . . . . . . 143 NaokoTakezaki PartII TheHumanGenomeViewedThroughGenes 8 GenesonXandYChromosomes. . . . . . . . . . . . . . . . . . . . . . . . . . 159 YokoSatta,YukakoKatsura,andMineyoIwase 9 HumanLeukocyteAntigen(HLA)RegioninHuman PopulationStudies. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 173 TimothyA.Jinam vii viii Contents 10 EvolutionofGenesforColorVisionandtheChemical SensesinPrimates. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181 ShojiKawamuraandAmandaD.Melin 11 GlobalLandscapesofHumanPhenotypicVariation inInheritedTraits. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 217 RyosukeKimura 12 TranscriptionFactorGenes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 241 MahokoUedaTakahashiandSoNakagawa 13 GeneticsofDiabetes:AreTheyThriftyGenotype?. . . . . . . . . . . . . 265 IturoInoueandHirofumiNakaoka 14 Disease-RelatedGenesfromPopulationGeneticAspect andTheirFunctionalSignificance. . . . . . . . . .. . . . . . . . . . . . . . .. 273 IturoInoueandHirofumiNakaoka 15 MicrobeGenomesAssociatedwithHumanBody. . . . . . . . . . . . . . 285 ChaochunWeiandBenJia Index. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 301 Part I Overview of the Human Genome
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