Evolutionary Biology – Concepts, Biodiversity, Macroevolution and Genome Evolution PDF
Preview Evolutionary Biology – Concepts, Biodiversity, Macroevolution and Genome Evolution
Evolutionary Biology – Concepts, Biodiversity, Macroevolution and Genome Evolution . Pierre Pontarotti Editor Evolutionary Biology – Concepts, Biodiversity, Macroevolution and Genome Evolution Editor Dr.PierrePontarotti UMR6632 Universite´d’Aix-Marseille/CNRS LaboratoireEvolutionBiologiqueetMode´lisation 3PlaceVictorHugo case19 13331MarseilleCedex03 France [email protected] ISBN978-3-642-20762-4 e-ISBN978-3-642-20763-1 DOI10.1007/978-3-642-20763-1 SpringerHeidelbergDordrechtLondonNewYork LibraryofCongressControlNumber:2011932535 # Springer-VerlagBerlinHeidelberg2011 Thisworkissubjecttocopyright.Allrightsarereserved,whetherthewholeorpartofthematerialis concerned,specificallytherightsoftranslation,reprinting,reuseofillustrations,recitation,broadcasting, reproductiononmicrofilmorinanyotherway,andstorageindatabanks.Duplicationofthispublication orpartsthereofispermittedonlyundertheprovisionsoftheGermanCopyrightLawofSeptember9, 1965,initscurrentversion,andpermissionforusemustalwaysbeobtainedfromSpringer.Violations areliabletoprosecutionundertheGermanCopyrightLaw. Theuseofgeneraldescriptivenames,registerednames,trademarks,etc.inthispublicationdoesnotimply, evenintheabsenceofaspecificstatement,thatsuchnamesareexemptfromtherelevantprotective lawsandregulationsandthereforefreeforgeneraluse. Coverdesign:deblik,Berlin,Germany Printedonacid-freepaper SpringerispartofSpringerScience+BusinessMedia(www.springer.com) Preface Forthe14thtime,theEvolutionaryBiologyMeetingatMarseilles(EBM)tookplace in the two-thousand-year old city. The aim of this congress is to allow scientists involvedintheresearchinevolutionarybiologyandintheapplicationofevolution- ary biology concepts, from mathematics to epistemology, to meet, exchange, and startinterdisciplinarycollaborations. TheorganizersseetheMarseille’smeetingasascientificexchangeplatformand aboosterfortheuseofevolutionarybasedapproachesnotonlyinbiology,butalso inotherscientificareas. The outputs of the meeting are proved by numerous collaborations initiated duringthe meeting andachieved byseveralpeer-reviewedarticlespublishedover thepastyears. Thisyear,morethan100presentations–talks,flashpresentationsandposters– were selected by the committee. Those works really reflected the epistemological positioning of the meeting. We have chosen one fifth of the most representative onestomakethisbook. The book will give the reader an overview of the state of the art in the evolutionary biology field. As during the congress, this area of science will be considered from an epistemological point of view. This work is the fourth that wehavepublishedfurthertotheEBM.Wewanttounderlinethatthefourbooksare complementaryandshouldbeunderstoodastomes. The19selectedarticlesareorganizedaccordingtothefollowingcategories: 1. Conceptsinevolution 2. Evolutionandbiodiversity 3. Macroevolution 4. Genomeevolution Wewouldliketothankthescientistswhocontributedtothisbook,themeeting participants as well as our sponsors: the University of Provence, the CNRS, the GDRBIM,theConseilGe´ne´ral13,theMunicipalityofMarseilleandGenoscreen. We also wish to thank the Springer’s Editions staff for its competences and help. v vi Preface Finally,wewanttogivethankstothemembersoftheAssociationpourl’Etudede l’Evolution Biologique (AEEB) and the members of the Evolutionary Biology ModelingLaboratory. We sincerely want to thank the AEEB coordinator, Axelle Pontarotti, for the remarkable coordination of the meeting. The scientific outputs of the meeting – initiated international collaborations, scientific exchanges – are due, of course, to the quality of the participants, but also to the Marseilles way of hosting of which Axelleisanoutstandingambassador. We wish to thank also our new coordinator, Marie-He´le`ne Rome, for her help withthebook. Marseilles,France Gae¨llePontarotti May2011 Associationpourl’Etudedel’Evolution Biologique(AEEB) PierrePontarotti DirecteurderechercheCNRS PresidentoftheAEEB Contents PartI Concepts 1 Site-SpecificSelf-CatalyzedDNADepurination,theBasis ofaSpontaneousMutagenicMechanismofWideEvolutionary Significance ................................................................ 3 JacquesR.Fresco,OlgaAmosova,PeterWei, JuanR.Alvarez-Dominguez,DamianGlumcher,andRafaelTorres 2 StochasticProcessesDrivingDirectionalEvolution ................... 21 SeanH.Rice,AnthonyPapadopoulos,andJohnHarting 3 EvolutionofSelf-FertileHermaphrodites ............................. 35 RonaldE.EllisandYiqingGuo 4 InsightsintoEukaryoticInteractingProteinEvolution .............. 51 SandipChakraborty,SoumitaPodder,BratatiKahali, TinaBegum,KamalikaSen,andTapashChandraGhosh 5 IntegrationofEvolutionaryBiologyConceptsforFunctional AnnotationandAutomationofComplexResearchinEvolution: TheMulti-AgentSoftwareSystemDAGOBAH ....................... 71 PhilippeGouret,JulienPaganini,JacquesDainat,DorraLouati, ElodieDarbo,PierrePontarotti,andAnthonyLevasseur PartII BiodiversityandEvolution 6 ANewAnimalModelforMergingEcologyandEvolution .......... 91 GabrieleProcaccini,OrnellaAffinito,FrancescoToscano, andPaoloSordino vii viii Contents 7 RapidEvolutionofSimpleMicrobialCommunities intheLaboratory ....................................................... 107 MargieKinnersley,JaredW.Wenger,GavinSherlock,and FrankR.Rosenzweig 8 UseofPaleontologicalandPhylogeneticDatainComparative andPaleobiologicalAnalyses:AFewRecentDevelopments ........ 121 MichelLaurin 9 SeasonalFloweringandEvolution:WillPlantSpecies BeUnderStressfromGlobalWarming? ............................. 139 RodW.King PartIII Macroevolution 10 TheEmergenceofCellularComplexityattheDawn oftheEukaryotes:ReconstructingtheEndomembrane SystemwithInSilicoandFunctionalAnalyses ....................... 153 LilaV.KoumandouandMarkC.Field 11 Neurophylogeny:RetracingEarlyMetazoanBrainEvolution ...... 169 RudiLoesel 12 ANewEarlyCambrianLobopod-BearingAnimal(Murero, Spain)andtheProblemoftheEcdysozoanEarlyDiversification .... 193 Jose´ AntonioGa´mezVintaned,EladioLin˜a´n,andAndreyYu.Zhuravlev PartIV GenomeEvolution 13 GenomicPerspectivesontheLong-TermAbsence ofSexualReproductioninAnimals ................................... 223 EtienneG.J.Danchin,Jean-Franc¸oisFlot, LaetitiaPerfus-Barbeoch,andKarineVanDoninck 14 EvolutionaryConstraintonDNAShapeintheHumanGenome ... 243 ThomasD.Tullius,StephenC.J.Parker,andElliottH.Margulies 15 EvolutionofFungiandTheirRespiratoryMetabolism ............. 257 MarinaMarcet-HoubenandToniGabaldo´n 16 GenomeStructureandGeneExpressionVariation inPlantMitochondria,ParticularlyintheGenusSilene ............ 273 HelenaStorchova Contents ix 17 EvolutionaryDynamicsandGenomicImpact ofProkaryoteTransposableElements ................................ 291 NicolasCerveau,Se´bastienLeclercq,DidierBouchon, andRichardCordaux 18 TransposableElementsinaMarginalPopulation ofAegilopsspeltoides:TemporalFluctuationsProvide NewInsightsintoGenomeEvolutionofWildDiploidWheat ....... 313 AlexanderBelyayevandOlgaRaskina 19 AnalysisoftheConservativeMotifsinPromotersofmiRNA Genes,ExpressedinDifferentTissuesofMammalians .............. 325 OlegV.Vishnevsky,KonstantinV.Gunbin,AndreyV.Bocharnikov, andEugeneV.Berezikov Index .......................................................................... 341 .
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