Evolutionary Biology from Concept to Application Pierre Pontarotti Editor Evolutionary Biology from Concept to Application 123 Editor: Dr.PierrePontarotti UMR6632 Universitéd’Aix-Marseille/CNRS LaboratoireEvolutionBiologiqueetModélisation,case19 3,PlaceVictorHugo 13331MarseilleCedex03 France [email protected] ISBN:978-3-540-78992-5 e-ISBN:978-3-540-78993-2 DOI:10.1007/978-3-540-78993-2 LibraryofCongressControlNumber:2008924864 (cid:1)c 2008Springer-VerlagBerlinHeidelberg Thisworkissubjecttocopyright.Allrightsarereserved,whetherthewholeorpartofthematerialis concerned,specificallytherightsoftranslation,reprinting,reuseofillustrations,recitation,broadcasting, reproductiononmicrofilmorinanyotherway,andstorageindatabanks.Duplicationofthispublication orpartsthereofispermittedonlyundertheprovisionsoftheGermanCopyrightLawofSeptember9, 1965,initscurrentversion,andpermissionforusemustalwaysbeobtainedfromSpringer.Violations areliabletoprosecutionundertheGermanCopyrightLaw. Theuseofgeneral descriptive names,registered names, trademarks, etc. inthis publication does not imply,evenintheabsenceofaspecificstatement,thatsuchnamesareexemptfromtherelevantprotective lawsandregulationsandthereforefreeforgeneraluse. Product liability: The publisher cannot guarantee the accuracy of any information about dosage and application contained inthisbook.Ineveryindividual casetheusermustcheck suchinformation by consultingtherelevantliterature. Coverdesign:WMXDesignGmbH,Heidelberg Printedonacid-freepaper 9 8 7 6 5 4 3 2 1 springer.com Preface Every biological system is the outcome of its evolutionary history; therefore, the decipheringoftheevolutionaryhistoryisoftremendousimportancetounderstand biology. Since1997,scientistsofdifferentdisciplineswhoshareadeepinterestinevolu- tionarybiologyconceptsandknowledgehaveheldan“evolutionarybiologymeet- ingatMarseilles”inordertodiscusstheirresearch,exchangeideas,andstartcollab- orations.Lately,scientistsinterestedintheapplicationoftheconceptshavejoined thegroup. ThisbookisaselectionofwhatIthinkarethemostrepresentativetalksof11th meetingastheyrepresentanup-to-dateoverviewofconceptsofevolutionandhow these conceptscan be used to understandbiologyin general.The bookcomprises severaltopicsthatwehavearrangedindifferentsubcategories:modelizationofevo- lution(Yu:Chap.1, Meadeand Pagel:Chap. 2),conceptsin evolutionarybiology (Toll-Riera et al: Chap. 3, Erenpreisa and Cragg: Chap. 4, Mikhalevich: Chap. 5, Raineri: Chap. 6), knowledge (Shimizu: Chap. 7, Hwang et al: Chap. 8), and ap- pliedevolutionarybiology(Barthe´le´myetal:Chap.9,HiluandBarthet:Chap.10, KrygerandScholtz:Chap.11,Swynghedauw:Chap.12,LevasseurandPontarotti: Chap.13).Ihopethatthisbookwillbeusefulnotonlytoevolutionarybiologistsbut alsotobiologistsingeneralandthatitwillhelptoproduceaneededepistemologi- calshiftinthedifferentdomainsofbiology—genomics,postgenomics,etc.—from correlativeapproachestoevolutionaryapproaches. I would like to express my sincere gratitude to the other members of the sci- entific committee—Etienne Pardoux, Philippe Monget, Bernard Swynghedauw, Etienne Danchin, Vincent Laudet, and Michel Milinkovitch, to the organiza- tional committee—Virginie Lopez-Rascol, Olivier Chabrol, and Julie Perrot, to the sponsor—Universite´ de Provence, CNRS, GDR BIM, Re´gion PACA, Conseil Ge´ne´ral 13, Marseille Provence Me´tropole, and to Association pour l’Etude de l’EvolutionBiologiquethatorganizesthemeetings.Ialsowishtothankthestaffat Springerfortheircooperation. v vi Preface LastbutnotleastIthankthemeetingcoordinatorAxellePontarottiforherwork andalso,asmanyparticipantssaid,formakingusfeelathomeduringthemeeting. Marseilles,France PierrePontarotti February2008 Contents PartI ModelizationofEvolution 1 RateofAdaptationofLargePopulations........................ 3 FengYuandAlisonEtheridge 2 APhylogeneticMixtureModelforHeterotachy .................. 29 AndrewMeadeandMarkPagel PartII ConceptsinEvolutionaryBiology 3 AcceleratedEvolutionofGenesofRecentOrigin................. 45 MacarenaToll-Riera,JoseCastresana,andM.MarAlba` 4 Life-CycleFeaturesofTumourCells ........................... 61 JekaterinaErenpreisaandMarkS.Cragg 5 GeneralEvolutionaryRegularitiesofOrganicandSocialLife ...... 73 ValeriaI.Mikhalevich 6 OldandNewConceptsinEvoDevo............................. 95 MargheritaRaineri PartIII Knowledge 7 OverturningthePrejudicesaboutHydraandMetazoanEvolution .. 117 HiroshiShimizu 8 The Search for the Origin of Cnidarian Nematocysts inDinoflagellates............................................ 135 JungShanHwang,SatoshiNagai,ShihoHayakawa,YasuharuTakaku, andTakashiGojobori vii viii Contents PartIV AppliedEvolutionaryBiology 9 APossibleRelationshipBetweenthePhylogeneticBranchLengths and the Chaetognath rRNA Paralog Gene Functionalities: Ubiquitous,Tissue-SpecificorPseudogenes...................... 155 Roxane-Marie Barthe´le´my( ), Michel Grino, Pierre Pontarotti, (cid:0) Jean-PaulCasanova,andEricFaure 10 Mode and Tempo of matK: Gene Evolutionand Phylogenetic Implications................................................ 165 KhidirW.HiluandMichelleM.Barthet 11 PhylogeographyandConservationoftheRareSouthAfricanFruit ChaferIchnestomastobbiai(Coleoptera:Scarabaeidae) ........... 181 UteKrygerandClarkeH.Scholtz 12 NothinginMedicineMakesSenseExceptintheLightofEvolution: AReview .................................................. 197 BernardSwynghedauw 13 AnOverviewofEvolutionaryBiologyConceptsforFunctional Annotation:AdvancesandChallenges.......................... 209 AnthonyLevasseurandPierrePontarotti Index .............................................................217 Contributors M.MarAlba` Research Unit on Biomedical Informatics, Institut Municipal d’Investigacio´ Me`dica,UniversitatPompeuFabra,E-08003Barcelona,Spain, and CatalanInstitutionforResearchandAdvancedStudies,08010Barcelona,Spain, [email protected] Roxane-MarieBarthe´le´my LaboratoireEvolutionBiologiqueetMode´lisation,Case19,UMR6632,Universite´ d’Aix-Marseille/CNRS,3PlaceVictorHugo,13331MarseilleCEDEX03,France, [email protected] MichelleM.Barthet ARCCentreofExcellenceinPlantEnergyBiology,School of BiologicalSciences, University of Sydney,Sydney,NSW 2006,Australia, [email protected] Jean-PaulCasanova LaboratoireEvolutionBiologiqueetMode´lisation,Case19,UMR6632,Universite´ d’Aix-Marseille/CNRS,3PlaceVictorHugo,13331MarseilleCEDEX03,France, [email protected] JoseCastresana InstituteofMolecularBiologyofBarcelona,CSIC,Barcelona,Spain, [email protected] MarkS.Cragg TenovusResearchLaboratory,SouthamptonUniversityHospital;TremonaRoad, SouthamptonSO166YD,UK,[email protected] JekaterinaErenpreisa LatvianBiomedicineResearch andStudyCentre, Ratsupitesstr. 1,1067Riga, Latvia,[email protected] ix x Contributors AlisonEtheridge DepartmentofStatistics,UniversityofOxford,1SouthParksRoad,OxfordOX1 3TG,UK,[email protected] EricFaure LaboratoireEvolutionBiologiqueetMode´lisation,Case19,UMR6632,Universite´ d’Aix-Marseille/CNRS,3PlaceVictorHugo,13331MarseilleCEDEX03,France, [email protected] MichelGrino InsermUMR626,UFRdeMe´decineSecteurTimone,27BdJeanMoulin,13385 MarseilleCEDEX5,France,[email protected] TakashiGojobori CenterforInformationBiologyandDDBJ,NationalInstituteofGenetics,Mishima, 411–8540Shizuoka,Japan,[email protected] ShihoHayakawa CenterforInformationBiologyandDDBJ,NationalInstituteofGenetics,Mishima, 411–8540Shizuoka,Japan,[email protected] KhidirW.Hilu DepartmentofBiologicalSciences,VirginiaTech,Blacksburg,VA24061,USA, [email protected] JungShanHwang CenterforInformationBiologyandDDBJ,NationalInstituteofGenetics,Mishima, 411–8540Shizuoka,Japan,[email protected] UteKryger DepartmentofZoologyandEntomology,UniversityofPretoria,Pretoria0002, SouthAfrica,[email protected] AnthonyS.G.Levasseur LaboratoireEvolutionBiologiqueetMode´lisation,Case19,UMR6632,Universite´ d’Aix-Marseille/CNRS,3PlaceVictorHugo,13331MarseilleCEDEX03,France, [email protected] AndrewMeade SchoolofBiologicalSciences,PhilipLyleBuilding,TheUniversityofReading, ReadingRG66BX,UK,[email protected] ValeriaI.Mikhalevich ZoologicalInstitute,RussianAcademyofSciences,Universitetskayanab.1,St. Petersburg199134,Russia,[email protected] SatoshiNagai NationalResearchInstituteofFisheriesandEnvironmentofInlandSea,Maruishi 2-17-5,Hatsukaichi,739-0452Hiroshima,Japan,[email protected] Contributors xi MarkPagel SchoolofBiologicalSciences,PhilipLyleBuilding,TheUniversityofReading, ReadingRG66BX,UK,[email protected] PierrePontarotti LaboratoireEvolutionBiologiqueetMode´lisation,Case19,UMR6632,Universite´ d’Aix-Marseille/CNRS,3PlaceVictorHugo,13331MarseilleCEDEX03,France, [email protected] MargheritaRaineri DepartmentofBiology,UniversityofGenoa,VialeBenedettoXV5,16132Genoa, Italy,raimrg@unige ClarkeH.Scholtz DepartmentofZoologyandEntomology,UniversityofPretoria,Pretoria0002, SouthAfrica,[email protected] HiroshiShimizu NationalInstituteofGenetics,1111Yata,Mishima,411-8540Shizuoka,Japan, [email protected] BernardSwynghedauw Centre de Recherches Cardiovasculaires de l’INSERM, Hoˆpital Lariboisie`re, 41 Bd de la Chapelle, 75475 Paris CEDEX, France, [email protected] YasuharuTakaku CenterforInformationBiologyandDDBJ,NationalInstituteofGenetics,Mishima, 411-8540Shizuoka,Japan,[email protected] MacarenaToll-Riera Research Unit on Biomedical Informatics, Institut Municipal d’Investigacio´ Me`dica,UniversitatPompeuFabra,Barcelona,Spain,[email protected] FengYu SchoolofMathematics,UniversityofBristol,UniversityWalk,BristolBS81TW, UK,[email protected]