Table Of ContentEvolutionary 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
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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
.
