Evolutionary Biology: Concept, Modeling, and Application

398 Pages·2009·8.205 MB·English

by  Fabiana Ciciriello, Giovanna Costanzo, Samanta Pino, Ernesto Di Mauro (auth.), Pierre Pontarotti (eds.)

Evolutionary Biology
Pierre Pontarotti
Editor
Evolutionary Biology
Concept, Modeling, and Application
Editor
Dr.PierrePontarotti
UMR6632
Universite´d’Aix-Marseille/CNRS
LaboratoireEvolutionBiologiqueetMode´lisation,case19
PlaceVictorHugo3
13331MarseilleCedex03
France
[email protected]
ISBN978-3-642-00951-8 e-ISBN978-3-642-00952-5
DOI:10.1007/978-3-642-00952-5
SpringerDordrechtHeidelbergLondonNewYork
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Preface
Since 1997, scientists of different disciplines who share a deep interest in evolu-
tionary biology concepts, knowledge and application have held the Evolutionary
BiologyMeetingatMarseillesinordertodiscusstheirresearch,exchangeideasand
startcollaboration.Latelyscientistsinterestedintheapplicationjoinedthegroup.
We start the book with the meeting report that gives a general idea of the
epistemologicalpostureofthemeeting;thisisfollowedby22articles.
Thesearticlesare,tomymind,aselectionofthemostrepresentativetalks,which
havebeenbroughtupduringthe12thEvolutionaryBiologyMeetingatMarseilles.
We decide to sort out the articles in several categories: evolutionary biology
concepts and knowledge, concepts and knowledge modeling and concepts and
knowledgeapplication.Thereaderwillnotethatevolutionaryapplicationtranscend
biology since two articles in the book show application of evolutionary biology
concepttoeconomyandastronomyannouncingotherfieldofapplications.
I would like to thank all the authors of the book, the meeting participants, the
sponsor-CNRS,Universite´deProvence,ConseilGe´ne´ral13,VilledeMarseilleand
GDRBIM.
I also wish to thank the staff of Springer for their cooperation and more
especiallyAndreaSchlitzbergerforherconsiderateness.
LastbutnotleastIwish tothankthe ‘‘Associationpourl’Etude del’Evolution
Biologique’’ and the meeting coordinator Axelle Pontarotti whose outstanding
workenhancedboththequalityandfriendlinessofthemeeting.
Marseilles,France PierrePontarotti
April2009
v
Meeting Report: 12th Evolutionary Biology
Meeting in Marseille
The12thEvolutionaryBiologymeetinginMarseille(EBM)wassupposedtobegin
onSeptember24,2008,althoughitactuallybegunatadinnertableonenightbefore
its official opening. People arriving one night before the beginning of the confer-
encegottogetherforinformalsocialactivities.Ofcourseitcouldnotbedifferent:a
number of passionate researchers seated together around a table must result in a
scientificdebate.DanielJohnLawson,apostdocstudentfromtheImperialCollege
of London, posed the central question: ‘‘Are there still any basic controversies in
evolutionarybiologythathavenotbeensolved?’’Thegeneralagreementoverthe
table,duringredwinetastingandadelicious‘‘Frenchrepas,’’wasaclearandsound
‘‘No.’’ Every single evolutionary biologist seems to be satisfied with the modern
view of the Darwinian paradigm. They all agreed that it presents the key and the
whole convergence point of the enormous research field in biology. Someone
rememberedDobzhansky:‘‘Nothinginbiologymakessenseexceptinthelightof
evolution.’’ At that point, it seems that the evolutionary biologists around that
restauranttableinthe‘‘VieuxPort’’atMarseillewereunderestimatingtherichness
and the deepness of the debates they would have in the following days regarding
long-termcontroversialpointsinevolutionarybiology.
During the very first morning session, a computational model for evolutionary
change raised the debate between the strength of natural selection opposed to the
application of nearly neutral Kimura-based models. Selectionism and neutralism
were under debate. In the afternoon, Guy Hoelzer from the University of Nevada
(USA)broughttodiscussiontherelevanceofallopatryforspeciationandhowthe
genomes of populations got incompatible after geographically specific mutations.
Confirming this computational simulated scenario, a group from London showed
that the presence of polymorphisms in the Hepatitis B virus is geographically
restrictedandcertainvirusstrainsareenclosedintosomedelimitedregionsofthe
planet. The following day, the relationship between kinship and fertility was also
computationally modeled and it was pointed out that the highest fecundity in
humanshasbeenobservedforcouplesrelatedatthelevelofthirdtofourthcousins
(inIceland??).StanislawCebratandcollaboratorsproducedamodelthatclaimsto
explain and prove the occurrence of sympatric speciation based on zygotic death
vii
viii MeetingReport:12thEvolutionaryBiologyMeetinginMarseille
associated to effects related a sort of intrapopulation outbreeding depression.
Furthermore,thealways-under-debatesubjectabouttheoriginoflifewasdiscussed
by researchers working in Italy, Russia and Japan. Di Mauro used physical infor-
mationaboutthemostcommonorganicmoleculesfoundininterstellarsystemsto
discussaputativeoriginallivingsystembasedontheformamidemolecule.Victor
Ostrovskiiagreedwithhimthatlifeshallemergewithoutanygreatunlikelyevent,
arising from thermodynamically favorable conditions. The point in their thought
couldberesumedasthefollowingquotationofVictorStengerin‘‘Thecomprehen-
sive cosmos’’: ‘‘Something came from nothing because it is more stable than
nothing.’’TadashiSugawaraaddressedthepointabouttheoriginofcellsshowing
howgiantlipidvesiclescoulddivideandputativelyreproducewithoutanyprecise
teleonomicformofinformationtoguidetheirduplication.Moreover,theevolution
of sex was simplistically explained and theorized using computational models to
describethebehaviorofpreysescapingpredators.RobertFrenchfromtheUniver-
sity of Burgundy presented an interesting model to describe his ‘‘Red-Tooth
Hypothesis,’’ theorizing on which sort of combined escape strategies should be
used for preys to escape being eaten. Using a computational model to describe
escape behaviors in sexual and asexual populations, he tried to approach the
question about how sexual reproduction could provide an advantage for preys,
allowing them to survive under the attack of starving predators at the population
level. Finally, the evolution of gene functions through neofunctionalization and
subfunctionalization was discussed by Ashley Byun McKay from the Fairfield
University(Canada).Sheshowedexamplesofduplicatedgenesonwhichasingle
nucleotide mutation in the signal peptide would be enough to change the cellular
compartment on which a given gene would be expressed and further the gene
function.Thedebateswerethanshiftedintotherelevanceofsaltacionistictheories
inevolution.Howfrequentshouldthesesinglemutationsproduceadrasticchange
ongenefunctionandorganisms’behavior?
Apart from these long-term discussions in evolutionary biology, new techno-
logiesforevolutionaryanalysiswerepresentedduringthistraditionalevolutionary
biology conference in France. Represented by one talk and three poster presenta-
tions, a group from Croatia headed by Tomislav Domazet-Lozo was probably the
biggerresearchgroupcomingtothemeeting.Theirinterestingworkwasbasedon
a technique they called phylostratigraphy, consisting in (1) the identification of
species-specific genes and (2) verifying the expression of these genes in different
tissues on these organisms. This way, this group could identify the relevance of
new-born genes in tissues and address questions about tissue and organ modifica-
tionalongtimeinanumberofspecies.Othernewtechnologypresentedduringthe
EBMwasperformedbyaconsortiumbetweenFranceandtheUnitedStates.They
described a conceptual model (ontology) allowing researchers to represent both
morphological and molecular characters observed in organisms and genes. They
claimed that the description of the most basic evolutionary biology concepts –
linked together through semantic relationships – will further allow automatic
algorithmicreasoning,helpingintheanalysisoftheenormousamountofcompara-
tiveandevolutionarybiologydataavailableforbiologyinthepetabyteera.
MeetingReport:12thEvolutionaryBiologyMeetinginMarseille ix
Regarding the evolution of gene families, a group in the Smurfit Institute of
Genetics in Ireland showed that immune-related genes are co-localized and puta-
tively co-expressed in the genomes of vertebrates. Selection constraints observed
using the number of synonym per non-synonym substitutions were studied by a
numberofgroupsaroundtheworld:inJapantheywerestudiedinfishgalactins;in
Ireland,theywererelatedtothethree-dimensionalstructureofproteins.TheKs/Ka
was also used in Germany to study the Asr gene family in tomato and a French-
Americangrouprelatedthesubstitutiontaxeswithvirulencefactorsinnematodes.
Changing the subject to the study of fossils, new researches made in USA
showed that the development of 14C datation techniques in the last decade have
helpedtorevealthatagreatpartofmolecularchangesinthehumangenomehave
happened during the Holocene period, encompassing the last 10,000 years of
Earth’s history. An interesting paleobotanics research made in China has shown
evidence of a putative new group of fossil Angiosperms. Another plant research
made in Belgium and Germany took profit of both morphological and molecular
data to study the evolution of basal perianthless Angiosperms species from the
family Piperales. ResearchersinFranceandItalyalsoreportedthatdensepopula-
tionsofplantsusuallyproducemoreviableseeds,aresearchthatcouldbelinkedto
the previously commented human population-genetics studies highlighting the
higher fertility between individuals presenting common ancestors not that far in
time. A group in Israel showed evidence for alotetraploydy events happening
during the molecular evolution of carps, maybe the single evidence for this sort
ofevent–socommoninplants–happeninginavertebratespecies.
Brian Kennedy presented an interesting aging study made in the USA. He
showed evidences that aging does not seem to be molecular programmed once
selectivepressuresdeclinewithage.Togetherwithhiscollaborators,theyshowed
that caloric restriction made late in the life of flies, worms and yeasts might help
theseorganismstoextendtheiraveragelifespan.
Moreover, a number of open-minded discussions were centered in new-born
interdisciplinary fields. The application of cladistic methods to reconstruct the
history of galaxies was approached by Didier Fraix-Burnet from the Laboratoire
d’AstrophysiquedeGrenoble.Hisastrocladisticsapproachhasbeenusedtoidentify
and map a number of putatively evolving characters in galaxies, allowing their
classification into phylogenetic trees. As expected, due the tradition of scientific
academy,hecomplainedaboutthedifficultiestopublishthesenewandinteresting
ideasinrespectedjournals.‘‘Galaxiesarenotlivingorganisms,’’arguedthereferees
whenrefusingthepapersfromhisgroup.Someoneworkingintheoriginoflifefrom
the audience pointed out: ‘‘if galaxies modify along time, if they can be born and
die, if they derive from a common ancestor since the Big Bang and if they may
interactwithothers...whytheyshouldnotbeconsideredalive?’’Thediscussion
about ‘‘what is life?’’ is still a controversy among scientists. By the way, it is
noteworthy to remember that the discussion about the main characteristics of a
livingsystemprobablyhadoneofitshighestpointswhenthephysicistSchrodinger
theorizedaboutaputative‘‘aperiodiccristal’’tostoregeneticinformationearlyin
1944. Interdisciplinary approaches were also discussed from the point of view of
x MeetingReport:12thEvolutionaryBiologyMeetinginMarseille
economics. Michael Turk came from the Fitchburg State College (USA) to speak
totheaudienceabouthowmostofthetheoriestryingtoscientifizeeconomywere
initially based on models inherited fromphysics. Nevertheless, a number of other
characteristicswouldmakethisdisciplineclosertobiology,suchas:(1)emphasis
on complexity; (2) its dynamic characteristic; (3) the focus on the cumulative
change; (4) the competitivity of market; and so on. He introduced a number of
philosophers – such as Brian Arthur, Paul David and Paul Krugman – that have
beeninfluencedbybiologistslikeJacquesMonodandbroughttheideasof‘‘Change
and Necessity’’ to the economics research field. At last, other interdisciplinary
topics were discussed during the conference concerning the relationship between
evolutionarybiologyandepistemology.Strictquestionscomingfromtheaudience
generated these off-topic discussions, since some researchers were arguing that a
presented given theory had already been ‘‘proved false’’ since a long time ago,
makingthestudypresentedunfruitfulandpointless.Thediscussionswerecentered
inquestionwhetherscienceactuallygivesornotsomesortofdefinitiveanswerto
thestudyofnature.Newtonianphysicshasbeenrememberedasthemostundoubt-
edly correct of all scientific theories and it has been proven – at least partially –
false. Shall scientists dogmatize their enterprise? The general agreement was that
opendiscussionsandempirical-basedfactsareactuallywhatmakescienceprogress
and dogmatism should not be kept in the science domain; mainly in the field of
evolutionarybiologythathassufferedsomuchatthehandofreligiousdogmas.
Last but not least, the variety of different computational, biological and philo-
sophical approaches presented during this meeting highlighted that Darwinian-
based thought keeps being at the center of evolutionary biology and encompasses
the mainstream linking point of all biological and medical research all over the
world.
FrancescoProsdocimiandPierrePontarotti
Contents
PartIConceptandKnowledge
1 SpontaneousGenerationRevisitedattheMolecularLevel ............. 3
FabianaCiciriello,GiovannaCostanzo,SamantaPino,
andErnestoDiMauro
2 MinimalCellModeltoUnderstandOriginofLifeandEvolution .... 23
TadashiSugawara
3 NewFossilsandNewHopefortheOriginofAngiosperms ............ 51
XinWang
4 VertebrateEvolution:TheStrangeCase
ofGymnophionanAmphibians ........................................... 71
Jean-MarieExbrayatandMichelRaquet
5 TheEvolutionofMorphogeneticSignallinginSocialAmoebae ....... 91
YoshinoriKawabeandElisaAlvarez-CurtoAllysonV.Ritchie,
andPaulineSchaap
6 OntheSurprisingWeaknessofPancreaticBeta-CellAntioxidant
Defences:AnEvolutionaryPerspective ................................ 109
ArminRashidi,ThomasB.L.Kirkwood,andDarylP.Shanley
7 TheImportanceofTranspositionsandRecombinationtoGenome
InstabilityAccordinghobo-ElementDistributionPatternin
CompletelySequenceGenomeofDrosophilamelanogaster .......... 127
L.P.Zakharenko,M.P.Perepelkina,andD.A.Afonnikov
xi