Table Of ContentPierre Pontarotti Editor
Evolutionary
Biology—A
Transdisciplinary
Approach
—
Evolutionary Biology A Transdisciplinary
Approach
Pierre Pontarotti
Editor
—
Evolutionary Biology A
Transdisciplinary Approach
123
Editor
Pierre Pontarotti
IHU Marseille MEPHI
AixMarseille UnivIRD, APHM
Marseille, France
SNC5039CNRS
Paris, France
ISBN978-3-030-57245-7 ISBN978-3-030-57246-4 (eBook)
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Preface
For the 13th time now, we publish a book on concepts and applications in evo-
lutionary biology.
Our aim is to capture the evolution and progress of this field, and the
EvolutionaryBiologyMeetinginMarseillesisaperfectbasistodoso.Thegoalof
this annual meeting is to allow scientists of different disciplines, who share a deep
interestinevolutionarybiologyconcepts,knowledgeandapplications,tomeetand
exchange and enhance interdisciplinary collaborations. The Evolutionary Biology
Meeting in Marseilles is now recognised internationally as an important exchange
platformandaboosterfortheuseofevolutionary-basedapproachesinbiologyand
also in other scientific areas.
The book chapters have been selected from the meeting presentations and from
propositions born by the interaction of meeting participants.
Thereadersoftheevolutionarybiologybooksaswellasthemeetingparticipants
would perhaps like to see a shift in the evolutionary biology concepts, which they
have witnessed year after year in the different meetings and also in the books.
However,thefactthatthechaptersofthebooksareselectedfromameetingenables
the quick diffusion of the novelties.
Wewouldliketoemphasisethatthe13booksarecomplementarytoeachother
and should be considered as tomes.
Marseille, France Marie Hélène Rome
June 2020 A.E.E.B. Director
Pierre Pontarotti
A.E.E.B. and CNRS
Acknowledgements We would like to thank all the authors and the reviewers of the different
chapters.
We thank the sponsors of the meeting. Aix Marseille Université, CNRS, ECCOREV
Federation,ConseilDépartemental13,ITMO,VilledeMarseille.
WewishtothanktheA.E.E.B.teamfortheorganisationofthemeeting.
WealsowishtothanktheSpringer’seditionstaffandinparticularAndreaSchlitzbergerforher
competenceandhelp.
v
Contents
1 Genetic and Morphological Differentiation of Common Toads
in the Alps and the Apennines . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Jan W. Arntzen, Wouter de Vries, Daniele Canestrelli,
and Iñigo Martínez-Solano
2 Molecular Phenotypes as Key Intermediates in Mapping
Genotypes to Fitness . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Aditya Ballal, Constantin D. Malliaris, and Alexandre V. Morozov
3 A Practical Guide to Orthology Resources . . . . . . . . . . . . . . . . . . . 41
Paul de Boissier and Bianca H. Habermann
4 Protein Recoding Through RNA Editing: Detection,
Function, Evolution. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
Eli Eisenberg
5 Most Successful Mammals in the Making: A Review
of the Paleocene Glires . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99
Łucja Fostowicz-Frelik
6 Continuous Spectrum of Lifestyles of Plant-Associated Fungi
Under Fluctuating Environments: What Genetic Components
Determine the Lifestyle Transition? . . . . . . . . . . . . . . . . . . . . . . . . 117
Kei Hiruma
7 Genome Evolution of Asexual Organisms and the Paradox
of Sex in Eukaryotes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133
Elvira Hörandl, Jens Bast, Alexander Brandt, Stefan Scheu,
Christoph Bleidorn, Mathilde Cordellier, Minou Nowrousian,
Dominik Begerow, Anja Sturm, Koen Verhoeven, Jens Boenigk,
Thomas Friedl, and Micah Dunthorn
vii
viii Contents
8 On the Origin of Life and Evolution of Living Systems
from a World of Biological Membranes . . . . . . . . . . . . . . . . . . . . . 169
Aditya Mittal, Suneyna Bansal,
and Anandkumar Madhavjibhai Changani
9 Orthology: Promises and Challenges. . . . . . . . . . . . . . . . . . . . . . . . 203
Yannis Nevers, Audrey Defosset, and Odile Lecompte
10 Prehistoric Stone Projectile Points and Technological
Convergence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 229
Michael J. O’Brien and George R. McGhee
11 Diversity and Evolution of RNase P . . . . . . . . . . . . . . . . . . . . . . . . 255
Isabell Schencking, Walter Rossmanith, and Roland K. Hartmann
12 An Unusual Evolutionary Strategy: The Origins, Genetic
Repertoire, and Implications of Doubly Uniparental Inheritance
of Mitochondrial DNA in Bivalves . . . . . . . . . . . . . . . . . . . . . . . . . 301
Donald T. Stewart, Sophie Breton, Emily E. Chase,
Brent M. Robicheau, Stefano Bettinazzi, Eric Pante, Noor Youssef,
and Manuel A. Garrido-Ramos
13 The Evolution of the FLOWERING LOCUS T-Like (FTL) Genes
in the Goosefoot Subfamily Chenopodioideae . . . . . . . . . . . . . . . . . 325
Helena Štorchová
14 DDE Transposon as Public Goods . . . . . . . . . . . . . . . . . . . . . . . . . 337
Louis Tsakou-Ngouafo, Célia Vicari, Laura Helou, Vivek Keshri,
Sabyasachi Das, Yves Bigot, and Pierre Pontarotti
15 Evolution of Milk Oligosaccharides of Carnivora
and Artiodactyla: Significance of the Ratio of Oligosaccharides
to Lactose in Milk. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 359
Tadasu Urashima, Yuri Mineguchi, Kenji Fukuda,
Katherine Whitehouse-Tedd, and Olav T. Oftedal
16 Making Sense of Noise . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 379
Shu-Ting You and Jun-Yi Leu
Chapter 1
Genetic and Morphological
Differentiation of Common Toads
in the Alps and the Apennines
JanW.Arntzen,WouterdeVries,DanieleCanestrelli,
andIñigoMartínez-Solano
Abstract Usingapanelof31diagnosticnuclearSNPmarkersin56toadpopula-
tionsfromthesouthernAlpsandthenorthernandcentralApennines,wedocument
that the range of the spined toad, Bufo spinosus, extends along the Mediterranean
coast from France into the northwest of Italy. This species, and the common toad
B. bufo, engage in a unimodal hybrid zone, with B. spinosus at the higher and B.
bufoattheloweraltitudesoftheLigurianAlps.Thewidthof24.0kmobservedin
the Italian section of the long hybrid zone is narrower than documented in France
(ca. 50 km). Using six mitochondrial SNP markers, we resolve several haplotype
groups,withapproximatedistributionsas‘bufo-e2’acrosstheFrench–Italianborder
region,‘bufo-e3’intheItalianAlps,‘bufo-e6’intheApenninesand‘spinosus’with
a single occurrence in Italy. We did not observe the northern European ‘bufo-e1’
haplogroup. The bufo-e2 haplogroup is frequently observed in B. spinosus, there-
with confirming a marked nuclear/mitochondrial discordance. The bufo-e3 and e6
haplogroupscorrespondtoseparatenucleargeneticlineagesofB.bufointheAlps
and the Apennines, respectively. These groups engage in a wide zone of intergra-
dation(109.3km).BufobufopopulationsfromthePovalleyremaintobestudied,
but presumably fall with the northern Alpine group. With data from the southeast
ofFranceasareference,weshowthatItalianB.bufo,inparticularthosefromthe
Electronicsupplementarymaterial Theonlineversionofthischapter
(https://doi.org/10.1007/978-3-030-57246-4_1)containssupplementarymaterial,whichis
availabletoauthorizedusers.
B
J.W.Arntzen( )·I.Martínez-Solano
NaturalisBiodiversityCenter,P.O.Box9517,2300RALeiden,TheNetherlands
e-mail:[email protected]
W.deVries
AsociationAmbor,Ctra.Constantina—Pedroso1,41450Constantina,Spain
D.Canestrelli
DepartmentofEcologicalandBiologicalScience,LargoDell’UniversitàS.N.C,01100Viterbo,
Italy
I.Martínez-Solano
DepartmentofBiodiversityandEvolutionaryBiology,MuseoNacionaldeCienciasNaturales,
CSIC,c/JoséGutiérrezAbascal,2,28006Madrid,Spain
©SpringerNatureSwitzerlandAG2020 1
P.Pontarotti(ed.),EvolutionaryBiology—ATransdisciplinaryApproach,
https://doi.org/10.1007/978-3-030-57246-4_1
2 J.W.Arntzenetal.
Apenninelineage,aremorphologicallymoresimilartoB.spinosusthantoB.bufo.A
two-speciesdistributionmodeldevelopedforFranceonthebasisofclimatevariables
wasextrapolatedovertheentireB.spinosus–B.buforange.Theresultsuggeststhat
largepartsofthecentralandeasternMediterraneanhaveclimatesthatinsouthern
France and the western Mediterranean region support the presence of B. spinosus.
Thisclarifiestaxonomicconfusionregardingspeciesassignmentofcommontoads
from southern European peninsulas and hints at possible processes of convergent
adaptivemorphologicalevolutionintheseareas.
1.1 Introduction
Manywidespreadtaxahave,overthelastdecades,turnedouttobeconglomerates
of distinct, but closely related and morphologically similar species, also known as
‘crypticspecies’.Amphibianexamplesinclude‘Tritoncristatus’,‘Tritontaeniatus’
and‘Ranaesculenta’intheOldWorldand‘Ranapipiens’intheNewWorld.These
taxaarecurrentlyconsideredspeciesgroupswithinthegeneraTriturus,Lissotriton,
PelophylaxandLithobates(Frost2019).Mostlybecauseoftheirubiquityandavail-
ability,theseveryspecieshavebeenpopularforteachingpurposesandformorpho-
logical, physiological and behavioural research (e.g., Rusconi 1821; Ecker 1864;
Eckeretal.1899;Donaldson1908;TinbergenandTerPelkwijk1938).Toillustrate
thepoint,onlysixtaxa(includingallfourlistedabove)wereinstrumentaltotheseven
Nobel Prize winning studies and 12 laureates that made use of amphibian models
(BurggrenandWarburton2007).Itremains,however,unclearwhichofthecurrently
recognizedspecieswereactuallyemployedinthesestudiesandhowtaxonomicaffil-
iationmightinfluencethereproducibilityofresultsintheseandotherinvestigations.
Thishighlightstheimportanceoftaxonomicknowledgelinkedtoarobustphyloge-
neticframework.Inthisrespect,molecularsystematicshasdecisivelycontributedto
delineatetaxaandresolvephylogeneticrelationshipsingroupscomprisingmorpho-
logicallysimilarspecies,whichhasledtorapidprogressintheresolutionofterminal
branchesinthetreeoflife,especiallywiththeadventofhigh-throughputsequencing
technologies(Hinchliffetal.2015).
One such example of hidden complexity is ‘Bufo bufo’ which comprises
four species of Eurasian toads. The species are unequivocally diagnosable from
geneticmarkersbutdifficulttoidentifyfrommorphology,atleastinsomeregions
(Litvinchuk et al. 2008; Recuero et al. 2012; Arntzen et al. 2013, 2016). Within
this group the spined toad Bufo spinosus Daudin, 1803 from North Africa and
south-western Europe and the common toad Bufo bufo (Linnaeus, 1758) from
western,northern,centralandeasternEurope,aregeneticallydeeplydifferentiated
butmorphologicallycrypticspecies.Thespeciesmeetupinadiagonallineacross
France,fromtheAtlanticOceantotheMediterranean(Arntzenetal.2018,2020).
They are not sister taxa, yet in the two areas where they were studied in detail,
they hybridize in ca. 50 km wide zones (Arntzen et al. 2016; Trujillo et al. 2017;
Van Riemsdijk et al. 2019a, b). Nuclear genetic data indicate the presence of B.
1 GeneticandMorphologicalDifferentiationofCommonToads... 3
spinosusalongtheFrenchMediterraneancoast,uptotheItalianborder,suggesting
thatthespecies’rangemayreachintoItaly(Arntzenetal.2016).Wehereinvesti-
gatethedistributionandpossiblegeneticadmixtureofbothspeciesoverthenorth
ofItalywithaneightfoldnumberofnucleargeneticmarkers(fromfourto31).We
confirmthatB.spinosusispresentinthenorthwestofthecountry(Liguria)andthat
itengageswithB.bufoinanarrowhybridzone.InItalianB.bufo,wediscerntwo
lineages,distributedalongtheAlpsandintheApennines,respectively.Thesouthern
ApenninelineageofB.bufoismorphologicallymoresimilartoB.spinosusthanis
thenorthernAlpinelineage,whichhintsatprocessesofconvergentmorphological
evolutiondrivenbyclimaticfactors.
1.2 MaterialsandMethods
Tissue samples were collected under licence as toe tips from adults and the tips
oftailfinsfromlarvaefor890individualsat56localitiesacrossthenorthofItaly
andadjacentFrance.Fluorescence-basedgenotyping(Semagnetal.2014)wasused
in the Kompetitive Allele-Specific PCR (KASP) system at the single nucleotide
polymorphism (SNP) genotyping facility (LGC genomics, UK) of the Institute of
Biology, Leiden University. Primer design, PCR setup and data visualization and
recording followed Arntzen et al. (2016) and Van Riemsdijk et al. (2019a). The
full panel of SNPs was studied with the exclusion of banp, c10orf2 and klhl that
lacked species diagnosticity and egflam that was strongly out of Hardy–Weinberg
equilibrium.DataforindividualswithmorethanfiveSNPsmissingwerediscarded.
Fortheremainder,missingdataamountedtoN=470(1.7%)over31nuclearmarkers.
WefurtherdesignedandappliedapanelofsixSNPmarkerstoasubsetofthematerial,
withtheaimtoidentifythedifferentmtDNAhaplogroupsthathavebeendocumented
forthewiderregion,namely‘spinosus’,‘bufo-e1’,‘bufo-e2’,‘bufo-e3’and‘bufo-
e6’(Garcia-Portaetal.2012;Arntzenetal.2017).Individualswithmorethanone
SNPdatapointmissingwereexcluded.Fortheremainder,missingdataamounted
toN =38(1.5%).Haplogroupinformationwascompiledfor620individualsfrom
33localities.
Wealsomeasuredadulttoadsinthefieldfortwocharactersthatarereportedto
discriminatebetweenBufobufoandB.spinosus(Arntzenetal.2013),namelybody
size(assnout-urostyllength,SUl,measuredwithcallipersat0.1mmprecision)and
parotoidangle(Pa,measuredwithaprotractorondigitalimagery,with0.5degree
precision),allbythesameobservers(WdeV,JWA).Speciesidentitywasdetermined
fromnucleargeneticdata,andindividualsfromstronglyadmixedpopulationswere
notanalysed.Thematerialstudiedinvolved213malesand45femalesofB.bufofrom
thesoutheastofFrance,207malesand88femalesofB.spinosusfromthesoutheast
ofFranceandadjacentItalyand254malesand41femalesofB.bufofromthenorth
ofItaly.Becauseofadocumentedsexualsizedimorphism,malesandfemaleswere
analysedseparately.
