What is an archaeon and are the Archaea really unique?

27 Pages·2017·2.34 MB·English

ManuscriptsubmittedtoeLife
What is an archaeon and are the
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Archaea really unique?
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AjithHarish1*
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*Forcorrespondence:
[email protected]( 1DepartmentofCellandMolecularBiology,StructuralandMolecularBiologyProgram,
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)
UppsalaUniversity,Uppsala,Sweden
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Abstract TherecognitionofthegroupArchaea40yearsagostimulatedresearchinmicrobial
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evolutionandmolecularsystematicsthatpromptedanewclassificatoryschemetoorganize
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biodiversity.AdvancesinDNAsequencingtechniqueshavesincesignificantlyimprovedthe
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genomicrepresentationofthearchaealbiodiversity.Inaddition,advancesincomputational
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modelingthatfacilitatelarge-scalephylogenomicshaveresolvedmanyrecalcitrantbranchesofthe
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TreeofLife.Despitethetechnicaladvancesandanexpandedtaxonomicrepresentation,two
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importantaspectsoftheoriginsandevolutionoftheArchaearemaincontroversial,evenaswe
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celebratethe40thanniversaryofthemonumentaldiscovery.Theissuesconcern(i)theuniqueness
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(monophyly)oftheArchaea,and(ii)theevolutionaryrelationshipsoftheArchaeatotheBacteria
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andtheEukarya;bothofthesearerelevanttothedeepstructureoftheTreeofLife.Acloserlook
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atrecentpublishedphylogenomicdatasetsthataddresstheseissuesshowsthattheconflicting
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conclusionsareprimarilyduetoascarcityofinformationinstandarddatasets—thecore-genes
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datasets—toreliablyresolvetheconflicts.However,theseconflictscanberesolvedefficientlyby
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employingcomplexgenomicfeaturesandgenome-scaleevolutionmodels—adistinctclassof
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phylogenomiccharactersandevolutionmodels,whichcanbeemployedroutinelytomaximizethe
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useofgenomesequencesfortestingevolutionaryhypotheses.Insightsfromthestudyofcomplex
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genomiccharactersraisequestionsaboutthecontinueduseoftheconventionalcore-gene
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phylogeneticapproach,thatis,ourrelianceonelementarycharacters(nucleotidesandamino
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acids)andonmodelsofsubstitutionmutationsalonetosolvedifficultphylogeneticproblems.
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Doesitneedtobesupplementedwithcomplexgenomiccharactersandcorrespondingmodelsof
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evolution?Orperhapssupplanted?Basedonacriticalanalysisofthepersistentdifficultyin
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resolvingthearchaealradiation,Iargueforthelatter.
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Introduction
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TherecognitionoftheArchaeaastheso-called“thirdformoflife”wasmadepossibleinpartbya
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newtechnologyforsequenceanalysis,oligonucleotidecataloging,developedbyFredrikSangerand
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colleaguesinthe1960s(1,2).CarlWoese’sinsightofusingthismethod,andthechoiceofthesmall
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subunitribosomalRNA(16S/SSUrRNA)asaphylogeneticmarker,notonlyputmicroorganisms
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onaphylogeneticmap(ortree),butalsorevolutionizedthefieldofmolecularsystematicsthat
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ZukerkandlandPaulinghaspreviouslyalludedto(3). Comparativeanalysisoforganism-specific
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(oligonucleotide)sequence-signaturesinSSUrRNAledtotherecognitionofadistinctgroupof
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microorganisms (2, 4). Initially referred to as Archaeabacteria, these unusual organisms had
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‘oligonucleotidesignatures’distinctfromotherbacteria(Eubacteria),andtheywerelaterfoundto
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bedifferentfromthoseofEukarya(eukaryotes)aswell.Manyotherfeatures,includingmolecular,
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biochemicalaswellasecological,corroboratedtheuniquenessoftheArchaea.Thusthearchaeal
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conceptwasestablished(2).
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Thestudyofmicrobialdiversityandevolutionhascomealongwaysincethen: sequencing
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microbial genomes, and directly from the environment without the need for culturing is now
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routine(5,6).Thiswealthofsequenceinformationisexcitingnotonlyforcatalogingandorganizing
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biodiversity,butalsotounderstandtheecologyandevolutionofmicroorganisms–archaeaand
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bacteriaaswellaseukaryotes–thatmakeupavastmajorityoftheplanetarybiodiversity.Since
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large-scaleexplorationbythemeansofenvironmentalgenomesequencingbecamepossiblealmost
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adecadeago,therehasalsobeenapalpableexcitementandanticipationofthediscoveryofa
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fourthformoflifeora“fourthdomain”oflife(7).Thereferencehereistoafourthformofcellular
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life,butnottoviruses,whichsomehavealreadyproposedtobethefourthdomainoftheTreeof
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Life(ToL)(7,8).Ifafourthformoflifeweretobefound,whatwouldthedistinguishingfeaturesbe,
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andhowcoulditbemeasured,definedandclassified?
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Ratherthanthediscoveryofafourthdomain,andcontrarytotheexpectations,however,current
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discussioniscenteredaroundthereturntoadichotomousclassificationoflife(9-11),despitethe
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rapidexpansionofsequencedbiodiversity–hundredsofnovelphyladescriptions(12,13). The
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proposeddichotomousclassificationsschemes,unfortunately,areinsharpcontrasttoeachother,
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dependingon:(i)whethertheArchaeaconstituteamonophyleticgroup—auniquelineofdescent
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thatisdistinctfromthoseoftheBacteriaaswellastheEukarya;and(ii)whethertheArchaeaform
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asistercladetotheEukaryaortotheBacteria.Boththeissuesstemfromdifficultiesinvolvedin
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resolvingthedeepbranchesoftheToL(10,11,14).
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Thetwinissues,firstrecognizedinthe80sbasedonsingle-gene(SSUrRNA)analyses,continue
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tobethesubjectsofalong-standingdebate,whichremainsunresolveddespitelarge-scaleanalyses
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ofmulti-genedatasets(5,15-19).Inadditiontothechoiceofgenestobeanalyzed,thechoiceof
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theunderlyingcharacterevolutionmodelisatthecoreofcontradictoryresultsthateithersupports
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theThree-domainstree(5,19)ortheEocytetree(17,20).Inmanycases,addingmoredata,either
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asenhancedtaxon(species)samplingorenhancedcharacter(gene)sampling,orboth,canresolve
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ambiguities (21, 22). However, as the taxonomic diversity and evolutionary distance increases
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amongthetaxastudied,thenumberofconservedmarker-genesthatcanbeusedforphylogenomic
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analysesdecreases.Accordingly,resolvingthephylogeneticrelationshipsoftheArchaea,Bacteria
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andEukaryaisrestrictedtoasmallsetofgenes—50atmost—inspiteofthelargeincreaseinthe
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numbersofgenomessequencedandtheassociateddevelopmentofsophisticatedphylogenomic
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methods.
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Based on a closer scrutiny of the recent phylogenomic datasets employed in the ongoing
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debate,Iwillshowherethatoneofthereasonsforthispersistentambiguityisthatthe‘information’
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necessarytoresolvetheseconflictsispracticallynonexistentinthestandardmarker-genes(i.e.core-
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genes)datasetsemployedroutinelyforphylogenomics. Further,Idiscussanalyticalapproaches
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thatmaximizetheuseoftheinformationthatisingenomesequencedataandsimultaneously
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minimizephylogeneticuncertainties.Inaddition,Idiscusssimplebutimportant,yetundervalued,
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aspectsofphylogenetichypothesistesting,whichtogetherwiththenewapproachesholdpromise
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toresolvetheselong-standingissueseffectively.
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Results
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Informationincoregenesisinadequatetoresolvethearchaealradiation
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Data-displaynetworks(DDNs)areusefultoexamineandvisualizecharacterconflictsinphylogenetic
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datasets,especiallyintheabsenceofpriorknowledgeaboutthesourceofsuchconflicts,ideally
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beforedownstreamprocessingofthedataforphylogeneticinference(23,24). Whilecongruent
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datawillbedisplayedasatreeinaDDN,incongruencesaredisplayedasreticulationsinthetree.
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Fig.1Ashowsaneighbor-netanalysisoftheSSUrRNAalignmentusedtoresolvethephylogenetic
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positionoftherecentlydiscoveredAsgardarchaea(20).TheDDNisbasedoncharacterdistances
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calculatedastheobservedgeneticdistance(p-distance)of1,462characters,andshowsthetotal
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amountofconflictinthedatasetthatisincongruentwithcharacterbipartitions(splits).Theedge
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(branch)lengthsintheDDNcorrespondtothesupportfortherespectivesplits.Accordingly,two
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well-supportedsetsofsplitsfortheBacteriaandtheEukaryaareobserved.TheArchaea,however,
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doesnotformadistinct,well-resolved/well-supportedgroup,andisunlikelytocorrespondtoa
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monophyleticgroupinaphylogenetictree.
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Figure1.Data-displaynetworksdepictingthecharacterconflictsindifferentdatasetsthatemploydifferent
charactertypes.(A)SSUrRNAalignmentof1,462characters.Concatenatedproteinsequencealignmentof(B)
29core-genes,8,563characters;(C)48core-genes,9,868charactersand(D)also48core-genes,9,868SR4
recodedcharacters(datasimplifiedfrom20to4character-states).Eachnetworkisconstructedfroma
neighbor-netanalysisbasedontheobservedgeneticdistance(p-distance)anddisplayedasanequalanglesplit
network.Edge(branch)lengthscorrespondtothesupportforcharacterbipartitions(splits),andreticulationsin
thetreecorrespondtocharacterconflicts.Datasetsin(A),(C)and(D)arefromRef.20,andin(B)isfromRef.17.
Likewise,theconcatenatedproteinsequencealignmentoftheso-called‘genealogydefiningcore
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ofgenes’(25)–asetofconservedsingle-copygenes–alsodoesnotsupportauniquearchaellineage.
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Fig.1BisaDDNderivedfromaneighbor-netanalysisof8,563charactersin29concatenatedcore-
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genes(17),whileFig.1C,Disbasedon9,868charactersin44concatenatedcore-genes(alsofrom
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(20)). Eventakentogether,noneofthestandardmarkergenedatasetsarelikelytosupportthe
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monophylyoftheArchaea—akeyassertionofthethree-domainshypothesis(26). Simplyput,
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thereisnotenoughinformationinthecore-genedatasetstoresolvethearchaealradiation,orto
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determinewhethertheArchaeaarereallyuniquecomparedtotheBacteriaandEukarya.However,
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othercomplexfeatures—includingmolecular,biochemicalandphenotypiccharacters,aswell
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asecologicaladaptations—supporttheuniquenessoftheArchaea.Theseidiosyncraticarchaeal
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charactersincludethesubunitcompositionofsupramolecularcomplexesliketheribosome,DNA-
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andRNA-polymerases,biochemicalcompositionofcellmembranes,cellwalls,andphysiological
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adaptationstoenergy-starvedenvironments,amongotherthings(27,28).
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Complex phylogenomic characters minimize uncertainties regarding the unique-
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nessoftheArchaea
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Anucleotideisthesmallestpossiblelocus,andanaminoacidisaproxyforalocusofanucleotide
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triplet.Unliketheelementaryaminoacid-ornucleotide-charactersinthecore-genesdataset(Fig.1),
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theDDNinFig. 2isbasedoncomplexmolecularcharacters–genomiclocithatcorrespondto
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proteindomains,typically~200aminoacids(600nucleotides)long.Neighbor-netanalysisofprotein-
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domaindatacodedasbinarycharacters(presence/absence)isbasedontheHammingdistance
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(identicaltothep-distanceusedinFig.1). HeretheArchaeaalsoformadistinctwell-supported
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cluster,asdotheBacteriaandtheEukarya.
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Figure2.Data-displaynetworks(DDN)depictingcharacterconflictsamongcomplexphylogenomiccharacters–
genomiclocicorrespondingtoprotein-domainsinthiscase.(A)Neighbor-netanalysisbasedonHamming
distance(identicaltothep-distanceusedinFig.1)of1,732characterssampledfrom141species.(B)DDNbased
onanenrichedtaxonsamplingof81additionalspeciestotaling222speciesandamodestincreaseto1,738
characters.Thedatasetin(A)isfromRef.10,whichwasupdatedwithnovelspeciestorepresenttherecently
describedarchaealandbacterialspecies(5,12,20).
Fig2AisaDDNbasedonthedatasetthatincludesprotein-domaincohortsof141species,used
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inaphylogenomicanalysistoresolvetheuncertaintiesattherootoftheToL(29). Comparedto
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thedatainFig.1,thetaxonomicdiversitysampledfortheBacteriaandEukaryaismoreextensive,
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butlessextensivefortheArchaea; itiscomposedofthetraditionalgroupsEuryarchaeotaand
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Crenarchaeota.Fig.2BisaDDNofanenrichedsamplingof81additionalspecies,whichincludes
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representativesofthenewlydescribedarchaealgroups:TACK(30),DPANN(5),andAsgardgroup
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includingtheLokiarchaeota(20).Inaddition,speciessamplingwasenhancedwithrepresentatives
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from the candidate phyla described for Bacteria, and with unicellular species of Eukarya. The
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completelistspeciesanalyzedisinSITable1.
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Notably, the extension of the protein-domain cohort was insignificant, from 1,732 to 1,738
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distinctdomains(characters).Basedonthewell-supportedsplitsintheDDNthatformadistinct
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archaealcluster,theArchaeaarelikelytobeamonophyleticgroup(clade)inphylogeniesinferred
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fromthesedatasets.
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Dataqualityaffectsmodelcomplexityrequiredtoexplainphylogeneticdatasets
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ResolvingtheparaphylyormonophylyoftheArchaeaisrelevanttodeterminingwhethertheEocyte
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tree(Fig. 3A)ortheThree-domainstree(Fig. 3B),respectively,isabetter-supportedhypothesis.
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RecoveringtheEocytetreetypicallyrequiresimplementingcomplexmodelsofsequenceevolution
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ratherthantheirrelativelysimplerversions(11).Ingeneral,complexmodelstendtofitthedata
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better. Forinstance, accordingtoamodelselectiontestforthe29core-genesdataset, theLG
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model(31)ofproteinsequenceevolutionisabetter-fittingmodelthanotherstandardmodels,
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such as the WAG or JTT substitution model (SI-Table 2), as reported previously (17). Further, a
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relativelymorecomplexversionoftheLGmodel,withmultiplerate-categorieswasfoundtobea
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better-fittingmodelthanthesimplersingle-rate-categorymodel(Fig.3C;SI-Table2).Thefitofthe
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dataisestimatedasthelikelihoodofthebesttreegiventhemodel.
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Acomplex,multiplerate-categoriesmodelaccountsforsite-specificsubstitutionratevariation.
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Substitution-rateheterogeneityacrossdifferentsitesinthemultiple-sequencealignment(MSA)
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wasapproximatedusingadiscreteGammamodelwith4,8or12ratecategories(LG+G4,LG+G8or
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LG+G12,respectively).TheArchaeaisconsistentwithaparaphyleticgroupintreesderivedfromthe
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rate-heterogeneousversionsoftheLGmodel(Fig.3A).Furthermore,thefitofthedataimproves
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withtheincreaseincomplexityofthesubstitutionmodel(Fig. 3C).Modelcomplexityincreases
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withanyincreaseinthenumberofratecategoriesand/ortheassociatednumbersofparameters
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thatneedtobeestimated. However,witharelativelysimplerversion–arate-homogeneousLG
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model,inwhichthesubstitution-ratesareapproximatedtoasinglerate-category,theArchaeaare
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consistentwithamonophyleticgroup(Fig.3B).
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Incontrast,treesinferredfromtheprotein-domaindatasetsareconsistentwithmonophyly
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oftheArchaeairrespectiveofthecomplexityoftheunderlyingmodel(Fig. 3D-F).TheMkmodel
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(Markovkmodel)isthebest-knownprobabilisticmodelofdiscretecharacterevolution,particularly
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ofcomplexcharacterscodedasbinary-statecharacters(32,33). SincetheMkmodelassumesa
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stochasticprocessofevolution,itisabletoestimatemultiplestatechangesalongthesamebranch.
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Implementingasimplerrate-homogeneousversionoftheMkmodel(Fig. 3D),aswellasmore
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complexrate-heterogeneousversionswith4,8or12ratecategories(Mk+G4,Mk+G8orMk+G12,
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respectively),alsorecoveredtreesthatareconsistentwiththemonophylyoftheArchaea(Fig.3E)
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ThetreederivedfromtheMk+G4modelisshowninFig. 3E.WhilethetreederivedfromMk+G8
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modelisidentical(SI-Fig. 1)totheMk+G4tree,theMk+G12treeisalmostidenticalwithminor
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differencesinthebacterialsub-groups(SI-Fig.2)
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Inallcases,bipartitionsforArchaeashowstrongsupportwithposteriorprobability(PP)of0.99
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whilethatofBacteriaandEukaryaissupportedwithaPPof1.0;inspiteofsubstantiallydifferent
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fitsofthedata.TheuniquenessoftheArchaeaisalmostunambiguousinthiscase(butseenext
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section).
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Figure3.Comparisonofconcatenated-genetreesderivedfromaminoacidcharactersandgenometrees
derivedfromprotein-domaincharacters.Branchsupportisshownonlyforthemajorbranches.Scalebars
representtheexpectednumberofchangespercharacter.(A),(B)Core-genes-treederivedfromabetter-fitting
model(LG+G4)andaworsefittingmode(LG),respectively,ofaminoacidsubstitutions.(C)Modelfittodatais
rankedaccordingtheloglikelihoodratio(LLR)scores.LLRscoresarecomputedasthedifferencefromthe
best-fittingmodel(LG+G12)ofthelikelihoodscoresestimatedinPhyML.Thus,largerLLRvaluesindicateless
supportforthatmodel/treerelativetothemost-likelymodel/tree.Substitutionrateheterogeneityis
approximatedwith4,8or12ratecategoriesinthecomplexmodels,butwithasingleratecategoryinthe
simplermodel.(D),(E)aregenome-treesderivedfromabetter-fittingmodel(Mk+G4)andaworsefittingmodel
(Mk),respectively,ofprotein-domaininnovation.(F)ModelfittodataisrankedaccordinglogBayesfactor(LBF)
scores,whichlikeLLRscoresarethelogoddsofthehypotheses.LBFscoresarecomputedasthedifferencein
likelihoodscoresestimatedinMrBayes.
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Siblingsandcousinsareindistinguishablewhenreversiblemodelsareemployed
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AlthoughaDDNisusefultoidentifyanddiagnosecharacterconflictsinphylogeneticdatasetsand
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topostulateevolutionaryhypotheses,aDDNbyitselfcannotbeinterpretedasanevolutionary
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network,becausetheedgesdonotnecessarilyrepresentevolutionaryphenomenaandthenodes
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donotrepresentancestors(23,24).Therefore,evolutionaryrelationshipscannotbeinferredfrom
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aDDN.Likewise,evolutionaryrelationshipscannotbeinferredfromunrootedtrees,eventhough
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nodesinanunrootedtreedorepresentancestorsandanevolutionmodeldefinesthebranches
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(seeFig.4A).
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Figure4.Effectofalternativeadhocrootingsonthephylogeneticclassificationofarchaealbiodiversity.(A)An
unrootedtreeisnotfullyresolvedintobipartitionsattherootofthetree(i.e.apolytomousratherthana
dichotomousrootbranching)andthusprecludesidentificationofsistergrouprelationships.Itiscommon
practicetoaddauser-specifiedrootaposterioribasedonpriorknowledge(orbelief)oftheinvestigator.Four
possible(ofmany)rootingsR1-R4areshown.(B)Operationally,addingaroot(rooting)aposterioriamountsto
addingnewinformation–anewbipartitionandanancestoraswellasanevolutionarypolarity–thatis
independentofthesourcedata.(C-F)ThedifferentpossibleevolutionaryrelationshipsoftheArchaeatoother
taxa,dependingonthepositionoftheroot,areshown.Rootingisnecessarytodeterminetherecencyof
commonancestryaswellthetemporalorderofkeyevolutionarytransitionsthatdefinephylogenetic
relationships.
Anunrootedtree,unlikearootedtree,isnotanevolutionary(phylogenetic)treeperse,sinceit
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isaminimallydefinedhypothesisofevolutionorofrelationships;itis,nevertheless,usefultorule
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outmanypossiblebipartitionsandgroups(34,35).Giventhataprimaryobjectiveofphylogenetic
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analyses is to identify clades and the relationships between these clades, it is not possible to
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interpretanunrootedtreemeaningfullywithoutrootingthetree(seeFig.4A).Identifyingtherootis
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essentialto:(i)distinguishbetweenancestralandderivedstatesofcharacters,(ii)determinethe
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ancestor-descendantpolarityoftaxa,and(iii)diagnosecladesandsister-grouprelationships(Fig.
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4).Yet,mostphylogeneticsoftwareconstructonlyunrootedtrees,whicharethenconsistentwith
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severalrootedtrees(Fig.4C-F).However,anunrootedtreecannotbefullyresolvedintobipartitions,
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becauseanunresolvedpolytomy(atrifurcationinthiscase)existsneartherootofthetree(Fig.4A),
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whichotherwisecorrespondstothedeepestsplit(root)inarootedtree(Fig.4,C-F).
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Resolving the polytomy requires identifying the root of the tree. The identity of the root
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corresponds,inprinciple,toanyoneofthepossibleancestorsasfollows:
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i.Anyoneoftheinferred-ancestorsattheresolvedbipartitions(opencirclesinFig.4A),or
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ii. Anyoneoftheyet-to-be-inferred-ancestorsthatliesalongthestem-branchesoftheunre-
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solvedpolytomy(dashedlinesinFig.4A)oralongtheinternal-braches.
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Inthelattercase,rootingthetreeaposteriorionanyofthebranchesamountstoinsertinganad-
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ditionalbipartitionandanancestorthatisneitherinferredfromthesourcedatanordeducedfrom
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theunderlyingcharacterevolutionmodel. Sincestandardevolutionmodelsemployedroutinely
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cannotresolvethepolytomy,rooting,andhenceinterpretingtheTreeofLifedependson:
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i.Priorknowledge—eg.,fossilsoraknownsister-group(outgroup),or
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ii.Priorbeliefs/expectationsoftheinvestigators—eg.,simpleisprimitive(36,37),bacteriaare
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primitive(38,39),archaeaareprimitive(1),etc.
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BothoftheseoptionsareindependentofthedatausedtoinfertheunrootedToL.Somepossible
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rootingsandtheresultingrooted-treetopologiesareshownascladogramsinFig.4,C-F.Iftheroot
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liesonanyoftheinternalbranches(e.g. R1inFig. 4,A-C),orcorrespondstooneoftheinternal
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nodes, withinthearchaelradiation, theArchaeawouldnotconstituteauniqueclade(Fig. 4C).
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However, if the root lies on one of the stem-branches (R2/R3/R4 in Fig. 4 A, B), monophyly of
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theArchaeawouldbeunambiguous(Fig.4D-F).Determiningtheevolutionaryrelationshipofthe
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Archaeatoothertaxa,though,requiresidentifyingtheroot.
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Directionalevolutionmodels,unlikereversiblemodels,areabletoidentifythepolarityofstate
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transitions,andthustherootofatree(40-42).Therefore,theuncertaintyduetoapolytomousroot
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branchingisnotanissue(Fig5A).Moreover,directionalevolutionmodelsareusefultoevaluatethe
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empiricalsupportforpriorbeliefsabouttheuniversalcommonancestor(UCA)attherootofthe
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ToL(29).ABayesianmodelselectiontestimplementedtodetectdirectionaltrends(42)choosesthe
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directionalmodel,overwhelmingly(Fig. 5B),overtheunpolarizedmodelfortheprotein-domain
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datasetinFig.2B,asreportedpreviouslyforthedatasetinFig.2A(29).Further,thebest-supported
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rootingcorrespondstorootR4(Fig. 4FandFig. 5A)—monophylyoftheArchaeaismaximally
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supported(PPof1.0). Furthermore,thesister-grouprelationshipoftheArchaeatotheBacteria
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ismaximallysupported(PP1.0). Accordingly,ahigherordertaxon,Akaryotes,proposedearlier
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(Forterre1992)formsawell-supportedclade. ThusAkaryotes(orAkarya)andEukaryaaresister
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cladesthatdivergefromtheUCAattherootoftheToL,alsoasreportedpreviously(29).
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Alternativerootingsaremuchlesslikely,andarenotsupported(Fig.5C).Accordingly,indepen-
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dentoriginoftheeukaryotesaswellakaryotesisthebest-supportedscenario.TheThree-domains
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tree(rootR3,Fig.4E)is10171timeslesslikely,andthescenarioproposedbytheEocytehypothesis
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(rootR1,Fig.5A)ishighlyunlikely.Thecommonbeliefthatsimpleisprimitive,aswellasbeliefsthat
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archaeaareprimitiveorthatarchaeaandbacteriaevolvedbeforeeukaryotes,arenotsupported
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either.
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Employingcomplexmolecularcharactersmaximizesrepresentationoforthologous,
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non-recombininggenomicloci,andthusphylogeneticsignal
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GenomiclocithatcanbealignedwithhighconfidenceusingMSAalgorithmsaretypicallymore
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conservedthanthoselociforwhichalignmentuncertaintyishigh.Suchambiguouslyaligned
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Figure5.(A)Rootedtreeoflifeinferredfrompatternsofinheritanceofuniquegenomic-signatures.A
dichotomousclassificationofthediversityoflifesuchthatArchaeaisasistergrouptoBacteria,whichtogether
constituteacladeofakaryotes(Akarya).EukaryaandAkaryaaresister-cladesthatdivergefromtherootofthe
treeoflife.Eachcladeissupportedbythehighestposteriorprobabilityof1.0.Thephylogenysupportsa
scenarioofindependentoriginsanddescentofeukaryotesandakaryotes.(B)Modelselectiontestsidentify,
overwhelmingly,directionalevolutionmodelstobebetter-fittingmodels.(C)Alternativerootings,and
accordinglyalternativeclassificationsorscenariosfortheoriginsofthemajorcladesoflife,aremuchless
probableandnotsupported.
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regionsofsequencesareroutinelytrimmedoffbeforephylogeneticanalyses(43). Typically,
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the conserved well-aligned regions correspond to protein domains with highly ordered three-
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dimensional(3D)structureswithspecific3Dfolds(Fig.6A).Regionsofsequencesthataretrimmed
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usuallyshowhighervariabilityinlength,arelessorderedandareknowntoaccumulateinsertion
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anddeletion(indel)mutationsatahigherfrequencythanintheregionsthatcorrespondtofolded
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domains(44).Thesevariable,structurallydisorderedregions,whichflankthestructurallyordered
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domains,linkdifferentdomainsinmulti-domainproteins(Fig.6A).Multi-domainarchitecture(MDA),
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theN-to-Cterminalsequenceofdomainarrangement,isdistinctforaproteinfamily,anddiffersin
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closelyrelatedproteinfamilieswithsimilarfunctions(Fig.6A).ThevariationinMDAalsorelatesto
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alignmentuncertainties.
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Figure6.Alignmentuncertaintyincloselyrelatedproteinsduetodomainrecombination.(A)Multi-domain
architecture(MDA)ofthetranslationalGTPasesuperfamilybasedonrecombinationof8modulardomains.57
distinctfamilieswithvaryingMDAsareknown,ofwhich6canonicalfamiliesareshownasaschematiconthe
leftandthecorresponding3Dfoldsontheright.Aminoacidsequencesofonly2ofthe8conserveddomains
canbealignedwithconfidenceforuseinphylogeneticanalysis.Thelengthofthealignmentvariesfrom
200-300aminoacidsdependingonthesequencediversitysampled(14,76).TheEF-Tu—EF-Gparalogouspair
employedaspseudo-outgroupsfortheclassicalrootingoftherRNAtreeishighlighted.(B)Phyleticdistribution
of1,738outthe2,000distinctSCOP-domainssampledfrom222speciesusedforphylogeneticanalysesinthe
presentstudy.About70percentofthedomainsarewidelydistributedacrossthesampledtaxonomicdiversity.
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