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    CSSForums>CSSOptionalsubjects>GroupV>ZoologyNotesforZoology

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    Sunday,September23,2007

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    zoologygeneticdrift

    Geneticdrift

    Inpopulationgenetics,geneticdrift(ormorepreciselyallelicdrift)isthestatisticaleffectthatresultsfromtheinfluencethatchancehasonthesurvivalofalleles(variantsofagene).Theeffectmaycauseanallele,andthebiologicaltraitthatitconfers,tobecomemorecommonorrareoversuccessivegenerations.Ultimately,thedriftmayeitherremovetheallelefromthegenepoolorremoveallotheralleles.Whereasnaturalselectionisthetendencyofbeneficialallelestobecomemorecommonovertime(anddetrimentaloneslesscommon),geneticdriftisthefundamentaltendencyofanyalleletovaryrandomlyinfrequencyovertimeduetostatisticalvariationalone,solongasitdoesnotcompriseallornoneofthedistribution.

    Chanceaffectsthecommonalityorrarityofanallele,becausenotraitguaranteessurvivalofagivennumberofoffspring.Thisisbecausesurvivaldependsonnongeneticfactors(suchasthepossibilityofbeinginthewrongplaceatthewrongtime).Inotherwords,evenwhenindividualsfacethesameodds,theywilldifferintheirsuccess.Araresuccessionofchanceeventsratherthannaturalselectioncanthusbringatraittopredominance,causingapopulationorspeciestoevolve.

    Animportantaspectofgeneticdriftisthatitsrateisexpectedtodependstronglyonpopulationsizeasaconsequenceofthelawoflargenumbers.Whenmanyindividualscarryaparticularallele,andallfaceequalodds,thenumberofoffspringtheycollectivelyproducewillonlyslightlydifferfromthe

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    expectedvalue,whichistheexpectedaverageperindividualtimesthenumberofindividuals.Butwithasmalleffectivebreedingsize,adeparturefromthenorminoneindividualcausesadisproportionatelygreaterdeviationfromtheexpectedresult.Thereforesmallpopulationsaresubjecttomoredriftthanlargeones.Thisisalsothebasisforthefoundereffect,aproposedmechanismofspeciation.

    Bydefinition,geneticdrifthasnopreferreddirection.Aneutralallelemaybeexpectedtoincreaseordecreaseinanygivengenerationwithequalprobability.Givensufficientlylongtime,however,themathematicsofgeneticdrift(cf.GaltonWatsonprocess)predicttheallelewilleitherdieoutorbepresentin100%ofthepopulation,afterwhichtimethereisnorandomvariationintheassociatedgene.Thusgeneticdrifttendstosweepgenevariantsoutofapopulationovertime,suchthatallmembersofaspecieswouldeventuallybehomozygousforthisgene.Inthisregard,geneticdriftopposesgeneticmutationwhichintroducesnovelvariantsintothepopulationaccordingtoitsownrandomprocesses.

    Allelefrequencies

    Fromtheperspectiveofpopulationgenetics,driftisa"samplingeffect."Toillustrate:onaverage,coinsturnupheadsortailswithequalprobability.Yetjustafewtossesinarowareunlikelytoproduceheadsandtailsinequalnumber.Thenumbersarenomorelikelytobeexactlyequalformanytossesinarow,butthediscrepancyinnumbercanbeverysmall(inpercentageterms).Asanexample,tentossesturnupatleast70%headsaboutonceineverysixtries,butthechanceofahundredtossesinarowproducingatleast70%headsisonlyaboutonein25,000.

    Similarly,inabreedingpopulation,ifanallelehasafrequencyofp,probabilitytheorydictatesthat(ifnaturalselectionisnotacting)inthefollowinggeneration,afractionpofthepopulationwillinheritthatparticularallele.However,aswiththecointossabove,allelefrequenciesinrealpopulationsarenotprobabilitydistributionsrather,theyarearandomsample,andarethussubjecttothesamestatisticalfluctuations(samplingerror).

    Whentheallelesofagenedonotdifferwithregardtofitness,onaveragethenumberofcarriersinonegenerationisproportionaltothenumberofcarriersinthepreviousgeneration.Buttheaverageisnevertallied,becauseeachgenerationparentsthenextoneonlyonce.Thereforethefrequencyofanalleleamongtheoffspringoftendiffersfromitsfrequencyintheparentgeneration.Intheoffspringgeneration,theallelemightthereforehaveafrequencyp',slightlydifferentfromp.Inthissituation,theallelefrequenciesaresaidtohavedrifted.Notethatthefrequencyofthealleleinsubsequentgenerationswillnowbedeterminedbythenewfrequencyp',meaningthatdriftisamemorylessprocessandmaybemodeledasaMarkovprocess.

    Asinthecointossexampleabove,thesizeofthebreedingpopulation(theeffectivepopulationsize)governsthestrengthofthedrifteffect.Whentheeffectivepopulationsizeissmall,geneticdriftwillbestronger.

    Driftingallelesusuallyhaveafinitelifetime.Asthefrequencyofanalleledriftsupanddownoversuccessivegenerations,eventuallyitdriftsuntilfixationthatis,iteitherreachesafrequencyofzero,anddisappearsfromthepopulation,oritreachesafrequencyof100%andbecomestheonlyalleleinthepopulation.Subsequenttothelatterevent,theallelefrequencycanonlychangebytheintroductionofanewallelebyanewmutation.

    Thelifetimeofanalleleisgovernedbytheeffectivepopulationsize.Inaverysmallpopulation,onlyafewgenerationsmightberequiredforgeneticdrifttoresultinfixation.Inalargepopulation,itwouldtakemanymoregenerations.Onaverage,anallelewillbefixedin4Negenerations,whereNeistheeffectivepopulationsize.

    AccordingtotheHardyWeinbergPrinciple,whichholdsthatallelefrequenciesinagenepoolwillnotchangeovertime,apopulationmustbesufficientlylargetopreventgeneticdriftfromchangingallelefrequenciesovertime.Thisiswhythelawisunstableinasmallpopulation.

    Driftversusselection

    Geneticdriftandnaturalselectionrarelyoccurinisolationfromeachotherbothforcesarealwaysatplayinapopulation.However,thedegreetowhichallelesareaffectedbydriftandselectionvariesaccordingtocircumstance.

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    Inalargepopulation,wheregeneticdriftoccursveryslowly,evenweakselectiononanallelewillpushitsfrequencyupwardsordownwards(dependingonwhetherthealleleisbeneficialorharmful).However,ifthepopulationisverysmall,driftwillpredominate.Inthiscase,weakselectiveeffectsmaynotbeseenatallasthesmallchangesinfrequencytheywouldproduceareovershadowedbydrift.

    Geneticdriftinpopulations

    Driftcanhaveprofoundandoftenbizarreeffectsontheevolutionaryhistoryofapopulation.Theseeffectsmaybeatoddswiththesurvivalofthepopulation.

    Inapopulationbottleneck,wherethepopulationsuddenlycontractstoasmallsize(believedtohaveoccurredinthehistoryofhumanevolution),geneticdriftcanresultinsuddenanddramaticchangesinallelefrequencythatoccurindependentlyofselection.Insuchinstances,manybeneficialadaptationsmaybeeliminatedevenifpopulationlatergrowslargeagain.

    Similarly,migratingpopulationsmayseeafoundereffect,whereafewindividualswithararealleleintheoriginatinggenerationcanproduceapopulationthathasallelefrequenciesthatseemtobeatoddswithnaturalselection.Founder'seffectsaresometimesheldtoberesponsibleforhighfrequenciesofsomegeneticdiseases.

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    Sunday,September23,2007

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    zoologynitrogencycle

    TheNitrogenCycle

    Allliferequiresnitrogencompounds,e.g.,proteinsandnucleicacids.Air,whichis79%nitrogengas(N2),isthemajorreservoirofnitrogen.Butmostorganismscannotusenitrogeninthisform.

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    Plantsmustsecuretheirnitrogenin"fixed"form,i.e.,incorporatedincompoundssuchas:

    nitrateions(NO3)ammonia(NH3)urea(NH2)2CO

    Animalssecuretheirnitrogen(andallother)compoundsfromplants(oranimalsthathavefedonplants).

    Fourprocessesparticipateinthecyclingofnitrogenthroughthebiosphere:

    1.nitrogenfixation2.decay3.nitrification4.denitrification

    Microorganismsplaymajorrolesinallfourofthese.

    NitrogenFixation

    Thenitrogenmolecule(N2)isquiteinert.Tobreakitapartsothatitsatomscancombinewithotheratomsrequirestheinputofsubstantialamountsofenergy.

    Threeprocessesareresponsibleformostofthenitrogenfixationinthebiosphere:

    AtmosphericfixationbylightningBiologicalfixationbycertainmicrobesaloneorinasymbioticIndustrialfixation

    AtmosphericFixation

    Theenormousenergyoflightningbreaksnitrogenmoleculesandenablestheiratomstocombinewithoxygenintheairformingnitrogenoxides.Thesedissolveinrain,formingnitrates,thatarecarriedtotheearth.

    Atmosphericnitrogenfixationprobablycontributessome58%ofthetotalnitrogenfixed.

    IndustrialFixation

    Undergreatpressure,atatemperatureof600C,andwiththeuseofacatalyst,atmosphericnitrogenandhydrogen(usuallyderivedfromnaturalgasorpetroleum)canbecombinedtoformammonia(NH3).Ammoniacanbeuseddirectlyasfertilizer,butmostofitsisfurtherprocessedtoureaandammoniumnitrate(NH4NO3).

    BiologicalFixation

    Theabilitytofixnitrogenisfoundonlyincertainbacteriaandarchaea.

    Someliveinasymbioticrelationshipwithplantsofthelegumefamily(e.g.,soybeans,alfalfa).

    Someestablishsymbioticrelationshipswithplantsotherthanlegumes(e.g.,alders).

    Someestablishsymbioticrelationshipswithanimals,e.g.,termitesand"shipworms"(woodeatingbivalves).

    Somenitrogenfixingbacterialivefreeinthesoil.

    Nitrogenfixingcyanobacteriaareessentialtomaintainingthefertilityofsemiaquaticenvironmentslikericepaddies.

    BiologicalnitrogenfixationrequiresacomplexsetofenzymesandahugeexpenditureofATP.

    Althoughthefirststableproductoftheprocessisammonia,thisisquicklyincorporatedintoprotein

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    andotherorganicnitrogencompounds.

    Decay

    Theproteinsmadebyplantsenterandpassthroughfoodwebsjustascarbohydratesdo.Ateachtrophiclevel,theirmetabolismproducesorganicnitrogencompoundsthatreturntotheenvironment,chieflyinexcretions.Thefinalbeneficiariesofthesematerialsaremicroorganismsofdecay.Theybreakdownthemoleculesinexcretionsanddeadorganismsintoammonia.

    Nitrification

    Ammoniacanbetakenupdirectlybyplantsusuallythroughtheirroots.However,mostoftheammoniaproducedbydecayisconvertedintonitrates.Thisisaccomplishedintwosteps:

    BacteriaofthegenusNitrosomonasoxidizeNH3tonitrites(NO2).

    BacteriaofthegenusNitrobacteroxidizethenitritestonitrates(NO3).Thesetwogroupsofautotrophicbacteriaarecallednitrifyingbacteria.Throughtheiractivities

    (whichsupplythemwithalltheirenergyneeds),nitrogenismadeavailabletotherootsofplants.

    Manysoilsalsocontainarchaealmicrobes,assignedtotheCrenarchaeota,thatconvertammoniatonitrites.Whilemoreabundantthanthenitrifyingbacteria,itremainstobeseenwhethertheyplayasimportantaroleinthenitrogencycle.

    Manylegumes,inadditiontofixingatmosphericnitrogen,alsoperformnitrificationconvertingsomeoftheirorganicnitrogentonitritesandnitrates.Thesereachthesoilwhentheyshedtheirleaves.

    Denitrification

    Thethreeprocessesaboveremovenitrogenfromtheatmosphereandpassitthroughecosystems.

    Denitrificationreducesnitratestonitrogengas,thusreplenishingtheatmosphere.

    Onceagain,bacteriaaretheagents.Theylivedeepinsoilandinaquaticsedimentswhereconditionsareanaerobic.Theyusenitratesasanalternativetooxygenforthefinalelectronacceptorintheirrespiration.

    Thustheyclosethenitrogencycle.

    Arethedenitrifierskeepingup?

    Agriculturemaynowberesponsibleforonehalfofthenitrogenfixationonearththrough

    theuseoffertilizersproducedbyindustrialfixationthegrowingoflegumeslikesoybeansandalfalfa.

    Thisisaremarkableinfluenceonanaturalcycle.

    Arethedenitrifierskeepingupthenitrogencycleinbalance?Probablynot.Certainly,thereareexamplesofnitrogenenrichmentinecosystems.Onetroublingexample:the"blooms"ofalgaeinlakesandriversasnitrogenfertilizersleachfromthesoilofadjacentfarms(andlawns).Theaccumulationofdissolvednutrientsinabodyofwateriscalledeutrophication.

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    zoologycellbiomitochondria

    Mitochondria

    Mitochondriaarerodshapedorganellesthatcanbeconsideredthepowergeneratorsofthecell,convertingoxygenandnutrientsintoadenosinetriphosphate(ATP).ATPisthechemicalenergy"currency"ofthecellthatpowersthecell'smetabolicactivities.Thisprocessiscalledaerobic

    respirationandisthereasonanimalsbreatheoxygen.Withoutmitochondria(singular,mitochondrion),higheranimalswouldlikelynotexistbecausetheircellswouldonlybeabletoobtain

    energyfromanaerobicrespiration(intheabsenceofoxygen),aprocessmuchlessefficientthanaerobicrespiration.Infact,mitochondriaenablecellstoproduce15timesmoreATPthantheycouldotherwise,andcomplexanimals,likehumans,needlargeamountsofenergyinordertosurvive.

    Thenumberofmitochondriapresentinacelldependsuponthemetabolicrequirementsofthatcell,andmayrangefromasinglelargemitochondriontothousandsoftheorganelles.Mitochondria,whicharefoundinnearlyalleukaryotes,includingplants,animals,fungi,andprotists,arelargeenoughtobeobservedwithalightmicroscopeandwerefirstdiscoveredinthe1800s.Thenameoftheorganelleswascoinedtoreflectthewaytheylookedtothefirstscientiststoobservethem,stemmingfromtheGreekwordsfor"thread"and"granule."Formanyyearsaftertheirdiscovery,mitochondriawerecommonlybelievedtotransmithereditaryinformation.Itwasnotuntilthemid1950swhenamethodforisolatingtheorganellesintactwasdevelopedthatthemodernunderstandingofmitochondrialfunctionwasworkedout.Theelaboratestructureofamitochondrionisveryimportanttothefunctioningoftheorganelle.Twospecializedmembranesencircleeachmitochondrionpresentinacell,dividingtheorganelleintoanarrowintermembranespaceandamuchlargerinternalmatrix,eachofwhichcontainshighlyspecializedproteins.Theoutermembraneofamitochondrioncontainsmanychannelsformedbytheproteinporinandactslikeasieve,filteringoutmoleculesthataretoobig.Similarly,theinnermembrane,whichishighlyconvolutedsothatalargenumberofinfoldingscalledcristaeareformed,alsoallowsonlycertainmoleculestopassthroughitandismuchmoreselectivethantheoutermembrane.Tomakecertainthatonlythosematerialsessentialtothematrixareallowedintoit,theinnermembraneutilizesagroupoftransportproteinsthatwillonlytransportthecorrectmolecules.Together,thevariouscompartmentsofamitochondrionareabletoworkinharmonytogenerateATPinacomplexmultistepprocess.Mitochondriaaregenerallyoblongorganelles,whichrangeinsizebetween1and10micrometersinlength,andoccurinnumbersthatdirectlycorrelatewiththecell'slevelofmetabolicactivity.Theorganellesarequiteflexible,however,andtimelapsestudiesoflivingcellshavedemonstratedthatmitochondriachangeshaperapidlyandmoveaboutinthecellalmostconstantly.Movementsoftheorganellesa...