w2 by jenny

8/7/2019 W2 by Jenny

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lecture2

• lagerstatten=motherlode;excellentfossilpreservationatthesite

• systemanaturaebycarolusLinnaeus(KingPhilipCameOverForGoodSex)

o impliesanorder,butdoesn’ttellyouhowthesespecies(spp)arerelated• hennig–phylogeneticsystematics–“cladistics”

• cladistics–amethodofclassifyinganimalsandplantsaccordingtotheproportionofmeasurablecharacteristicstheyhaveincommon

• assumptionsofcladistics:o iforganismsarerelatedbydescent,thecloserdescent=themorerecent

commonancestry

o becauseorganismschangethroughevolutionarytime,theypassontheir

changestotheiroffspring

o therefore,organismsthataremostcloselyrelatedshouldsharethemost

derivedcharacters,acquiredbyevolution,thatarenotpresentinother

groupso

thesearchforthesesetsoftraitsshouldgiveusthebestapproximationofthe

evolutionarysequence(aphylogeny)• branchlengthusuallyreferstomoleculardatasuchthatlongerbranches=longer

timeperiods

• clade=agroupthatincludesMRCAandallcommondescendents• parsimony=usethefeweststepsnecessarytoconstructalegitimatetree–makeit

assimpleaspossible

o lookforthesimplestpossibleexplanationsoyouonlyhaveafewtraitsuniquetoataxa

o thisisahypothesisaboutevolution

• crown-baseddefinition–unifyyourcladesoitincorporateseverythingdescended

fromtheMRCA

• trait-baseddefinition–includeeveryanimalthathadfur,oranopposablethumbo worksforextanttaxa,butnotalwaysforextincttaxa

• monophyleticgroup–includestheMRCAandallitsdescendants

• paRaphyleticgroup–includestheMRCA,butdoesn’tincludeallofitsdescendants

• pOlyphyleticgroup–nOMRCAoralldescendents;2mono-orpara-phyleticclades

incorrectlygroupedtogether

• systematics–thescientificstudyofthediversityoforganisms,whichrevealsthe

evolutionaryrelationshipsbetweenorganisms

• taxonomy–(asubdivisionofsystematics)–thetheoryandpracticeofclassifyingorganisms

• rejectingthesppapproach–somepplsuggesttrashingallnamesandusingaunique

numbertoIDeverythingonearth–orperhapsusingcytochrome1todefineaspp• phylogeny–ahypothesisthatdescribesthehistoryofdescent ofagroupoforganismsfromtheircommonancestor

• bifurcatingtree–alineageisrepresentedasabranchingtree,inwhicheachsplitor

noderepresentsaspeciationevent

o branchinginto2,notmany

o doesn’tnecessarilyhappenthatway,butit’sthemostparsimonious

explanation



• starburstphylogenies

• phylogenetictreesareconstructedbyanalyzingevolutionarychangesinthetraitsoforganisms

• cladogenesis;node;stem;crowngroup• ancestraltraits–inheritedfromacommonancestor(hair,milkformarsupials,

monotremesandeutheria)• derivedtraits–atraitthatdiffersfromitsancestralform(placentaforeutheria

(non-marsupial/monotrememammals),hairandmilkformammaliaasagroup)

• homologous–anyfeatures(DNAsequences,behavioral,anatomical)sharedby2+

sppthatbothinheritedthetraitfromacommonancestor

o thesimilarityisduetotheirsharedancestry

o thevertebralcolumninvertebrates

o bonesinbird/batwings

• analogous–performingasimilarfunctionbuthavingadifferentevolutionaryorigin

(wings/flightinpterosaurs,batsandbirds)•

convergentevolution–whenindependentlyevolvedfeaturessubjectedtosimilar

selectivepressuresbecomesuperficiallysimilaro convergenttraitsareindependentlyderived

• evolutionaryreversal–whenacharacterrevertsfromaderivedstatebacktoan

ancestralstate• homoplasies–traitsthataresimilarforsomereasonotherthaninheritancefroma

commonancestor

o lossofeyesincaecilians=evolutionaryreversalandahomoplasy(they’reamphibiansthatlooklikeeyelesssnakes)

• outgroup–alineagethatiscloselyrelatedtoaningroup(thelineageofinterest)buthasbranchedofffromtheingroupbelowitsbaseontheevolutionarytree

o ancestraltraitsshouldbefoundintheoutgroupandtheingroup;derived

traitsarefoundonlyintheingroup• toreconstructaphylogeny:

o 1.selectagroupoforganismstoclassify(theingroup)andanappropriate

outgroup

o 2.choosethecharactersthatwillbeusedintheanalysisandidentifythe

possibleforms(traits)ofthecharacter

o determinetheancestralandderivedtraits

o distinguishhomologousfromhomoplastictraits

• systematistsusephysiological,behavioral,molecular,andstructuralcharactersoflivingandfossilorganismstoreconstructphylogenies

• richness=numberofdifferenttaxa(alpha,betadiversity,etc)• diversity=numberofdifferenttaxaandtheirrelativeabundances

evolutionarythoughtlecture

• homology–anysimilaritybetweencharactersthatareduetotheirsharedancestry

• homoplasy–whencharactersaresimilar,butnotderivedfromacommonancestor

• synapomorphy–charactersthataresharedbyagroupoforganisms,butarenotfoundintheancestorsofthatgroup



• parsimony–adoptionofthesimplestassumptionintheformulationofatheoryor

intheinterpretationofdata

• Lamarckianevolution–sppcouldchangethroughtheuseordisuseofstructures

duringtheindividualorganism’slifetimeo theenvironmentpresentsconditionswhichproduce“needs”inorganisms

o needsleadtomodificationoforgansandbehaviorso usedpartsincreaseinsize,disusedpartsdecreaseinsize

o modificationoccursduringthelifespanoftheorganismandarepassedonto

theorganism’soffspring

• uniformatarianism–thesamenaturallawsandprocessesthatoperateintheuniversenow,havealwaysoperatedintheuniverseinthepastandapply

everywhereintheuniverse

• Malthus–humansreproduceatahigherratethantheirresourcescansustainthem;

theonlythingkeepingthemincheckisdeathanddisease(competition)

• darwin’sargumentfornaturalselectiono

1.organismshaveagreatpotentialfertility,permittingexponentialgrowthof

popns(Malthus)o 2.naturalpopnsdon’tnormallyincreaseexponentially,butremainfairly

constantinsize(Darwin)

o 3.naturalresourcesarelimited(Malthus)o 4.astruggleforexistenceoccursamongorganismsinapopulation

(competition,Malthus)

o 5.variationoccursamongorganismswithinpopns(darwin’spigeons,barnacles)

o 6.variationisheritable(animalbreeding)o 7.varyingorganismsshowdifferentialsurvivalandreproduction,favoring

advantageoustraits=naturalselection(Darwin)

o 8.naturalselection,actingovermanygenerations,graduallyproducesnewadaptationsandnewspecies

• Wallace

• thejointletter–hookerandlyell

• themodernsynthesis–Mendel;THmorgan–genesonchromosomes(theflylab);

mutationssupplytherawmatlfornaturalselectiontoactupon

o JBSHaldane,SewallWright,andRonaldFisher

o mathematicscanexplainhowselectionandmutationcanaffectgene

frequencieswithinpopulationso populationgeneticsyieldsagenotypeexpressedinthephenotype

o populationsaregenepoolswithvariationingeneticfrequencieso geneticvariationisaresultofrandomsubstitutionsofbasepairsinthe

genotypebymutation,andinsexualorganisms,thevariationcanalsobe

introducedwithrecombinationo thevariationingenotyperesultsinavariationinthephenotype,whichis

thenactedonbynaturalselection

o naturalselectioncullsthe‘lessfit’oftherandomvariants



o thus,evolutionhasno‘direction,’excepttowardsincreasingfitness,whichin

anextremeformmeansthateveryfeatureinanorganismishonedbynaturalselection(panselectionism)

ReadingsforWeekTwoNote:Ioutlinedthepapersinthe1,2,3formMattsuggested,where1)isthequestionposed

inthepaper,2)isthemethodology,and3)isthemainconclusion.Hippopotamusandwhalephylogeny,Thewissenetal.2007

1. Arehipposandcetacea(whales,dolphins,porpoises)placedcorrectlyontheirmammalianphylogeny?

2. GeislerandTheodorperformedanewanalysisusingweightedcharacters

(homoplasiesweredown-weighted)tocreatewhattheythoughtwasthemostparsimonioustree.Theyemphasizetheimportanceofincludingmoleculardataas

well.

3. Theauthorsofthebriefcommentary(GeislerandTheodor)thinkhippposarethemostcloselyrelatedextanttaxontoCetacea.Theauthorsoftheinitialpaper

(Thewissenetal.)respondedbysayingthatGeislerandTheodorupheldtheirmainfinding,whichwasthatraoellids(nowextinct)arethesistergrouptocetaceans.

“Herbivorousecomorphologyandspecializationpatternsintheropoddinosaurevolution,”

ZannoandMakovicky20111. Howdoweusemorphologicalfactorstodetermineifsomethingwascarnivorousor

herbivorous?

2. TheauthorsidentifiedlotsofcharactersreliablefortheindicationofherbivoryusingthreestatisticalanalysesandthentestedthesetraitsinCoelurosauria.

3. Usingstats,youcanhavesomefairconfidenceaboutthefeedingbehaviorsoflong-extinctanimals.WithinCoelurosauria,thereisevidenceofincreasingspecialization

toherbivoryinsomeclades,indicatingthatthecoelurosaurianbeakwaslikely

correlatedwithanherbivorousdiet.Thisisanexampleofecomorphology,whichisthestudyoftherelationshipbetweentheecologicalroleofanindividualandits

morphologicaladaptations(structureandfunction).

Evolutionofanatomyandgenecontrol,Koentges20081. Shouldtherebemorecommunicationbetweenthesubdisciplinesofbiology?

2. Koentgesdidadetailedliteratureviewandprovidedalotofhisownanalysisandsuggestionsforpotentialcollaborations.

3. Weneedtointegratedifferentdisciplines(e.g.,paleontology,evodevo,taxonomy,

genomics,molecularbio,etc.)toanswerthebigquestionsingenomicsystemsbiology.Wealsoneedalargecentralizeddatabasetointegratedataacross

subdisciplines.

StudyingFunctionandBehaviorintheFossilRecord,Benton20101. Howdopaleobiologistsuseformtostudyfunction?

2. Bentondiscusses/analyzesthethreemaintechniquesusedtoinferfunctionandbehaviorfromfossils:empiricalevidence,comparisonwithmodernanalogs,and

biomechanicalmodeling.Hedoesn’treallycritiquethesemethods,though.

3. Usingthesethreemaintechniques,paleobiologistscamakeevidence-basedreconstructionsandreallyinferfunctionfromform.

w2 by jenny

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