Ch 26 Phylogeny
Transcript of Ch 26 Phylogeny
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PhylogenyBIOL221
Ch.26
Fig.26-1
Overview:Inves8ga8ngtheTreeofLife• Phylogeny
• evolu1onaryhistoryofaspecies
• orgroupofrelatedspecies
• Systema8cs
• classifiesorganismsanddeterminestheirevolu1onaryrela1onships
• Systema1sts
• usefossil,molecular,andgene1cdatatoinferevolu1onaryrela1onships
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Fig.26-2
BinomialNomenclature
• CarolusLinnaeus
• 18thcentury
• publishedasystemoftaxonomybasedonresemblances
• Twokeyfeaturesofhissystemremainusefultoday
• two-partnamesforspecies
• Binomialnomenclature
• hierarchicalclassifica1on
• binomial
• two-partscien1ficnameofaspecies
• genus
• firstpartofthename
• specificepithet-secondpart
• Uniqueforeachspecieswithinthegenus
• ThefirstleKerofthegenusiscapitalized
• andtheen1respeciesnameisitalicized
• Bothpartstogethernamethespecies
• notthespecificepithetalone
BinomialNomenclature
Ophisaurusventralis
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HierarchicalClassifica8on• Linnaeus
• introducedasystemfor
groupingspecies
• inincreasinglybroad
categories
• domain,kingdom,phylum,class,
order,family,genus,species
• Topdown
• taxon
• Taxonomicunitatanylevelof
hierarchy
Fig.26-3
Species: Panthera pardus
Genus: Panthera
Family: Felidae
Order: Carnivora
Class: Mammalia
Phylum: Chordata
Kingdom: Animalia
Archaea Domain: Eukarya Bacteria
LinkingClassifica8onandPhylogeny• phylogene8ctrees
• Usedbysystema1ststodepictevolu1onaryrela1onships
Species
Canis lupus
Pantherapardus
Taxidea taxus
Lutra lutra
Canis latrans
Order Family Genus
Carnivora
Felidae M
ustelidae C
anidae
Canis
Lutra Taxidea
Panthera
• Linnaeanclassifica1onandphylogeny
• candifferfromeachother
• Systema1stshaveproposedthePhyloCode
• whichrecognizesonlygroupsthatincludeacommonancestor
• andallitsdescendants
• Ar1odactyla/Cetacea/Cetar1odactyla???
LinkingClassifica8onandPhylogeny
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• Aphylogene1ctree
• representsahypothesisaboutevolu1onaryrela1onships
• Eachbranchpoint
• representsthedivergenceoftwospecies
• Sistertaxa
• aregroupsthatshareanimmediatecommonancestor
LinkingClassifica8onandPhylogeny
Species
Canis lupus
Pantherapardus
Taxidea taxus
Lutra lutra
Canis latrans
Order Family Genus
Carnivora
Felidae M
ustelidae C
anidae
Canis
Lutra Taxidea
Panthera
• Arootedtree
• includesabranchto
representthelast
commonancestorofall
taxainthetree
• Apolytomy
• isabranchfromwhich
morethantwogroups
emerge
LinkingClassifica8onandPhylogeny
Sister taxa
ANCESTRAL LINEAGE
Taxon A
Polytomy Common ancestor of taxa A–F
Branch point (node)
Taxon B
Taxon C
Taxon D
Taxon E
Taxon F
WhatCanandCan’tLearnfromPhylogene8cTrees
• Phylogene1ctrees
• doshowpaKernsofdescent
• donotindicatewhenspeciesevolved
• orhowmuchgene1cchangeoccurredinalineage
• Itshouldn’tbeassumed
• thatataxonevolvedfromthetaxonnexttoit
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Sor8ngHomologyfromAnalogy• Organismswithsimilar
morphologiesorDNAsequences
• arelikelytobemorecloselyrelated
• thanorganismswithdifferentstructuresorsequences
• Homology
• similarityduetosharedancestry
• Analogy
• similarityduetoconvergentevolu1on
• Batandbirdwings
• arehomologousasforelimbs,butanalogousasfunc1onalwings
• Homoplasies
• Analogousstructuresormolecularsequencesthatevolvedindependently
• Homology
• canbedis1nguishedfromanalogybycomparingfossilevidenceandthedegreeofcomplexity
• Themorecomplextwosimilarstructuresarethemorelikelyitisthattheyarehomologous
Sor8ngHomologyfromAnalogy
Cladis8cs• Cladis8cs
• groupingorganismsbycommondescent
• Clade
• groupofspeciesthatincludesanancestralspeciesandallitsdescendants
• canbenestedinlargercladesbutnotallgroupingsoforganismsqualifyasclades
• Avalidcladeismonophyle8c
• signifyingthatitconsistsoftheancestorspeciesandallitsdescendants
A A A
B B B
C C C
D D D
E E E
F F F
G G G
Group III Group II
Group I
(a) Monophyletic group (clade) (b) Paraphyletic group (c) Polyphyletic group
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SharedAncestralandSharedDerivedCharacters• Comparedtoanancestor
• anorganismhasbothsharedanddifferentcharacteris1cs
• sharedancestralcharacter
• originatedinanancestorofthetaxon
• sharedderivedcharacter
• evolu1onarynoveltyuniquetoapar1cularclade
• Acharactercanbebothancestralandderived
• dependingonthecontext
InferringPhylogeniesUsingDerivedCharacters
• Wheninferringevolu1onaryrela1onships
• itisusefultoknowinwhichcladeasharedderivedcharacterfirst
appeared
TAXA
Lanc
elet
(o
utgr
oup)
Lam
prey
Sala
man
der
Leop
ard
Turt
le
Tuna
Vertebral column (backbone)
Hinged jaws
Four walking legs
Amniotic (shelled) egg CH
AR
AC
TER
S
Hair
(a) Character table
Hair
Hinged jaws
Vertebral column
Four walking legs
Amniotic egg
(b) Phylogenetic tree
Salamander
Leopard
Turtle
Lamprey
Tuna
Lancelet (outgroup)
0
0 0
0
0
0
0 0
0
0
0 0
0 0 0 1
1 1
1 1 1
1
1 1
1
1
1 1
1 1
• outgroup
• speciesorgroupofspeciesthatiscloselyrelatedtothe
• Ingroup
• thevariousspeciesbeingstudied
• Systema1sts
• compareeachingroupspecieswiththeoutgroup
• todifferen1atebetweensharedderivedandsharedancestralcharacteris1cs
InferringPhylogeniesUsingDerivedCharacters
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PhyloTreeswithPropor8onalBranchLengths• Insometrees
• Branchlengthcanreflectthenumberofgene1cchangesthathavetakenplaceinapar1cularDNAsequenceinthatlineage
Drosophila
Lancelet
Zebrafish
Frog
Human
Chicken
Mouse
• Inothertrees
• branchlengthcanrepresentchronological1me
• branchingpointscanbedeterminedfromthefossilrecord
Drosophila
Lancelet
Zebrafish
Frog
Human
Chicken
Mouse
CENOZOIC
Present 65.5
MESOZOIC
251 Millions of years ago
PALEOZOIC
542
PhyloTreeswithTimeScale
MaximumParsimonyandMaximumLikelihood• Systema1sts
• Canneverbesureoffindingthebesttreeinalargedataset
• Cannarrowpossibili1es
• byapplyingtheprinciplesofmaximumparsimonyandmaximumlikelihood
• Maximumparsimony
• thetreethatrequiresthefewestevolu1onaryevents(appearancesofsharedderivedcharacters)
• isthemostlikely–Occam’srazor
• Maximumlikelihood
• givencertainrulesabouthowDNAchangesover1me
• atreecanbefoundthatreflectsthemostlikelysequenceofevolu1onaryevents
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Fig.26-14
Human
15%
Tree 1: More likely Tree 2: Less likely (b) Comparison of possible trees
15% 15%
5%
5%
10%
25% 20%
40%
40%
30% 0
0
0
(a) Percentage differences between sequences
Human Mushroom
Mushroom
Tulip
Tulip
Phylogene8cTreesasHypotheses• Thebesthypothesesforphylogene1ctrees
• fitthemostdata:morphological,molecular,andfossil
• Phylogene8cbracke8ng
• allowsustopredictfeaturesofanancestorfromfeaturesofitsdescendents
Common ancestor of crocodilians, dinosaurs, and birds
Birds
Lizards and snakes
Crocodilians
Ornithischian dinosaurs
Saurischian dinosaurs
Fig.26-17
Eggs
Front limb
Hind limb
(a) Fossil remains of Oviraptor and eggs
(b) Artist’s reconstruction of the dinosaur’s posture
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evolu8onaryhistoryinthegenome
• Comparingnucleicacidsorothermoleculestoinferrelatedness
• isavaluabletoolfortracingorganisms’evolu1onaryhistory
• DNAthatcodesforrRNA
• changesrela1velyslowlyandisusefulforinves1ga1ngbranchingpointshundredsofmillionsofyearsago
• mtDNAevolvesmorerapidly
• canbeusedtoexplorerecentevolu1onaryevents
GeneDuplica8onsandGeneFamilies• Geneduplica1on
• increasesthenumberofgenesinthegenome
• providingmoreopportuni1esforevolu1onarychanges
• Likehomologousgenes
• duplicatedgenescanbetracedtoacommonancestor
• Orthologousgenes
• foundinasinglecopyinthegenome
• homologousbetweenspecies
• candivergeonlya^erspecia1onoccurs
• Paralogousgenes
• resultfromgeneduplica1on
• soarefoundinmorethan
onecopyinthegenome
• candivergewithintheclade
thatcarriesthem
• ando^enevolvenew
func1ons
GeneDuplica8onsandGeneFamilies
(b) Paralogous genes
(a) Orthologous genes
Ancestral gene
Paralogous genes
Ancestral species
Speciation with divergence of gene
Gene duplication and divergence
Species A after many generations
Species A Species B
Species A
Orthologous genes
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GenomeEvolu8on• Orthologousgenes
• arewidespreadandextend
acrossmanywidelyvaried
species
• Genenumberandthecomplexityof
anorganism
• arenotstronglylinked
• Genesincomplexorganisms
• appeartobeveryversa1leand
eachgenecanperformmany
func1ons
MolecularClocks• Molecularclock
• usesconstantratesofevolu1oninsomegenes
• toes1matetheabsolute1meofevolu1onarychange
• Inorthologousgenes
• nucleo1desubs1tu1onsarepropor1onal
• tothe1mesincetheylastsharedacommonancestor
• Inparalogousgenes
• nucleo1desubs1tu1onsarepropor1onal
• tothe1mesincethegenesbecameduplicated
• Molecularclocksarecalibratedagainstbrancheswhosedatesareknownfromthefossilrecord
Divergence time (millions of years)
Num
ber o
f mut
atio
ns
120
90
90
60
60
30
30 0
0
MolecularClocks
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NeutralTheory
• Neutraltheory
• statesthatmuchevolu1onarychangeingenesandproteins
• hasnoeffectonfitnessandthereforeisnotinfluencedbyDarwinian
selec1on
• therateofmolecularchangeinthesegenesandproteins
• shouldberegularlikeaclock
Difficul8eswithMolecularClocks• Themolecularclock
• doesnotrunassmoothlyasneutral
theorypredicts
• Irregulari1esresultfromnaturalselec1on
• inwhichsomeDNAchangesarefavored
overothers
• Es1matesofevolu1onarydivergencesolder
thanthefossilrecord
• haveahighdegreeofuncertainty
• Theuseofmul1plegenesmayimprove
es1mates
Fig.26-20
Year
Inde
x of
bas
e ch
ange
s be
twee
n H
IV s
eque
nces
1960
0.20
1940 1920 1900 0
1980 2000
0.15
0.10
0.05
Range
Computer model of HIV
FromTwoKingdomstoThreeDomains• Earlytaxonomists
• classifiedallspeciesaseitherplantsoranimals
• Later,fivekingdomswererecognized
• Monera(prokaryotes),Pro1sta,Plantae,Fungi,andAnimalia
• Morerecently
• thethree-domainsystemhasbeenadopted
• Bacteria,Archaea,andEukarya
• Thethree-domainsystemissupportedbydatafrommanysequencedgenomes
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Fig.26-21
Fungi
EUKARYA
Trypanosomes
Green algae Land plants
Red algae
Forams Ciliates
Dinoflagellates
Diatoms
Animals
Amoebas Cellular slime molds
Leishmania
Euglena
Green nonsulfur bacteria Thermophiles
Halophiles
Methanobacterium
Sulfolobus
ARCHAEA
COMMON ANCESTOR
OF ALL LIFE
BACTERIA
(Plastids, including chloroplasts)
Green sulfur bacteria
(Mitochondrion)
Cyanobacteria
Chlamydia Spirochetes
• Therehavebeensubstan1al
interchangesofgenes
• betweenorganismsindifferent
domains
• Horizontalgenetransfer
• movementofgenesfromone
genometoanother
• Verycommoninprokaryotes
• Virusesandeukaryotesdo
ittoo
• complicateseffortstobuilda
treeoflife
FromTwoKingdomstoThreeDomainsFig.26-22
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Archaea
Bacteria
Eukarya
Billions of years ago
4 2 1 0
• Someresearchers
• suggestthateukaryotes
arose
• asanendosymbiosis
betweenabacterium
andarchaean
• Ifso,earlyevolu1onary
rela1onships
• mightbebeKerdepicted
byaringoflife
• insteadofatreeoflife
RingofLife?
Archaea Bacteria
Eukarya
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Youshouldnowbeableto:
1. Explainthejus1fica1onfortaxonomybasedonaPhyloCode
2. Explaintheimportanceofdis1nguishingbetweenhomologyandanalogy
3. Dis1nguishbetweenthefollowingterms:monophyle1c,paraphyle1c,andpolyphyle1cgroups;sharedancestralandsharedderivedcharacters;
orthologousandparalogousgenes
4. Definehorizontalgenetransferandexplainhowitcomplicatesphylogene1ctrees
5. Explainmolecularclocksanddiscusstheirlimita1ons