1

PhylogenyBIOL221

Ch.26

Fig.26-1

Overview:Inves8ga8ngtheTreeofLife•  Phylogeny

•  evolu1onaryhistoryofaspecies

•  orgroupofrelatedspecies

•  Systema8cs

•  classifiesorganismsanddeterminestheirevolu1onaryrela1onships

•  Systema1sts

•  usefossil,molecular,andgene1cdatatoinferevolu1onaryrela1onships

2

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

3

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

4

•  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

5

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

6

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

7

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

8

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

9

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

10

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

11

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

12

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

3

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

13

Youshouldnowbeableto:

1.  Explainthejus1fica1onfortaxonomybasedonaPhyloCode

2.  Explaintheimportanceofdis1nguishingbetweenhomologyandanalogy

3.  Dis1nguishbetweenthefollowingterms:monophyle1c,paraphyle1c,andpolyphyle1cgroups;sharedancestralandsharedderivedcharacters;

orthologousandparalogousgenes

4.  Definehorizontalgenetransferandexplainhowitcomplicatesphylogene1ctrees

5.  Explainmolecularclocksanddiscusstheirlimita1ons