3. The reconstruction of phylogeny

The first Darwinian principle told that every phylogenetic tree has one common ancestor.

Phylogenetic analysis is the study of taxonomic relationships among lineages.

Willi Hennig (1913-1976)

Phylogenetic systematicsCladistics (greek κλάδος: branch)

Numerical taxonomy

Robert Sokal(1927-)

http://www.eol.org/http://tolweb.org/tree/phylogeny.htmlhttp://www.faunaeur.org/

Ancestor

a

b

c ee

d

f

The cladistic methodology

A B C D Apomorphies are common derived characters.

Autapomorphies are characters that are restricted to single lineages.

Plesiomorphies are ancestral derived characters.

adf ade abc abd

b: Synapomorphy of lineage C+D d: Plesiomorphy of lineage A It is a symplesiomorphya: Apomorphy of the whole tree It is the ancestral state.

e: Autapomorphy of lineage D

The collective set of plesiomorphies defines the ground plan of a phylogenetic tree.

Ancestor

a

b

de

d

f

A B Cadf ade abd C is the sister taxon of A and B

Character a in lineages A, B, and C is homologous because it synapomorph

Character d in lineages A, B, and C is not homologous because it derived twice. It is homoplasious

Ancestor

b

de

d

f

A B C D E

Monophyletic taxon Paraphyletic taxon

f

bPolyphyletic taxon

The ultimate aim of taxonomy is to group

higher taxa into monophyletic subtaxa.

For this task we have to infer autapomorphies

Autapomorphy defines monophyly

Actino-pterygia Dipnoi Anura Urodela Mammalia Squamata

Therosauria

Aves

Tetrapoda

Amniota

Reptilia(paraphyletic)

Archosauria

Common ancestor Lungsplesiomorph

Tetrapod limbsapomorph

Amnionapomorph

Mammaeautapomorph

Feathersapomorph

Loss of tailapomorph

The evolutionary change within a lineage is called anagenesis

The diversification of an evolutionary tree is called cladogenesis

Linnean systematics and cladistics

Linnean approachHierachical encaptive system

Phenomenological method based on similarity

It uses grades (groups of similar body plan)

Different taxonomies are possible

There is no clear decision intrument for taxonomies

The number of higher taxa is rather small (Pisces, Amphibia, Reptilia, Aves, Mammalia)

It does not assume common evolutionary history

It does not reconstruct evolution

Taxonomy is independent of evolution

Hennigean approachHierachical encaptive system

Analytical method based on lineage branching

It uses clades (groups of identical root)

Only one taxonomic solution is allowed

Autapomorphies decide about taxonomic position

The number of higher taxa is large (Pisces, Amphibia, Reptilia are not valid taxa )

It is based on common evolutionary history

It does reconstruct evolution

Taxonomy is a part of evolutionary theory

Low resolution trees High resolution trees

Phylogenetic tree of winged insect orders

Devonian TriassianPermianCarboniferous CretaceousJurassic Paleogene to recent

PalaeodictyopteraOdonata

EphemeropteraDictyopteraPlecopteraZorapteraEmbiopteraIsoptera

GrylloblatodeaDermaptera

PhasmidaOrthopteraMallophagaPsocopteraThysanopteraHeteropteraHymenopteraNeuropteraColeoptera

MecopteraSiphonaptera

Diptera

LepidopteraTrichoptera

Devonian origin

Radiation

Radiation

Low resolution

In the Triassic period all extant taxa already existed

The tree lacks 9 orders that went extinct by the end of the Permian

Rhyniognatha hirsti

The principle of maximum parsimony (Occam’s razor) holds that we should accept that phylogenetic tree that can be constructed with the least number of morphological

changes.

The construction of phylogenetic trees from numerical methods

CSpecies 1 2 3 4 5 6A 1 1 0 1 1 1B 1 1 1 1 1 1C 0 1 0 0 1 0D 0 0 1 1 0 1E 1 0 1 1 0 1

CharactersThe raw data

Species A B C D EA 0 1 3 4 3B 1 0 5 3 2C 3 4 0 5 6D 4 3 5 0 1E 3 2 6 1 0

Distance matrix

We are looking for such a tree that minimizes the sum of distances.

A B ED

010010

110111101101

001101

8 changes

111111

A B CD E

110111010111

010010111111

101101

001101

7 changes

Outgroup

How to define the root?

Parsimony analysis

To find the most parsimonious tree we have to cross all combinations of lineages (trees) with all character combinations at the root.

SpeciesNumber of

trees2 13 34 155 1056 9457 103958 1351359 202702510 34459425

The number of possible trees

S 1

(2S 2)!N2 (S 1)!

Neighbour joining

A

F

DE

C

B

Root

A

F

DE

C

B

RootX

A

F

DE

C

B

RootX

Y

Neighbour joining is particularly used to generate phylogenetic trees

in

(X) (X,Y )

(X,Y)Q (n 2) (X,Y) (X) (Y)

AB(X,A) (X,B) (A,B)(X, U )

2

(n 2) (A,B) (A) (B)(A, U)2(n 2)

(n 2) (A,B) (A) (B)(B, U)2(n 2)

Dissimilarities

You need similarities (phylogenetic distances) (XY) between all elements X and Y.

Select the pair with the lowest value of Q

Calculate new dissimilarities

Calculate the distancies from the new node

Calculate

Distance matrixMouse Raven Octopus Lumbricus

Mouse 0 0.2 0.6 0.7Raven 0.2 0 0.6 0.8Octopus 0.6 0.6 0 0.5Lumbricus 0.7 0.8 0.5 0

Delta values 1.5 1.6 1.7 2

Q-valuesMouse/Raven -2.7Mouse/Octopus -2Mouse/Lumbricus -2.1Raven/Octopus -2.1Raven/Lumbricus -2Octopus/Lumbricus -2.7

Distance matrixMouse Raven Protostomia

Mouse 0 0.2 0.4Raven 0.2 0 0.45Protostomia 0.4 0.45 0

Delta values 0.6 0.65 0.85

Q-valuesMouse/Raven -1.25Mouse/Protostomia -1.05Raven/Protostomia -0.6

Distance matrixVertebrata Protostomia

Vertebrata 0 0.075Protostomia 0.075 0

in

(X) (X,Y )

(X,Y)Q (n 2) (X,Y) (X) (Y)

AB(X,A) (X,B) (A,B)(X, U )

2

(X,Y)Q (n 2) (X,Y) (X) (Y)

in

(X) (X,Y )

Mouse

Lumbricus

Raven

Octopus

Mouse

Protostomia

Raven

Protostomia

Vertebrata

Assumption of the numerical methods

Characters (or transitions) have to be independent.

Impossible character states have to be excluded.

Scales

Hairs

Feathers

Loss of feathersLoss of hairsFish

MammalsBirds

Incompatible

Characters are assumed to have equal importance. In reality transitions are not comparable.

To overcome this problem you give character weights. Technically you multiply the occurrence of a character in a distance matrix

A B C1 C2 DA 1 0 1 1 6B 1 2 4 4 2C1 4 5 2 2 1C2 4 5 2 2 1D 1 0 3 3 2

http://evolution.genetics.washington.edu/phylip/software.html

Species SequenceA A A T T A A C C C A A T AB C A T T A A C C C A A T AC C G T T T G G A A T G A CD C G T G T G G A A T A A AE G G T G T G C C C A A T A

Trees from molecular data

A B C D EA 0 1 11 10 5B 1 0 10 9 5C 11 10 0 3 9D 10 9 3 0 6E 5 5 9 6 0

Distance matrix

Linus Pauling (1901-1994)

Motoo Kimura(1924-1994)

Emile Zuckerkandl(1922-)

Evolutionary time scalesThe molecular clock

Numbers of amino acid substitutions and therefore trespective numbers of nucleotide substitutions are for many proteins and genomes approximately

proportional to time.

Hence, numbers of substitutions are a measure of time of divergence from

the latest common ancestor.

Substitutions alone provide a relative time scale

An appropriate calibration adds the absolute time scale

0

10

20

30

40

50

60

70

80

0 200 400 600 800 1000Paleontological divergence

estimate

Nuu

mbe

r of a

min

o

c a

cid

diffe

renc

es

c

Superoxide dismutase

Tomoko Ohta(1933-)

Errors

A B C D

Ancestor

The length of a tree segment is a measure of the duration of a lineage 1

4

3

2Is it possible to convert numbers of character

changes into evolutionary time scales?

T→CTCA→GAG→C→GTG→C→AAACG

TTCA→GAGTGCCCT

Single substitution

Parallel substitution

Back substitution

Multiple substitution

The Jukes Cantor model now assumes that the probabilities l of any transition within these 4

nucleotides is the same.

Assuming that transition probability is time independent (every period has the same

transition probability). The probability distribution follows an Arrhenius

model. t

transp 1 e l

 A

TC

G

l/3

l/3

l/3

l/3

Applying the molecular clock

ttransp 1 e l

A→T:

1 4xt ln(1 )3n

l

t ttrans

1 3p 3( (1 e )) (1 e )4 4

l l

x n x

t t

nL(x; t) p (1 p)

x

n 3 3 3 3ln(L(x; t)) ln x ln( e ) (n x) ln(1 ( e ))x 4 4 4 4

l l

A→G: t1 (1 e )4

l A→C: t1 (1 e )4

l A→A:

What is the probability to get exactly x differences out of n possible?

We apply the binomial:

We are interested in the time that maximizes this function. Hence we need the root of

the first derivative

We apply the principle of maximum likelihood.

t1 (1 e )4

l

The distances t are now used in distance matrices to construct the phylogenetic tree

)431(

41)1(

431 tt ee ll

Paleontological versus molecular timescales

Morphological change

Gen

etic

al c

hang

e Time axis

Molecular divergence of placental orders (120-140 mya)

First fossils of placental orders (65 mya)

Eomaia (125 mya)

Morphological change

Gen

etic

al c

hang

e Time axis

Molecular divergence (4-5 mya)

First fossils of erect hominids(6-7 mya)

Gene flow up to 2 mya

Molecular estimates point frequently much more ancient divergences of lineages than estimates based on the fossil record.

The reason are different speeds of morhological and genetical changes.

Changes in genetic constitution accumulate to a point where basic regulatory elements are

involved

Changes in genetic constitution involve first basic regulatory elements.

Paleontological versus molecular timescales

Matching of molecular and paleontological timescales in Echinodermata

For the majority of Echinoderm subtaxa molecular divergence estimates are higher than

the paleontological estimates.

Taxon First record Duration of record

Missing records

Euechinoidea Serpianotiaris coaeva 235–240 45 15Acroechinoidea Diademopsis serialis 205–210 0 0Acrosalenia chartroni Lambert 200–205 0 0Diadematoida Gymnotiara varusense 190–195 10 5Plesiechinus hawkinsi Jesionek 195–200 5 5Irregularia Plesiechinus hawkinsi 195–200 15 0Microstomata Galeropygus sublaevis 180–185 0 0Neognathostomata Galeropygus sublaevis 180–185 80 10Cassiduloida Hungaresia ovum 85–90 90 15Clypeasteroida Nucleopygus angustatus 100–105 50 0Scutellina Eoscutum doncieuxi 50–55 0 0Laganiformes Sismondia logotheti 50–55 0 0Scutelliformes Eoscutum doncieuxi 50–55 25 0Atelostomata Hyboclypus ovalis 175–180 25 0Spatangoida Disaster moeschi 160–165 65 5Paleopneustina Polydesmaster fourtaui 90–95 0 5Brissidea Micraster distinctus 95–100 45 0Meoma antiqua Arnold 40–45 0 0Eupatagus haburiensis Khanna 50–55 15 0Stirodonta Atlasaster jeanneti 195–200 30 0Camarodonta Glyptocyphus difficilis 115–120 0 0Echinoida Pseudarbacia archaici 90–95 65 65Echinoida Lytechinus axiologus 45–50 0 5Cidaroidea Eotiaris keyserlingi 250–255 255 0Echinothurioida Pelanechinus oolithicum 170–175 175 45Pedinoida Hemipedina hudsoni 205–210 210 0Aspidodiadematidae Gymnotiara varusense 190–195 195 35Diadematidae Farquharsonia crenulata 165–170 170 0Echinoneoida Pygopyrina icaunensis 160–165 165 5Cassidulidae Rhyncholampas macari 65–70 70 30Echinolampadidae Hungaresia ovum 85–90 90 35Clypeasterina Clypeaster calzadai 40–45 45 20Fibularidae Echinocyamus gurnahensis 50–55 55 0Laganidae Sismondia logotheti 50–55 55 10Mellitidae Encope ciae 20–25 25 0Astriclypeidae Amphiope duffi 25–30 30 0Holasteroida Collyrites ellipticus 165–170 170 5Schizasteridae Periaster elatus 90–95 95 0Paleopneustidae Polydesmaster fourtaui 90–95 95 0Archaeopneustids Heterobrissus salvae 40–45 45 0Brissidae Meoma antiqua 40–45 45 0Spatangidae Granopatagus lonchophorus 35–40 40 0Loveniidae Hemimaretia subrostrata 35–40 40 0Arbacioida Atopechinus cellensis 165–170 170 0Somopneustids Phymechinus mirabilis 155–160 160 0Temnopleuridae Zeuglopleurus costulatus 95–100 100 0Echinidae Psammechinus dubius 15–20 20 0Strongylocentrotidae Strongylocentrotus antiquus 20–25 25 0Echinometridae Plagiechinus priscus 25–30 30 10Toxopneustidae Lytechinus axiologus 45–50 50 5Trigonocidaridae Arbacina monilis 15–20 20 30Sum 3210 360

Species

0

50

100

150

200

250

300

0 100 200 300Paleontological divergence

estimate

Mol

ecul

ar d

iver

genc

e

z

est

imat

e

Data from Smith et al. (2006)

Data from Qun et al. (2007)

Divergences Earliest fossil record

Molecular estimates

Placental-marsupials 175–145 185–161Amniotes-amphibians 310 375–345Myriapods-chelicerates 530 705–579Mosses-vascular plants 450 899–515Crustaceans-insects 530 726-539Echinoderms-chordates <530 1001–586Spiralian-Ecdysozoans 560–540 643–544Protostomes-deuterostomes 560–540 678–556Arthropods-chordates 560–540 1200–588Cnidaria-bilaterians <600 724–615Sponges-chordates <600 1350–592

Paleontological versus molecular timescales

Have all phylogenetic trees a single root?

Darwin’s first principle: All species of a given taxon have a common ancestor.

Parsimony analysis cannot answer this question. A brush would always have a lower number of character changes

TimeSpontaneous origin of simple life forms

Sca

le o

f org

aniz

atio

n

Scala naturae

A brush means:• No speciation.• If we except that extinction occurs this

would mean a constant decrease in the number of species.

• Character change within whole species.• No genetic (character) variability within

populations.• Extreme longevity of lineages.

Theory of Lamarck

But horizontal gene transfer and might at least in bacteria result in networks and rings!

Evolution and development (EvoDevo)

August Weismann (1834-1914)

The soma - germ line distinction

makes it impossible to transmit acquired characters

to the next generation

Ernst Haeckel(1834-1919)

Theory of recapitulation The ontogeny of advanced species

recapitulates respective stages in ancestral

forms.In fact, only basic genetic programs are conserved and modifications at all stages of ontogenesis

appear. Haeckel’s rule is only a crude approximation.

Today’s reading

Phylogenetic systematics: http://evolution.berkeley.edu/evolibrary/article/phylogenetics_01

Cladistics: http://en.wikipedia.org/wiki/Cladistics

Ernst Haeckel: Kunstformen der Natur (Internet exhibition of original drawings: http://caliban.mpiz-koeln.mpg.de/~stueber/haeckel/kunstformen/liste.html

The modern molecular clock: http://awcmee.massey.ac.nz/people/dpenny/pdf/BromhamPenny_2003.pdf