Molecules as documents of evolutionary historyevolution.unibas.ch/teaching/molec_evol/doc/Mol_Evol_2.pdf · 2008-10-13 · Molecules as documents of evolutionary history Dr. Walter

Moleculesas documents of

evolutionary history

Dr. Walter Salzburger

“The most rational, universal and informative

molecular phylogeny will be built on

semantophoretic molecules alone”

Zuckerkandl and Pauling (1965)

Documents of Evolutionary History | 2

Linus Carl Pauling (1901-1994)

! quantum chemistry (USA)

! Nobel Prize (1954) for his work “on the

nature of chemical bonds”

! Nobel Peace Price (1962) for his campaign

against nuclear testing

! founder of molecular biology; influential in

the fields of molecular evolution, molecular

medicine, etc.


Emile Zuckerkandl (1922-)

! biologist (Austria, USA)

! protein chromatography and

electrophoresis in Linus Pauling’s lab

! Zuckerkandl & Pauling (1962): concept of

molecular clocks

! founder of molecular evolution; founding

editor of the Journal of Molecular Evolution


! Semantophoretic molecules, semantides are molecules that

carry information of genes of transcripts thereof: DNA,

mRNA, polypeptides (proteins)

! Episemantic molecules are synthesized under the control of

(tertiary) semantides but in the absence of a template.

! Asemantic molecules are not produced by the organism and

do not express information that this organism contains (e.g.

vitamins, phosphate ion).

“It is plain that asemantic molecules are not worthy in inquiries about

phylogenetic relationships.”



The comparison of homologous semantophoretic molecules

yields threefold information:

! the approximate time of existence

! the probable amino-acid sequence of the ancestor

! the lines of descent along which changes occurred



Nucleic acids: basis of all life on Earth


Three domains of life


16S rRNA

Three domains of life

Carl Woese (1928-)


cellular processes: rRNA subunits


genomic architecture: Hox gene clusters

Sw

alla

(2

00

6)

anterior

posterior


mutational difference: foxp2 in apes

Fis

her

& M

arc

us (2

00

6)


molecular evolution of foxp2 in apes

Enard et al. (2002)


chimpanzee

human

gorillaorangutan

rhesus

1 mutation

chimpanzee

human

gorillaorangutan

rhesus

1 mutation

diagram of evolutionary history


(phylogenetic) tree

phylogeny

evolutionary tree

“The stream of heredity makes phylogeny: in a

sense, it is phylogeny. Complete genetic analysis

would provide the most priceless data for the

mapping of this stream”

Simpson (1945)

George G. Simpson (1902-1984)


mutational change inheritance

+


...CAGGCTTATTC...

time

spa

ce

...CCGGCCTATTC...

...CCGGCCTATTC......CCGGCCTATTC...

...CCGGCCTATTC...

...CCGGCCTATTC......CCGGCCTATTC...

...CCGGCCTATTC......CCGGCCTATTC......CCGGCCTATTC...

...CCGGCCTATTC......CCGGCCTATTC......CCGGCCTATTC......CCGGCCTATTC......CCGGCCTATTC...

...CCGGCTTATTC......CCGGCTTATTC......CCGGCTTATTC......CCGGCTTATTC...

...CCGGCTTATTC...

...CCGGCTTATTC...

...CCGGCTTATTC...

...CCGGCTTATTC......CCGGCTTATTC...

...CAGGCTTATTC...

...CAGGCTTATTC...

...CAGGCTTATTC...

...CCGGCCTAGTC......CCGGCCTAGTC......CCGGCCTAGTC......CCGGCCTAGTC...

...CCGGCTTATTC...


...CCGGCCTATTC...

...CCGGCCTATTC...

...CCGGCTTATTC...

time

...CCGGCTTATTC...

...CAGGCTTATTC...

...CCGGCCTAGTC...


Ernst Haeckel

(1834-1919)


liverworts hornworts mosses tracheophyta

elaters in sporangium !

oil bodies !

lunularic acid !

pseudo-elaters !

non-synchr.

spore production !

multicell.

rhyzoids !

!stomates

!ability to distinguish D-methionine

!true lignin

!branched sporoph.

!xylem

!phloem

!perine layer on spores

! Phylogeny of plants based on morphological characters


Bremer (1985)

Molecular phylogeny of Cetacea and Artiodactyla

Ursing & Arnason (1998)


root

internal node

terminal node

phylogeny, evolutionary tree “leaf”, operational

taxonomic unit (OTU)


root

phylogeny, evolutionary tree


terminal node

A B C D E

phylogeny, evolutionary tree


A B C D E

Venn diagram


A B C D E

Venn diagram

((A , B), (C, (D , E))

Nested parentheses


((A , B), (C, (D , E))

A B C D E E D C B A

A

BC

E

D

A

B C

E

D


E D C B A

rooted tree

Rooted and unrooted trees

E

DC

B

A

unrooted tree

- has a defined “root”

- and therefore a defined

direction

TIM

E

- no information about

ancestry

- no defined direction


polytomy

E D C B A

unresolved (star-tree)

E D C B A

fully resolved

E D C B A

partially resolved

The resolution of trees


The basic kinds of threes

A B C D

cladogram phylogram(“additive tree”)

A B C D

2 1

11

2 4

A B C D

dendrogram(“ultrametric tree”)

0

4

shows relative

recency of

common ancestry

shows branch

lengths/amount of

evolutionary change

tips are aequidistant

from the root, nodes

reflect evoluionary time


ingroup

Tree terminology I: outgroup, ingroup and sistergroup

A B C D E

sistergroup outgroup

root


! A character can be - in relative terms - ancestral or derived.

Ancestral character stages are referred to as plesiomorphies,

derived ones as apomorphies.

Sarcopterygii Polypteriformes TeleosteiChondrostei

swimm bladder

lung


Tree terminology II: ancestral/derived character states

GG

G

G

A

A A GG

G

G

A G

G

autapomorphyplesiomorphyapomorphy

GG

G

G

A

A A

synapomorphy

G

G

G

A G

G

A

homoplasy

muta

tion


! A monophyletic group contains a common ancestor and all of

its descendants

Deuterostomia et al.:

Monophyletic groups are natural.

Looking at the animal phylogeny

on the right, many of the major

animal clades* are monophyletic,

e.g.,:

! Deuterostomia

! Ecdysozoa

! Lophotrochozoa

*clade is in fact a synonym

of monophyletic group

Ho

fer

& S

alz

burg

er

(2005)

Deu

tero

sto

mia

Ecd

yso

zoa

Documents of Evolutionary History | 34Lo

ph

otr

och

ozo

a

! A paraphyletic group contains a common ancestor and some,

but not all of its descendants

‘Reptilia’:

The ‘Reptilia’ are a paraphyletic

group. The species included in

the ‘Reptilia’ still resemble their

ancestor morphologically. The

birds, however, have evolved

more rapidly and no longer

resemble their ancestor but

have evolved a variety of

derived characters. Note that if

a group is not monophyletic, its

name is put in quotation marks.b

ird

s

cro

co

dil

es

liza

rds

turt

les

‘reptiles’


! A polyphyletic group is a set of taxa descended from more than

one common ancestor

‘Vultures’:

‘Vultures’ are a polyphyletic

grouping comprised of birds

that have independently evolved

similar morphology and habits

from different ancestors.

New

Wo

rld

Vu

ltu

res

sto

rks

bir

ds

of

pre

y

Old

Wo

rld

Vu

ltu

res‘Vultures’

ww

w.h

aveyo

useenm

yb

ird

.co

m

ww

w.w

ikip

ed

ia.c

om


Molecular clocks

“The persistence of memory”, Salvador Dalí (1931)


“Soft watches, biologically speaking, are the giant

Dalinian DNA molecules which constitute the

factors of eternity”

Dalí (~1961)

Salvador Dalí

(1904-1989)


! Molecular clock is the theory that molecules evolve at an

approximately constant rate

! The difference between the form of a molecule in two

species is then proportional to the time since divergence

from a common ancestor

! The molecular clock hypothesis is a testable prediction


Kim

ura

(1993)

Millions of years ago

Nu

cleo

tid

e s

ub

stit

uti

on

s

0 25 50 75 100 125

0

25

50

75

100

horse/donkey

goat/cow

sheep/cow

llama/cow

pig/cow

horse/cow

dog/cow

rabbit/rodent

human/cow

human/rodent

human/kangaroo

molecular clock in hemoglobin


molecular clock in hominoids as revealed by DNA hybridiation

1

0

2

3

4

5

6

7

8

% d

iffe

ren

ce i

n D

NA

befo

re p

rese

nt

(in

Myr

)

0

5

10

15

20

25

30

35

co

mm

on

ch

imp

pyg

my

ch

imp

hu

ma

n

go

rill

a

ora

ng

uta

n

co

mm

on

gib

bo

n

sia

ma

ng

gib

bo

n

Old

Wo

rld

mo

nk

eys

Sib

ley &

Ahlq

uis

t (1

987)


Is there a universal molecular clock?L

i (1

99

7), R

idle

y (2

00

4)

GeneRate of amino acid

evolution

Rate of nucleotide

evolution

Albumin 0.92 6.08

"-globin 0.56 4.92

#-globin 0.78 3.36

Immunoglobin V 1.1 5.87

Parathyroid hormone 1.0 4.57

Relaxin 2.59 8.98

Ribosomal S14 0.02 2.18

average (45 genes) 0.74 4.25

in changes per 10" years for an average site

no!


Relative rate test: rate constancy in a molecule in two

independent lineages?

Sarich

an

d W

ilso

n (1

97

7)

k=x+y

l=y+z

m=x+z


Bin

ind

a-E

mo

nd

s e

t al. (2

00

7)

ma

mm

ali

an

ra

dia

tio

n a

nd

K/T

bo

un

dary
