Transcript Slajd 1

The discovery of the past
To study evolution means to dig in
the past.
The science of past organims is
paleontology (greek: palaews:
old, logos: science)
Paleontology deal with fossils (lat.
fodere = to dig)
Charles Lyell
Georges Cuvier
Early paleontology mainly described ancient
life within the Linnean framework
Modern paleontology tries to reconstruct
ancient life.
It links therefore ecology and taxonomy.
Mary Anning (1799-1847)
Richard Owen (1804-1892)
How do animals fossilize?
Taphonomy (Greek: tafos: burial; nomos: law)
Immediate
burial
Death
Living organism
Remains
Mineralization
Fossil
Buried remains
Decomposition
Decay
Bleaching
Delayed
burial
Exposed remains
Ginkgo biloba
Stratinomy
Ginkgo adiantoides
Much less than 1% of all
organisms fossilize
Coral fish
Coral fish from Jura
Bioerosion
A fossil forest in Dorset, England formed by
fossilized bacteria around old tree stumps.
A fossilized dinosaur footprint from New Mexico
Fossilized Cyanobacteria (stromatolites) from
South Africa
A mammoth coprolith (fossilized excrements)
What fossilizes?
Hard body materials
Substance
Examples
Calcite (CaCO3)
Octocorallia
Bryozoa
Brachiopoda
Polychaeta
Ammonita
Belemnita
Echinodermata
Aragonite (CaCO3)
Hydrozoa
Gastropoda
Calciumphosphate
(Ca5(OH)(PO4)3)
Vertebrata
Trilobita
Crustacea
Opal (SiO2.H2O)
Radiolaria
Diatomea
Porifera
Chitin
Algae
Fungi
Arthropoda
Cnidaria
Priapulida
Annelida
Cellulose
Plantae
Tunicata
Soft body materials
Soft tissues very seldom fossilize
(of about half of all major evolutionary
lines no fossils are known)
Exceptions are
Fast drying out in very arid climates
Permanent frozen
Preservation in amber or asphalt
A feathered
Dinosaur:
Sinosauropteryx
Under what conditions do organisms fossilize?
Moisture gradient
Nutrient rich soils
River sediments
Anaerobic conditions
(moorlands)
Volcanic ashes
Probability of fossilization
Salinity gradient
How complete is the fossil record?
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0
SCI
Divergence
time inferred
from
cladogram
GER
Divergence
time inferred
from fossils
RCI
SCI: Quotient of consistent to inconsistent nodes
0
5
10
15
20
25
30
PZ PZ/MZ NZ MZ/CZ CZ
Older
-----Younger
RCI: Relative completeness index
GAP: Gap excess index
100%
Completeness
Metrics
Benton MJ, Willis MJ, & Hitchin R. 2000. Quality of the fossil record through time. Nature 403: 534-537.
?
At the family level about
50% of all taxa are known
from fossils.
50%
0%
Species
Family
Order
Class
Taxonomic levels
Type
Fossils of soft-bodied
types are not well
known
Continental drift
Alfred Lothar Wegener
(1880-1930)
The tectonic plates (from David Sanfwell, Scripps Inst. Oceanography)
Evidence for plate tectonics:
Fit of coastlines
Distribution of mountains
Continuity of fossils
Continuity of geological features
Isostasy: Earth acts like a fluid
From Press et al.. 2004. Understanding earth, http://www.whfreeman.com/presssiever/con_index.htm?99iex
Continental drift
From C. R. Scotese: http://www.scotese.com/future.htm
How to match phylogeny and plate tectonics
Cassowary
35
62
Emu
New Guinea
0.1
65
Kiwi
Australia
55
69
Ostrich
82
South America
79
Rhea
100
New Zealand
Moa
Africa
Tinamou
Fossil dating
Relative dating methods
Relative dating uses geological strata to infer whether
fossils are older or younger than a given stratum
Layer 1
Younger
Layer 2
Time
Layer 2
Older
Stratigraphy
Morphological primitivism
Absolute dating methods
Radiometric absolute dating
Radioactive Element
Potassium 40
Rubidium 87
Thorium 232
Uranium 235
Uranium 238
Carbon 14
Stable element
Argon 40
Strontium 87
Lead 208
Lead 207
Lead 206
Nitrogen 14
Half time
1.25 billion yrs
48.8 billion yrs
14 billion years
704 million years
4.47 billion years
5730 years
Most minerals which contain radioactive
isotopes are in igneous rocks.
The dates they give indicate the time the
magma cooled.
Potassium 40 is found in:
potassium feldspar (orthoclase)
muscovite
amphibole
glauconite
Surviving
atoms C14
Daugther
atoms N14
Volcanic rocks
Sometimes in sediments
Uranium may be found in:
zircon
urananite
monazite
apatite
sphene
Volcanic rocks
Carbon 14 is used for bones
Radiometric dating
Stratigraphy
Raw data
Relative time
scale
Absolute time
scale
Recognition of
unique events to
subdivide time
Geological time scale
Post
eruption 2
time
Depth [m]
Volcanic ash 2
Calibrating
geological
time
Radiomtric
dating of layers
Post fossil
B time
160 ± 10 mya
165 mya
Fossil B
time
Last occurrence of B:
First occurrence of
Pre fossil
B time
Volcanic ash 1
190 ± 8 mya
Last occurrence of A:
First occurrence of
180 mya
Pre eruption
1 time
Fossil B
time
Older than
190 mya
Pre fossil
B time
Modified from Andy MacRae: Radiometric Dating and the Geological Time Scale. http://www.talkorigins.org/faqs/dating.html
Fission track
Fission Tracks (FT) are micrometer-sized,
linear damage tracks that occur in insulating
minerals and that are caused by the
spontaneous fission of heavy, unstable
nuclides (mostly 238U in natural minerals).
Dendrochronology
Dendrochronology analyses treering growth patterns.
History of the earth
Steno founded stratigraphy by stating that
geological layers are horizontal and superposed.
Deeper layers are older.
Nicolas Steno (1638-1686)
The Red Rock Canyon, California
The geological time scale
Eon
Era
Phanerozoic Cenozoic
Mesozoic
Paleozoic
Proterozoic
Neoproterozoic
Mesoproterozoic
Palaeproterozoic
Archean
Hadean
Period
Quarternary
Neogene
Paleogene
Cretaceous
Jurassic
Triassic
Permian
Carboniferous
Devonian
Silurian
Ordovician
Cambrian
Ediacaran (Vendian)
Cryogenian
Tonian
Age at Base (Mya) Duration (Mya)
2
2
23
21
65
42
140
75
205
65
250
45
290
40
355
65
410
55
440
30
490
50
540
50
630
90
850
220
1000
150
1600
600
2500
900
3800
2950
4550
750
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.
Phylogenetic systematics
Cladistics (greek κλάδος: branch)
Willi Hennig
(1913-1976)
Numerical taxonomy
Robert Sokal
(1926-2012)
http://www.faunaeur.org/
http://tolweb.org/tree/phylogeny.html
http://www.eol.org/
The cladistic methodology
A
B
adf
ade
e
f
C
D
abc
c
d
e
b
a
Ancestor
abd
Apomorphies are common derived
characters.
Autapomorphies are characters that are
restricted to single lineages.
Plesiomorphies are ancestral derived
characters.
e: Autapomorphy of lineage D
b: Synapomorphy of lineage C+D
d: Plesiomorphy of lineage A
It is a symplesiomorphy
a: Apomorphy of the whole tree
It is the ancestral state.
The collective set of plesiomorphies defines the ground plan of a phylogenetic tree.
A
B
C
adf
ade
abd
e
f
C is the sister taxon of A and B
Character d in lineages A, B, and C is not
homologous because it derived twice. It
is homoplasious
d
d
Character a in lineages A, B, and C is
homologous because it synapomorph
b
a
Ancestor
Monophyletic taxon Paraphyletic taxon
B
A
e
f
Polyphyletic taxon
C
D
f
d
b
d
Ancestor
b
E
The ultimate aim of
taxonomy is to group
higher taxa into
monophyletic subtaxa.
For this task we have to
infer autapomorphies
Autapomorphy defines
monophyly
Tetrapoda
The diversification
of an evolutionary
tree is called
cladogenesis
Actinopterygia
Dipnoi
Amniota
Archosauria
Anura Urodela
Mammalia
Squamata
Aves
Therosauria
Loss of tail
apomorph
Mammae
autapomorph
Reptilia
(paraphyletic)
Feathers
apomorph
Amnion
apomorph
Common ancestor
Tetrapod
limbs
apomorph
Lungs
plesiomorph
The evolutionary
change within a lineage
is called anagenesis
Linnean systematics and cladistics
Linnean approach
Hennigean approach
Hierachical encaptive system
Hierachical encaptive system
Phenomenological method based on similarity Analytical method based on lineage branching
It uses grades (groups of similar body plan)
It uses clades (groups of identical root)
Different taxonomies are possible
Only one taxonomic solution is allowed
There is no clear decision intrument for
taxonomies
Autapomorphies decide about taxonomic
position
The number of higher taxa is rather small
The number of higher taxa is large
(Pisces, Amphibia, Reptilia, Aves, Mammalia) (Pisces, Amphibia, Reptilia are not valid taxa )
It does not assume common evolutionary
history
It is based on common evolutionary history
It does not reconstruct evolution
It does reconstruct evolution
Taxonomy is independent of evolution
Taxonomy is a part of evolutionary theory
Low resolution trees
High resolution trees
The construction of phylogenetic trees from numerical methods
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 raw data
Species
A
B
C
D
E
1
1
1
0
0
1
2
1
1
1
0
0
Characters
3
4
0
1
1
1
0
0
1
1
1
1
5
1
1
1
0
0
6
1
1
0
1
1
A
B
D
E
C
001101
110111
101101
010010
8 changes
Distance matrix
Species
A
B
C
D
E
A
0
1
3
4
3
B
1
0
4
3
2
C
3
5
0
5
6
111111
D
4
3
5
0
1
E
3
2
6
1
0
We are looking for such a tree that
minimizes the sum of distances.
A
Outgroup
B
D
E
C
001101
101101
010010
111111
How to define the
root?
010111
110111
7 changes
Parsimony analysis
To find the most parsimonious tree we have to cross all combinations of lineages (trees)
with all character combinations at the root.
The number of possible
trees
Number of
trees
Species
2
1
3
3
4
15
5
105
6
945
7
10395
8
135135
9
2027025
10
34459425
N
(2S  2)!
2S1 (S  1)!
Assumption of the numerical methods
Birds
Characters (or transitions) have to be
independent.
Impossible character states have to be
excluded.
Fish
Loss of hairs
Mammals
Loss of feathers
Hairs
Feathers
Scales
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
Incompatible
Trees from molecular data
Distance matrix
Species
A
B
C
D
E
Sequence
A
A
C
A
C
G
C
G
G
G
T
T
T
T
T
T
T
T
G
G
A
A
T
T
T
A
A
G
G
G
C
C
G
G
C
C
C
A
A
C
C
C
A
A
C
A
A
T
T
A
A
A
G
A
A
T
T
A
A
T
A
A
C
A
A
A
B
C
D
E
A
0
1
11
10
5
B
1
0
10
9
5
C
11
10
0
3
9
D
10
9
3
0
6
E
5
5
9
6
0
Evolutionary time scales
The molecular clock
Numbers of amino acid substitutions
and therefore trespective numbers of
nucleotide substitutions are for many
proteins and genomes approximately
proportional to time.
Motoo Kimura Emile Zuckerkandl Tomoko Ohta
(1933-)
(1924-1994)
(1922-2013)
80
Hence, numbers of substitutions are a
measure of time of divergence from
the latest common ancestor.
Substitutions
alone
provide a
relative time
scale
70
acid differences
Nuumber of amino
c
c
Linus Pauling
(1901-1994)
60
50
40
30
20
Errors
10
0
0
200
400
600
800 1000
Paleontological divergence
estimate
Superoxide dismutase
An appropriate
calibration
adds the
absolute time
scale
Paleontological versus molecular timescales
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
First fossils of
placental orders (65
mya)
Eomaia (125 mya)
Molecular divergence of
placental orders (120-140 mya)
Morphological change
Gene flow up to 2 mya
Genetical change
Genetical change
Time axis
Changes in genetic constitution involve first
basic regulatory elements.
First fossils of erect hominids
(6-7 mya)
Morphological change
Time axis
Molecular
divergence
(4-5 mya)
Paleontological versus molecular timescales
z
Matching of molecular and paleontological
timescales in Echinodermata
250
estimate
Molecular divergence
300
200
150
100
50
0
0
100
200
300
Paleontological divergence
estimate
For the majority of Echinoderm subtaxa
molecular divergence estimates are higher than
the paleontological estimates.
Data from Smith et al. (2006)
Paleontological versus molecular timescales
Divergences
Placental-marsupials
Amniotes-amphibians
Myriapods-chelicerates
Mosses-vascular plants
Crustaceans-insects
Echinoderms-chordates
Spiralian-Ecdysozoans
Protostomes-deuterostomes
Arthropods-chordates
Cnidaria-bilaterians
Sponges-chordates
Data from Qun et al. (2007)
Earliest fossil
record
175–145
310
530
450
530
<530
560–540
560–540
560–540
<600
<600
Molecular
estimates
185–161
375–345
705–579
899–515
726-539
1001–586
643–544
678–556
1200–588
724–615
1350–592
Have all phylogenetic trees a single root?
Darwin’s first principle: All species of a given taxon have a common ancestor.
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.
Theory of Lamarck
Scale of organization
Parsimony analysis cannot answer this
question. A brush would always have a lower
number of character changes
Scala
naturae
Spontaneous origin of simple
life forms
• No genetic (character) variability within
populations.
• Extreme longevity of lineages.
But horizontal gene transfer and might at least in bacteria result in
networks and rings!
Time
Today’s reading
History of palaeontology: http://en.wikipedia.org/wiki/History_of_paleontology
History of earth: http://wiki.cotch.net/index.php/History_of_the_Earth
Radiometric dating details: http://www.tulane.edu/~sanelson/eens211/radiometric_dating.htm
Geological time scale: http://en.wikipedia.org/wiki/Geologic_time_scale
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