Slajd 1

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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.
Phylogenetic systematics Cladistics (greek
???d?? branch)
Numerical taxonomy
Robert Sokal(1927-)
Willi Hennig (1913-1976)
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http//www.faunaeur.org/
http//tolweb.org/tree/phylogeny.html
http//www.eol.org/
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The cladistic methodology
Apomorphies are common derived characters. Autapom
orphies are characters that are restricted to
single lineages.
B
C
D
A
ade
abc
abd
adf
Plesiomorphies are ancestral derived characters.
c
e
e
f
b
d
e Autapomorphy of lineage D
b Synapomorphy of lineage CD
a
d Plesiomorphy of lineage A It is a
symplesiomorphy
Ancestor
a Apomorphy of the whole tree It is the
ancestral state.
The collective set of plesiomorphies defines the
ground plan of a phylogenetic tree.
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B
C
A
C is the sister taxon of A and B
ade
abd
adf
Character d in lineages A, B, and C is not
homologous because it derived twice. It is
homoplasious
d
e
f
Character a in lineages A, B, and C is homologous
because it synapomorph
b
d
a
Ancestor
Monophyletic taxon
Paraphyletic 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
B
A
C
D
E
d
f
e
f
b
b
Polyphyletic taxon
d
Ancestor
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Tetrapoda
The diversification of an evolutionary tree is
called cladogenesis
Amniota
Archosauria
Actino-pterygia
Dipnoi
Anura
Urodela
Mammalia
Squamata
Aves
Therosauria
Loss of tailapomorph
Mammaeautapomorph
Reptilia(paraphyletic)
Feathersapomorph
Amnionapomorph
Tetrapod limbsapomorph
The evolutionary change within a lineage is
called anagenesis
Common ancestor
Lungsplesiomorph
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Linnean systematics and cladistics
Linnean approach Hierachical 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 approach Hierachical 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
High resolution trees
Low resolution trees
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Phylogenetic tree of winged insect orders
Devonian
Triassian
Permian
Carboniferous
Cretaceous
Jurassic
Paleogene to recent
Palaeodictyoptera
Odonata
Ephemeroptera
Devonian origin
Dictyoptera
Plecoptera
Low resolution
Zoraptera
Embioptera
Isoptera
In the Triassic period all extant taxa already
existed
Dermaptera
Radiation
Grylloblatodea
Phasmida
Orthoptera
Mallophaga
Psocoptera
Thysanoptera
Heteroptera
Hymenoptera
Rhyniognatha hirsti
Neuroptera
Coleoptera
The tree lacks 9 orders that went extinct by the
end of the Permian
Siphonaptera
Mecoptera
Radiation
Diptera
Trichoptera
Lepidoptera
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The construction of phylogenetic trees from
numerical methods
The principle of maximum parsimony (Occams
razor) holds that we should accept that
phylogenetic tree that can be constructed with
the least number of morphological changes.
The raw data
C
A
B
E
D
001101
110111
101101
010010
8 changes
Distance matrix
111111
A
B
C
D
E
001101
Outgroup
101101
010010
111111
We are looking for such a tree that minimizes the
sum of distances.
010111
How to define the root?
110111
7 changes
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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
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Neighbour joining
Neighbour joining is particularly used to
generate phylogenetic trees
You need similarities (phylogenetic distances)
d(XY) between all elements X and Y.
Dissimilarities
Calculate
Select the pair with the lowest value of Q
Calculate new dissimilarities
Calculate the distancies from the new node
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Raven
Mouse
Lumbricus
Octopus
Raven
Mouse
Protostomia
Vertebrata
Protostomia
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Assumption of the numerical methods
Mammals
Birds
Characters (or transitions) have to be
independent. Impossible character states have to
be excluded.
Fish
Loss of hairs
Loss of feathers
Hairs
Incompatible
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
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http//evolution.genetics.washington.edu/phylip/so
ftware.html
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Trees from molecular data
Distance matrix
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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. Hence, numbers of
substitutions are a measure of time of divergence
from the latest common ancestor.
Tomoko Ohta(1933-)
Linus Pauling (1901-1994)
Motoo Kimura(1924-1994)
Emile Zuckerkandl(1922-)
Substitutions alone provide a relative time scale
Errors
An appropriate calibration adds the absolute time
scale
Superoxide dismutase
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Applying the molecular clock
A
B
C
D
The length of a tree segment is a measure of the
duration of a lineage
1
3
Is it possible to convert numbers of character
changes into evolutionary time scales?
4
2
The Jukes Cantor model now assumes that the
probabilities l of any transition within these 4
nucleotides is the same.
Ancestor
l/3
G
A
 
l/3
l/3
C
T
l/3
Assuming that transition probability is time
independent (every period has the same transition
probability). The probability distribution
follows an Arrhenius model.
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A?T
A?G
A?C
A?A
What is the probability to get exactly x
differences out of n possible?
We apply the binomial
We apply the principle of maximum likelihood.
We are interested in the time that maximizes this
function. Hence we need the root of the first
derivative
The distances t are now used in distance matrices
to construct the phylogenetic tree
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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
Changes in genetic constitution involve first
basic regulatory elements.
Gene flow up to 2 mya
Time axis
Time axis
First fossils of placental orders (65 mya)
Genetical change
Genetical change
Molecular divergence (4-5 mya)
Eomaia (125 mya)
First fossils of erect hominids(6-7 mya)
Molecular divergence of placental orders (120-140
mya)
Morphological change
Morphological change
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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.
Data from Smith et al. (2006)
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Paleontological versus molecular timescales
Data from Qun et al. (2007)
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Have all phylogenetic trees a single root?
Darwins 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
Theory of Lamarck

• 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.

Scale of organization
Scala naturae
Spontaneous origin of simple life forms
Time
But horizontal gene transfer and might at least
in bacteria result in networks and rings!
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Evolution and development (EvoDevo)
August Weismann (1834-1914)
Ernst Haeckel(1834-1919)
Theory of recapitulation
The ontogeny of advanced species recapitulates
respective stages in ancestral forms.
The soma - germ line distinction makes it
impossible to transmit acquired characters to the
next generation
In fact, only basic genetic programs are
conserved and modifications at all stages of
ontogenesis appear. Haeckels rule is only a
crude approximation.
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Todays reading
Phylogenetic systematics http//evolution.berkele
y.edu/evolibrary/article/phylogenetics_01 Cladist
ics http//en.wikipedia.org/wiki/Cladistics Erns
t 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/pd
f/BromhamPenny_2003.pdf