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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.

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Presentation on theme: "3. The reconstruction of phylogeny The first Darwinian principle told that every phylogenetic tree has one common ancestor. Phylogenetic analysis is the."— Presentation transcript:

1 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 systematics Cladistics (greek κλάδος: branch) Numerical taxonomy Robert Sokal (1927-)

2 http://www.eol.org/ http://tolweb.org/tree/phylogeny.html http://www.faunaeur.org/

3 Ancestor a b c e e d f The cladistic methodology A BCD Apomorphies are common derived characters. Autapomorphies are characters that are restricted to single lineages. Plesiomorphies are ancestral derived characters. adf adeabcabd 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. e: Autapomorphy of lineage D The collective set of plesiomorphies defines the ground plan of a phylogenetic tree.

4 Ancestor a b d e d f A BC adf adeabd 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 d e d f A B CDE Monophyletic taxonParaphyletic 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

5 Actino- pterygia DipnoiAnuraUrodelaMammaliaSquamata Therosauria Aves Tetrapoda Amniota Reptilia (paraphyletic) Archosauria Common ancestor Lungs plesiomorph Tetrapod limbs apomorph Amnion apomorph Mammae autapomorph Feathers apomorph Loss of tail apomorph The evolutionary change within a lineage is called anagenesis The diversification of an evolutionary tree is called cladogenesis

6 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 Low resolution trees High resolution trees

7 Phylogenetic tree of winged insect orders DevonianTriassianPermianCarboniferousCretaceousJurassicPaleogene to recent Palaeodictyoptera Odonata Ephemeroptera Dictyoptera Plecoptera Zoraptera Embioptera Isoptera Grylloblatodea Dermaptera Phasmida Orthoptera Mallophaga Psocoptera Thysanoptera Heteroptera Hymenoptera Neuroptera Coleoptera Mecoptera Siphonaptera Diptera Lepidoptera Trichoptera Devonian origin 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

8 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 C The raw data Distance matrix We are looking for such a tree that minimizes the sum of distances. ABED 010010 110111 101101 001101 8 changes 111111 ABCDE 110111 010111 010010 111111 101101 001101 7 changes Outgroup How to define the root?

9 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

10 Neighbour joining Neighbour joining is particularly used to generate phylogenetic trees 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

11 Mouse Lumbricus Raven Octopus Mouse Protostomia Raven Protostomia Vertebrata

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13 Assumption of the numerical methods Characters (or transitions) have to be independent. Impossible character states have to be excluded. Scales Hairs Feathers Loss of feathers Loss of hairs Fish 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

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

15 Trees from molecular data Distance matrix

16 Linus Pauling (1901-1994) Motoo Kimura (1924-1994) Emile Zuckerkandl (1922-) 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. Substitutions alone provide a relative time scale An appropriate calibration adds the absolute time scale Superoxide dismutase Tomoko Ohta (1933-) Errors

17 ABCD Ancestor The length of a tree segment is a measure of the duration of a lineage 1 4 3 2 Is it possible to convert numbers of character changes into evolutionary time scales? The Jukes Cantor model now assumes that the probabilities 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. A T C G  Applying the molecular clock

18 A→T:A→T: A→G:A→G: A→C:A→C: A→A: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. The distances t are now used in distance matrices to construct the phylogenetic tree

19 Paleontological versus molecular timescales Morphological change Genetical change Time axis Molecular divergence of placental orders (120-140 mya) First fossils of placental orders (65 mya) Eomaia (125 mya) Morphological change Genetical change 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.

20 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)

21 Data from Qun et al. (2007) Paleontological versus molecular timescales

22 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 Time Spontaneous origin of simple life forms Scale of organization 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!

23 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.

24 Today’s reading Phylogenetic systematics: http://evolution.berkeley.edu/evolibrary/article/phylogenetics_01 http://evolution.berkeley.edu/evolibrary/article/phylogenetics_01 Cladistics: http://en.wikipedia.org/wiki/Cladisticshttp://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 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 http://awcmee.massey.ac.nz/people/dpenny/pdf/BromhamPenny_2003.pdf


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