3. The reconstruction of phylogeny

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3. The reconstruction of phylogeny. The first Darwinian principle told that every phylogenetic tree has one common ancestor . Phylogen e tic analysis is the study of taxonomic relationships among lineages . Phylogenetic systematics Cladistics (greek κλάδος : branch). Numerical taxonomy. - PowerPoint PPT Presentation

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3. The reconstruction of phylogenyThe 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 : branch)Numerical taxonomy

Robert Sokal(1927-)

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http://www.eol.org/

http://tolweb.org/tree/phylogeny.html

http://www.faunaeur.org/2AncestorabceedfThe cladistic methodologyABCDApomorphies are common derived characters.Autapomorphies are characters that are restricted to single lineages.Plesiomorphies are ancestral derived characters.adfadeabcabdb: 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.3AncestorabdedfABCadfadeabdC is the sister taxon of A and BCharacter 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 AncestorbdedfABCDEMonophyletic taxonParaphyletic taxonfbPolyphyletic taxonThe ultimate aim of taxonomy is to group higher taxa into monophyletic subtaxa.For this task we have to infer autapomorphiesAutapomorphy defines monophyly4Actino-pterygiaDipnoiAnuraUrodelaMammaliaSquamataTherosauriaAvesTetrapodaAmniotaReptilia(paraphyletic)ArchosauriaCommon ancestorLungsplesiomorphTetrapod limbsapomorphAmnionapomorphMammaeautapomorphFeathersapomorphLoss of tailapomorphThe evolutionary change within a lineage is called anagenesisThe diversification of an evolutionary tree is called cladogenesis5Linnean systematics and cladisticsLinnean approachHierachical encaptive systemPhenomenological method based on similarityIt uses grades (groups of similar body plan)Different taxonomies are possibleThere is no clear decision intrument for taxonomiesThe number of higher taxa is rather small (Pisces, Amphibia, Reptilia, Aves, Mammalia)It does not assume common evolutionary historyIt does not reconstruct evolutionTaxonomy is independent of evolutionHennigean approachHierachical encaptive systemAnalytical method based on lineage branching It uses clades (groups of identical root)Only one taxonomic solution is allowedAutapomorphies decide about taxonomic positionThe number of higher taxa is large (Pisces, Amphibia, Reptilia are not valid taxa )It is based on common evolutionary history

It does reconstruct evolutionTaxonomy is a part of evolutionary theoryLow resolution treesHigh resolution trees6Phylogenetic tree of winged insect ordersDevonianTriassianPermianCarboniferousCretaceousJurassicPaleogene to recentPalaeodictyopteraOdonataEphemeropteraDictyopteraPlecopteraZorapteraEmbiopteraIsopteraGrylloblatodeaDermapteraPhasmidaOrthopteraMallophagaPsocopteraThysanopteraHeteropteraHymenopteraNeuropteraColeopteraMecopteraSiphonapteraDipteraLepidopteraTrichopteraDevonian originRadiationRadiationLow resolutionIn the Triassic period all extant taxa already existedThe tree lacks 9 orders that went extinct by the end of the Permian

Rhyniognatha hirsti7The 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 construction of phylogenetic trees from numerical methodsC

The raw data

Distance matrixWe are looking for such a tree that minimizes the sum of distances.ABED010010110111101101001101 8 changes111111ABCDE110111010111010010111111101101001101 7 changesOutgroupHow to define the root?8Parsimony analysisTo 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

9Neighbour joining

Neighbour joining is particularly used to generate phylogenetic trees

DissimilaritiesYou need similarities (phylogenetic distances) d(XY) between all elements X and Y.Select the pair with the lowest value of QCalculate new dissimilaritiesCalculate the distancies from the new nodeCalculate10

MouseLumbricusRavenOctopusMouseProtostomiaRavenProtostomiaVertebrata11

12Assumption of the numerical methodsCharacters (or transitions) have to be independent. Impossible character states have to be excluded.ScalesHairsFeathersLoss of feathersLoss of hairsFishMammalsBirdsIncompatibleCharacters 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/software.html14

Trees from molecular data

Distance matrix15

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 scaleAn appropriate calibration adds the absolute time scale

Superoxide dismutase

Tomoko Ohta(1933-)ErrorsFitch W. M., Ayala F. J. 1994. The superoxide dismutase molecular clock revisited. Proc. Natl. Acad. Sci. USA 91: 6802-6807.16ABCDAncestorThe length of a tree segment is a measure of the duration of a lineage 1432Is it possible to convert numbers of character changes into evolutionary time scales?

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.

ATCGl/3l/3l/3l/3Applying the molecular clock17

AT:

AG:

AC:

AA: 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

18Paleontological versus molecular timescalesMorphological changeGenetical changeTime axisMolecular divergence of placental orders (120-140 mya)First fossils of placental orders (65 mya)

Eomaia (125 mya)

Morphological changeGenetical changeTime axisMolecular 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 involvedChanges in genetic constitution involve first basic regulatory elements.19Paleontological versus molecular timescalesMatching of molecular and paleontological timescales in EchinodermataFor the majority of Echinoderm subtaxa molecular divergence estimates are higher than the paleontological estimates.

Data from Smith et al. (2006)Smith A. B. et al. (2006) Testing the Molecular Clock: Molecular and Paleontological Estimates of Divergence Times in the Echinoidea (Echinodermata). Molecular Biol. Evol. 23: 1832-1851.20Data from Qun et al. (2007)

Paleontological versus molecular timescalesQun Y., Yunye M., XiaoyanS., Peiyun C. 2007. Phylochronology of early metazoans: combined evidence from molecular and fossil data. Geol. J. 42: 281-295. 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 changesTimeSpontaneous origin of simple life forms Scale of organizationScala naturaeA 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 LamarckBut horizontal gene transfer and might at least in bacteria result in networks and rings!22

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. Haeckels rule is only a crude approximation.23Todays readingPhylogenetic 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

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