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Computational phylogenetics

Computational phylogenetics. computational phylogenetics uses algorithms to assemble phylogenetic trees. Phylogenetic trees. a phylogenetic tree is a branching diagram representing evolutionary relationships between taxa or biological molecules.

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Computational phylogenetics

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  1. Computationalphylogenetics computational phylogenetics uses algorithms to assemble phylogenetic trees.

  2. Phylogenetictrees a phylogenetic tree is a branching diagram representing evolutionary relationships between taxa or biological molecules. Hedges & Kumar 2009. Timetree of Life. Oxford UniversityPress

  3. Phylogenetictrees depending on the input data and the algorithm used, trees can be rooted or unrooted. Alpha Delta Gamma Beta Epsilon Gamma Beta Alpha most recent common ancestor Delta Epsilon

  4. Phylogenetictrees depending on the input data and the algorithm used, trees can be scaled to time or not 1Mya 2Mya 3Mya 4Mya 5Mya

  5. Phylogenetictrees trees can be bifurcating or multifurcating.

  6. Characters different types of traits can be used to infer phylogenies. Phenotypicaldata Morphologicaltraits Physiological traits Cytological traits Behavioural traits Moleculardata Immunologicaltechniques Proteines (amino acid sequences) DNA DNA-DNA hybridisation Restriction enzyme sites Nucleotide sequence comparisons

  7. Characters Friedman 2008. Nature 454: 209-212.

  8. Characters morphological traits can be measured in both extant and extinct taxa. 10mm Friedman 2008. Nature 454: 209-212.

  9. Characters cytogenetic traits include the number, size and morphology of the chromosomes, behavior in meiosis and total DNA content Zeltneraexaltata Zeltneracalycosa Zeltneravenusta Mansion & Zeltner 2004. Am. J. Botany 91: 2069-2086.

  10. Characters behavioural characteristics can be used to build trees. Elk – Cervuscanadensis Moose – Alcesalces Fallow deer – Damadama Cap et al. 2008 Cladistics 24: 917-932.

  11. Characters behavioural characteristics can be used to build trees. Elk – Cervuscanadensis Moose – Alcesalces Fallow deer – Damadama Cap et al. 2008 Cladistics 24: 917-932.

  12. Characters in immunological taxonomy, antibody-antigen recognition is used to estimate relatedness. B A C species A antigens species A antibodies species B antigens precipitation species C antigens precipitation+++

  13. Characters trees can be build by comparing amino acid sequences for the same protein in different species. amino acid sequence of aspartatetransaminase P=proline, A=alanine, L=leucine, F=tryptophan, D=aspartic acid, T=threonine, S=serine, K=lysine, N=asparagine, M=methionine, G=glycine, Y=tyrosine, E=glutamic acid, R=arginine, V=valine

  14. Characters DNA hybridisation techniques allow the comparison of a billion of nucleotides. determine melting temperature dissociate into single strands dissociate into single strands radioactive labeling isolate hybrid double strands add to incubation mixture

  15. Characters restriction enzymes cleave DNA at specific short nucleotide sequences, producing distinctive patterns of fragments. EcoRI 5’ 3’ … … N N N N G C A T A T T A T A C G N N N N … … 3’ 5’ A A T C G N N N N … … 3’ 5’ 5’ 3’ … … N N N N G C T A A T

  16. Characters restriction enzymes cleave DNA at specific short nucleotide sequences, producing distinctive patterns of fragments. EcoRI Bg/II XbaI EcoRI Bg/II XbaI SmaI HindIII SmaI Hpa1 Hpa1

  17. Characters comparing nucleotide sequences among species is the most precise way of inferring phylogenetic relationships. April 2011: 135 440 924 sequences 126 551 501 141 bases

  18. Characters since1995, 180 organisms were sequenced genome-wide Drosophilamelanogaster Rattusnorvegicus Caenorhabditisbriggsae Apismellifera Takifugurubripes Canisfamilaris Oryzasativa Tetraodonnigroviridis Populustrichocarpa Cionaintestinalis Caenorhabditeselegans Arabidopsisthala Anophelesgambiae Mus musculus Pan troglodytes Gallus gallus Homo sapiens

  19. Characters some types of DNA evolve faster than others. NuclearDNA Mitochondrial DNA Microsatellites • easy to isolate • evolves at a faster rate • e.g. CAACAACAA… • evolve at an even faster rate

  20. Charactercoding continuous quantitative characters are often reverted into discrete ones, e.g. by gap coding. state 0 state 1 state 2 a b c d

  21. Inferringphylogenies different approaches exist for inferring phylogenies Parsimonymethods Distance methods Maximum likelihood methods Bayesian inference methods

  22. Testingphylogenies specific hypotheses about trees, evolutionary models and clocks can be tested statistically. Testingmodels, trees and clocks Bootstrap, jackknife and permutation tests

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