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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. Hedges & Kumar 2009. Timetree of Life. Oxford University Press depending on the input data and the algorithm used, trees can be rooted or unrooted. Phylogenetic trees Alpha Delta Gamma Beta Epsilon Gamma Beta Alpha most recent common ancestor Delta Epsilon Phylogenetic trees depending on the input data and the algorithm used, trees can be scaled to time or not 1Mya 2Mya 3Mya 4Mya 5Mya Phylogenetic trees trees can be bifurcating or multifurcating. Characters different types of traits can be used to infer phylogenies. Phenotypical data Morphological traits Physiological traits Cytological traits Behavioural traits Molecular data Immunological techniques Proteines (amino acid sequences) DNA DNA-DNA hybridisation Restriction enzyme sites Nucleotide sequence comparisons Characters Friedman 2008. Nature 454: 209-212. morphological traits can be measured in both extant and extinct taxa. Characters 10mm Friedman 2008. Nature 454: 209-212. Characters cytogenetic traits include the number, size and morphology of the chromosomes, behavior in meiosis and total DNA content Zeltnera exaltata Zeltnera calycosa Zeltnera venusta Mansion & Zeltner 2004. Am. J. Botany 91: 2069-2086. Characters behavioural characteristics can be used to build trees. Elk – Cervus canadensis Moose – Alces alces Fallow deer – Dama dama Cap et al. 2008 Cladistics 24: 917-932. Characters behavioural characteristics can be used to build trees. Elk – Cervus canadensis Moose – Alces alces Fallow deer – Dama dama Cap et al. 2008 Cladistics 24: 917-932. in immunological taxonomy, antibody-antigen recognition is used to estimate relatedness. Characters B A species A antigens species A antibodies species B antigens precipitation precipitation+++ species C antigens C trees can be build by comparing amino acid sequences for the same protein in different species. Characters amino acid sequence of aspartate transaminase 1 2 3 4 5 6 7 8 9 1 0 1 1 1 2 4 0 4 1 4 2 4 3 4 4 4 5 4 6 4 7 4 8 4 9 5 0 Bacteria P L F D F A Y Q G F A R … K N F G L Y N E R V G Yeast A L F D T A Y Q G F A T … K N A G M Y G E R V G Alfaalfa P F F D S A Y Q G F A S … K N M G L Y G E R V G Chicken P F F D S A Y Q G F A S … K N F G L Y N E R V G Rat P F F D S A Y Q G F A S … K N F G L Y N E R V G Horse P F F D S A Y Q G F A S … K N F G L Y N E R V G Pig P F F D S A Y Q G F A S … K N F G L Y N E R V G Human P F F D S A Y Q G F A S … K N F G L Y N E R V G 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 DNA hybridisation techniques allow the comparison of a billion of nucleotides. Characters dissociate into single strands dissociate into single strands radioactive labeling add to incubation mixture isolate hybrid double strands determine melting temperature restriction enzymes cleave DNA at specific short nucleotide sequences, producing distinctive patterns of fragments. Characters EcoRI 5’ … N N G A A T T C N N … 3’ 3’ … N N C T T A A G N N … 5’ 5’ … N N G 3’ … N N C T T A A restriction enzymes cleave DNA at specific short nucleotide sequences, producing distinctive patterns of fragments. Characters EcoRI HindIII Hpa1 Bg/II XbaI SmaI EcoRI Hpa1 Bg/II XbaI SmaI Characters April 2011: comparing nucleotide sequences among species is the most precise way of inferring phylogenetic relationships. 135 440 924 sequences 126 551 501 141 bases since 1995, 180 organisms were sequenced genome-wide Characters Drosophila melanogaster Ciona intestinalis Rattus norvegicus Caenorhabdites elegans Caenorhabditis briggsae Arabidopsis thala Apis mellifera Anopheles gambiae Takifugu rubripes Mus musculus Canis familaris Oryza sativa Pan troglodytes Tetraodon nigroviridis Gallus gallus Homo sapiens Populus trichocarpa Characters Nuclear DNA Mitochondrial DNA Microsatellites some types of DNA evolve faster than others. • easy to isolate • evolves at a faster rate • e.g. CAACAACAA… • evolve at an even faster rate Character coding state 0 a continuous quantitative characters are often reverted into discrete ones, e.g. by gap coding. state 1 b c state 2 d Inferring phylogenies Parsimony methods Distance methods Maximum likelihood methods Bayesian inference methods different approaches exist for inferring phylogenies Testing phylogenies specific hypotheses about trees, evolutionary models and clocks can be tested statistically. Testing models, trees and clocks Bootstrap, jackknife and permutation tests