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

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

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

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

5. trees can be bifurcating or multifurcating. Phylogenetic trees

6. Characters different types of traits can be used to infer phylogenies. Phenotypical data Molecular data Morphological traits Physiological traits Cytological traits Behavioural traits Immunological techniques 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 Zeltnera exaltata Zeltnera venusta Zeltnera calycosa Mansion & Zeltner 2004. Am. J. Botany 91: 2069-2086.

10. 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.

11. 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.

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

13. Characters trees can be build by comparing amino acid sequences for the same protein in different species. 12345678910101 1212 4040 4141 4242 43434 4545 4646 4747 4848 4949 5050 Bacteria PLFDFAYQGFAR…KNFGLYNERVG Yeast ALFDTAYQGFAT…KNAGMYGERVG Alfaalfa PFFDSAYQGFAS…KNMGLYGERVG Chicken PFFDSAYQGFAS…KNFGLYNERVG Rat PFFDSAYQGFAS…KNFGLYNERVG Horse PFFDSAYQGFAS…KNFGLYNERVG Pig PFFDSAYQGFAS…KNFGLYNERVG Human PFFDSAYQGFAS…KNFGLYNERVG 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 amino acid sequence of aspartate transaminase

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

15. Characters restriction enzymes cleave DNA at specific short nucleotide sequences, producing distinctive patterns of fragments. NNNN NNNN GCGC ATAT ATAT TATA CGCG NNNN NNNN ………… 3’ 5’ ………… 3’ TATA A A T CGCG NNNN NNNN ………… 5’ NNNN NNNN GCGC ………… 3’ A A T T EcoRI

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

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 since 1995, 180 organisms were sequenced genome-wide Drosophila melanogasterRattus norvegicusCaenorhabditis briggsaeApis melliferaTakifugu rubripesCanis familarisOryza sativa Tetraodon nigroviridis Ciona intestinalisCaenorhabdites elegansArabidopsis thalaAnopheles gambiaeMus musculusPan troglodytesGallus gallusHomo sapiens Populus trichocarpa

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

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

21. Inferring phylogenies different approaches exist for inferring phylogenies Parsimony methods Distance methods Maximum likelihood methods Bayesian inference methods

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