Phylogenetics Introduction and Methodologies

FBW 24-11-2011 Wim Van Criekinge

Inhoud Lessen: Bioinformatica ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Phylogenetics ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

[object Object],[object Object],[object Object],[object Object],[object Object]

Trees ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Clade: A set of species which includes all of the species derived from a single common ancestor

Species I. Definitions: Species = the basic unit of classification > Three different ways to recognize species:

Definitions: > Three different ways to recognize species: 1) Morphological species = the smallest group that is consistently and persistently distinct (Clusters in morphospace) species are recognized initially on the basis of appearance; the individuals of one species look different from the individuals of another Plant Species

Definitions: > Three different ways to recognize species: 2) Biological species = a set of interbreeding or potentially interbreeding individuals that are separated from other species by reproductive barriers species are unable to interbreed Species

Definitions: > Three different ways to recognize species: 3) Phylogenetic species = the boundary between reticulate (among interbreeding individuals) and divergent relationships (between lineages with no gene exchange) Species

reticulate divergent Phylogenetic species recognized by the pattern of ancestor - descendent relationships boundary

Definitions: > Three different ways to recognize species: 4) Phylogenomics species = ability to transmit (and maintain) a (stable) gene pool Adresses the Anopheles genome topology variations Species

[object Object],[object Object],[object Object]

[object Object],[object Object],[object Object],Branch node, internal node Edge, Branch Leafs Tips external node

Outgroups, rooted versus unrooted An unrooted reptilian phylogeny with an avian outgroup and the corresponding rooted phylogeny. The R i represent modern reptiles; the A i , inferred ancestors and the B a bird.

[object Object],[object Object],[object Object],Examples

[object Object],[object Object],[object Object],[object Object],Examples

[object Object],[object Object],[object Object],[object Object],[object Object],Examples

Origin of the Universe 15 billion yrs Formation of the Solar System 4.6 " First Self-replicating System 3.5 " Prokaryotic-Eukaryotic Divergence 2.0 " Plant-Animal Divergence 1.0 " Invertebrate-Vertebrate Divergence 0.5 " Mammalian Radiation Beginning 0.1 " ,[object Object]

[object Object],[object Object],[object Object],[object Object]

Carl Woese ,[object Object],[object Object]

[object Object],[object Object],Name a Size (nucleotides) Location 5S 120 Large subunit of ribosome 16S 1500 Small subunit of ribosome 23S 2900 Large subunit of ribosome a The name is based on the rate that the molecule sediments (sinks) in water. Bigger molecules sediment faster than small ones.

[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

[object Object],[object Object]

[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Rate of Change Theoretical Lookback Time (PAMs / 100 myrs) (myrs) Pseudogenes 400 45 Fibrinopeptides 90 200 Lactalbumins 27 670 Lysozymes 24 850 Ribonucleases 21 850 Haemoglobins 12 1500 Acid proteases 8 2300 Cytochrome c 4 5000 Glyceraldehyde-P dehydrogenase 2 9000 Glutamate dehydrogenase 1 18000 PAM = number of Accepted Point Mutations per 100 amino acids. ,[object Object]

[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

[object Object],Since we start with A,p(A)=1

[object Object],D=evolutionary distance ~ tijd F = dissimilarity ~ (1 – P X (t)) F ~ 1 – d

[object Object],http://www.bioportal.bic.nus.edu.sg/phylip/neighbor.html

[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Maximum Parsimony ,[object Object],[object Object],[object Object],The best tree is the one which requires the least number of substitutions

Maximum Parsimony: Branch Node A or B ?

Maximum Parsimony: A requires 5 mutaties

Maximum Parsimony: B (and propagating A->B) requires only 4 mutations

Comparison of methods ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Rooting the Tree ,[object Object],[object Object],[object Object],[object Object]

Automatic rooting ,[object Object],[object Object],[object Object]

Rooting Using an Outgroup ,[object Object],[object Object],[object Object]

How confident am I that my tree is correct? ,[object Object],[object Object]

Bootstrapping phylogenies ,[object Object],[object Object],[object Object],[object Object]

Bootstrapping - an example Ciliate SSUrDNA - parsimony bootstrap Majority-rule consensus Ochromonas (1) Symbiodinium (2) Prorocentrum (3) Euplotes (8) Tetrahymena (9) Loxodes (4) Tracheloraphis (5) Spirostomum (6) Gruberia (7) 100 96 84 100 100 100

[object Object],[object Object],[object Object],[object Object],[object Object],Bootstrap - interpretation

Jack-knifing ,[object Object],[object Object],[object Object]

Weblems ,[object Object],[object Object],[object Object],[object Object]

Phylogenetics Introduction and Methodologies

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Phylogenetics Introduction and Methodologies