Phylogenetic genome analysis, phylogenomics Bas E. Dutilh

What we can see

Family tree → species tree Offspring looks like its parents Darwin: species evolve like families

Species tree

Tree of life Archaea Bacteria Eukaryota

Phylogeny Term coined by Ernst Haeckel (1866) Phylon (Greek: fulon) Tribe Race Genus (Latin) Birth Origin

Phenotype ↔ genotype Infinite # features Subjective choice Value can depend on observation (etc.) Gene/genome is finite Objective choice A sequence is absolute

Convergence Contrary to phenotype or structure, sequences do not converge Highly dimensional: every residue is a dimension

Phylogenetic markers Available/easy to sequence Present in all species Cytochrome C Present in all species Constant function Slowly evolving SSU rRNA Fitch, Science1967 Woese et al, PNAS 1977

SSU rRNA Phylogeny of SSU rRNA discovered the three domains Representative for the evolutionary history of species Archaea Bacteria Eukaryota

Phylogenetic assumptions Sequences are homologous – have a common ancestor Sequences diverge in a binary fashion Each position evolves independently

Phylogenetics Neighbor joining Maximum parsimony Maximum likelihood Which tree assumes the fewest mutations? Maximum likelihood For a given model, which tree has the highest probability of generating observed alignment?

Bootstrapping Jackknifing Randomly re-sample all columns in the alignment with replacement Re-create trees Count presence of each branch Jackknifing Delete fraction of columns Re-create tree

Different genes tell different stories Conflict between trees based on single genes Unrecognized paralogy Horizontal gene transfer Mutation saturation, biases, divergent rates spec B spec A - Paralogs - Orthologs ancestor spec C

More data → more consistent trees Combine information from more genes to average out these anomalies Complete genomes contain the maximum phylogenetic information Dutilh et al, Bioinformatics 2007

Chimeric genomes Is a tree the right representation of the evolutionary history of a genome? Endosymbiosis (mitochondrion, chloroplast) Horizontal gene transfer (many examples, often adaptations to environment) Darwin, 1859 Doolittle, Science 1999

Densitree “Fuzzy” trees Draw the tree lots of times Bootstrap Different genes Use transparency to make fuzziness

Splitstree Tries to accommodate non-bifurcating nodes Some positions evolve independently Parallel edges are related

Genomic properties Word frequency Sequence (nt/aa) Gene content Gene order

Dutilh et al, Bioinformatics 2007 Fungi Yeasts, filamentous and dimorphic fungi Fungi are the eukaryotic clade with largest number of completely sequenced genomes S. cerevisiae is a well studied model organism Much consensus about phylogeny Dutilh et al, Bioinformatics 2007

Consensus phylogeny (literature) 19 target nodes Dutilh et al, Bioinformatics 2007

13 trees 14 trees 15 trees 12 trees

Gene content methods Presence/absence matrix (0/1) Similarity: number of shared orthologous groups Genomes that share few OGs are distantly related Genomes that share many OGs are closely related OG1 OG2 OG3 OG4 … sp1 1 1 0 1 … sp2 0 1 0 0 … sp3 0 0 1 1 … … … … … … but… Snel et al, Nat Genet 1999 Tekaia et al, Genome Res 1999

Genome size correction Large genomes have more genes, so they also share more genes Divide number of shared genes by Average genome size Smallest of two genomes Weighted average genome size P. chrysosporium # shared genes genome size Korbel et al, TiG 2002

Saitou et al, Mol Biol Evol 1987 Gene content methods Similarity: corrected number of shared genes Distance: (1 – similarity) Neighbour joining ( ) # shared OGs (spA, spB) weighted average size (spA, spB) d 0.8 0 0.6 0.1 0 0.8 0.9 0.7 0 dist (spA, spB) = 1 – \s sp1 sp2 sp3 sp4 … sp1 \1 0.2 0.4 0.2 … sp2 \1 0.9 0.1 … sp3 \1 0.3 … sp4 \1 … … … … … … Saitou et al, Mol Biol Evol 1987

Superalignment methods Multiple alignment Concatenate alignments (1:1:1) A missing gene in a certain species (row) can be seen as a gap in the alignment

Select positions Percentage gaps Percentage conservation GBlocks Slow-fast Castresana, Mol Biol Evol 2000 Brinkmann et al, Mol Biol Evol 1999

Gene content vs. sequence Gene content supertrees are different than sequence based supertrees Dutilh et al, Bioinformatics 2007

“Hot” origin of life? Protein sequence Gene content

Other evidence Membrane composition Gene structure Plötz et al, J Biol Chem 2000 Gene structure Gribaldo et al, J Bact 1999

Light from different angles Sequence Phylogenetic trees (marker genes) Phylogenomic trees Gene content Gene content trees Signature genes Phenotype Morphology Metabolism / chemistry

Highly similar strains Almost identical gene content Low recombination rate Whole genome alignment Mauve Nucmer Extract positions that are not completely conserved from the genome alignment SNPs Small indels Abundance Recombination rate