1. Study phylogeny in the context of species evolution
Phylogenies of 5154 syntenic 1:1 orthologs ?
Systematic errors in existing methods
Lack of informative sites in short genes
Long-branch-attraction in fast-evolving lineages
Gene trees of syntenic orthologs are similar
Genes maintain common rate across different species
Each genome has species-specific acceleration
Correct
phylogeny

2. The two forces of gene-family evolution
Mutation rate of gene j in species i = gene-rate * species rate
bij = Fj * Si
1. Family rate
2. Species-specific rates Fj Si
~gamma(a,b)
~normal(ui,si)
Selective pressures on gene function
Population dynamics of the species

3. Evolutionary history of all genes in 17 fungi
Each branch
Mean and stdev
Num genes
Gains, losses
Features
Few events !
Gain vs. loss
Acceleration
Churning
Applications
Recover WGD
Pathogenicity
Mating evolution
Codon capture
Evol. parallels

4. Resolving power in mammals, flies, fungi
0.3 sub/site
Post-duplication
9 Yeasts
Pre-dup P
Diploid P P
8 Candida P P
Haploid P
10 mammals
12 flies
17 yeasts
Neutral: 2.57 subs/site
(opp: sps: 4.87)
Coding: 1.16 subs/site
Detect: 6-mer at FP 10-6
Neutral: 4.13 subs/site
Coding: 1.65 subs/site
Detect: 6-mer at 10-11
Neutral: 15.5 subs/site
(Yeast: Candida: 6.5)
Coding: 7.91 subs/site
Detect: 3-mer at 10-21

5. Resolving power in mammals, flies, fungi
0.3 sub/site P P P P P P P
0.1 s
0.8 sub/site
10 mammals
12 flies
17 yeasts
Neutral: 2.57 subs/site
(opp: sps: 4.87)
Coding: 1.16 subs/site
Detect: 6-mer at FP 10-6
Neutral: 4.13 subs/site
Coding: 1.65 subs/site
Detect: 6-mer at 10-11
Neutral: 15.5 subs/site
(Yeast: Candida: 6.5)
Coding: 7.91 subs/site
Detect: 3-mer at 10-21

6. Extensive conservation of synteny
Mammals
Flies
Candida
Global mapping of orthologous segments
Nucleotide-level alignments span complete genomes
Study properties / patterns of nucleotide conservation