Assessing evolutionary relationships among species from whole-genome analysis

1. Assessing evolutionary relationships among species from whole-genome analysis

2. Intro and history • Evolutionary history inferred from comparison of gene sequences (1965, Zuckerland and Pauling) • First universal tree of life from rRNA (1977-8, Woese) (is that true?)

3. Horizontal Gene Transfer • Clarification by analysis of complete genome sequences • Answer: each lineage has its own combination of vertical descent, gene transfer, gene and genome duplication, gene invention, gene loss and degradation, recombination, convergence and selection.

4. Inferring evolutionary history is dependent on genomes being analyzed.

5. Methods for assessing evolutionary relationships from genome sequences • Comparing phylogenetic trees of universal genes • Patterns of best matches to different species • Clustering species by oligonucleotide relative abundance • Identifying regions of the genome with unusual compositions • Using patterns of shared homologous proteins to build whole genome trees

6. 1. Comparing phylogenetic trees of universal genes • Generate and compare phylogenetic trees for every gene in every genome • (Problems?)

7. 2. Patterns of best matches to different species • Assess the degree of similarity of genes between genomes • Proportion of genes that show best matches to those of different species is used as a measure of relatedness. • Suggestion of extensive HGT between Bacteria and Archaea. • Fast but dependent only on sequence similarity.

8. 3. Clustering species by oligonucleotide relative abundance • Each species has unique(!) biases in nucleotide composition of its genome. • e.g. codon usage, GC nucleotide content, di-nucleotide frequency • Use relative abundance of dinucleotides as a measure of evolutionary relatedness (Karlin et al. 1995) • Dinucleotide abundance too prone to convergence

9. 4. Identifying regions of the genome with unusual compositions • Nucleotide composition within a species is relatively constant. • Takes time for newly transferred genes from other species (HGT) to become adapted to the new genome signature. • Detect foreign genes in a genome through identification of unusual nucleotide composition.

10. 5. Using patterns of shared homologous proteins to build whole genome trees • Number of shared genes between genomes to construct “whole genome trees”. • Number of shared genes between species is affected by genome size in addition to evolutionary relatedness.

11. Difficulty in detecting HGT • Genes from t. maritima (from microbial group of Bacteria) • Branches close to archaeal group • Cluster together • Biased nucleotide structure => HGT from Archaea to t. Maritima • Any rules for HGT?

12. Relationships between species • Average nature of genomes is similar in related major taxa • What about smaller phylogenetic groups? • Ambiguity due to transfers and difficulty of inferring events long ago • e.g. Predicting a root for tree of life

13. Genome reduction and degradation • Challenge vs. opportunity

14. How far should the compared genomes be? • Distantly related species => events from long ago or rarely happened • Closely related species => recent and frequent events

15. Conclusions • Models for genome evolution • From detection to understanding • Whole genome sequences are valuable

16. Reference • Eisen, Jonathan A. "Assessing evolutionary relationships among microbes from whole-genome analysis." Current opinion in microbiology 3.5 (2000): 475-480.