Lior Pachter: Challenges in combinatorial phylogenomics

The term 'homology' in biology was defined by Richard Owen as ‘the same organ in different animals under every variety of form and function’, and is used to refer to ‘common ancestry’. This important concept relies on the identification of evolutionary ‘characters’, distinct entities between which we may assign ancestral relationships. First used in reference to morphological characters, such as eye color or petal number, homology has since been used in reference to characters of all levels, from the behavioral to the molecular. Our recently acquired ability to identify the nucleotides in genomes of different species allows us to specify homology at the smallest scale. The identification of homology among nucleotides of genomes requires inference of ancestral evolutionary events such as mutations, recombinations and duplications, and is the central problem in the field of phylogenomics. 

I will present a brief (mathematical) introduction to phylogenomics, together with a survey of the algebraic and topological combinatorics that is central to its study.