Applying Topological Principles to Genomic Analysis: Topological data analysis helps to overcome difficulties that conventional tree-based phylogenetic analyses have with horizontal gene transfers

In On the Origin of the Species in 1859, Charles Darwin proposed phylogenetic trees to depict evolutionary relationships on the basis of phenotypic attributes. Since then, biologists have shifted to using molecular traits to characterize evolutionary relationships between and among species. These approaches typically assume that traits are inherited vertically, and that evolution is strictly clonal. However, several other modes of genetic exchange add complexity to this process, including lateral gene transfers in bacteria, recombination and reassortment in viruses, viral integration in eukaryotes, and fusion of genomes of symbiotic species.