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Chapter 1 : Introduction: a Personal Homage to Tom Whittam
This chapter presents the author's interaction with Tom Whittam who had worked on statistical methods and evolutionary biology, and written a review article on Escherichia coli population genetics. Tom's review on the author's manuscript on Helicobacter pylori had suggested the use of the program Reticulate to display homoplasies, i.e., mutations that existed along multiple independent branches of a phylogenetic tree. Based on the suggestions, the author included the output from Reticulate analyses in the revised version, and the paper was accepted by Proceedings of the National Academy of Sciences of the USA, and published later that year. The author says that Tom's insights into phylogenetics in the late 1980s continued to influence how we calculated the ages of clonal lineages until very recently. The calculations used the assumption that a universal clock rate, which was calibrated by the genetic distance between E.coli and Salmonella enterica serovar Typhimurium and an estimated time of separation of 160 million years, could be applied to date the coalescent of a clonal lineage. This clock rate was used to calculate that the Mycobacterium tuberculosis complex evolved 20,000 years ago and that the E.coli O157:H7 lineage evolved from O55:H7 some 40,000 years ago. The author concludes that Tom was one of the few early founders of modern bacterial population genetics and has left a lasting impression on the field, particularly so on those who met him.