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Frank R. Lillie was born in Toronto, Canada, on 27 June 1870. His mother was Emily Ann Rattray and his father was George Waddell Little, an accountant and co-owner of a wholesale drug company. While in high school Lillie took up interests in entomology and paleontology but went to the University of Toronto with the aim of studying ministry. He slowly became disillusioned with this career choice and decided to major in the natural sciences. It was during his senior year that he developed his lifelong interest in embryology.