Morgan was born in Lexington, Kentucky, to Charlton Hunt Morgan and Ellen Key Howard Morgan. Part of a line of Southern planter elite on his father's side, Morgan was a nephew of Confederate General John Hunt Morgan and his great-grandfather John Wesley Hunt had been the first millionaire west of the Allegheny Mountains. Through his mother, he was the great-grandson of Francis Scott Key, the author of the "Star Spangled Banner", and John Eager Howard, governor and senator from Maryland. Following the Civil War, the family had fallen on harder times with the temporary loss of civil and some property rights for those who aided the Confederacy. His father had difficulty finding work in politics and spent much of his time coordinating veterans reunions.
Beginning at age 16 in the Preparatory Department, Morgan attended the State College of Kentucky (now the University of Kentucky). He focused on science; he particularly enjoyed natural history, and worked with the U.S. Geological Survey in his summers. He graduated as valedictorian in 1886 with a bachelor in science. Following a summer at the Marine Biology School in Annisquam, Massachusetts, Morgan began graduate studies in zoology at the recently founded Johns Hopkins University, the first research-oriented American university. After two years of experimental work with morphologist William Keith Brooks and writing several publications, Morgan was eligible to receive a master of science from the State College of Kentucky in 1888. The College required two years study at another institution and an examination by the College Faculty. The College offered Morgan a full professorship; however, he chose to stay at Johns Hopkins and was awarded a relatively large fellowship to help him fund his studies.
Under Brooks, Morgan completed his thesis work on the embryology of sea spiders—collected during the summers of 1889 and 1890 at the Marine Biological Laboratory in Woods Hole, Massachusetts—to determine their phylogenetic relationship with other arthropods. He concluded that with respect to embryology, they were more closely related to spiders than crustaceans. Based on the publication of this work, Morgan was awarded his Ph.D. from Johns Hopkins in 1890, and was also awarded the Bruce Fellowship in Research. He used the fellowship to travel to Jamaica, the Bahamas and to Europe to conduct further research.
Nearly every summer from 1890 to 1942, Morgan returned to the Marine Biological Laboratory to conduct research. He became very involved in governance of the institution, including serving as an MBL trustee from 1897-1945.
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