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Male Jonathan Smith Click to view Jonathan Smith in the family tree

Jonathan was born after 1684.1   Jonathan's father was Benjamin Smith and his mother was Ruth Loomis.  His paternal grandmother was Elizabeth Stanley; his maternal grandparents were Samuel Loomis and Elizabeth Judd. He had four brothers and four sisters, named William, Benjamin, Samuel, Job, Ruth, Elizabeth, Rachel and Mary.  He was the third youngest of the nine children.1 

1 phelps.FTW @ Tree #0105
Further sources/citations:
World Family Tree Vol. 3, Ed. 1 @ Tree #3669, 3669.ftw