This family was in Jennings Co., 1850 and 1860. I suspect there were TWO wives named Mary--the first, Mary Ann, born about 1829 KY, mother of Matilda, William, Lucinda, John. Then Thomas Jones married Mary Ann Short, Feb. 1855, Jennings Co. She was born about 1833, Indiana; mother of the younger children, Thomas, Eugenia, Hellen.
Thomas Jones is almost certainly a son of Thomas Jones, Sr., born 1798, died Nov. 29, 1853, buried in Edwards Cemetery in Jennings Co.
Can't find any of your family in 1880--I'm sure you've tried also! I did go through all marked burials in Wayne Twp. Bartholomew Co.; they are not there. Thomas was a railroad clerk in 1870, a job that might well have moved him around a lot. It's POSSIBLE he's the "Mr. Jones" who was killed in Indianapolis in 1888 and buried in the old Edwards cemetery back in Jennings Co.: http://www.findagrave.com/cgi-bin/fg.cgi?page=gr&GScid=2...