Several genealogists have come to the conclusion that Edward Tipton and Amy Phillips were the parents of Jonathan. This Edward was born about 1617 in Pontesbury, Shropshire, England. This might fit if we assume that Jonathan was born in 1639. However, there is no indication that this Edward and Amy ever came to America. However, their son, also named Edward, did come to America. This son was born 7 Nov 1650, and was 18 when he arrived in Maryland on the ship Friendship. He returned to England in 1700. There is no indication that Edward, Jr, went to Jamaica. While it might be possible that Jonathan was a brother to Edward, Jr, it is highly unlikely that he would be his son.
I (Bob Tipton) am a co-administrator of the Tipton Family DNA Project. We currently have about 60 male members who have taken Y-DNA tests. Almost all of them have closely matching STRs and are members of the I1 haplogroup. Those that have done SNP testing are confirmed I-L813. So far, we do not have any tested members from England, so have not been able to prove or disprove a connection to either Edward.
The Tipton surname is location-based, so it would not be unusual to find several different DNA signatures, but so far almost everybody seems to be a close match to Jonathan (or a close ancestor of his). 
We have no inkling as to the identity of the parents of Jonathan Tipton, and we can only speculate about how they arrived on the island of Jamaica. Jonathan's father could well have been one of the men in Penn and Venable's Haitian expedition force that conquered Jamaica in the campaign that extended from 1650 to 1655. A scenario (totally speculative) that appeals to this writer is one wherein Jonathan's father was one of the 4,200 to 5,200 men that Penn and Venable recruited in the Windward and Leeward Islands prior to the assault of Jamaica who survived the campaign, saw an opportunity to improve his lot in this new British possession, and settled on the island. Once hostilities ceased he could have either returned to his home island for his wife or sweetheart or bought her passage from there to Jamaica. No English were on Jamaica prior to 1650. The fact that no Spanish given names are found in any of Jonathan's descendants leads one to conclude that his mother was of English descent, probably from one of the nearby Lesser Antilles or some other British West Indies possession. 
Immigration to United States if America: (1671 1676). The year range 1671-1676 puts the age of Jonathan Tipton at the time he entered this country at somewhere between 12 and 17 years. The writer is inclined toward the latter end of this bound for several reasons. First, it is more believable that a 16- or 17-year-old young man would want or need to leave his homeland than it is for a stripling of 12 or 13 years. Second, somewhere along the way, Jonathan learned the art of barrel making, for we find him described as a "cooper" in many of the early Maryland records; and, in 1830, he gave bond that he would have William and Richard Cross taught to read and learn the trade of cooper. How did he learn this trade? We can only speculate, but it seems more likely to this student of the family that he learned from his father or had nearly completed his apprenticeship at age 16 or 17 when he departed the Jamaican shores than it is that a 12- or 13-year-old friendless youth could manage to get taken on as an apprentice in this country. 
Birth Date: about 1659
Place of Birth: Jamaica , ,  (what are these bracketed numbers?)
Supporting this birth estimate:
The following obituary appeared in the January 27, 1757 issue of the Maryland Gazette:
"We are informed that at the beginning of this month, died in Baltimore County, Mr. Jonathan Tipton, aged 118 years. He was born at Kingston on Jamaica, which place he left while young, and lived almost ever since in this province, and had his perfect senses to the last, especially a remarkable strength of memory. His youngest sons are reckoned among the oldest men in Baltimore County."
Charles D Tipton, in his book TIPTON The First Five American Generations, discusses several of the problems with this short obituary. One of the most telling is the fact that Jamaica was under Spanish control until it was conquered by Venable in 1655. It is unlikely that an English child was born in Jamaica prior to that time. Tipton says that 1659 is a much more likely date of birth:
""Fortunately, new evidence regarding Jonathan's date of birth has surfaced in the past few years that brings Jonathan's lifespan into harmony with history and makes his level of activity more in keeping with his age. Taking all things into consideration, the year 1659 would seem, to this student of the Tipton family, to be the most likely for the date of birth of Jonathan Tipton for the following reasons." 
Another element in Jonathan's obituary that seems to be in error is the statement that he was born in Kingston on Jamaica. Kingston, Jamaica, was not built until after the destruction of Port Royal by an earthquake in 1692, several years after Jonathan's arrival in America.
A 1966 letter from the librarian for the Institute of Jamaica to the writer (Bob Tipton?) contains the following statement:
"The English conquered Jamaica from Spain in 1655, and before that time the English settlers were not allowed in the Island, so Jonathan Tipton could not have been born in Kingston in 1639."
Jonathan Tipton's birthplace was almost certainly Jamaica, not only because it was so reported in a contemporary article in the Maryland Gazette, but also because of Jonathan's strong sense of identity with the island as demonstrated by his naming one of his farms "Poor Jamaica Man's Plague," and another "Port Royal."
3. Chronicles of a Nation: Founding Fathers, Families, and Patriots
July 11, 2015 by Joan Wheeler LaGrone (Author)
Publisher: WIN Publishers of Colorado
WAPI (Tower ID): 136603289
Release Date: July 11, 2015
Maryland, Church Records, 1668-1995, database, FamilySearch (https://familysearch.org/pal:/MM9.1.1/F4ZN-GRF : 24 February 2016), Jonathan Tipton in entry for Jonathan Tipton, 25 Mar 1699; citing Birth, St. James Parish, Anne Arundel, Maryland, United States, various libraries, churches, historical and national societies, private and public records; FHL microfilm 13,280.
"Maryland Births and Christenings, 1650-1995," database, FamilySearch (https://familysearch.org/pal:/MM9.1.1/F4ZJ-297 : 12 December 2014), Jonathan Tipton in entry for Thomas Tipton, 08 Apr 1693; citing Saint James Parish, Anne Arundel, Maryland; FHL microfilm 13,280.
"Maryland Births and Christenings, 1650-1995," database, FamilySearch (https://familysearch.org/pal:/MM9.1.1/F4ZJ-2ZX : 12 December 2014), Jonathan Tipton in entry for William Tipton, 27 Jul 1696; citing Saint James Parish, Anne Arundel, Maryland; FHL microfilm 13,280.
Maryland, Church Records, 1668-1995, database, FamilySearch (https://familysearch.org/pal:/MM9.1.1/F4JM-W5D : 24 February 2016), Jonathan Tipton and Mary Chilcoat, 15 Dec 1709; citing Marriage, Saint James Parish , Anne Arundel, Maryland, United States, various libraries, churches, historical and national societies, private and public records; FHL microfilm 13,280.
Stevens, Mary Edith, (1984) "Family History of John Stanley Stevens, with geneaologies of the families who settled in Union and Wayne Counties, Indiana. Route 3, Box 237, Flowery Branch, GA 30542, Note: Most of the Stevens, Tipton side of Marguerite Steven's family researched and listed in book by Margie's step mother, Mary Edith Stevens.
It may be possible to confirm family relationships with Jonathan by comparing test results with other
carriers of his Y-chromosome or his mother's mitochondrial DNA.
However, there are no known yDNA or mtDNA test-takers in his direct paternal or maternal line.
It is likely that these autosomal DNA test-takers will share DNA with Jonathan:
There is no doxumentation that Jonathan Tipton had a son named John. The only proven children of Jonathan Tipton are Thomas, William and Jonathan,II. This is evidence explained by the definitive authority on the Tiptons during this time period, Charles Dawes Tipton. If anyone can document that Jonathan had a son, John, by all means include him.
Is Elizabeth Jane Tipton, who married John Hunt the daughter of this Jonathan Tipton? Tipton-369 https://www.wikitree.com/wiki/Tipton-369 It looks like there is not a Elizabeth Tipton. That John Tipton Hunt is not a relative on paper records, that he received his middle name Tipton for his father or grandfather being a friend of the Tiptons. Was their any Tipton's that also named their children after their friend Hunt? http://www.genealogy.com/ftm/j/e/f/Lora-Jeffries/WEBSITE-0001/UHP-0034.html One of the pages said the Hunts were in the tobaco business and moved from Maryland for fresh fields. Were the tipton's also in tobacco? In respect to DNA... I think the Hunt line that has the Denton line in it... May have gotten to think Elizabeth Tipton... I may be related to Tipton's through marriage to son Jonathan Tipton 1699 then grandson Joseph Tipton 1738-1842 that married Elizabeth Denton? I am going to see if I can connect the Denton lines. I am checking the trees to make sure I do not have any other common ancestors. I have a 8.4cM match who has line through Thomas Tipton and his Steptoe wife, I am about to source the line that match comes through, there is one other match I can see so far through this line. I found another Elizabeth Tipton that married a William Amiss in 1760 in Shropshire, England they seem to be in England, so I would need to finish my England lines to see if I had any other matches with them. I am trying to organize these matches Had another match with a Lavina Tipton born 1765 and married Isaac Whitecotton. The son's middle name was Tipton. I am working on this now. Might make a forum post to look for these lines. I now have a match also with the William Tipton line through Sarah Tipton that married Christopher Cole a 7.4cM match, I will try and message these matches and see if thy are on gedmatch.com.
Saro, I don't think I said anything about two sons named Jonathan. Prior to 23 Sep 2014, this entry for Jonathan Tipton-63 [CDT LoD (A)] correctly listed all four sons (Thomas (AA), William (AB), Jonathan (AC) and John (AD). If you look at the change history for Tipton-62, you can see where it was proposed to merge Tipton-199 (John) into Tipton-62 (Jonathan). My comment suggesting that these were not the same person can still be seen on in the public comment area of Tipton-62. The merge still took place. So, now there is no sign of John Tipton (AD). What I suggested here on July 9 was that somebody might want to add John (AD) back in as a son of Jonathan (A) Tipton-63.
I have considered asking that this profile be protected due to so many incorrect suppositions about the Tipton family in general. Please, if you have cause to believe some information needs to be changed or added, be so kind as to contact me and we can discuss it. I don't know EVERYTHING, by all means. But I have worked very hard cleaning up Tipton-63 with documentation and we can certainly discuss it and exchange ideas and sources. Thanks and Happy Hunting.
Hi Bob Tipton, Are you referring to Jonathan (A) or Jonathan Tipton-63 (husband of Sarah Pearce) or Jonathan Tipton-62 (husband of 4 wives) having two sons named Jonathan??? I worked Tipton-62 thoroughly using Charles D Tipton's book and less thoroughly Tipton-63 and I do not see anywhere that it states there were two sons named Jonathan. I just checked again!Please clarify. BTW, the merge of Tipton-199 and Tipton-62 wasn't at my iniation. :-} Thanks
Somebody might also want to add Jonathan's fourth son, John, back in. He used to have an entry (Tipton-199), but due to overzealous merging that entry was merged into Jonathan-62, and the information has now been lost. Charles has a section in his book which will provide most of the details needed to recreate the entry.
Could we please unlink these parents since the definitive authority who has done extensive research and documentation on the 1st 5 generation of Tipton's says there just is no proof of any ancestry past this Tipton. This myth was perpetrated from Hord Tipton's 1948 book and has been carried down until now.