Sometimes testing the Y chromosome can help when you are looking for a missing father, grandfather, or further back as long as you have a tester descended on the male only line. Remember the Y is passed father to son, so any changes are rare and are caused by mutations not recombination. Typically a man would start with a Y 37 STR marker test at Family Tree DNA to see if this avenue is worth pursuing. A STR test gets the most recent changes rather than the haplogroup, thus can suggest a surname. Click here for my article explaining Y testing.
The Y results will not help if no other men from that Y lineage have tested unless you have a theory. In that case you need to test someone else descended on the male only line from the presumed ancestor.
Y testing can be very useful when the unknown parentage occured many generations ago, such that autosomal testing may not be able to solve it.
If your ancestors have been in the USA for some time then a Y 37 STR marker test may find a probable last name. In that case there may be a surname project with other Y testers at Family Tree DNA. I recommend contacting the admins of that project as they can often be a great help in your quest. However if you are from a population group which has only had inherited surnames for two hundred years or less, quite likely you will have no luck.
Here is an example from the Y test of a Jewish man with Polish Galician roots, surnames only happened there in about 1815.
As you can see, not a single surname is in common despite all being one step matches. Family Tree DNA has a nice chart in their help center to give you a feel for what a genetic distance number means (click here). For surname research, I have found that a distance in the range 0-3 on a 37 marker test is the desired target. Warning, that number cannot be tied to a specific number of years. My second cousin has a 0 step match to a cousin sharing an ancestor born in the 1600s while my Dad has a 3 step match to a cousin sharing an ancestor born around the same time. I also know of a case where a son has a 2 step match to his father, a relationship proven in the autosomal DNA.
In my own family, my DNA research started by trying to find the ancestors of my Norwegian 4th grandfather. There were ten men with his name, Lars Monsen, born in the Bergen area in the right time frame; our hope was that a Y test would help figure this out. Unfortunately there were no close Y matches, so we needed to test another man descended from his possible grandfather. Click here to read that story.
Recently I was working on a case of an unknown father of an unknown father. Barry had figured out who his unknown father was, call him Lionel, but Lionel’s father was also unknown. Autosomal DNA pointed to a Smith family in Pearl River, Mississippi. However when Barry did a Y DNA test his closest matches had the surname Gilliland!
So we joined him to the Gilliland project where we found a number of Smiths, one of whom was a good autosomal match, although a 2 step Y match. Correspondence with him confirmed that some unknown Gilliland fathered this Smith line back during the American Revolution and yes, some of those descendants ended up in Pearl River!
On the other hand, in a number of cases that have been mainly solved with autosomal DNA, the Y STR test has confirmed the expected surname. If you have a male line descendant, it is always worth trying a Y test when working with unknown parentage, but you may find extra surprises like Barry did!
My Dad would be 101 today and I thank him again for doing every DNA test I asked for, including his Y to solve our own family mystery.