Deep ancestry research plays a much larger role for genealogists than I ever realized. In the future, deep ancestry (Y-SNPs) will cross over into the genealogical time frame (200 to 600 years). Here are some major usages of Y-SNPs for genealogists:
1) For surnames with a lot of different genetic origins, it is very difficult for admins to separate clusters based on Y-STRs only. For better groupings, sponsors should also get deep clade tests. They should also test for newly discovered Y-SNPs that are not included in the deep clade (haplogroup) test to get the most recently discovered haplotree branch. This will help admins better break up groupings by haplogroups which in turns helps sponsors see which submissions are related. If you do not share a deep ancestry (1,000 to 2,000 years ago), you obviously can share genealogical connections in the 200 to 600 year range.
2) Deep ancestry researchers are primarily only interested in finding new Y-SNPs that are broadly found that will reveal new major branches on the haplotree. These branches are now approaching the genealogical time frame as my L226+ is believed to originate only 1,300 years ago. A big surprise was the discovery of "private" SNPs. These are not widely found and are believed to be anywhere to 200 to 1,000 years old. These private SNPs can be used and are being used by genealogists as very recent DNA fingerprints of common ancestry. They could potentially separate genealogical clusters into two major branches or could reveal good NPE candidates.
3) Once you test positive for a pretty recent haplogroup (1,000 to 2,000 years ago), you can determine the MRCA of the haplogroup (published at most Y-SNP projects). The MRCA of your surname cluster will generally have only 2 to 10 mutations from haplogroup MRCA. It can difficult for some surname clusters to determine the MRCA for some markers as there is sometimes no clear "majority rules" winner to determine the MRCA value for some markers. By comparing both possible marker values of the surname cluster MRCA to the haplotype MRCA can help determine the MRCA of the surname cluster. Also, the off-modal modal values (mutations) from the haplogroup MRCA to the surname cluster MRCA can be very revealing as a DNA fingerprint for your cluster. This DNA fingerprint can be used for NPE candidates searching.
Family Tree DNA offers a test called the "Walk the Y" test for $750. This is a partial Y-chromosome test that is looking for new mutations of Y-SNPs. In only 2 or 3 years, full Y-chromosome tests will fall to under $1,000 or much less. With this test, you will never have to upgrade either your Y-STR markers or Y-SNP markers since all will be already be tested. Most researchers think that there are enough Y-SNP mutations to identify every living person uniquely. Researchers think that Y-SNP testing will eventually replace Y-STR testing. However, I do not think genealogists will give up census records (Y-STRs) for probate records (Y-SNPs). We like lots of different sources and already have a massive Y-STR database being created. I highly recommend joining your haplogroup project and hang around deep ancestry researchers for a while. Both crowds have a lot to learn from each other. There are now discovered a lot parallel Y-SNP mutations (L159.1, L159.2, etc.) Welcome to the world of genealogists where independent mutations to the markers to the same marker value happen regularly.