Harold Casey

Harold Casey, ca. 1944, Elk City, OK

How To - Y-SNPs (Deep Ancestry Viewpoint)


For deep ancestry researchers, it is primarily about discovering new branches to add to the descendancy chart of mankind (known as the Y-DNA haplotree). Once a new Y-SNP is discovered, then the new Y-SNP must be tested via special order Y-SNP testing to determine the breadth and age of the newly discovered Y-SNP and how it relates to existing Y-SNPs. There are a myriad of diverse and interesting other reasons that deep ancestry researchers are involved. Many just like the mathematical and logical challenge behind analyzing Y-SNPs. Others have interest geographic origins of their ancestry or are researching the origins of their surnames. Others are more interested in the migration patterns of mankind in the last 2,000 years. For those with Scottish and Irish ancestors, many are attempting to determine and establish the connection of various surnames associated with clans. For many genealogists, it is gathering more genetic information in order to connect many diverse lines of related individuals beyond what traditional documentation reveals by itself. We all share the common feeling of accomplishment with our small collective contributions in adding another branch to the descent of mankind.

Deep ancestry research focuses on discovering the broadest and oldest branches possible. There is a strong desire to discover and document broad branches so that the branches are orderly that do not leave any researchers stranded with only R-L21 as their most recent Y-SNP. Since the R-L21 Plus project and the R-L21 WTY project are the primary projects where researchers share their discoveries, there is natural bias to discover and document new sons of R-L21. This natural bias also exists since there is a strong desire to find new sons of R-L21 that are inclusive all the researchers that contribute to the R-L21 project. Deep ancestry researchers tend to move on to other topics once a Y-SNP has been determined to be broad in nature or once a Y-SNP is been determined to be much smaller in scope. Once any Y-SNP is discovered to be broad in nature, it becomes the responsibility of a new haplogroup project that has its own members and new goals.

There are some major differences between the goals of deep ancestry researchers and genealogists that need to be understood by both parties. The primary differences are the age of the Y-SNP and the breadth of Y-STR submissions under any Y-SNP. Finding new sons of R-L21 that include descendants what was previously sons of R-L21 is a major find for deep ancestry researchers as it organizes the R-L21 genetic descendancy chart into orderly and evenly distributed tree like structure. These older Y-SNPs also reduce the number of Y-STR submissions that are stuck with only R-L21 as their most recent Y-SNP. Once a Y-SNP is determined to be very limited in scope, interest in the Y-SNP wanes as these Y-SNPs will have less impact of including any large quantity of researchers that are researcher R-L21 related Y-SNPs. Genealogists are just the opposite, the smaller the scope and the more recent the origin of the Y-SNP, the higher the impact will be on genealogical research. Although deep ancestry researchers and genealogists have some major differences in their objectives, both parties are so dependent on each others research that any real difference become less important since each group benefits so much from each others work.



For those just starting out in deep ancestry research, the methodology of research is radically different from genealogical genetic research. The first step for deep ancestry researchers is to build a significant database of Y-STR submissions that are believed to be R-L21 descendants. Once a database is established, researchers look for patterns of common Y-STR mutations that may reveal common ancestry. Since Y-SNPs and Y-STRs track each other, these Y-STR patterns are DNA signatures that reveal good candidates future "Walk the Y" testing. Once a major pattern is discovered, leaders of the R-L21 projects encourage researchers of these DNA signatures to pool their funds for a partial Y chromosome test offered by Family Tree DNA that reveals new Y-SNP mutations. This leadership of the R-L21 research also datamines other scientific and academic databases for new Y-SNP mutations that are positive for R-L21. This first phase of Y-SNP analysis and specialized "Walk The Y" tests from Family Tree DNA (and datamining other genetic databases) are the seeds of discovering new Y-SNPs that were previously unknown.

Once a new Y-SNP has been discovered that appears to be a descendant of R-L21, there is a small waiting period for Family Tree DNA to add the newly discovered Y-SNP as a special order Y-SNP test. Since Y-DNA ladder rungs are added and deleted on such a regular basis, Family Tree DNA has to determine a "primer" which similar to a fixed landmark that shows you have now arrived near the newly discovered Y-SNP and that the new Y-SNP is a fixed distance from the landmark. Occasionally, primers can not be determined as the area of the Y-DNA strand may be to volatile to reliably find the new Y-SNP. Unlike other DNA testing companies that only offer static Y-SNP tests, Family Tree DNA is constantly adding new special order Y-SNPs on a monthly basis. Once the primer has been determined, the new primer has to be added to the production DNA scanners and the Family Tree DNA web site has to be updated to accept orders for the newly discovered Y-SNPs.

Once the new Y-SNP is available for researchers to order, deep ancestry researchers now enter the second phase of analysis that determines the breadth of the Y-SNP and how the new Y-SNP relates to other existing Y-SNPs that are already known. As with most newly discovered Y-SNPs, there is a flurry of testing immediately after the new Y-SNP becomes available for ordering. If the scope is found to be narrow via testing, the testing becomes more focused by only a few interested researchers. If the scope the new Y-SNP remains broad, testing continues until the final scope of the new Y-SNP is better known. This phase of deep ancestry analysis determines the breadth and age of the Y-SNP as well as any connections of the new Y-SNP with existing Y-SNPs. This phase of analysis takes three to six months of initial testing depending on the complexity and breadth of the new Y-SNP. After this time frame of testing, the Y-SNP either becomes a well defined wide-spread Y-SNP where interest drops off over time or becomes a narrow scope Y-SNP where interest falls rapidly since the scope is much less.

Once a new Y-SNP is determined to be somewhat broad, attention is switched to getting the new Y-SNP qualified for addition to the Y-DNA haplotree. "Private" SNPs will never qualify for the haplotree as the haplotree as defined by the ISOGG organization. "Private" Y-SNPs are those fail the following criteria: 1) the Y-SNP has been observed more than once; 2) Y-STR submissions testing positive for the Y-SNP must have a Y-STR variance of more than a 15 % (must have 10 or more mutations between two 67 marker Y-STR submissions); 3) must be proven to be broader than 0.05 % of the population that has tested (with around 105,000 37 marker FTDNA submissions, this equates to demonstrating that around 50 Y-STR submissions could test positive for the new Y-SNP). Other rules require that the connection between the new Y-SNP and existing Y-SNPs must be proven via testing (all sons of R-L21 must be tested for the new Y-SNP to see if they are descendants of existing Y-SNPs found on the haplotree).

After Y-SNPs have been added to the haplotree or after the Y-SNP has been determined to be more limited in scope due to initial testing, deep ancestry researchers switch their primary focus back to the myriad of new Y-SNPs being discovered every week. For most broader scope Y-SNPs, spin-off projects are formed to address additional research. For those that are more "private" in nature, interest becomes limited to those researchers who are usually related to the "private" Y-SNP with the assistance of R-L21 leadership as time allows. In the past, there were many fewer Y-SNPs being discovered on a weekly basis, so "private" Y-SNPs received much more attention in the past. With the tremendous increase in the rate of new Y-SNP discovery, these more "private" SNPs are receiving less attention since addressing all the new Y-SNP discoveries is hard to keep up with. However, these new "private" Y-SNPs are gaining interest with genealogical researchers where their impact could be extremely important to genealogical research. This web site is evidence of the increasing interest of genealogists in deep ancestry research as "private" and "near private" Y-SNPs now plays a major role in the analysis of genealogical surname clusters.