A boom in direct-to-consumer Next Generation Sequencing tests has seen an explosion in the genetic genealogy community’s understanding of the Y tree. ISOGG’s tree has exploded in the last year. As consumers continue to compare and match their results the defining SNPs move from the Bronze Age to the emergence of surnames to the 1800s. The later growing group brings to focus a need to rethink genealogical Y DNA testing strategies.
Traditionally, the advice to new testers has always been to start testing STR markers to a level where valid hypothesis can be formed for relatedness of matches. As the STR marker databases grow in a manner that begins to mirror the actual population, a new phenomenon has been identified. Convergence of STR marker is a growing concern in well-tested subclades. These groups note clusters of men who share a genetic distance of ten or less at 111 markers, who clearly haven’t shared a common ancestor since prior to the adoption of surnames. SNP-based trees are needed to structure these men in any meaningful manner.
This blog entry proposes a new methodology, which will yield a budding genetic genealogist a lower cost solution.
Step 1: Take a Autosomal Panel
Wait! You may be saying to yourself. How will an autosomal panel help identify my paternal ancestry?
The answer is that you will not be taking just any autosomal panel. The key is to order the test from one of three vendors who also provide sufficient Y and mtDNA markers to establish your haplogroups. In order of cost the options are:
- 23andMe offers a $99 Ancestry Service. The test includes ancestry composition, cousin matching in the second largest database, and most importantly your Bronze Age Y DNA haplogroup. The test omits the health reports and is not available in all countries however.
- National Geographic offers a $199.95 option. The test includes ancestry composition and a Y DNA haplogroup using a more current selection of SNPs. The results can be transferred to FTDNA for cousin matching and inclusion of your Y SNPs in their matching database.
- BritiansDNA offers Chromo2 Complete for $345. This test is mentioned for completeness and not recommended as part of this strategy. The Y SNPs tested are more complete than 23andMe’s but NatGeo’s Geno2 Next Gen is more recent. The other factor is BritiansDNA testing panel is not suitable for cousin matching.
The importance of autosomal matching when connecting the paternal line is often overlooked in closing out the last five generations in Y DNA matching. Shared segments are a much more precise confirmation than randomly alternating STR values.
Step 2: Take a Specialized Y-DNA Panel
YSEQ’s Thomas Krahn introduced a concept of creating specialized test panels from Next Generation Sequencing tree results in 2014. Today the company offers 41 Y Haplogroup panels ranging from $77 to $99. The more expensive options are the Superclade panels, which bundle a subpanel when initial testing reveals it is appropriate to the tester.
FTDNA followed suit with an alternate take they refer to as SNP Packs. These tests are run on a new multiplexing technology that allows up to 160 targeted locations be sampled. At present that are 77 of these tests available from the Advanced Testing options. The prices range from $99 to $119. Unlike YSEQ’s Superclade tests a second pack may be necessary to reach the most recent shared SNP branch.
An example of this approach is a tester found to be R-L21 via a 23andMe Ancestry Only test would take the R1b-L21 Super-Clade Orientation Panel. YSEQ’s lab runs a protocol of Sanger sequencing steps starting with DF13 and Z39589. As the results become known additional tests are staged until no more progress can be made. Testers are then notified of their terminal branch in YSEQ’s tree.
Step 3: Research the Results
YFULL maintains a Y DNA tree that includes estimation of branch ages. If your branch is less than 5 generations old, your SNP testing journey may have come to an end. Communicate with your autosomal matches who share a surname and same general haplogroup. See if they may be interested in testing the single SNP you already identified to see if there is a Y connection.
Look for Internet communities like Anthrogenica and a diverse assortment of Yahoo and Facebook groups where discussions about your branch may be happening right now.
ISOGG maintains a list of projects related to your Haplogroup branch as well. Look through the public results in these projects. If you see surnames and related SNPs in the public results, it may be time to consider Step 4a.
Step 4a: Everything Turned on Its Head
Assuming you have not turned up satisfactory results in your SNP testing, it’s time to consider going back to the STR matching systems. Order the largest STR panel test from FTDNA that you can afford and join the Surname and Haplogroup projects found in your research above. Having the static SNP markers from your panel test in step 2 helps ensure that you are placed in the correct subgroup.
Other labs also offer STR testing but there is not currently an independent matching service anywhere close to FTDNA’s size.
Step 4b: Just Can’t Get Enough SNPs
STR tests at the end of the day are a hypothesis that must be proven by paper trail or testing a common stable marker. The random nature of their transition over the generations ensures there will be false positive and negatives due to convergence and divergence of signatures. In larger haplogroups such as R-CTS4466 or R-M222 it is not uncommon for STR testers to have 800 to 1200 67-marker matches.
When the low cost options fail to find such a SNP in the last 300 years, it is a sign your branch of the Y DNA tree has not seen adequate exploratory testing. Pricing for NGS testing, which will reveal the mutations specific to your lineage, ranges between $575 and $1250. The results must be compared with other testers on similar branches to effectively isolate your SNPs. A comparison of current options is available from Haplogroup-R.org’s Statistics Page. The lower estimated years per SNP is better, but the cost increases rapidly.
As to how you can compare your NGS test results, it all depends on which test you take and which branch is closest to you. YFULL is a very attractive service for this purpose. They accept results from all labs, identify SNPs private to your lineage, extract over 400 STRs, and provide matching with other members.
Jumping straight into STR testing is rapidly becoming outdated advice. The problem of convergence and divergence mandates SNP testing in subclades where genetic genealogy is well established. Calls to increase panels to 400 markers are frankly unnecessary. It will likely make the cost of STRs more expensive than simply ordering a Big Y, which is already capable of resolving branching at the 5-generation level using the SNPs alone.
Taking a low-cost autosomal test as a springboard into low-cost Y DNA panels reduces the complexity of interpreting the non-precise STRs in matches. Depending on the final results this may be all one really needs to establish male lineage connections in databases much larger than specialized Y STR databases.
Of course exploration of the Y DNA tree outside of those with western European origins is not as advanced. STR testing may still become necessary to recruit more men with similar origins to advance the state of knowledge in your line. For personal discovery when cost is not an object NGS testing and waiting for future matches is a better long-term strategy.