FAQs collection

Collection of questions and answers mostly based on Y-DNA J2 and Alpine DNA research and communication.

JS, May 2016: I don’t know whether to keep advising paternal clan project members to do the Big Y test at Family Tree DNA or to advise them to do the Full Genomes Y-Elite 2.1. It is extremely difficult to get project members to test, and even more difficult if they have to send in a new sample.  We tested one member at Full Genomes and did the YFull analysis. Every time I ask a project member to pay for a test I have to convince him that the test results will be worth the money we spend on it, and that it furthers the goals of the project. Justin Loe offered us a discount at Full Genomes if we can get five project members to test. But I cannot find five project members who agree to do Full Genomes. Soon we will have the opportunity to do a NGS Y test on project member who has interesting ancestry.  It may not be possible to get a new sample so we are probably limited to doing Big Y.  In your opinion, should I try to convince the person managing the account to try to get a new sample to send to Full Genomes or would it be good enough to do a Big Y.

I think this is not easy to answer. Personally I’m trying to get a FGC WGS (at least 4x) for every so far untested person to get also mt and autosomal/X data. Upgrades are possible, so this is good. Less good is that saliva samples are less easy to do for old people then the check swabs.
Seeing how many BigY results close by STR-results share the same terminal haplogroup I do not anymore recommend BigY for research in genealogical time (last 600 years). There is a possibility that the 400+ Y-STRs (from YFull analysis) in the BigY data in the future allow some better tree reconstruction but I prefer to have the SNP evidence as good as Y-DNA allows and Y-Elite is now the test giving the maximum the current technology allows.
I would either focus on trying to do Y-Elite now (maybe on lineages that are dying out) or wait until Y-Elite will be cheaper or FTDNA will make a coverage-upgrade (BigY 2) or another new DNA test will become interesting.
In the long term I think every serious genetic genealogist will seek to get the “Full Y sequence” of lineages of interest, so with current testing we are not yet there, even the best NGS machines are not able to sequence all regions of the Y yet and we do not know how much SNPs those repetitive regions have and how stable they are, but I think some useful data might be there.
Hint: After having maybe three Y-Elite it may be possible to better evaluate “how much more” Y-Elite delivers in comparison to several BigY results.

JS, September 2015: Since I have not found any close matches I’d like as much information as possible. So I’m wondering if it might be a better idea to just have the BigY testing done?

Since no kits in your haplotype cluster (see J2@FTDNA project grouping) have done BigY it would help if you order it.
See here the researched subhaplogroups – we don’t know where your cluster falls into: tree.j2-m172.info
Most likely you belong to the [X] branch since it was discovered only in the last year and not much results are available yet. NextGenSequencing of the Y allows to detect all SNPs down to very recent ones (BigY has a coverage of ca. one SNP per 150 years). So BigY and an additional YFull analysis allow to put your paternal lineage on the J2 tree and refine the branches as new nearer matches do the same type of test. FTDNA usually at Xmas time has great discounts also for BigY which currently is $575.
Since I see your kit has not yet ordered an mtDNA and autosomal test (FamilyFinder) you could consider a whole genome sequencing test which will give you Y, mt and autosomal/X sequenced with the SNPs for your genome. In case this seems interesting I would suggest the Full Genomes Corp WGS 10X test for $675, see a draft comparison table (not yet finished) by me. You see BigY detects ca. 2000 Y-SNPs, since some of the other tests are new, we have not yet a comparison, but for the WGS 10X I would expect ca. 2500 Y-SNPs.

JG, August 2015: I still remain very interested in and committed to building testing strategies for our y-DNA cluster. […] I can’t help but wonder if now is the time to consider NGS testing for […]’s kit with the goal of subsequent testing for his terminal SNPs against all other group members? We currently have an aggregate of 6 y-kits that should help to maximize new SNP discovery and branching into your working tree models. Although I am a layperson in DNA science, you may consider me a willing go-to citizen scientist.
Answer: yes, in the long term NGS is the only way that allows to  reconstruct the paternal lineage tree in pre- and genealogical time (accuracy currently 60-200 years).
Mind that the [X]? grouping is speculative (based on a haplotype similarity on only 20 Markers). Even if certified by single testing [X] is expected to be only slightly younger then [Y] (ca. 5,500 years) and so not much more information will be given by this SNP only. IMHO I think helping by testing to find haplogroups younger then 3,000 years really supports to build hypotheses about the paternal lineage history.
The decision of when to spent how much money I can’t make for you but maybe this comparison is interesting for you:
When focusing on the Y-sequencing IMHO the amount of detectable derived Y-SNPs is one of the most important features.
In the future I think WGS testing will become the major genetic genealogy test. The question is just how much read depth is needed for the average user (2X, 4X, 10X, etc.).
EG, August 2015:I began in 1998 to try to discover my paternal side and thought DNA might break the brickwall. I have made access available to […] to my Familytree.com [including BigY with three matches of other surnames approx. at the same distance] account and to my 23andme one. My closest DNA matches in FF and RF (relative finder in 23andme) do not give any information or respond to my queries. I ramble because I don’t think I will ever break through that brickwall. Therefore I will try to organize my files so any family member who ever becomes interested will have some background.
Answer: YFull analysis […] could maybe reveal one informative SNP which is not seen by FTDNA analysis only. It could also be that the informative SNP is outside of the BigY capture range (ca. 25% of the Y, not more then 45% is possible currently). About time estimates it currently remains difficult to nail down a very precise date of MRCA. That could become better if YFull applies an algorithm combining their existing SNP TMRCA estimate with a mutation estimate based on the ca. 400+ STR markers they extract. YFull has announced to be on this. Lets see how the current estimate will change:  www.yfull.com/tree/J2/
For the paternal lineage history older then 8 generations ago you probably have to stick to Y-DNA testing because Autosomal fades out to detect distant cousins after 5 generations (at least for the current chip testings like FF, 23andMe, Ancestry). See www.isogg.org/wiki/Autosomal_DNA_statistics#Identical_by_descent_segments
Trying to make available what is known to you for other researchers is very important.