STRs and SNPs – Are STR Markers Still Useful for Y DNA?

Some time back, I wrote an article titled, STRs vs SNPs, Multiple DNA Personalities, which you can read, here. In that article, I explained the difference between STR and SNP markers.

Y DNA is extremely useful for men to track their direct paternal line via the Y chromosome that they inherited from their father. You can see how various types of DNA are inherited, here. By way of comparison, mitochondrial DNA (red) is inherited from your matrilineal line, and autosomal DNA (green) is inherited from all lines.

The Y chromosome, shown in blue above, is passed from father to son without mixing with the DNA of the mother, so it is in essence tracked intact for generations – with the exception of occasional mutations.

Two kinds of mutations make Y DNA genealogically useful. They are STRs, short tandem repeat markers and SNPs, single nucleotide polymorphisms, pronounced as “snips.” If you’re looking for in-depth information about Y DNA, I have provided a Y DNA resource guide here.

How is Y DNA Useful?

For Estes males, we have identified several genetic lineages using these markers that show us where testers fit into the tree of Estes males, which of course in turn fits into the larger tree of mankind.

In some cases, Y DNA is the only clue people have as to their genealogy. In other situations, these tests confirm and further refine both the genetic tree and genealogy.

Let’s look at how these two types of Y DNA markers work, separately and together at FamilyTreeDNA.

STR Markers, Results and Matching

Y DNA STR results are returned in panels when men take Y DNA tests.

Every man who takes a Y DNA test at FamilyTreeDNA receives STR results, shown above. How many marker results he receives depends on the level of the test he orders. In the past, 12, 25, 37, 67 and 111 marker tests were available to purchase individually. Men could also upgrade to higher level tests. 500 and 700 STR marker results are only available when the Big Y test has been purchased.

Today, men can order the entry level 37 Y DNA test or a 111 marker test individually. However, a minimum of 700 STR markers are included in the Big Y-700 test, in addition to SNP results, which we will talk about in a minute.

Matching is Key

However, the benefit isn’t in the STR markers themselves, but in matching to other men. The markers are just the tool used – but the more information you have, the better the result.

STR results are used to match all Y DNA testers against each other. Matches are shown at each marker level.

My Estes male cousin has tested at the Big Y 700 level. He is matched against all other men who have taken a Y DNA test. He can see who he matches at 12 through 111 markers separately. For each man that he matches, if they have taken the Big Y test, he can see how closely he matches at the 500 or 700 marker level too.

This Estes match to my Estes cousin, shown above, has tested at 111 markers, but has not taken the Big Y test, so he has no STR markers above 111. He mismatches my cousin with 1 STR marker difference at 111 markers. That’s pretty close.

Additionally, we can see that the match’s haplogroup has been estimated as R-M269 based on STR results. For a more specific haplogroup, either individual SNP markers must be tested, or an upgrade to the Big Y-700 test can be ordered. I don’t recommend individual SNP marker testing anymore because the Big Y gives you so much more for your money by scanning for all Y DNA mutations.

Big Y-700 and SNPs

The only way to obtain the most detailed Y DNA haplogroup is to take a Big Y test. The Big Y test scans the Y chromosome to search for SNP mutations. The Big Y test doesn’t test any one specific location, like STRs or individual SNP tests, but scans for all mutations – currently known and previously unknown. That’s the beauty. You don’t have to tell it what to look for. The Big Y test scans and looks for everything useful.

More than 200,000 men in the FamilyTreeDNA database have been SNP tested and more than 450,000 variants, or mutations, have been found in Big Y tests. The database grows every single day. Sometimes DNA matching is a waiting game, with your DNA available for matching 24X7. When your DNA is working for you, you just never know when that critical match will be forthcoming.

The Big Y test keeps giving over time, because new variants (mutations) are discovered and eventually named as haplogroups. Many new haplogroups are based on what can best be called family line mutations.

Initially, SNP results and haplogroups were so far up the tree that often, they weren’t genealogically relevant, but that’s NOT the case anymore.

Today, SNP results from the Big Y-700 test are sometimes MORE relevant and dependable than STR results.

Each man receives a very refined personal haplogroup, known colloquially as their terminal SNP, often FAR down the tree from the estimated haplogroup provided with STR testing alone.

After Big Y testing, my cousin is now haplogroup R-ZS3700 instead of R-M269. R-M269 was accurate as far as it went, but only the Big Y test can provide this level of detail which is quite useful.

The Block Tree Divides Lines for You

The Block Tree is provided for all Big Y testers.

Looking at the Block Tree for my cousin, you can see that he and several other primarily Estes men either share the same haplogroup or parent/child haplogroups.

My cousin in R-ZS3700, while R-BY490 is the parent haplogroup of R-ZS3700, and R-BY154784 is a child haplogroup of R-ZS3700.

R-M269 is more than 15 haplogroup branches upstream of my cousin’s R-ZS3700.

You can also easily see that Estes men fall onto different “twigs” of the tree, and those twigs are very genealogically significant. Each column above is a twig, representing a distinct genealogical lineage. Taking the Big Y test separates men into their ancestral branches which can be genealogically associated with specific men.

My cousin is R-ZS3700, along with one other man. Two more men form R-BY154784, a subgroup of R-ZS3700, which means they descend from a specific man who descends from Moses Estes. All of these men descend from R-BY490 and all of those men descend from R-BY482, the parent of R-BY490, as shown on the public haplotree, here.

Men who take the Big Y test ALSO receive separate SNP matching – meaning they have BOTH STR and SNP matching which provides testers with two separate tools to use.

Of course, the only men who will be shown as SNP matches are the men who have taken the Big Y test.

Ok, how is this information useful?

Project View

Looking at the Estes DNA project, you can see that two men who have joined the project carry haplogroup R-ZS3700. Several others descend from that same genealogical line according to their paper trail, and STR matches, but have not taken the Big Y-700 test.

As the project administrator, I’ve grouped these men by their known ancestor, and then, in some cases, I’ve used their terminal SNP to further group them. For example, one man, kit 491887, doesn’t know which Estes line he descends from, but I can confidently group him in Estes Group 4 based on his haplogroup of R-ZS3700.

I can also use STR matching and autosomal matching to further refine his match group if needed for the project. But guaranteed, he’ll need to use both of those additional tools to figure out who his Estes ancestors are.

He was absolutely thrilled to be grouped under Moses Estes, because at least now he has something to work his paper trail backwards towards.

Test Summary

Men who take STR tests alone, meaning 12-111 only, receive STR matching and an estimated haplogroup.

Men who take the Big Y test receive STR results and matches, PLUS the most refined haplogroup possible, many additional STR markers, separate SNP matches and block tree placement.

STR 12-111 Tests Only Big Y-700 Test
STR markers through 111 Yes, depending on test level purchased Yes
STR marker matching with other men Yes Yes
STR markers from 112-700 Only if the tester purchases a Big Y upgrade Yes
Estimated haplogroup Yes Haplogroup is fully tested, not estimated
Tested, most refined haplogroup Not without an upgrade to the Big Y-700 test Yes
SNP Matching No Yes
Block Tree No Yes

Genealogy

Recently, someone asked me how to use these tools separately and together. That’s a great question.

First, if there is a data conflict, SNP results are much more stable than STRs. STRs mutate much more often and sometimes back mutate to the original value which in essence looks like a mutation never happened. Furthermore, sometimes STR markers mutate to the same value independently, meaning that two men share the same mutation – making it look like they descend from the same line – but they don’t.

Before the Big Y tests were available, the only Y DNA tools we had were STR matches and individual SNP mutations. From time to time, one of the STR markers would mutate back to the original value which caused me, as a project administrator, to conclude that men without that specific line-marker mutation were not descended from that line, when in fact, that man’s line had experienced a back-mutation.

How do I know that? When the men involved both took the Big Y-700 test, they have a lineage defining haplogroup that proved that there had been a back-mutation in the STR data and the men in question were in fact from the line originally thought.

Thank goodness for the Big Y test.

STRs and SNPs Working in Tandem

Click any image to enlarge

Looking at the Estes project again, the R-ZS3700 SNP defines the Moses Estes (born 1711) line, a son of the immigrant, Abraham Estes. The men grouped together above are descendants of Moses’s great-grandson. You can see that if I were to use STR markers alone, I would have divided this group into two based on the values of the two bottom kits. However, both genealogy and SNP/haplogroups prove that indeed, the genealogy is accurate.

STR markers alone are inconclusive at best and potentially deceptive if we used only those markers without additional information.

However, we don’t always have the luxury of upgrading every man to the right and Big Y-700 test. Some testers are deceased, some don’t have enough DNA left and cannot submit a new swab, and some simply aren’t interesting.

When we don’t have the more refined Big Y test, the STR markers and matches are certainly valuable.

Furthermore, STR markers can sometimes provide lineages WITHIN haplogroups.

For example, let’s say that in the example above the two men at the bottom were a distinct line of men descended from one specific descendant of Moses Estes. If that were the case, then the STR markers would be very valuable within the R-ZS3700 haplogroup. Maybe I need to reevaluate their genealogy and see if there are any new clues available now that were not available before.

STRs Within Match Groups

Using a different example, I can’t group these Estes men any more closely based on their genealogy or SNP results.

Only two men in this group have taken a Big Y test – those with haplogroup R-BY490. Unfortunately, this haplogroup only confirms that these men descend from the Estes lineage that immigrated to America and that they are NOT from the Moses Estes line. That’s useful, but not enough.

Two other men have taken individual SNP tests, R-DF49 and R-L21 which are not useful in this context. They don’t reach far enough down the tree.

We need more information. Fortunately, we have some.

We have two clusters of STR markers. We can see that three men have a purple grouping of 24 at marker DYS390 (the header with STR marker names is not shown in the screen shot) and a grouping of men that share a mutation of 12 at marker DYS391.

It’s likely, but not a given, that the men clustered together at the bottom with the 12 value descend from the same Estes male common ancestor. The men at the top with a value of both 12 and 24 could belong to that same cluster, with an additional small cluster of 24 further delineating their ancestor – OR – the mutation to 12 at location DYS391 could have arisen independently in two separate lines.

It’s also possible that back-mutations have occurred in some of the other men. We just don’t know.

If I were to advise these men, I’d strongly suggest that they all upgrade to the Big Y-700 with the hope that at least some of them would have SNPs that define existing or new haplogroups that would positively sort their lines.

Then, within those haplogroup groups, I’d focus on STR groupings, genealogy and possibly, autosomal results.

Evaluate All Three, Separately and Together

We have three separate tools (plus autosomal) that need to be considered together as well as separately.

  1. The first, of course, is known genealogy. However, Y DNA testing works well even without genealogy.
  2. Big Y haplogroup information combined with the block tree should be evaluated to define genetic lineages.
  3. STR groupings need to be evaluated separately from and within haplogroups and allow us to add people to the SNP-defined groups of testers. Known genealogy is important when using STR markers.

As a bonus, if the men have also taken the Family Finder test, some men may match each other autosomally as well as Y DNA, if the connection is close enough in time. Of course, Y DNA matches reach much further back in time than autosomal matching because Y DNA is never divided or combined with any DNA from the other parent.

Confirm or Refute

Genealogy can be either confirmed or refuted by either STR or SNP tests, independently or together.

Looking again at the public Estes DNA project, you can see that the first person in that group provided his genealogy as descending from the same Moses Estes line as the other men. However, the STR mutations clearly show that indeed, his genealogy is incorrect for some reason. He does not match any of the other men descended from Moses’s grandson or the rest of the Estes lineage.

This man’s haplogroup is estimated as R-M269, but were he to take the Big Y test, he would assuredly not be R-ZS3700. In fact, his STR markers match two men who have taken the Big Y-700 test and those two men share an entirely different haplogroup, not in the Estes or related branches at all. If this man were to take the Big Y-700 test, he would likely match that haplogroup.

Both STRs and SNPs can disprove a lineage relationship. As I mentioned earlier, of the two, SNPs are more reliable. Often SNPs are required to conclusively divide a group of men descended from a common ancestor.

STRs may or may not be useful, or correct, either without SNP-defined haplogroups, or within those haplogroups.

However, STRs, even alone, are a tool that should not be ignored, especially when we don’t have SNP data or it’s not conclusive.p

A Different View

To literally look at this a different way, I prepared a pedigree type Y DNA haplogroup spreadsheet for the Estes Project at WikiTree. I’ve divided the information by ancestor and included haplogroups. You can view that spreadsheet, here, and you can then compare the colored groups with the Estes DNA Project at FamilyTreeDNA which are grouped by ancestral line.

This is only a small portion of that pedigree showing the Moses lineage. The image is large, but you can see the entire spreadsheet (as of August 2020) here.

Of note, R-BY490 defines the entire Abraham Estes line (green above). Within that line, other SNP lineages have been defined, including R-ZS3700 and R-BY154784.

However, many lines have additional STR motifs that define or suggest associations with specific genealogical ancestral lines, as you can see in the Estes FamilyTreeDNA project, here. I’ve included only a snippet above.

Bottom Line

To answer the original question – yes you can and should use STR and SNP markers both separately and together. If you don’t have enough SNP data, use STR matches along with genealogy information and Family Finder results to augment what you do have.

The more Y DNA information you have in hand, the better prepared you are to analyze and utilize that information for genealogical purposes.

Do you have genealogical questions that Y DNA could potentially solve? What are they and can you find someone to test?

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24 thoughts on “STRs and SNPs – Are STR Markers Still Useful for Y DNA?

  1. Hi. I saw you used a method for analyzing B-Y700 in another of your posts. You attributed it to Göran. Do you still recommend that method? When using it for two people in the same column, do you count that column twice? That’s what I’ve been doing. And when using that method compared to the tips calculator, Big Y and tips don’t seem too far apart. So you seem to be saying here that we shouldn’t try to match them because strs are too unreliable.

    Thanks

  2. Roberta, when I tried to view your Estes Project at WikiTree spreadsheet that you say we can “view that spreadsheet, here” (https://www.wikitree.com/photo.php/c/c6/Estes_Name_Study.png), I got the message below, even after I signed into WikiTree, saying
    the image is privacy protected and viewers need to be in your Trusted List. I presume there is a way to make it publicly viewable, but I don’t know what that is.

    Protected Image: Estes_Name_Study.png
    Estes_Name_Study.png
    Comments: 1. Popularity: 1.

    This image is privacy protected. Only the thumbnail is open.

    To view the full image and its details you need to be in the Trusted List of
    someone or something tagged in the photo. If you’re a family member:

  3. I tested Y-DNA with 37 markers a few years ago. I still have matches only on 25-markers-level (although those matches have tested with more than 25 markers).
    What does that mean?
    Does buying Big-Y makes any sense in this situation (besides knowing the most detailed haplogroup) ?

    • You may match other surnames. You will also know where the haplogroup or nearby haplogroups are found geographically.

  4. I have a brick wall on my paternal line. My father’s father’s father’s father’s parents are unknown. My half brother, uncle, 3 of my uncle’s first cousins and a half 3rd cousin, all descendants on that male line, have have taken the Y111 test, and two of the first cousins also did the BigY500 and formed a new twig at Yfull. Would we benefit at all from upgrading their BigY from 500 to 700, or upgrade the others from 111 to BigY? Wouldn’t they all probably end up in the same haplogroup anyway? We have no really close matches on Y111 or BigY yet.
    I hesitate to use up the remaining DNA from my uncle and the half 3rd cousin because they have already passed away. Does the BigY700 require a lot of DNA?

  5. Thank you for this post. My sons Big Y results came in this morning and I was overwhelmed. A little more confident now .

  6. Hi. Many posts I have seen regarding BigY explain how a lot of very close matches and/or known relatives fit into the picture. I have zero close matches at 111 markers – would BigY add anything to advance my genealogical research?

    • You would see which surnames your match a bit further back in time. You would know where the line came from geographically. You could match men with a similar surname. You just don’t know if you don’t test.

    • I have zero matches even at 12 STR markers. But I did the Big Y700 to find out a bit more about where I fit. Earlier work with 67 STRs had suggested that the closest other lines were a long way back. Big Y showed it was even further back – around First Farmers, and something like 95 SNP mutations back.
      I can do more by finding those 3C and 4C matches from autosomal matches on this line and getting some tested for BigY. That would sort out which of those 95 SNP mutations are fairly close.
      There is someone with my Y line surname who left from nearby and went to a different country. A 12 STR test would tell me if they are family, and if they are I could upgrade to Big Y. That would get me back another SNP mutation or two.
      But I have already gorged myself on the other things my rare haplogroup has achieved and where they went. And looking at the Most Distant Ancestor on that line’s wife, have managed to get back further and re-unite over a dozen separate families with that surname on that distaff line.
      So there is so much elsewhere that my Yline is a low priority just now.

  7. Roberta, thank you for putting this together. I am in a 15-member surname project and we have just finished our 6th Big Y. Your article should certainly help some of our upgrade-reluctant members realize why we need to look at SNP paths first, then STRs.

  8. I did a DNA test some years ago and was able to find a lot of contacts through my mothers side and also on my fathers mothers side but I have not been able to identify any ancestors on my father’s father and back along that paternal line. I have some theories and anecdotal evidence however at this time it is inconclusive. I wish to go further with DNA testing however I am not clever enough to interpret the information above.
    Can you assist me please.

  9. I posted a comment but it never showed up, so I try again and apologize if it turns up twice.
    I have a brick wall – my father’s father’s father’s father’s parents are unknown. Several of my close male relatives, descendants on a direct male line from the unknown father, have taken the Y111 test: my brother, uncle, a 3rd cousin and two of my uncle’s 1st cousins. My uncle and one of his 1st cousins have also done the BigY-500 and formed a new twig in Yfull’s tree. They have no really close Y-DNA matches, the closest has a genetic distance of 6 on Y111. Would we benefit at all from upgrading the BigY-500 tests to 700, or having more of the cousins upgrade from Y111 to BigY? I suspect that they would all have the same haplogroup and we wouldn’t learn anything more than we already know. I am also afraid of using up the remaining DNA, since my uncle and the 3rd cousin have passed away.

    • I would suggest upgrading someone to the Big Y-700. Preferably someone still living who can submit a new sample if necessary. I don’t think you need to do everyone. I might do another one from a different line just to be sure the haplogroup is the same.

  10. Your excellent series of articles on Y tests has been invaluable to me when trying to explain away all of the Y confusion to others!!

    THANK YOU Roberta!!

  11. Roberta, Question about the parent/child relationships in SNP testing. Above you say, “My cousin is R-ZS3700, along with one other man. Two more men form R-BY154784, a subgroup of R-ZS3700, which means they descend from a specific man who descends from Moses Estes.” Did you determine men who were R-BY154784 descended from Moses Estes from y700 testing or genealogical records?
    In other words when there is a parent/child result (which I understand will be on the left side of “my results”) can we determine who they descend from?

  12. This post was very influential in getting several of our Moore testers to upgrade to y700, but when I want to share or review it I cannot find it by searching your blog for Big Y or y700.

    • I just verified that it’s tagged with those words. Maybe because it’s not in the title? I’m glad the article is useful.

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