By: Katy Rowe-Schurwanz
There are several reasons your paternal haplogroup may change. Understand why these changes happen and how new Y-DNA research and testing upgrades refine your haplogroup placement.
What are haplogroups?
A haplogroup is a branch on either the paternal or maternal Tree of Humankind. Each haplogroup represents an ancestor on that tree, with many being so far back the names of those ancestors have been lost to time.
Haplogroups can help you determine when you share a common ancestor with your matches, where your ancestors are from, and how they got there.
Your Y-DNA haplogroup is your placement on the Y-DNA Tree of Humankind. Your placement on your family tree doesn’t typically change, so why does your placement on the genetic tree change?
Your placement (i.e., haplogroup) might change for several reasons, including:
- Variations between test types and companies
- Naming conventions
- New phylogenetic information
Y-DNA haplogroup nomenclature
As mentioned above, one of the reasons your haplogroup can change or has changed is because of different naming conventions.
In the early years of Y-DNA testing, Y-DNA haplogroups typically had a longhand name. Longhand haplogroup names started with the letter for the root of the haplotree you belonged to, like R, followed by alternating numbers and letters based on where your branch fell below that root.
For example, R had two child branches, R1 and R2. Below R1, you’d have more child branches, R1a and R1b. From there, you would have more child branches, like R1a1 and R1a2. This pattern continued for every root branch from the top of the tree to the bottom of the tree.
You can still see examples of the longhand nomenclature when looking at mtDNA haplogroups on the Phylotree or Y-DNA haplogroups on the ISOGG Haplogroup Tree.
When FamilyTreeDNA launched our updated Y-DNA haplotree in 2014, we conducted Y-SNP testing through SNP Packs for several years, and thousands of Y-DNA branches and variants were added to the haplotree.
This made the longhand terminology unwieldy, so FamilyTreeDNA began using shorthand names for Y-DNA haplogroups. Instead of alternating numbers and letters like the longhand names, the shorthand names are comprised of the root branch followed by a hyphen and then the variant or SNP name. So instead of R1b1a2, your haplogroup was now R-M269.
If you tested before 2014, you may have received a longhand Y-DNA haplogroup. The name of that haplogroup may have changed before adopting the shorthand name for your branch.
This was a fortuitous change, as we also launched the Big Y in 2014. Since then, we have added tens of thousands of branches and hundreds of thousands of variants to the Y-DNA Tree of Humankind.
If all the new branches and variants added to the haplotree were phylogenetically below what was already on the haplotree, continuing to use the longhand terminology would not have been difficult.
However, we often discover new branches that split parts of the haplotree high up on the root branch, like the new branch discovered immediately below R-M269 in June. Discoveries like that would require the longhand for all branches below to change. When using the shorthand terminology, the new branches and variants are easily inserted into their place on the tree instead.
Y-DNA test differences
There are multiple different types of tests you can take to receive a Y-DNA haplogroup. Each type of test will cover a different amount of the Y chromosome, which can cause you to receive a different haplogroup and placement on the haplotree.
Y-STR tests like the Y-37 and Y-111 do not look at Y-SNPs. These tests will provide a predicted haplogroup based on your Y-STR signature. The predicted haplogroup will always be close to the top of your root branch. Sometimes, Y-STR testing cannot provide a reliable prediction. In those cases, FamilyTreeDNA will run an SNP test that covers the top of each root branch automatically and at no additional cost.
Many companies, including FamilyTreeDNA, offer autosomal tests run on a microarray chip. Each company customizes its chip to determine what SNP locations it wants to cover. Most of these are autosomal SNP locations found on chromosomes 1-22. Most chips also include Y-DNA and mtDNA SNP locations—enough to provide an intermediate-level haplogroup. FamilyTreeDNA’s chip also includes locations on the X chromosome.
The major autosomal testing companies, including FamilyTreeDNA, MyHeritage, Ancestry, and 23andMe, originally used the Illumina OmniExpress chip and have now switched to the Illumina Global Screening Array chip. National Geographic’s discontinued Genographic Project test also used the Illumina OmniExpress chip. Alternatively, LivingDNA uses an Affymetrix chip from Thermo Scientific.
Each company has used different versions of their customized chips over the years. Depending on when and where you tested, some Y-DNA SNPs may or may not have been included on your test’s chip. Early chip versions may have fewer Y-DNA SNP locations due to new SNPs being discovered later.
FamilyTreeDNA also previously offered individual Y-SNP tests and SNP Pack tests. Individual Y-SNP tests would look at a single variant and test to see if you were positive, negative, or received no call for that variant. SNP Packs would look at groups of Y-SNPs and report if you were positive, negative, or received no call for each of the included variants.
Individual Y-SNP or SNP Pack results may have placed you above or below your haplotree placement from a different test.
Other tests, like the Big Y-700, scan the entire Y chromosome to find your most specific haplotree placement.
FamilyTreeDNA has offered three versions of the Big Y test since 2014: the Big Y, which only looked at Y-SNPs; the Big Y-500, which increased Y-SNP coverage and added bonus STRs above the Y-111; and the current Big Y-700, which maximized Y-SNP coverage and added even more bonus STRs.
Because the Big Y-700 looks at more of the Y chromosome than any other test, you will receive a haplogroup below your placement on the tree received from other tests. They can also discover SNPs unique to your line and not yet found in other testers. As those unique SNPs are found in more testers over time, they’ll be added to the haplotree, and your placement may change again.
Despite the differences in Y chromosome coverage, you should rarely ever receive haplogroup assignments from two different root branches. For example, if you’re placed on the R branch with one test, you should not be placed on J, I, or another branch besides R with a different test.
There are some exceptions:
- If limited Y chromosome information was tested and your coverage was poor for your root branch, you may be placed on a root higher up on the haplotree.
- If you received both a predicted haplogroup and a confirmed haplogroup, predictions may not always be 100% correct.
Types of Y-DNA haplogroups
Depending on the type of test you took, you may have received different types of haplogroups.
Predicted vs. confirmed
A predicted haplogroup is a haplogroup you have been assigned without Y-SNP testing based on your Y-STR results. The values for your first 12 STRs can reliably inform what major root branch of the haplotree you belong to. A prediction will place you near the top of that branch with a broad haplogroup assignment.
Predicted haplogroups typically will not change. If you receive a predicted haplogroup from a Y-37 and upgrade to the Y-111, your prediction will remain the same. If FamilyTreeDNA adjusts the science behind our predictions, your prediction may change at that time; however, this is an extremely rare occurrence.
A confirmed haplogroup is a haplogroup you have been assigned from Y-SNP testing. With a confirmed haplogroup, you will always be placed on the branch furthest downstream for which you tested positive. Confirmed haplogroups can come from individual Y-SNP or SNP Pack tests, autosomal tests like the Family Finder, or the Big Y.
Confirmed haplogroups can change over time, depending on if you take a more extensive test later (like upgrading from the Family Finder to the Big Y-700) or through changes to the haplotree with the Big Y-700’s Lifetime Analysis.
Partial vs. full haplogroups
Except for the Big Y-700, most tests will provide a partial haplogroup. A partial haplogroup means that you have been placed on a branch on the haplotree but that there are more branches below you where you could belong with further testing.
A full haplogroup from the Big Y-700 will place you as far down the haplotree as possible. This is the most specific and refined placement you can receive. However, this placement can still change over time with new phylogenetic evidence and Big Y-700’s Lifetime Analysis.
What are broad, intermediate, and refined haplogroups?
FamilyTreeDNA often describes haplogroups as broad, intermediate, or refined.
A broad haplogroup is one that originated typically in the Stone Age. It’s likely to be high up on your root branch of the haplotree. A predicted haplogroup will always be broad. Broad haplogroups will provide you with the early parts of your father’s father’s father’s story, showing migration paths from Y Adam across or out of Africa to the continent your ancestors called home.
An intermediate haplogroup typically originated in the Metal Age. It’s likely to be somewhere in the middle of your root branch of the haplotree. You will likely receive an intermediate haplogroup with an autosomal test like the Family Finder or the discontinued SNP Packs. These provide a little more granularity for your father’s father’s father’s story, expanding your ancestors’ migration path often to a particular region of a continent, but not typically much further than that.
A refined haplogroup typically originated in the Middle Ages or the Modern Age. It’s likely to be as far down on your root branch as you can get without additional phylogenetic evidence from more testers. These haplogroups come from the Big Y-700. They provide the most information possible about where your ancestors are from and how they got there. Many refined haplogroups formed within genealogical times, and when compared with the results of other Big Y testers, can sometimes narrow down the location where your father’s father’s father’s line is from to a country, region of a country or even to a village.
Private variants
The Big Y-700 also provides you with private variants. These are SNPs on the Y chromosome that were found in your results but have not yet been found in other testers’ results. Depending on how many testers from your lineage have Big Y results, you may have many, very few, or no private variants. When new testers receive results and match your private variants, those SNPs may be named and placed on the haplotree, further refining your placement.
Coverage
Your haplogroup can also vary depending on your coverage for specific SNPs. Different types of tests provide different amounts of coverage of Y-SNPs. Y-STR tests provide no coverage. Individual SNP tests provide coverage for only one SNP. SNP Packs and autosomal tests provide coverage for selected SNPs. The Big Y-700 looks at all of the genealogically relevant portions of the Y chromosome, providing the maximum possible coverage.
Coverage can also vary based on how many reads of a position were obtained from your results. A read refers to how many times a particular position was examined during testing.
With the Big Y-700, we require at least 10 high-quality reads to automatically call an SNP positive or negative. SNPs with fewer than 10 high-quality reads will be no-called. Our phylogenetic expert can adjust no-call SNPs if there is enough evidence to call them positive.
Other analysis sites may have differing quality control requirements, meaning they may call something positive where FamilyTreeDNA’s quality control standards and our phylogenetic expert would not.
With individual, SNP Pack, and autosomal testing, an SNP has or doesn’t have a read. You may be called positive or negative for a particular SNP or receive a “no call,” meaning that we could not read a result at that position. Our phylogenetic expert will not alter these results, and additional SNP testing would be required to potentially receive a call.
Haplotree differences
Your haplogroup may also change when the Y-DNA haplotree changes. Y-DNA haplotrees are built based on the results of testers. FamilyTreeDNA has the largest database of Y-DNA testers in the world and has built the largest Y-DNA Tree of Humankind in the world.
Other haplotrees may have been built based on academic research and data or data from transferred results. Because of this, those haplotrees are less complete than FamilyTreeDNA’s, and the placement you received from us may not exist on another haplotree. You may receive a less refined placement on another site.
The FamilyTreeDNA haplotree is constantly being updated. As new results come in, our phylogenetic expert uses those to split existing branches and add new branches to the tree. This may cause your haplogroup to become more refined as these changes are implemented.
About the Author
Katy Rowe-Schurwanz
Product Manager at FamilyTreeDNA
Katy Rowe-Schurwanz has always been interested in genealogy, inspired by her maternal grandparents, who told her stories about their family and family history when she was little. After studying anthropology and history in college, she joined FamilyTreeDNA in 2015 and became the trainer for Customer Support. Katy created and improved training processes and was fundamental in the creation of the Big Y Specialist team. In September 2021, she became Product Manager and has focused closely on improving FamilyTreeDNA’s genetic genealogy products.