The differences between Y-DNA STR and Y-DNA SNP testing

Jul 19th, 2014 | By | Category: Joyce DNA Research, Laurie's Blog

stock-footage-dna-strand

There are two types of YDNA markers that can be tested for.   Familytree DNA does both types of tests but you must test for STR markers first in order to then have the SNP testing done.   STR tests can be for 37, 67 or 111 markers but what exactly does that mean?

When we test for STR markers we are looking for short repeats of DNA that are repeated over and over and those number of repeats are called allele values.  As stated on genebase[1] “Some STR markers contain a wide range of repeats, like Y-STR marker DYS385a/b which has a repeat range of 6 to 28.  On the other hand, some STR markers like DYS 426 contain a narrow range of repeats, spanning from 10 to 13.”

As a general rule of thumb if you share the same number of repeats with another person across a wide range of STR markers then you are related to them and the more you share the more recent your most common ancestor is likely to have been.

The following tables are from emily D.Aulicino’s book Genetic Genealogy (2013 Authorhouse, Bloomington).

  YDNA12 YDNA25 YDNA37 YDNA67 YDNA111 Interpretation
Very tightly related N/A N/A 0 0 0 Your exact match means your relatedness is extremely close.  Few people achieve this close level of a match. All confidence levels are well within the time frame that surnames were adopted in Western Europe
Tightly related N/A N/A 1 1-2 1-2 Few people achieve this close level of a match.  All confidence levels are well within the time frame that surnames were adopted in Western Europe
Related 0 0-1 2-3 3-4 3-5 Your degree of matching is within the range of most well established surname lineages in Western Europe.  If you have tested with the YDNA12 or YDNA25 test, you should consider upgrading to additional STR markers.  Doing so will improve your time to common ancestor calculations.
Probably related 1 2 4 5-6 6-7 Without additional evidence, it is unlikely that you share a common ancestor in recent genealogical times (1 to 6 generations).  You may have a connection in more distant genealogical times (less than 15 generations).  If you have traditional genealogy records that indicate a relationship, then by testing additional individuals you will either prove or disprove the connection.
Only possibly related 2 3 5 7 8-10 It is unlikely that you share a common ancestor in genealogical times (1-15 generations).  Should you have traditional genealogy records that indicate a relationship, then by testing additional individuals you will either prove or disprove the connection.  A careful review of your genealogical records is also recommended.
Not related 3 4 6 >7 >10 You are not related on your Y-Chromosome lineage within recent or distant genealogical times (1 to 15 generations).

 

Number of Matching Markers Probability that the MRCA was not more than this number of generations ago
  50% 90% 95%
10 of 10 16.5 56 72
11 0f 12 17 39 47
12 of 12 7 23 29
23 of 25 11 23 27
24 of 25 7 16 20
25 of 25 3 10 13
35 of 37 6 12 14
36 0f 37 4 8 10
37 of 37 2 – 3 5 7
65 0f 67 6 12 14
66 of 67 4 8 9
67 0f 67 2 4 6
107 0f 111 7 11 13
108 0f 111 5 10 11
109 of 111 4 8 9
110 of 111 2 6 7
111 of 111 1 3 – 4 5

 

If you have tested at FTDNA go to your YDNA Matches page and you will see who your matches are.  At 67 markers I have two –

The first is my son Luke and not surprisingly we match exactly.  The second is a person I match on 60 of 67 markers which is therefore not likely to be in genealogical times.  If I then click on the “TiP” icon I find the following estimate.

Again, if we assume roughly 3 generations per 100 years then we are somewhere in excess of 800 years since we had a common ancestor.

The traditional explanation of the difference between STR and SNP testing is that STR markers are useful for comparing recent paternal ancestry and that SNP markers are for identifying deep ancient paternal ancestry.   And until recently that was a fair comment.  However the development of National Geographic’s Geno 2.0 test, followed by Britain’s DNA Chromo 2 and now FTDNA’s Big Y tests are significantly altering the landscape.

These tests have led to the discovery of thousands of new SNP markers and hold great promise for identifying some markers that relate to specific surname groups.  But what are they?

Genebase states that “…SNP markers are mutations in a single nucleotide (represented as a letter, either A, T, C or G).  For example, the ancestral allele for Y-SNP marker M207 is A, and the mutation for this marker is known to be A to G.  If result of testing M207 is G, then it is considered a mutation.  Unlike Y-STR markers which can have multiple repeats, SNP markers often only exist in 2 forms – the ancestral and the mutated allele.”

The following table from dnahaplogroups.org shows a comparison between STR and SNP tests.

What is the difference between Y-DNA STRs and Y-DNA SNPs?[2]

Y-DNA STR Y-DNA SNP
Stands for Short Tandem Repeat Single Nucleotide Polymorphism
Where it’s found Y-DNA Y-DNA
Rate of mutation (change) ~ one change every 20 generations ~ one change every few thousand years
Line traced Tracing recent ancestry and predicting haplogroup (ancient ancestry) • Confirming haplogroup (ancient ancestry)
• Confirming subclade
• Fine tuning placement in phylogenetic tree
Other uses Database comparisons:
• DNA Reunion
• Indigenous DNA
• DNA Archaeology
Only used for haplogroup and subclade classification / confirmation
Advantages Good starting point. Has many general uses and can predict haplogroup. The only way to confirm a haplogroup. Can give further refinement through Subclade determination.
Disadvantages Cannot confirm haplogroup. Haplogroup prediction is not always strong. Weak predictions are not reliable. Only provides haplogroup and subclade classification information. Not useful for recent ancestry.[3]
Comparisons Individuals who share the same STR profile likely recently related. Individuals who share the same SNPs not necessarily recently related as SNPs are used to trace deep ancestry.
Test types Y-DNA STR marker test
Choose from 20, 44, 67 or 91 markers. You can either test all 91 markers at once or you can start with less markers and then upgrade and test more markers at a later date as needed.
Y-DNA SNP Backbone test
Y-DNA SNP Subclade test (Subclade tests available for haplogroups A, B, C, D, I and R).
Y-DNA SNP Stand Alone Test
(order one SNP at a time as new SNPs are discovered in the future to refine your results)

 

What are subclades?

Many of you may be familiar with the nomenclature of YDNA genealogy.   FTDNA and 23andme traditionally displayed a person’s haplogroup as a combination of alphanumerics, e.g. R1b1a2 etc.  This was an indicator of what your terminal or most recent Haplogroup is.   If you were in the same Haplogroup as another person you shared an ancestor with them.  Your subclade is the terminal haplogroup you belong to

Haplogroup R1b1a2 is the sign of a person being positive for SNP M269.   In other words if your haplogroup starts with that combination of alphanumerics then you know that you are positive for M269.  Each successive number and letter marks another different SNP.  The first person who had that particular mutation passed it on father to son to all of his male descendants.   Now that there has been an explosion in the number of SNP’s discovered the companies are starting to use the shorthand version of the haplogroup name and thus R1b1a2 is now more commonly written as R-M269.

The aim for most of us though is to try and break through our documented paper trail and DNA research is one way in which we hope to do that.  But remember that we only assist in those aims by both sharing our own results and by exporing new tests as they become available.   Whilst you will continue to get matches as more people test and as databases grow, if you truly wish to explore the full opportunities you do need to attempt to find out what your terminal SNP really is.

Let’s take M269 as an example.   It is believed that this marker is around 15,000 years old, interesting but hardly significant as a marker that will help recent genealogy research.

If we look at the Joyce Project DNA results you will see that a lot of members are still sitting with M269 as their terminal SNP, so certainly all related but more testing is required to help start sorting those people into more recent groups.

 

Advice

For those who wish to read a bit more detail about SNPs then I recommend this link –

http://dna-explained.com/2014/02/10/strs-vs-snps-multiple-dna-personalities/

 

The following table comes from here http://www.goggo.com/terry/HaplogroupI1/y-Haplogroups_I1_and_R1b_in_European_Countries,_plus_Ancient_Migrations.pdf

 

European I1 STR Cluster/Clan MRCA[4]

Time Period 16,000 BC to13,000 BC 13,000 BC to10,000 BC 10,000 BC to7,000 BC 7,000 BC to4,000 BC 4,000 BC to1,000 BC 1,000 BC to2000 AD
Europe Events Expansion out of Refugiaafter LastGlacial Maximum at 16,000 BC End of Last Glacial Period by 10,000 BC Sea Levels Rise 120misolating Britain from Continent by 7,000 BC Expansion of Farming from Near Eastto all of Europe by 4,000 BC Expansion of Indo-Europeans out of Ukraine into Europe by 1,000 BC Migration of “Celts”, “Germanics”,

“Barbarians”,

“Vikings”

SNP Events   R1b-P25  E1b-M78  J2-M172   R1a-M17  I2b-M436  I2b-M223

  N1c-P105

  R1a-M458  R1b-M269  R1b-L23

  G2a-P15

  R1b-M412  R1b-L11  I1-M253

  I2a-P37.2

  I2a-M423

  R1b-S116  R1b-U152  R1b-M529

  I1-L22

  R1b-U106   R1b-M222

The above timeline shows approximately when some SNP mutations occurred in the major European y-Haplogroups, and places them into historical context. Note, some authors have computed different SNP event dates to these.

The following table comes from Haplotypes of R1b1a2-P312 and related subclades: origin and “ages” of most recent common ancestors; Anatole A. Klyosov http://aklyosov.home.comcast.net

A detailed analysis of a 2299 of 67 marker haplotype dataset provided by Michael Walsh, administrator of R1b1a2-L21 site http://www.familytreedna.com/public/R-L21/default.aspx?section=yresults has allowed to identify base (ancestral) 67 marker haplotypes and timespans to their common ancestors as follows:

 

  • •       •      •       •      R1b1a2   L265, M269, M520, S3, S10, S13, S17                            ~ 7000 ybp1
  • •       •      •       •      •       R1b1a2a   L23/S141, L49.1                                                                             ~ 6200 ybp1
  • •       •      •       •      •       •      •       R1b1a2a1a   L51/M412/S167                                                     5300±700 ybp1
  • •       •      •       •      •       •      •       •       R1b1a2a1a1   L11, P310, P311 ~ 4800 ybp (in Europe)2
  • •       •      •       •      •       •      •       •      •       R1b1a2a1a1a   M405/S21/U106         4175±430 ybp
  • •       •      •       •      •       •      •       •      •       •       null mutation U106                                          3325±450 ybp
  • •       •      •       •      •       •      •       •      •       R1b1a2a1a1b   P312/S116                                        ~ 4800 ybp
  • •       •      •       •      •       •      •       •      •       •       null mutation P312                                          3575±400 ybp
  • •       •      •       •      •       •      •       •      •       •       R1b1a2a1a1b1   M65                                        ~ 1800 ybp
  • •       •      •       •      •       •      •       •      •       •       R1b1a2a1a1b2   M153                                      ~ 3640 ybp
  • •       •      •       •      •       •      •       •      •       •       R1b1a2a1a1b3   S28/U152          4125±450 ybp[5]
  • •      •       •      •       •      •       •      •       •      •      •      null mutation U152                                   3525±460 ybp
  • •       •      •       •      •       •      •       •      •       •      •      R1b1a2a1a1b3c   L2/S139    4025±410 ybp
  • •      •       •      •       •      •       •      •       •      •       •      •       •       R1b1a2a1a1b3c1   L20 3650±400 ybp
  • •       •      •       •      •       •      •       •      •       •      •       R1b1a2a1a1b3d   L4/S178 1275±290 ybp
  • •       •      •       •      •       •      •       •      •       •       R1b1a2a1a1b4   L21/M529/S145                  3750±380 ybp
  • •       •      •       •      •       •      •       •      •       •      •       null mutation L21                                     3025±460 ybp
  • •      •       •      •       •      •       •      •       •      •       •      •      •      null mutation L21                    1500±325 ybp
  • •      •       •      •       •      •       •      •       •      •       •      •       Unidentified clade    1650±175 ybp
  • •       •      •       •      •       •      •       •      •       •      •       R1b1a2a1a1b4b   M222      1450±160 ybp
  • •       •      •       •      •       •      •       •      •       •      •       R1b1a2a1a1b4e   L144         ~ 4000 ybp
  • •       •      •       •      •       •      •       •      •       •      •       R1b1a2a1a1b4f    L159.2     1775±200 ybp
  • •      •       •      •       •      •       •      •       •      •       •      •       R1b1a2a1a1b4g   L193                    1275±170 ybp
  • •      •       •      •       •      •       •      •       •      •       •      •       R1b1a2a1a1b4h   L226                    1500±170 ybp
  • •       •      •       •      •       •      •       •      •       •      •       R1b1a2a1a1b4i    P314.2     2225±300 ybp
  • •       •      •       •      •       •      •       •      •       •       R1b1a2a1a1b5   L176.2/S179.2 3675±560 ybp
  • •       •      •       •      •       •      •       •      •       •      •       R1b1a2a1a1b5a   SRY2627 3150±320 ybp
  • •       •      •       •      •       •      •       •      •       •      •      •      null mutation SRY        ~ 2800 ybp
  • •       •      •       •      •       •      •       •      •       •      •       R1b1a2a1a1b5b   L165/S68                    ~ 3000 ybp
  • •       •      •       •      •       •      •       •      •       •       R1b1a2a1a1b6   L238/S182         ~ 1000 ybp

 

[1] http://www.genebase.com/support/index.php?_m=knowledgebase&_a=viewarticle&kbarticleid=153

[2] http://www.dnahaplogroups.org/ydnaHaplogroup.php?page=5&l=n&__atoken=__NONE__

[3] Note that as I said earlier this statement is not strictly correct anymore because the advances in SNP testing are beginning to make it far more valuable as a tool for recent genealogical time frame ancestry.

[4] MRCA is the most-recent-common-ancestor, and TMRCA is the time-to-most-recent-common-ancestor.

[5] 3800±380 (a different dataset)

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