R-L21 Haplogroups
SNPs and STRs


R-L21 Haplogroups
SNPs and STRs

SNPs and STRs - the ancestor breadcrumb trail

What are Genes

What are STRs?

What does the YDNA test?

What are SNPs?

Evaluating SNPs and STRs

SNPs through History

Other tutorials

As man moved out of Africa they moved to areas, grew in size then some would break with the group and move into a new area.   Each moving group would become the founders in the new area taking with them a subset of the genes from the African population.  Time and distance created mutations in SNPs and STRs, called genetic drift, as the migrant survivors changed in the process of natural selection of the best traits meeting the relevant environmental conditions.

What are Genes?  top

Chromosomes are the structures that contain Genes.  Genes are the set of instructions inside each cell.  Humans have 46 chromosomes or 23 pairs that are randomly inherited from a mother and father.  22 pairs of chromosomes, somatic cells, are recombinant so a child does not inherit the exact chromosomes of the parent.  The 23rd pair, gametes, decide the sex of the child.  A child can inherit an X chromosome from the mother and either an X or Y chromosome from the father.  Only a tip of the YDNA is recombinant with the rest being non-recombinant.  The non-recombinant portion of YDNA is referred to as junk DNA because it doesn't decide anything such as indicate eye or hair color.  However, it does mutate at a predictable rate and is therefore excellent for genealogy studies for estimating mutation rates.

What use the YDNA test? Our project uses the YDNA for testing purposes because a son's surname and YDNA, usually without any changes, are inherited from the father which enables us to trace the surname heritage. 

What are STRs?  Tracking recent ancestry in immediate family history for several generations. top

STRs, Short Tandem Repeat, markers provide information that can help you understand the origins of your ancestors.  This is what is being tested when you order a YDNA test.  The differences in STRs between individuals reflect mutations of the marker allele values. 

The YSTRs (aka markers such as 393, 390, and 19 for example) are short fragments of DNA, 2 to 6 base pairs, that are repeated over and over again.  An STR on the Y chromosome is called DYS (DNA Y-chromosome Segment number).  STRs change at a faster rate than SNPs.

In GAP 1.0 FTDNA uses 67 markers (more advanced markers are available).  Each marker can have several different values called alleles and will vary between different individuals.  Click on this list of markers to see the range of possible allele values.

Color coding legend:

slow fast recLOH
448 449 464

The markers are either slow moving (mutate slowly and help track family ancestry - white background), fast moving (mutate more quickly and which track family branches - 385/439/389i/389ii/458/449/576/570) or subject to recLOH events (459/464/CDY). 

Currently FTDNA uses 58 markers (GAP 2.0) with several markers combined into multi-allele markers.

When a male takes a YDNA test, the allele values are specific to him and his immediate male relatives.  The entire set of specific alleles are his haplotype.  The genetic distance between haplotypes can be determined using the following chart.  The genetic distance (GD) below was determined using 67 single allele markers.  The GD for the 58 markers (GAP 2.0) has not been provided by FTDNA to date.

Genetic distance between donors can be used to identify close genetic matches:

Gap 1.0

Member close matches

Gap 1.0

Member close matches

Gap 1.0

Member close matches

Gap 1.0

Member close matches

Gap 1.0

Member close matches

Gap 1.0

Member close matches

Gap 2.0*

Haplogroup close matches

probably related
possibly related
probably not related
not related Multi-allele Markers

GD = 0 related

  GD = 1 possibly related GD = 2 probably not related GD = 3 not related GD = 1

GD = 1 related

GD = 2 probably related


GD => 3 probably not related

GD => 4 not related GD = 2
GD = 0 very tightlyrelated
GD = 1 tightly related
GD = 2 or 3 related

GD = 4 probably related

GD = 5 possibly related


GD => 6 not related

GD = 5
GD = 0 very tightlyrelated
GD = 1 or 2 tightly related
GD = 3, 4, 5 ,6 related


GD = 7 possibly related

= 8 or 9 only possibly related

  GD => 10 not related GD = 9
111           GD = 9

Haplotypes are studied to find their Most Recent Common Ancestor which builds broader groups known as haplogroups.  Haplogroups, genetic populations with a direct ancestor, are assigned letters in the alphabet; see the Y-DNA Haplogroup Tree 2011.   Your haplotype can then be compared to known haplogroups.  You compare your haplotype to another's haplotype to find your closest matches to another family or within it's branches.   

Frequent haplotypes, commonly known as modal haplotypes can often be associated with defined populations and geographical areas, and can be informative or predictive of haplogroups that also show geographic preferences.

FTDNA discusses SNPs and haplogroups and provides a high level overview of the subject.  Useful information is found in the:

The Atlantic Modal Haplogroup, R1b, is the most common haplogroup in Atlantic Europe. 

"It reaches the highest frequencies in the Iberian Peninsula and in Great Britain and Ireland. In the Iberian Peninsula it reaches 70% in Portugal as a whole, more than 90% in NW Portugal and nearly 90% in Galicia (NW Spain), while the highest value is to be found among Spanish Basques." see Wikipedia

It is further refined in the Western Atlantic Modal Haplogroup which exists in high or very high frequencies in all of Western Europe from Spain in the south to the British Isles and western Scandinavia in the north.

  393 390 19 391 385 426 388 439 389-i 392 389-ii
AMH Atlantic Modal Haplogroup 13 24 14 11     12     13  
WAMH Western Atlantic Modal Haplogroup 13 24 14   11-14 12 12 12 13 13 29

There are 40 current and speculative haplogroups in the R-L21 Projects

Generally if you are within a genetic distance of any identified R-L21 haplogroup, you can assume that you are most likely in the haplogroup.  If your genetic distance is greater than 10 (not an absolute rule) to a haplogroup, you are very likely in another haplogroup.  If you do not have a high genetic distance to any of the known haplogroups, most likely your specific haplogroup has not yet been identified or studied. 

The South Irish haplogroup includes Dr. Nordvedt's 12 marker version over the Atlantic Modal Haplogroup creating the 67 marker version of the South Irish.

Color coding legend:

Dr. Nordvedt's 12 marker South Irish haplogroup 11
mutations from the South Irish 23

What are SNPs(Single Nucleotide Polymorphism)? Tracking deep ancestry top

SNPs are mistakes in the copying of the genome when one letter is changed to another letter (example when a T changes to an A).  In YDNA these mistakes, mutations, occur at a relatively low rate and can be used to determine ancestry.  YDNA is passed from father to son so the son will inherent these mutations.  Identifying your SNPs can help you find whether you belong to a certain ancestral group.  SNPs can be used to identify ancestral haplogroups and visa versa.  SNPs define a whole chromosome and becomes it's signature.

Many haplogroups have identified unique SNPs such as M222 for the North Irish or L226 for the West Irish.  The unique SNP for the South Irish has not been identified in testing, however Dr. Ken Nordvedt has identified the STRs for the South Irish Haplogroup. 

The WTY test is an advanced sequencing test that examines the entire YDNA strand in order to find new haplogroup-defining SNPs (Single Nucleotide Polymorphisms).  Sometimes SNPs are found in the test process before the haplogroup is identified.  At other times haplogroups are first identified and only later confirmed through SNP testing.  Once the SNP of an ancestral haplogroup is found and you think you belong to this ancestral haplogroup, you can take the advanced SNP test to confirm it.

You log into to your account. From the left navigation bar select:
  • Order tests & Upgrades
    • Select Order Advanced tests
      • Select 'SNP' in the test type box;
      • Enter the SNP Name in the marker box;
        • Add the test ($29)

Evaluating SNPs and STRs top

The graphic above (http://www.genebase.com/learning/article/8) shows the relationship between SNPs (ancestral) and STRs (more recent).

Illustration from The Migration History of Humans: DNA Study Traces Human Origins by Scientific American by Gary Stix

Haplogroups are defined by a common ancestor.  Y-DNA haplogroups are defined by slowly evolving SNPs, and each SNP characterizes or identifies a particular paternal haplogroup or branch of the Y-DNA phylogenetic tree.

SNPs through History top

Migration of Man through SNPs

Tracing Human Migration through YDNA (excellent summary, stops at P312.  L21 is just below P312)

The ancestry of all L21+ men, in terms of SNPs, runs like this: 

M207+. .M173+. . M343+. . P25+. . P297+ . . M269+. . L23+. . L51+. . P310+. . P312+. . L21+ 

The current FTDNA SNP tree (L459 needs to be added and should be R1b1a2a1ab4; equivalent to L21):

R1b-Haplogroup tree:

Insight into SNP testing by Alex Williamson

"SNPs are rare.  There is nothing special about when they occur.  Just one man in history acquires a mutation his father didn't have.  He doesn't have to go on to found any great clusters, etc.  A SNP may occur before an STR cluster, and include slightly more than we might "want", or it may occur inside a cluster, and include less than what we "want".  That many of the SNPs we found so far just happen to fit exactly with an STR cluster, isn't because of a special relationship between clusters and SNPs, instead, it is because of something special about the real world history of many of the clusters we've identified so far.

I have no doubt that a SNP corresponding to the bulk of the South Irish will be found.  As far as I know, only a small fraction of the Y-chromosome has been carefully examined for SNPs thus far.  New tests are always being developed to look at more and more of the Y.  It is just a matter of having the right spot examined to find your SNP.  It just hasn't happened yet.

There aren't necessarily any good or bad candidates.  Ideally, all of your South Irish men will either have the SNP or they won't.  It is possible as I've alluded to above that you might find a SNP that will include only a fraction of your South Irish men, or perhaps it will include a larger piece of R-L21 which includes the South Irish.  The Scots cluster is a very large R-L21 cluster, and it doesn't have an associated SNP yet, despite attempts to find one.  Recently a SNP has been found which looks to identify a part of the Scots cluster, but not all of it.

There is no reason why one hasn't been found for the South Irish men yet.  Many men have tried to find SNPs for various groups, some found them, most did not.  There is a lot of Y-DNA however, so there is still plenty of potential for the future.  What you need to do is keep trying.  Don't try right away though, give some time for new tests to be developed, then try again.  Eventually it will just happen."


Other tutorials: Excellent tutorials by 23andMe, DNAHeritage Oglekin, Genebase National Institute of Health  top

Where do your Genes come from ?

What are phenotypes?

Understanding Deep Haplogroups "Deep Ancestry"

How is genetic distance calculated to YSTR markers?

SNP mutation

It's a revolution

The Migration History of Humans: DNA Study Traces Human Origins by Scientific American by Gary Stix

 R-L21 South Irish Project 2011
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Last updated: 03/19/11.

 R-L21 South Irish Project 2011
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Last updated: 08/10/13.