SNPs and STRs - the ancestor breadcrumb trail - development in progress

"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?  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.  When a mutation does occur, it occurs at a predictable rate making yDNA an excellent source of information regarding the time to the most common ancestor (TMRCA).

What are STRs?  Tracking recent ancestry in immediate family history for several generations. 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 2.0 FTDNA uses up to 111 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. 

Markers and Alleles

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 111 markers (GAP 2.0) with several markers combined into multi-allele markers.  Mutations between the multi-allele markers are counted as a single mutation.

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 individual haplotype.  When comparing individual haplotypes, they are placed in a group to study their Most Recent Common Ancestor.  This list of individual haplotypes that share common STR signatures is called a haplogroup, a genetic populations with a direct ancestor.  Haplogroups, are assigned letters in the alphabet; see the Y-DNA Haplogroup Tree 2013.  

To understand your individual haplotype better, your haplogroup is ordered in a phylogenetic tree.  This phylogenetic tree has numerous branches.  All known critical SNP for your haplogroup, in this case 4466+ for the South Irish (closely related 4466- members are being studied for also being in the South Irish tree), must be identified.  The CTS4466+ critical SNPs are CTS5714, CTS3974, CTS8358, F2517, Z454, PF112, L270, and L247.  Each member in the research group is tested for all these critical SNPs then they build into separate phylogenetic trees and branches by critical SNPs.  Those that do not test are in a general list which has a lower chance of being placed into their correct sub branch.  A individual's yDNA is then studied in their sub branch to find common characteristics such as STR signature and family history based on location, time frame, migration pattern etc.

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.



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

    • Migration map View Y-DNA Migration map

      How different DNA labs name the SNPs

      Download a detailed copy of the Y-DNA Haplogroup Tree 2009

      Haplogroup R  FTDNA R-L21 is under R1b1a2a1a1b4*  ISOGG R1b1b2a1a2f* 

      ISOGG and FTDNA/YCC use different naming conventions for the same information for Deep Clade testing.

      Morley SNP tree, Dr. Krahns tree, ISOGG tree

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

      • Initially it was thought that if you are within a genetic distance of any identified R-L21 haplogroup, you could assume that you are most likely in the haplogroup.  FTDNA measures their member Close matches by counting mutations from member to member.  On closer scrutiny I have found that counting mutations puts an individual in a pool that may or may not be within the same haplogroup or sub branch.  FTDNA uses a statistical analysis for the probability that these are, in fact a members close matches.

      • Every male on earth is in a single phylogenetic tree.  A person may have the same STR signature as another but be identified as belonging to another group by SNPs which occur randomly.  Each male descendant will inherit these SNPs.  For the South Irish, the unique SNP is CTS4466+.  CTS3974 seems to occur whenever CTS4466+ occurs.