Methodology of marker analysis
The main task in analysing the marker set is to determine the deepest branch on the world Y tree.
First of all we need a set of markers. In the example below is a set of 37 markers
Such a set is called a haplotype. Accordingly, a set of 37 markers is a 37 marker haplotype.
Tools used in the analysis:
Nevgen haplogroup calculator (predictor)
STR Match Finder service, it allows to compare sets of markers and determine the closest matches.
Nevgen
Nevgen is a service that predicts haplogroup based on a set of markers, sometimes with high detail.
The screenshot below shows the interface of the Nevgen calculator.
In the field marked with number 1 you should copy a set of markers, wait a little while until the area marked with number 3 is filled with digits and click Calculate. The screenshot below shows an example filled in
After the calculation, the prediction appears.
In this example, the calculator only predicted the haplogroup. Haplogroup R1a was predicted with 100% probability. Now when we know the haplogroup we can switch Nevgen to the mode of work on a specific haplogroup. To do this, click on the settings (number 4 on the first screenshot).
Here you should select the desired haplogroup, in this example R1a and click Calculate again.
Now not just a haplogroup is predicted, but its deep branch.
STR Match Finder
STR Match Finder allows you to compare sets of markers and determine the closest matches. The list of matches is arranged in such a way that the most probable matches are at the top. The main thing to pay attention to is the 6th column GD. This is the sum of different markers. The smaller the number is, the more likely the relationship is.
Further in the table specific markers are indicated and visually it is possible to estimate on what markers someone differs. Rare values are highlighted in colour. The rarest ones are dark red. This colour highlighting shows that for a particular sample the marker value is very rare. Sometimes it allows you to deepen the prediction.
The markers themselves are arranged by mutation rate. The ones on the left are less likely to mutate, they are more stable. The ones on the right are the fastest. Some markers differ by several positions at once.
For 37 marker haplotype close matches usually differ up to 3-5 markers.
A group of closely related results is clearly visible in the picture. The first 3 with GD = 2 (first column) are representatives of the same surname. They have a small genetic distance and also the most recent marker (CDY) is the same. This indicates a close relationship. CDY is the most rapidly changing marker and when values of this marker coincide at those at whom distance on markers is not very big, it speaks about close kinship. In contrast to this it is necessary to pay attention to the bottom lines. There the marker distance is 11-12 steps and CDY is also the same. Here, on the contrary, CDY has coincidentally matched, and with such a long distance it is better to remove this marker from the comparison (by removing it from the filled table on the STR Match Finder site).
Also pay attention to the YCAII marker. It is highlighted in dark red colour. This rare value is a manifestation of the marker pattern. This pattern allows to detect more exact matches on the basis of rare marker values.
Yfull
The Yfull haplotree contains a number of tools that aid in research.
First, let's focus on searching. Yfull allows you to find the subclade to which the SNP belongs by the name of a SNP.
To do this, go to the site and open the tree:
At the very bottom of the page is a link to the current version of the tree.
In the top right corner, click on search and type in the SNP name
For example, the SNP that in our example was predicted by the Nevgen calculator, namely YP451.
The result is a link to the appropriate branch and the name of the SNP. In this example, 2 names are specified, they are synonyms.
Thus, using a symbiosis of different tools we (not always) can predict this or that branch on the Y tree.