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Contents
The Y Chromosome
Part I - STR Markers– Short Tandem Repeat Markers. 1
Part II - SNP – Single Nucleotide Polymorphism.. 1
Part III - Comparing Tilley Family Genealogy project member matches. 1
Comparing 12 Markers. 1
Comparing 25 Markers. 1
Comparing 37 Markers. 1
Comparing 67 Markers. 1
Comparing 111 Markers. 1
Comparing Big Y. 1
Sources and Learning. 1
There are 23 pairs of chromosomes in each cell. (46 chromosome)
Of those 23, 1 is the sex chromosome. Either X in females, or Y in males.
All chromosome pairs are made up of two chromosome strands connected by a pair of base nucleotides, typically illustrated as the 3d spiral ladder.
A = Adenine
C = Cytosine
G = Guanine
T = Thymine
Nucleotides are typically paired with their complements on the opposing strand of DNA to form base pairs.
"A" typically pairs with "T" on the opposing strand, and "C" typically binds only with "G" on the opposing strand. But on rare instances that may differ.
The illustration below is to represent the total length of the Y-DNA Chromosome and the ~59 million base pairs of nucleotides.
A representation of a very small segment is illustrated below, beginning at nucleotide or base #15,175,642 with the base pairs identified with their respective letter designations.
There is the top strand represented as red.
There is a bottom strand represented as blue
The light gray lines that look similar to ladder rungs represent the alleles or base pair of nucleotides.
The letter designation for given for each nucleotide.
To simplify expressing and illustrating the results, only one strand and a single base sequence is shown when illustrating a location along the chromosome.
This is typically the way you will see the results visualized, and typically numbered to illustrate the exact base location.
The sequence of the base pairs remains fairly constant from generation to generation, but occasionally mutate.
Meaning that as the DNA is reproduced (copied) and change occurs somewhere along the base.
In testing Y-DNA, basically one strand of base nucleotide is examined to identify those changes or variations.
The next two sections explain those mutations and variations and how they are expressed and used in comparisons.
Within the sequence of base pairs, can be found short tandem repeats. Repeats may be a single nucleotide (AAAAAAAA) or two nucleotide (ATATATATA) or six or more.
The process of determining these sequences and finding variations is DNA Sequencing.
The National Institute of Standards define and name the positions along the DNA, and each testing lab follows those standards to large degree.
In a 12 Marker test, 12 STRs are examined and reported. Likewise, in the 111 Marker test, 111 named STRs are examined and reported
For example, one standard STR is named DYS393 and can be found at the beginning of the 12 Marker results. The base sequence AGAT is repeated 13 times in our group, but is known to vary, repeating 9-17 times. 12 being the most common. That STR region is located near the beginning of the Y chromosome near position 3,100,000, and can be illustrated as below.
When this sequence varies, it will repeat as little as 9 times or as many as 17 times. Typically, 12 times.
Examples;
1. The image below illustrates 4 repeats of the sequence AGAT. 4 base pairs in length repeated 4 times
2. The image below illustrates 8 repeats of the sequence TT. 2 base pairs in length repeated 8 times
3. The image below illustrates 16 repeats of the the sequence CGT, 3 base pairs in length repeated 16 times
The illustration below shows the positions of some of the STRs along the first half (more or less) of the Y chromosome. Notice the position of DYS393 which was just discussed.
National Institute of Standards & Technology
Using the above and below illustration we can see something in the tests results which typically brings questions.
In the Illustration below, notice the marker labeled DYS464. Rather than a single column of values, there are 4 columns.
Now notice in the illustration above, you will find DYS464a, DYS464b, DYS464c, and DYS464d.
The 4 columns simply represent four different Markers, all with the label DYS464, but with the suffixes a,b,c & d. This is of no importance to us, other than to understand why some of the markers have more than a single column. Those STRs which contain multiple columns are consider as one change, regardless of which values or how many values change.
STR or Marker Values
Below is an illustration of how the STR or Marker Values are recorded, and made available for us to utilize in our personal comparisons. Typically the way Ftdna displays them in a project.
The chart heading below illustrates the colors you see from a results chart. The various shades of blue indicate the various testing levels, 12-25-37-67 and 111. Testing level 12 being the darkest, and level 111 being the lightest. The Dark red shading indicates faster changing STR markers.
Notice the 4th row of values from the bottom. It shows that only 32 Strs or Markers were used in that members test.
Tilley Family Genealogy
The values given are the total count of how many short tandem repeats at each marker along the each person’s Y-DNA strand.
Looking at the first STR you notice the DYS393 (DNA Y Segment # 393) mentioned above. It received the value of 13. The short tandem repeat, repeated 13 times along that segment. And for all 10 of the person’s results shown here, that value was the same.
These values, compared against each other, help us determine how closely we are related. For example, an exact match as shown with rows 2, 3 & 4, is known to be a high probability of those three people having their MRCA within 3-5 generations.
MRCA = Most Recent Common Ancestor, or the first ancestor going back in their line that all of them share
More details of comparisons and interpretations will be covered in other reports.
Y-DNA tests such as Y12-Y111 return STR results only. The more markers tested, the more results are returned for comparison. Typically Y67 is considered a good base test.
Your STR results will also show the Haplogroup you that you match.
The initial group placement being at a higher level in the Haplotree. (defined later)
As the name implies, that is simply a grouping of people who match based on several match criteria.
Further and more extensive testing would be needed to determine more precisely the lower sub groups.
The lower tests much better help to define family Surnames, and are necessary for project groups studying multiple Y-DNA results.
STR variances occur frequently and can be used to identify branches of a family within 5 generations more or less.
STRs values are what we utilize most in comparing against our matches/relatives.
STRs define the various Haplotypes
STRs are used in our most recent genetic research. (5 generations more or less)
SNPs are used in far more distant or ancestral genetic research.
A single-nucleotide polymorphism (SNP) is a change (mutation) to a single nucleotide in a DNA sequence, as opposed to the previously discussed STR which looks at changes to a sequence.
SNPs occur far less frequently ( 1,000 years more or less) and are used to determine far more ancestral branches of a family, beyond 5 generations.
STRs help define more recent family branches.
SNPs are at different locations than STSs.
An STR described prior is a mutation or variance of how many times a sequence is repeated.
A SNP is a mutation or change in only a single nucleotide (nucleotide is also referred to as a base)
In the DNA sequence illustrated above, the single nucleotide C was found to be different in some tests, compared to a reference sample. This then is noted as an SNP
That same change will be found in all of our project group member results, unless there was a mutation in a more recent branch.
Ftdna illustrates this in test results as follows. This also provides the exact location and number of the nucleotide which changed.
This nucleotide change occurred at 16,750,037. The location is not relevant when comparing results, and is seldom provided, and is only pointed out here in case you encounter it.
The relative mutation rate for an SNP is extremely low. Meaning they occur once in periods of 1,000 years more or less.
This makes them ideal for marking the history of the human genetic tree.
SNPs are named with a letter code and a number.
The letter indicates the lab or research team that discovered the SNP. The number indicates the order in which it was discovered.
For example, M173 is the 173rd SNP documented by the Human Population Genetics Laboratory at Stanford University, which uses the letter M.
SNPs define the various Haplogroups (discussed later)
These include project members, and matches found in the L-38 project
The same process will likely be done in the future for Tilley NPEs as well as other matching groups as they come into the project.
Below is an image a comparison of the first 12 markers.
· Shading; each marker testing level is shaded slightly different. Marker level 12 below being the darkest shade of blue.
· Maroon shading indicates the STRs which mutant more frequently.
· The MIN, MAX, and MODE row headings indicate the value ranges found in each STR.
Ex: The STR named DYS393 will have values that range from 12 being the minimum to 14 being the maximum, and 13 being the modal or most common when comparing our group.
· Tilley mode is an additional row heading which indicates values more unique to current matches, and documented Tilley descendants.
The image to the right illustrates how the table would appear using the typical mode.
Notice that DYS385 there is shaded black to indicate the values are different than the Mode.
The STRs that have a unique variation from the Mode make up the unique Tilley mode values, and those values are highlighted orange with the red border, as illustrated below.
· Drop down arrows (
· Haplogroups which have been designated for each match is shown here, and will be an important part in the end results.
The different haplogroups indicate that not all matches have been specifically tested to identify their lowest or most downstream Haplogroup (terminal SNP).
To clarify those with the Haplogroup I-M170 did not request a specific SNP test, and are projected to be in that group based on the result values known for that SNP level
Those with Haplogroup I-Y17121 requested to be tested at that SNP level
Those with Haplogroup I-BY117260, requested the Big Y test which tests for the lowest or most downstream Haplogroup (terminal SNP)
As testing progresses, more extensive test will be made available, and may eventually reveal a lower terminal SNP which will help define our more recent ancestral branches.
· Genetic distance is simply how many variations there are at each test level.
Here, it shows that all of these members and their matches are perfect matches at the 12 Marker level and therefore their genetic distance is 0.
· DYS385 & DYS447 are shown here to also have a unique Tilley mode value. The value unique to our Project group matches for DYS447 is 23, where the overall mode value for this STR or marker is 24. Because this match group all share the same variation at these markers, they are NOT variances within the group. That is the standard or mode for the project group.
· DYS437 shows that two people have a variation at this marker. Each of those persons compared to the others, have a genetic distance of 1 at the 25 marker level. They are currently the only two people in the group that have that variation.
· Compared to each other, those two people would not have a genetic difference because they are the same. They are only different to the rest of the group. In the genetic distance table, they show a genetic distance between them of 0 at 25 markers
These two people are uncle and nephew, and at this point, this variation will be considered as a family branch within this project.
Their designated Haplogroups are different, only because one tested to find the terminal SNP, where the other’s haplogroup was assigned to a known and much higher parent group. The Haplogroup I-M170 in our Project group matches can be projected to the confirmed most downstream SNP I-BY117260
Later, on our Haplogroup chart, you will see these two people listed in their unique family branch.
· DYS464. This is actually a combined marker and that is why it has 4 columns of values.
DYS464i, DYS464ii, DYS464iii, and DYSiii. But they are grouped under the main heading DYS464, and considered to only be one variation, when any one or more value differs.
· Note that there is also a variation at marker DYS464, unique to only one person in this group.
Here again, this variation can be considered as a family branch within this project, and will be shown in the Haplogroup chart later.
This persons Haplogroup was assigned a known much higher parent group, but for this project will be shown as projected to be in the confirmed terminal SNPs or Haplogroups.
Everyone being considered in the current comparison, has tested at least to the 37 Marker level.
That level then currently will be used as our minimal comparison level.
Segment DYS576 reveals one variation which indicates 19 short tandem repeats, rather than 18 which is our Project group matches standard.
This variation may be considered to be unique to the line descending from Lazarus Tilley 1765-1850 who migrated from Kings Creek in North Carolina to the mountains of western North Carolina and then into Rabun County Georgia. He is the son of Edmund Tilley Sr 1747-1800 of Kings Creek. The variation may have occurred much later than Lazarus and even earlier. There is inadequate data to determine much more about that variation, but it IS unique to that line.
Segment CDY reveals two variations unique from the group standard, but different to each other.
The 35-36 seems to be unique to a line descending from Stephen Tilley 1742-1781 of Kings Creek, and likely more specifically to his son Lazarus Tilley 1770-1834 who finally settled in Anderson, South Carolina ca 1800.
The 34-37 variation seems to be unique to a line descending from Henry Tilley Jr 1754-1833 of the Dan River Settlement in Stokes County North Carolina. However, this Y-DNA donor and the Project group are still researching the possibilities of that line.
Marker DYS438 is very unique to the Tilley descendants with its value of 8.
First notice that two people did not test beyond the 37 Marker level. (The empty rows)
Segment DYS531 reveals a variation from 11 to 12 short tandem repeats.
This person is not a member of our group as yet, but has for some time been very much of interest, they are a descendant of the White family and likely the result of an NPE, and possibly in the area of Logan West Virginia. This variation may be considered unique to a Tilley / White NPE, although apparent, that is speculation.
Segment DYS617 reveals a variation from 13 to 14, and is in the line descending from John Tilley 1763-1842 of the Granville Settlement of Orange County North Carolina.
Notice that only 4 in this current group tested at the 111 Marker level
DYS716 reveals that TWO people share this variation.
What is interesting is that both are known descendants of Henry Tilley 1714-1790 of the Dan River Settlement. This variation apparently occurring with Henry Tilley 1714-1790 passed on to these the two sons of which these two people descended. Therefore, this STR / Variant will be considered a unique Identifier, unique to descendants of Henry Tilley1714-1790.until proven otherwise.
DYS650
DYS552
These two segments both reveal a variation, and both for the same individual
These may later compare to other test results and reveal more possibilities of sub grouping.
PENDING ONE MORE BIG Y-700 RESULT
The primary sources for much of this information was compiled from the sources listed below. A few others sources are credited throughout. Many of the illustrations were developed by Tilley Family genealogy and this compilation is intended for that private group and not for public circulation.
In search of the Origin of I2a2b-L38 - Hans De Buele Highly recommended for future learning, the title may be misleading to fact that this is a great “from the ground up” learning aid.
ISOGG
Ftdna
Roberts Estes - DNA Explained – blog
STRs vs SNPs - a much more detailed explanation