HAM Surname DNA
Project
Group 1
I1-M253 atDNA Largest Shared Autosomal Match
Group 1 I1-M253 atDNA Largest Shared
Autosomal Segment Match
12/28/2017
updated: Jan 30, 2018, Mar 31, 2018
Taking a little
inspiration from Dean McGee, I did a Dean McGee style table
of the largest shared autosomal segments from the tiny
segment
study of HAM DNA Group #1 -
I1-M253.
Basically, the autosomal DNA testing
companies set a low threshold, meaning they usually do not
show much beyond 5th cousins for the
autosomal DNA. As most of you know the
Y-DNA goes much further back.
We have had folks in our Y-DNA group
upload their autosomal DNA to GEDMatch, and I have lowered
the thresholds by using GEDMatch utilities.
The results from the largest shared
segments roughly follow the Y-DNA, except that the autosomal
DNA has totally separated out the line of our
William HAM, Sr. of Grayson County. You
can almost make out his three sons.
The problem we have had with the Y-DNA is
that not everybody has tested to the same number of markers,
and you have to adjust for that. Not
having the same number of Y-DNA markers
means the lines of Wm, Sr. are jumbled up a bit.
Here, the problem with this autosomal
tree is that that there has been no attempt to separate out
the males and females. Also, some folks
descend more than once, which makes the
autosomal segments sometimes appear to be larger than they
normally would be.
First off is to create a
table of the largest autosomal shared segments from the tiny
segment study. FTDNA, Ancestry, and GEDMatch have a lower
threshold of 7 cMs, and that cuts us off at about the 5th or
6th cousin level. I used the utilities at GEDMatch to lower
the threshold to one (1.0) centimorgans (cMs).
Then, I created a program to create a
table of the largest shared segments for the autosomal DNA
of the HAM Group #1 autosomal participants.
| Largest Shared Segment |
| ID |
T
6
1
1
x
x
x
|
T
6
8
2
x
x
x
|
T
1
8
1
x
x
x
|
A
5
0
0
x
x
x
|
A
9
8
4
x
x
x
|
A
2
7
4
x
x
x
|
T
1
3
3
x
x
x
|
T
0
7
4
x
x
x
|
A
4
3
8
x
x
x
|
A
6
5
8
x
x
x
|
T
1
0
3
x
x
x
|
T
3
6
8
x
x
x
|
A
4
0
4
x
x
x
|
A
1
7
1
x
x
x
|
T
4
6
3
x
x
x
|
A
7
4
0
x
x
x
|
T
6
3
0
x
x
x
|
T
3
8
4
x
x
x
|
M
8
0
4
x
x
x
|
| T611xxx |
|
25.5 |
10.1 |
28.5 |
21.1 |
4.3 |
21.8 |
14.1 |
4.7 |
11.8 |
6.8 |
3.6 |
8.5 |
4.8 |
6.3 |
4.7 |
4.5 |
6.1 |
3.9 |
|
| T682xxx |
25.5 |
|
29.3 |
24.8 |
5.5 |
4.9 |
4.4 |
4.6 |
13.8 |
3.5 |
3.5 |
5.0 |
4.9 |
4.9 |
4.5 |
3.5 |
6.3 |
3.5 |
|
|
| T181xxx |
10.1 |
29.3 |
|
52.1 |
4.5 |
5.0 |
11.4 |
9.6 |
4.3 |
5.6 |
4.2 |
4.2 |
4.6 |
3.6 |
4.3 |
3.9 |
3.6 |
3.9 |
|
|
| A500xxx |
28.5 |
24.8 |
52.1 |
|
3.7 |
4.8 |
4.5 |
22.0 |
7.1 |
4.0 |
8.6 |
5.7 |
4.1 |
4.5 |
3.4 |
4.0 |
3.4 |
6.6 |
1.8 |
|
| A984xxx |
21.1 |
5.5 |
4.5 |
3.7 |
|
4.3 |
10.8 |
11.6 |
6.7 |
6.8 |
4.8 |
5.1 |
4.9 |
3.8 |
5.5 |
3.8 |
3.9 |
4.8 |
|
|
| A274xxx |
4.3 |
4.9 |
5.0 |
4.8 |
4.3 |
|
24.2 |
18.1 |
5.1 |
6.2 |
4.5 |
3.8 |
5.8 |
4.9 |
5.0 |
3.8 |
4.2 |
4.0 |
4.3 |
|
| T133xxx |
21.8 |
4.4 |
11.4 |
4.5 |
10.8 |
24.2 |
|
125.9 |
11.9 |
15.3 |
4.3 |
6.2 |
6.3 |
5.9 |
5.0 |
5.3 |
3.8 |
5.1 |
1.1 |
|
| T074xxx |
14.1 |
4.6 |
9.6 |
22.0 |
11.6 |
18.1 |
125.9 |
|
3.9 |
10.7 |
4.9 |
4.9 |
4.6 |
5.6 |
5.7 |
3.9 |
4.3 |
6.6 |
|
|
| A438xxx |
4.7 |
13.8 |
4.3 |
7.1 |
6.7 |
5.1 |
11.9 |
3.9 |
|
4.2 |
8.7 |
4.6 |
6.2 |
4.8 |
3.8 |
4.5 |
3.8 |
3.4 |
4.6 |
|
| A658xxx |
11.8 |
3.5 |
5.6 |
4.0 |
6.8 |
6.2 |
15.3 |
10.7 |
4.2 |
|
37.7 |
3.9 |
3.8 |
6.8 |
4.7 |
4.9 |
5.1 |
4.8 |
|
|
| T103xxx |
6.8 |
3.5 |
4.2 |
8.6 |
4.8 |
4.5 |
4.3 |
4.9 |
8.7 |
37.7 |
|
4.8 |
3.9 |
4.6 |
5.9 |
4.1 |
5.5 |
4.0 |
1.6 |
|
| T368xxx |
3.6 |
5.0 |
4.2 |
5.7 |
5.1 |
3.8 |
6.2 |
4.9 |
4.6 |
3.9 |
4.8 |
|
281.5 |
5.0 |
4.1 |
4.0 |
6.0 |
3.8 |
|
|
| A404xxx |
8.5 |
4.9 |
4.6 |
4.1 |
4.9 |
5.8 |
6.3 |
4.6 |
6.2 |
3.8 |
3.9 |
281.5 |
|
4.4 |
4.5 |
4.7 |
4.9 |
4.6 |
5.1 |
|
| A171xxx |
4.8 |
4.9 |
3.6 |
4.5 |
3.8 |
4.9 |
5.9 |
5.6 |
4.8 |
6.8 |
4.6 |
5.0 |
4.4 |
|
3.6 |
4.1 |
4.7 |
4.2 |
|
|
| T463xxx |
6.3 |
4.5 |
4.3 |
3.4 |
5.5 |
5.0 |
5.0 |
5.7 |
3.8 |
4.7 |
5.9 |
4.1 |
4.5 |
3.6 |
|
3.7 |
7.6 |
5.3 |
2.2 |
|
| A740xxx |
4.7 |
3.5 |
3.9 |
4.0 |
3.8 |
3.8 |
5.3 |
3.9 |
4.5 |
4.9 |
4.1 |
4.0 |
4.7 |
4.1 |
3.7 |
|
7.5 |
3.6 |
|
|
| T630xxx |
4.5 |
6.3 |
3.6 |
3.4 |
3.9 |
4.2 |
3.8 |
4.3 |
3.8 |
5.1 |
5.5 |
6.0 |
4.9 |
4.7 |
7.6 |
7.5 |
|
4.4 |
2.1 |
|
| T384xxx |
6.1 |
3.5 |
3.9 |
6.6 |
4.8 |
4.0 |
5.1 |
6.6 |
3.4 |
4.8 |
4.0 |
3.8 |
4.6 |
4.2 |
5.3 |
3.6 |
4.4 |
|
46.3 |
|
| M804xxx |
3.9 |
|
|
1.8 |
|
4.3 |
1.1 |
|
4.6 |
|
1.6 |
|
5.1 |
|
2.2 |
|
2.1 |
46.3 |
|
| Closely Related |
2nd to 4th Cousin |
4th to 6th Cousin |
| Minimum threshold
size to be included in total = 500 SNPs
Mismatch-bunching Limit = 100
SNPs
Minimum segment cM = 1.0 cM
Some values are roughly 25%
larger than given by FTDNA. |
| Largest Shared
Segment cannot be graphed as Genetic Distance.
Genetic Distance increases with time. Largest
Shared Segment decreases with time.
Also, Largest Shared Segment
is not an indication of strictly males or
females.
|
| Examples of
largest segment sizes and cousin level at HAM
Country:.
Autosomal DNA Cousin Calculator |
| HLA region on
Chromosome 6 is between 25 and 35 million base
pairs (Mb) - and is not considered to be a valid
comparison.
Chromosome 17 has an excess
IBD region between 59 and 64 Mb - and may not be
a valid comparison.
Chromosome 22 has an excess
IBD region between 16 and 25 Mb - and may not be
a valid comparison.
Reference:
Relationship Estimation from Whole-Genome
Sequence Data
|
|
I then wanted to
graph that out, so I had to invent some form of Genetic
Distance for the autosomal DNA.
For the purpose of creating a tree,
I used 100/(x) for genetic Distance, where 'x' is given in
cMs.
My threshold values were down to 1
cM, but I suppose that for less than one, I could use
100/SQRT(x)
| Genetic DIstance for Largest Shared Segment
|
| ID |
T
6
1
1
x
x
x
|
T
6
8
2
x
x
x
|
T
1
8
1
x
x
x
|
A
5
0
0
x
x
x
|
A
9
8
4
x
x
x
|
A
2
7
4
x
x
x
|
T
1
3
3
x
x
x
|
T
0
7
4
x
x
x
|
A
4
3
8
x
x
x
|
A
6
5
8
x
x
x
|
T
1
0
3
x
x
x
|
T
3
6
8
x
x
x
|
A
4
0
4
x
x
x
|
A
1
7
1
x
x
x
|
T
4
6
3
x
x
x
|
A
7
4
0
x
x
x
|
T
6
3
0
x
x
x
|
T
3
8
4
x
x
x
|
M
8
0
4
x
x
x
|
| T611xxx |
|
3 |
9 |
3 |
4 |
23 |
4 |
7 |
21 |
8 |
14 |
27 |
11 |
20 |
15 |
21 |
22 |
16 |
25 |
|
| T682xxx |
3 |
|
3 |
4 |
18 |
20 |
22 |
21 |
7 |
28 |
28 |
20 |
20 |
20 |
22 |
28 |
15 |
28 |
99 |
|
| T181xxx |
9 |
3 |
|
1 |
22 |
20 |
8 |
10 |
23 |
17 |
23 |
23 |
21 |
27 |
23 |
25 |
27 |
25 |
99 |
|
| A500xxx |
3 |
4 |
1 |
|
27 |
20 |
22 |
4 |
14 |
25 |
11 |
17 |
24 |
22 |
29 |
25 |
29 |
15 |
55 |
|
| A984xxx |
4 |
18 |
22 |
27 |
|
23 |
9 |
8 |
14 |
14 |
20 |
19 |
20 |
26 |
18 |
26 |
25 |
20 |
99 |
|
| A274xxx |
23 |
20 |
20 |
20 |
23 |
|
4 |
5 |
19 |
16 |
22 |
26 |
17 |
20 |
20 |
26 |
23 |
25 |
23 |
|
| T133xxx |
4 |
22 |
8 |
22 |
9 |
4 |
|
0 |
8 |
6 |
23 |
16 |
15 |
16 |
20 |
18 |
26 |
19 |
90 |
|
| T074xxx |
7 |
21 |
10 |
4 |
8 |
5 |
0 |
|
25 |
9 |
20 |
20 |
21 |
17 |
17 |
25 |
23 |
15 |
99 |
|
| A438xxx |
21 |
7 |
23 |
14 |
14 |
19 |
8 |
25 |
|
23 |
11 |
21 |
16 |
20 |
26 |
22 |
26 |
29 |
21 |
|
| A658xxx |
8 |
28 |
17 |
25 |
14 |
16 |
6 |
9 |
23 |
|
2 |
25 |
26 |
14 |
21 |
20 |
19 |
20 |
99 |
|
| T103xxx |
14 |
28 |
23 |
11 |
20 |
22 |
23 |
20 |
11 |
2 |
|
20 |
25 |
21 |
16 |
24 |
18 |
25 |
62 |
|
| T368xxx |
27 |
20 |
23 |
17 |
19 |
26 |
16 |
20 |
21 |
25 |
20 |
|
0 |
20 |
24 |
25 |
16 |
26 |
99 |
|
| A404xxx |
11 |
20 |
21 |
24 |
20 |
17 |
15 |
21 |
16 |
26 |
25 |
0 |
|
22 |
22 |
21 |
20 |
21 |
19 |
|
| A171xxx |
20 |
20 |
27 |
22 |
26 |
20 |
16 |
17 |
20 |
14 |
21 |
20 |
22 |
|
27 |
24 |
21 |
23 |
99 |
|
| T463xxx |
15 |
22 |
23 |
29 |
18 |
20 |
20 |
17 |
26 |
21 |
16 |
24 |
22 |
27 |
|
27 |
13 |
18 |
45 |
|
| A740xxx |
21 |
28 |
25 |
25 |
26 |
26 |
18 |
25 |
22 |
20 |
24 |
25 |
21 |
24 |
27 |
|
13 |
27 |
99 |
|
| T630xxx |
22 |
15 |
27 |
29 |
25 |
23 |
26 |
23 |
26 |
19 |
18 |
16 |
20 |
21 |
13 |
13 |
|
22 |
47 |
|
| T384xxx |
16 |
28 |
25 |
15 |
20 |
25 |
19 |
15 |
29 |
20 |
25 |
26 |
21 |
23 |
18 |
27 |
22 |
|
2 |
|
| M804xxx |
25 |
99 |
99 |
55 |
99 |
23 |
90 |
99 |
21 |
99 |
62 |
99 |
19 |
99 |
45 |
99 |
47 |
2 |
|
| Closely Related |
2nd to 4th Cousin |
4th to 6th Cousin |
| Minimum threshold
size to be included in total = 500 SNPs
Mismatch-bunching Limit = 100
SNPs
Minimum segment cM = 1.0 cM
Some values are roughly 25%
larger than given by FTDNA.
|
| Hypothetical
Genetic Distance given as:
- for Size in cMs GE 1:
(100/Size)
- for Size in cMs GT 0 and LT
1: (100/SQRT(Size))
- for Size in cMs EQ 0: set
to 99 for an arbitrary upper limit
Largest Shared Segment cannot
be graphed as Genetic Distance. Genetic Distance
increases with time. Largest Shared Segment
decreases with time.
Also, Largest Shared Segment
is not an indication of strictly males or
females.
|
| Examples of
largest segment sizes and cousin level at HAM
Country:.
Autosomal DNA Cousin Calculator |
| HLA region on
Chromosome 6 is between 25 and 35 million base
pairs (Mb) - and is not considered to be a valid
comparison.
Chromosome 17 has an excess
IBD region between 59 and 64 Mb - and may not be
a valid comparison.
Chromosome 22 has an excess
IBD region between 16 and 25 Mb - and may not be
a valid comparison.
Reference:
Relationship Estimation from Whole-Genome
Sequence Data
|
|
As usual, I used the kitsch program from Phylip to sort the
resulting tree. I removed M804xxx (Lauren), because she does not
have valid match here, even though she is related to
Lynette. Here, Lauren matches only 9 of the HAM kits, and
5 of those kits are on the HLA region of chromosome 6 (not a
valid match).
Basically, with Lauren included, the resulting tree wanted to
pull Lynette out of the Patrick County HAM group and put it
outside to Lauren's group.
So, Lauren was removed for the purposes of creating the atDNA
genetic tree for the HAM surname group.
Update March, 31. 2018: What I have found
regarding the problem with the kit for Lauren (M804xxx) is
that it's a "vendor conversion" problem at GEDMatch.
The problem has to do with SNP overlays, as I have been
informed by Andreas West. Basically, you currently can use the
"One to One' comparison utility at GEDMatch and lower the
number of SNPs to "250" when you lower the number of cMs to
'1.' That much greatly improves the comparison to the 23AndMe
vendor (kits numbered Mxxxx at GEDMatch).
One thing that the tree points out is that our NPE to the LOVIN
surname apparently came out of Amelia County, VA. We have no
Y-DNA from Amelia County, just autosomal DNA. My guess is that
his ancestor died in war and he was adopted. His line is more
recently (since 1800) from Wayne County, NC, and he doe not
match the Y-DNA of Wayne County HAM lines.
I am fairly happy with this initial tree. Even though I did
not separate out the male and female lines, the tree does
separate out the various lines in separate geographic areas.
Also the timeline suggests that my Grayson County, VA line
separated from the line in Somerset later on, and that the
Amelia County HAM line separated out earlier (As does the
Franklin County, NC HAM line).
This is not so clear from the Y-DNA, because we have no
Y-DNA participants from Amelia County, VA but we do have
autosomal DNA from Amelia County. This tree shows that our LOVIN
surname NPE should be from Amelia Co., VA.
Andrew Millard suggested that because the Genetic Distance
value of 1/cMs is not linear, I might try an exponential
equation of the form -ln(cm/7200).
That formula suggestion was tried that, and I was not real
happy with the results. The Genetic Distance did not correspond
well to cousin level, and the upper limit for data greater than
1 cM appeared to be about 8 (generations), even for the results
for Lauren Shutt (M804xxx).
Andrew had also suggested that I do not use kitsch, but I have
not yet found different program that works with Genetic
Distance.
So, here, I have used the equation for the half life decay
rate, typically used in radioactive decay under the presumption
that we are looking at Half Identical Regions (HIRs). The
results mostly returned the expected cousin level (or number of
generations).
Hypothetical Genetic Distance derived from
half life decay rate:
Nt = No*e^kt
Solvng for t, Hypothetical Genetic
Distance given as:
t = -1*ln(cMs*0035524)/0.693147
- where "ln" is the natural log
function
Largest segment (i.e., most obvious) for mother/son or
parental half life calculations (for size) is:
a = 1/281.5 cMs = 0.0035524
and for parent/child half life decay:
k = ln(N0/Nt) = ln(1/2) = 0.693147
Below is a description of the half life decay
rate calculations, and the resulting phylogenetic tree.
| Exponential
Decay for Largest Shared Segment |
| ID |
T
0
7
4
x
x
x
|
T
1
3
3
x
x
x
|
A
2
7
4
x
x
x
|
A
9
8
4
x
x
x
|
T
6
1
1
x
x
x
|
T
6
8
2
x
x
x
|
T
1
8
1
x
x
x
|
A
5
0
0
x
x
x
|
A
4
3
8
x
x
x
|
T
1
0
3
x
x
x
|
A
6
5
8
x
x
x
|
T
4
6
3
x
x
x
|
T
3
8
4
x
x
x
|
A
1
7
1
x
x
x
|
T
3
6
8
x
x
x
|
A
4
0
4
x
x
x
|
A
7
4
0
x
x
x
|
T
6
3
0
x
x
x
|
M
8
0
4
x
x
x
|
| T074xxx |
|
2.2 |
3.9 |
5.4 |
4.8 |
6.6 |
6.2 |
4.0 |
6.8 |
7.8 |
5.1 |
5.8 |
5.7 |
5.9 |
6.4 |
6.9 |
6.9 |
6.3 |
99 |
|
| T133xxx |
2.2 |
|
3.5 |
4.9 |
3.8 |
7.2 |
6.0 |
6.3 |
5.9 |
6.3 |
5.1 |
6.8 |
5.9 |
5.8 |
5.3 |
6.0 |
6.9 |
6.9 |
11.2 |
|
| A274xxx |
3.9 |
3.5 |
|
6.5 |
6.6 |
6.2 |
6.7 |
6.7 |
5.9 |
7.3 |
5.8 |
6.8 |
6.6 |
6.4 |
7.1 |
5.4 |
6.8 |
6.9 |
6.3 |
|
| A984xxx |
5.4 |
4.9 |
6.5 |
|
4.1 |
5.7 |
6.5 |
6.8 |
5.2 |
6.3 |
5.2 |
6.6 |
6.5 |
6.9 |
6.7 |
6.8 |
6.8 |
6.6 |
99 |
|
| T611xxx |
4.8 |
3.8 |
6.6 |
4.1 |
|
4.6 |
5.5 |
4.6 |
6.1 |
5.0 |
5.4 |
5.4 |
5.7 |
6.8 |
7.2 |
6.0 |
6.2 |
6.9 |
7.1 |
|
| T682xxx |
6.6 |
7.2 |
6.2 |
5.7 |
4.6 |
|
4.5 |
4.6 |
4.9 |
7.4 |
7.2 |
6.4 |
6.9 |
6.1 |
6.6 |
6.6 |
7.1 |
5.2 |
99 |
|
| T181xxx |
6.2 |
6.0 |
6.7 |
6.5 |
5.5 |
4.5 |
|
3.4 |
6.8 |
6.4 |
5.7 |
6.7 |
6.6 |
7.2 |
6.7 |
6.2 |
7.8 |
7.1 |
99 |
|
| A500xxx |
4.0 |
6.3 |
6.7 |
6.8 |
4.6 |
4.6 |
3.4 |
|
5.6 |
5.5 |
6.8 |
7.8 |
5.4 |
6.6 |
5.5 |
6.6 |
7.1 |
10.5 |
10.3 |
|
| A438xxx |
6.8 |
5.9 |
5.9 |
5.2 |
6.1 |
4.9 |
6.8 |
5.6 |
|
5.1 |
6.3 |
7.4 |
7.1 |
6.3 |
6.9 |
6.4 |
6.2 |
6.7 |
6.4 |
|
| T103xxx |
7.8 |
6.3 |
7.3 |
6.3 |
5.0 |
7.4 |
6.4 |
5.5 |
5.1 |
|
3.9 |
5.3 |
6.8 |
6.5 |
6.2 |
7.5 |
6.8 |
6.5 |
10.5 |
|
| A658xxx |
5.1 |
5.1 |
5.8 |
5.2 |
5.4 |
7.2 |
5.7 |
6.8 |
6.3 |
3.9 |
|
6.1 |
6.5 |
5.9 |
6.8 |
6.9 |
6.9 |
6.1 |
99 |
|
| T463xxx |
5.8 |
6.8 |
6.8 |
6.6 |
5.4 |
6.4 |
6.7 |
7.8 |
7.4 |
5.3 |
6.1 |
|
5.9 |
6.9 |
7.3 |
7.3 |
7.0 |
5.5 |
9.5 |
|
| T384xxx |
5.7 |
5.9 |
6.6 |
6.5 |
5.7 |
6.9 |
6.6 |
5.4 |
7.1 |
6.8 |
6.5 |
5.9 |
|
7.5 |
6.7 |
6.3 |
7.0 |
6.3 |
2.7 |
|
| A171xxx |
5.9 |
5.8 |
6.4 |
6.9 |
6.8 |
6.1 |
7.2 |
6.6 |
6.3 |
6.5 |
5.9 |
6.9 |
7.5 |
|
6.2 |
7.1 |
6.4 |
6.3 |
99 |
|
| T368xxx |
6.4 |
5.3 |
7.1 |
6.7 |
7.2 |
6.6 |
6.7 |
5.5 |
6.9 |
6.2 |
6.8 |
7.3 |
6.7 |
6.2 |
|
1.0 |
6.9 |
6.1 |
99 |
|
| A404xxx |
6.9 |
6.0 |
5.4 |
6.8 |
6.0 |
6.6 |
6.2 |
6.6 |
6.4 |
7.5 |
6.9 |
7.3 |
6.3 |
7.1 |
1.0 |
|
6.0 |
6.1 |
5.9 |
|
| A740xxx |
6.9 |
6.9 |
6.8 |
6.8 |
6.2 |
7.1 |
7.8 |
7.1 |
6.2 |
6.8 |
6.9 |
7.0 |
7.0 |
6.4 |
6.9 |
6.0 |
|
5.1 |
99 |
|
| T630xxx |
6.3 |
6.9 |
6.9 |
6.6 |
6.9 |
5.2 |
7.1 |
10.5 |
6.7 |
6.5 |
6.1 |
5.5 |
6.3 |
6.3 |
6.1 |
6.1 |
5.1 |
|
9.8 |
|
| M804xxx |
99 |
11.2 |
6.3 |
99 |
7.1 |
99 |
99 |
10.3 |
6.4 |
10.5 |
99 |
9.5 |
2.7 |
99 |
99 |
5.9 |
99 |
9.8 |
|
| Closely
Related |
2nd
to 4th Cousin |
4th
to 6th Cousin |
| Minimum threshold size to be included
in total = 500 SNPs
Mismatch-bunching Limit = 100 SNPs
Minimum segment cM = 1.0 cM
Some values are roughly 25% larger than given by
FTDNA.
|
| Largest Shared Segment cannot be
graphed as Genetic Distance. Genetic Distance
increases with time. Largest Shared Segment
decreases with time.
Also, Largest Shared Segment is not an indication
of strictly males or females.
Hypothetical Genetic Distance derived from half
life decay rate:
Nt = No*e^kt
Solvng for t, Hypothetical Genetic Distance
given as:
t = -1*ln(cMs*0035524)/0.693147
where largest segment (i.e., most obvious) for
mother/son or parental half life calculations (for
size) is:
a = 1/281.5 cMs = 0.0035524
and for parent/child half life decay:
k = ln(N0/Nt) = ln(1/2) = 0.693147
which can be used if you have mapped out the
segment in question.
However, here we are searching for the segment
to be mapped out, and the relationship is not
always clear. We are using the largest segment as
being the most obvious, but due to endogamy, we do
not yet know if the largest segment is
appropriate. Therefore, if endogamy is present,
the largest segment may not be the segment that we
had expected. So, I have introduced an endogamy
correction factor, just for the purpose of
discovery.
- Endogamy correction factor: [(100*cMs)/SNPs]
t = -1*ln[(cMs*0035524*100*cMs)/SNPs]/0.693147
- for Size in cMs and number of SNPs
- for Size in cMs EQ 0: set to 99 for an
arbitrary upper limit
The endogamy corrction factor is only intended
to be used for estimating the expected
relationship. The equation without the endogamy
correction factor should be used if the
relationship is already mapped out properly.
|
Half Life Equation for use with a
spreadsheet: HAM
DNA Half Life Equation
Examples of largest segment sizes and cousin level
at HAM Country and my search for an equation:. Autosomal
DNA Cousin Calculator |
| HLA region on Chromosome 6 is between
25 and 35 million base pairs (Mb) - and is not
considered to be a valid comparison.
Chromosome 1 has an excess IBD region between
118 and 153 Mb - and may not be a valid
comparison.
Chromosome 2 has an excess IBD region between 85
and 99 Mb - and may not be a valid comparison.
Chromosome 2 has an excess IBD region between
132 and 141 Mb - and may not be a valid
comparison.
Chromosome 2 has an excess IBD region between
192 and 198 Mb - and may not be a valid
comparison.
Chromosome 6 has an HLA region between 25 and 35
Mb - and may not be a valid comparison.
Chromosome 8 has an excess IBD region between 10
and 13 Mb - and may not be a valid comparison.
Chromosome 9 has an excess IBD region between 38
and 72 Mb - and may not be a valid comparison.
Chromosome 10 has an excess IBD region between
44 and 53 Mb - and may not be a valid comparison.
Chromosome 15 has an excess IBD region between
20 and 25 Mb - and may not be a valid comparison.
Chromosome 15 has an excess IBD region between
27 and 30 Mb - and may not be a valid comparison.
Chromosome 16 has an excess IBD region between
19 and 24 Mb - and may not be a valid comparison.
Chromosome 17 has an excess IBD region between
59 and 64 Mb - and may not be a valid comparison.
Chromosome 17 has an excess IBD region between
77 and 78 Mb - and may not be a valid comparison.
Chromosome 21 has an excess IBD region between
16 and 19 Mb - and may not be a valid comparison.
Chromosome 22 has an excess IBD region between
16 and 25 Mb - and may not be a valid comparison.
Reference:
Relationship Estimation from Whole-Genome
Sequence Data
|
|
For my data, the resulting sizes given
by the decay rate are about what is expected for the cousin
level, or number of generations.
Personally I am aware of some of the endogamy, and that
the largest segment is not always the segment that we have an
interest in (to trace the HAM male lineage). Otherwise, Excess
IBD regions have not yet been removed from these tables.
The resulting half life decay rate tree moves the LOVIN NPE more
toward the Patrick County, VA line whereas the previous tree
(above) had him closer to Amelia County, VA. This exponential
decay tree appears to separate out the sons of William HAM, Sr.
better than the previous tree (GD=1/cMs, above), and also breaks
up the LINEBERRY female autosomal DNA.
Finally, the gap or Genetic Distance from Jon of Somerset
appears to be much closer, and the upper limit for a 1 cMs
segment for this data appears to be at around 11th cousin (using
the endogamy factor). Genetic Distance for Jon of Somerset now
appears to be around 6th or 7th cousin.
My thoughts are that it would be useful to concatenate the trees
by using the genetic distance of each segment, not just the
largest segment. Concatenating the trees may also be useful for
the triad
study as well.
Notes:
If you wand the mouse over the tables, it should show the shared chromosome and location. For example, a wand over of the horizontal for
A274xxx (Roxanne) and her largest segment for T133xxx (Mary Ann ), it shows the largest shared segment to be:
Chr Start Location End Location Centimorgans (cM)
12 123,996,713 130,079,716 24.2
Moving the mouse to the right for A274xxx (Roxanne) andT074xxx (Wendell ) it shows the largest shared segment to be:
Chr Start Location End Location Centimorgans (cM)
12 123,996,713 128,587,277 18.1
Which is pretty much the same segment, meaning that Roxanne, Mary Ann, and Wendell share the same largest tiny segment from the same ancestor.
The idea is to figure out which ancestor is at that location on that chromosome.
More importantly for the group, the largest shared segments to Jon of Somerset can be seen by wanding over the values for Jon (A171xxx).
For the current group, that should give us something like this:
Chr Start Location End Location cMs SNPs
M804xxx A171xxx (no results)
A274xxx A171xxx 1 160,250,821 162,571,709 4.9 709
T384xxx A171xxx 1 182,770,426 189,420,715 4.2 1,145
A404xxx A171xxx 2 192,671,921 199,153,199 4.4 923
A658xxx A171xxx 2 128,826,835 133,892,598 6.8 972
T368xxx A171xxx 3 149,237,723 151,910,260 5.0 656
A500xxx A171xxx 5 149,006,726 150,972,778 4.5 682
T630xxx A171xxx 5 15,419,156 18,178,723 4.7 598
T181xxx A171xxx 6 154,506,891 156,712,811 3.6 663
A171xxx F47412 7 71,024,792 76,755,130 5.0 621
T133xxx A171xxx 8 137,114,169 139,806,479 5.9 706
T611xxx A171xxx 8 50,226,545 55,406,314 4.8 893
T463xxx A171xxx 9 2,706,921 4,167,109 3.6 540
A740xxx A171xxx 13 19,948,575 21,637,260 4.1 517
T074xxx A171xxx 13 24,622,475 26,808,122 5.6 663
T103xxx A171xxx 15 96,947,636 99,124,055 4.6 696
T682xxx A171xxx 15 98,242,381 99,754,243 4.9 582
A984xxx A171xxx 17 50,189,302 52,179,232 3.8 594
A438xxx A171xxx 18 13,544,095 19,922,062 4.8 662
Group Contact information for the HAM Surname
DNA Project Participants
---------------------------------------------------------------------------------------------------
HAM Y-DNA Group #1:
Contact Dave Hamm for further contact information.
Dave Hamm odoniv (at)
yahoo.com
---------------------------------------------------------------------------------------------------
ANCESTRY:
A171xxx 413276 Jon of Somerset
A274xxx Roxanne of the Ashe County, NC line HAM line
A404xxx Jamison relates to Sintha HAM, daughter of Jordan
HAM of Patrick County, VA.
The documentation
implies Jamison is Lynette's 4th cousin (T384xxx via a female)
Jamison is the son
of C_Godby (T368xxx)
A438xxx Robin relates to Roxanne via the HAM line Ashe County, NC
A500xxx Joan D. C., relates to Cindy Q. of the Grayson County, VA
line via a female LINEBERRY.
A658xxx Nancy descends from Isaac HAM (1825-1908), Ashe County, NC
The son of John HAM
(1780-1850) and Sarah LANDRETH.
She relates to Jimmy (T103xxx) as 3rd cousin via
John Alley HAM.
Nancy relates to Mary
Ann (T133xxx) as 4th cousin, twice removed.
Nancy relates to
Wendell (T074xxx) as 5th cousins, once removed.
Nancy relates to Dave
(T611xxx) as 5th cousin, once removed.
A740xxx Martha Jane descends from the orphans of John Hamm
in Rowan
County, NC (1779),
supposedly in Rowan Co. & later Iredell Co.
before moving to TN in
the 1870s. Connection to Group #1 is UNKNOWN
A984xxx Cindy Q. of Grayson Co, VA via Dave Hamm's LINEBERRY
line.
of Grayson County, VA.
We should expect matches to be female.
She is listed as Cindy
(A.) at FTDNA
She is listed as Cindy
(Q.) at Ancestry
-----------------------------------------------------------
M804xxx Lauren - related to Lynette, her father descends
from the Ham lines via Bernard Blaine Shutt m. Allene Ray Wagner
> Nora Ellen Bowman
m. Nelson Edward Shutt
> Martha Ann Ham m.
Peter "Babe" Bowman
> William Jordan Ham
m. Columbia McMillan
> William Ham m.
Martha (?).
FTDNA:
-----------------------------------------------------------
T842xxx FTDNA kit 47412 Arnold (Control Group, Wayne Co., NC
Group #4)
-----------------------------------------------------------
T074xxx FTDNA kit 214726 Wendell is nephew to Mary Ann and 5th cousin to
Dave (kit T611xxx)
Wendell descends twice via Thomas HAM of Ashe Co., NC (1795-1865).
Wendell is nephew to Mary Ann
Wendell is 5th cousin, once removed to Nancy (A658xxx)
Wendell is 5th
cousin to Dave (kit T611xxx)
T103xxx 478168 Jimmy descends from John Ham of Grayson County, VA
(1780-1850) - son of William HAM, Sr.
Jimmy relates to Nancy (A658xxx) as 3rd cousin via John Alley HAM.
Jimmy and Dave (T611xxx) are 5th cousin once removed.
T133xxx F245261 Mary Ann
Mary Ann descends twice via Thomas HAM (1795-1865) of Ashe Co.,
NC.
Mary Ann is aunt to Wendell
(T074xxx)
Mary Ann and Nancy (A658xxx) are 4th cousin, twice removed.
Mary Ann is 4th cousin, once removed to Dave (kit T611xxx)
T181xxx Y-DNA kit #21554 Todd
T368xxx F321643 C_Godby - C. would be the mother
of Jamison (A404xxx).
Documentation indicates that C. is related to Lynette (T384xxx)
via Sintha HAM 4th cousin, 2R Patrick County, VA
T384xxx F414920 Lynette is 1st cousin to Michael, kit #212352 in
HAM DNA Group #1 Lynette descends from
William Ham b. abt 1780 d abt 1860 Patrick County, VA
Jamison (A404xxx) is
Lynette's 4th cousin (via a female)
T463xxx F300269 Ramsey - Ramsey looking for his VA connection
during
the 1700's. His line has been from Wayne Co., NC.
T611xxx F40777 Dave Hamm of the Ashe County, NC HAM line
Dave Hamm odoniv (at) yahoo.com
T630xxx F475840 Linda, Pittsylvania & Amelia Co., VA
T682xxx F226396 Deborah Michelle (Debb P.), the HAM line out
of Washington County, VA. Her uncle is Carl, Y-DNA Kit #226942.
Updates:
Mar 31, 2018:
Additional information regarding 23AndMe vendor conversion
problems at GEDMatch
Added additional list of Excess IBD regions
Removed some last names and pseudo emails in an effort to
improve GDPR compliance.
References:
HAM
Group #1 Information
HAM
Y-DNA Project Phylogenetic Tree
HAM
DNA Half Life Equation
HAM
Group #1 Initial Tiny Autosomal Segment Triad Study
HAM
DNA Project Dean McGee's Utility output
HAM
DNA Project Y-DNA Results at HAM Country
HAM
DNA Project at FTDNA
How to Read HAM DNA Phylograms
(video)
Back to
HAM Country