I have updated the FAQ list in areas that deal with Mathematica's production of
the dated phylogenetic tree. Some conclusions about what the program does, its
comparison with the RCC matrix, and how it groups testees on the tree are given,
with some statistics about the positioning of testees on the tree.

The web site is the same, and if there are future updates, the URL will remain
the same but the date at the end will be changed.

Again, the URL is:  http://mysite.verizon.net/weh8/FAQ.pdf

- Bye from Bill Howard

The announcement that was just sent out was an error.  I apologize.  I
apparently let my automatic calender run to far.  There is no meeting in July,
August, or September.  Hope to see you in October.

For those that might be interested, Colleen Fitzpatrick, the forensic
genealogist, will be at Bull Run Library on September 17.  She is
sponsored by RELIC, the local history library.  Their description is
provide in the attached and in the following source:

*http://www.pwcgov.org/library/relic/PDF/relic_programs/Aug%20%20Sept%20%202011.\
pdf*



--
====================
J. J. (Jim) Logan
Group Administrator, J-mtDNA and Logan DNA Projects at FTDNA
Owner/Moderator, J-mtDNA and GenGen-NV Discussion Groups on Yahoo
===================================================================

DYS 464 could have additional copies other then the standard 4.  Does anyone
know how the genetic distances is computed when comparing two persons with
different number of copies on this marker?  Also in John F. Chandler's
"Estimating Per-Locus Mutation Rates", does anyone know how he handled the
mutation rate for extra copies on DYS 464?

Thanks,

Sidney Sachs

Hi, Jim,

How about sending me your 104 unsorted Y-DNA haplotypes and I will run my RCC
correlation procedure to produce the RCC matrix as well as a time-calibrated
phylogenetic tree?
Then we can compare the results and the group can discuss the differences we
find and possible reasons for those differences.
This will be an interesting exercise if you are willing to do it.

Ideally I would like to get the haplotypes ASAP in an Excel spreadsheet with the
following format, but if it is too much for you to do, I will try to do it
myself.

Put Kit No in Column A
Put any other indicator in Column B - your choice
Put haplotype strings in Columns C to AM
Other than Cols A and B, leave rows 1 and 2 blank
Insert testee results in rows down the page. The order of the haplotypes does
not matter.
Insert your 104 testee results, row by row. (My approach can handle at least
five time more than this)
Don't enter rows that are not haplotypes
The columns to the right of Column  AM are not used by my program. You can
further identify the haplotypes by inserting other information there -- country
of ancestor, haplotype or group, your running identification, comments, etc.
Send only 37 markers, in the same order as FTDNA reports them.
Please also check and be sure that the values in the DYS column 389ii are in the
high range, not the lower values that are sometimes reported.

This promises to be a very interesting comparison.

Thanks,

- Bye from Bill Howard

Jim has kindly sent me his set of haplogroups and I am working on it now.
I think his analysis, combined with mine, will allow us to do a very good
comparison.
I am particularly interested in comparing our trees. They will be different
because of our different approach, but we may gain some valuable insight from
the comparison.
- Bye from Bill Howard

Hi, Jim,

Thanks for sending me your 100+ Logan haplotypes.
I have analyzed them in an RCC time-sliced matrix, in a time-calibrated
phylogenetic tree, and have analyzed the junction points on the tree to estimate
the time when your various Logan family groups (which I call clusters) shared a
most recent common ancestor.

You can find a narrated 12 minute movie entitled "Evolution of Y-DNA Haplotypes
Using RCC Correlation Technique" which shows the results at the following web
site:

http://gallery.me.com/weh8/100550

(The first frame lasts for a longer time but it includes my narration, so turn
the volume up).
The movie requires QuickTime to be on your computer, but it has been checked out
on both PCs and Macs.

I hope we will be able to compare our analyses at the SIG meeting on Wednesday,
since they were both done independently. I am hoping that the differences will
give us some insight into the way we are doing the analysis.

- Bye from Bill Howard

This note is written for readers who are interested in the details of how
pedigrees and Y-DNA results can be made to work together to yield vastly more
complete information than either approach can give alone. We now have an
approach that can compare pedigrees with clusters on the tree. Moreover, both
pedigrees and trees now have compatible time scales.

As part of my study of haplotypes and how they can be used to form dated
phylogenetic trees, I recently concentrated on two clusters of Hamiltons, one
called Hamilton A and the other called Hamilton B. My Maymore Hamilton line is
among those in Hamilton B. The Hamilton B lines connect through both pedigrees
and Y-DNA to Scottish royalty around the time of James I of Scotland. You can
read about this fascinating pedigree line, complete with its non-paternal event
at: http://dl.dropbox.com/u/59120192/HamiltonBHistory.pdf
and the note (just below) contains the URL that ties the pedigrees to the tree.

I belong to a Hamilton chat room and I recently sent to their members the
following notice about the phylogenetic tree containing Hamilton As and Bs. Here
is the note I sent:
--------------------------------------------------------------------------------\
----------------------------
There has been considerable discussion recently about the genetic relationship
between the Hamilton A and B groups. Here is a brief discussion of what I have
found. First, open the phylogenetic tree located at:
http://dl.dropbox.com/u/59120192/HamiltonTree.pdf
The tree contains Kit Numbers vertically on the right, along the time line RCC=0
which is about 1945 CE. The RCC time scale is at the bottom of the chart and
time increases to the left so that 10 RCC is about 433 years. My application
program uses 37 marker haplotypes to place the testee results on the tree, and
it optimizes the positions of the testees on the tree. Just to the right of the
Kit Number is the Hamilton Group designation. A and B are Hamilton A and B. You
will note that the program has separated the A group into subclusters A1 and A2.
These subclusters, as well as A and B, are well-separated from each other on the
tree. The designation AR shows where the haplotypes of the Group A Robertsons
fit on the tree. They are quite mixed among the Hamilton A; some are listed
among the A1 sub-clustering and some are among the A2 sub-clustering. The A1
subcluster tends to group near the bottom of the tree, although some appear
mixed among the A2 group. While the AR group is scattered, you can see a
grouping of 6 or 7 of them among the A1 subcluster at the bottom of the tree.
Now, what about the time relationships? We now look at the junction points on
the tree. Those junction points show where mutations have caused evolutionary
branching from the progenitors down to today's testees.
The B group shows
little, if any, sub-clustering. But there appear to be groups of B that are
probably related by pedigree because they are within an RCC of 5-10. There are
about 4-5 of these groups in B that probably tie together with pedigrees. The
most recent common ancestor (MRCA) of most of the Bs is at RCC ~ 8, but then
other MRCAs show up at RCC ~ 12 (the lower half of the B are tied with the
middle B at that point). The MRCA of all the B group is at RCC ~ 22 (an
estimated 950 years ago). Then the MRCA of the B group AND the A group is
estimated to be at RCC ~ 66 (2850 years ago, or about 2850-1945=900
BC).
Similarly, the MRCA of the A1 and A2 groups is located at about RCC ~
10 (430 years ago) with the CA of the A2 group at RCC ~ 18-23 and the CA of the
A1 group at RCC ~ 10.
In the papers I have written in which pedigrees are
compared with the clusters on the phylogenetic tree, there is virtually a
one-to-one correspondence between each cluster and the pedigrees of their
cluster members. Note, however, that mutations still cause uncertainties in the
placements on the tree, particularly when single pairs are compared. But the
overall form of the tree should match reality pretty well. Individual
uncertainties amount to a standard deviation of RCC=3 or less. Statistically,
out of 100 placements one might expect a couple of testee pairings to be off by
an RCC of about 9.
I invite the testees and Gordon Hamilton to comment on these clusters and
pedigree groupings. 

- Bye from Bill Howard (Hamilton B line, with Tom Hamilton, Kit No. 111729, my
2d cousin, once removed, as my tie to this group.
--------------------------------------------------------------------------------\
----------------------------
Gordon Hamilton is the Hamilton surname administrator. You can view his Hamilton
website at the following URL:
http://www.personal.psu.edu/faculty/g/a/gah4/HamDNA/H1.html
This is one of the very best web sites I have seen that deals with this topic.
It investigates various Hamilton pedigree lines and haplogroups analyzing the
differences in marker values in detail. My investigation of the Hamilton A and B
lines treats only those lines. This web site extends the analysis to additional
lines in different haplogroups. I commend this site to you. It's an excellent
tutorial. Gordon Hamilton responded to my note in the Hamilton Clan chat room.
Here is his commentary of my analysis and the Hamilton A and B phylogenetic
tree.
--------------------------------------------------------------------------------\
----------------------------
Bill:


Your analysis of results for Groups A and B certainly indicates that they
separated some time back as expected from the differences in the STR values.
Your time to a most recent common ancestor for the two groups of about 3000
years is similar to what others have estimated as well.
Turning specifically to the Group A results first, the two outliers at the
beginning (kits 46116 and 9248) are almost certainly due to RecLOH** events in
each of their lines. Participant H-123 (46116) is known to be closely related to
H-046 (15116), and participant H-014 (9248) is known to be closely related to
H-054 (19325). You will note that 15116 and 19325 are far removed from their
close relatives in your phylogenetic tree as one would expect if a RecLOH event
occurred in the two lines. What this is really telling us is that the results
for the two outliers (46116 an 9248) should be ignored. This then gives a tree
for Group A which looks reasonable with the most recent common ancestor for this
group living about 17 RCC or about 730 years ago. Since we believe that those in
Group A are derived from Walter Fitzgilbert who was born about 1270, this number
is almost too good to be true. However, it is certainly consistent with our
earlier conclusions.
As indicated on our web site, the separation of Group A into two tables, A1 and
A2, is fairly arbitrary; attempts were made to cluster those with similar STR
results close to one another. Your finding that the A1 and A2 results separate
to some extent is therefore consistent with that.
Turning to the Group B results, the first three results (14095, 21774, and
18060) are clearly outliers but for these I do not have a good explanation for
why this should be the case. I note that in two of these cases (14095 and 21774)
the value for one of the STR sites (CDYb) is off by two (35) from the modal
(37). Possibly your program does not allow for the possibility that this
difference may be due to only one mutation event. The other outlier (18060) is
known to be closely related to H-053) which has two less mutations so maybe
something unusual happened in the case of 18060. In any event I would tend to
ignore the three outliers, in which case the rest of the tree looks reasonable
with a most recent common ancestor of about 12 RCC or about 520 years. Again
this is not too far off from what is expected if all of Group B, as we suspect,
is derived from one man (James1) who lived about 1400.
As you imply, one should not put too much emphasis on the exact position of each
person in your tree but overall the trees look reasonable with the foregoing
caveats.
-- Gordon (H-003, Group B)
--------------------------------------------------------------------------------\
----------------------------
**  A good description of what is meant by the term RecLOH can be found at:
http://www.dna-fingerprint.com/modules.php?op=modload&name=Sections&file=index&r\
eq=viewarticle&artid=9
--------------------------------------------------------------------------------\
----------------------------
I would appreciate any comments that our chat room may have on this work and
these exchanges.  – Bye from Bill Howard

 

This note is written for readers who are interested in the details of how pedigrees and Y-DNA results can be made to work together to yield vastly more complete information than either approach can give alone. We now have an approach that can compare pedigrees with clusters on the tree. Moreover, both pedigrees and trees now have compatible time scales.

As part of my study of haplotypes and how they can be used to form dated phylogenetic trees, I recently concentrated on two clusters of Hamiltons, one called Hamilton A and the other called Hamilton B. My Maymore Hamilton line is among those in Hamilton B. The Hamilton B lines connect through both pedigrees and Y-DNA to Scottish royalty around the time of James I of Scotland. You can read about this fascinating pedigree line, complete with its non-paternal event at: http://dl.dropbox.com/u/59120192/HamiltonBHistory.pdf
and the note (just below) contains the URL that ties the pedigrees to the tree.

I belong to a Hamilton chat room and I recently sent to their members the following notice about the phylogenetic tree containing Hamilton As and Bs. Here is the note I sent:
----------------------------------------------------------
There has been considerable discussion recently about the genetic relationship between the Hamilton A and B groups. Here is a brief discussion of what I have found. First, open the phylogenetic tree located at:
http://dl.dropbox.com/u/59120192/HamiltonTree.pdf
The tree contains Kit Numbers vertically on the right, along the time line RCC=0 which is about 1945 CE. The RCC time scale is at the bottom of the chart and time increases to the left so that 10 RCC is about 433 years. My application program uses 37 marker haplotypes to place the testee results on the tree, and it optimizes the positions of the testees on the tree. Just to the right of the Kit Number is the Hamilton Group designation. A and B are Hamilton A and B. You will note that the program has separated the A group into subclusters A1 and A2. These subclusters, as well as A and B, are well-separated from each other on the tree. The designation AR shows where the haplotypes of the Group A Robertsons fit on the tree. They are quite mixed among the Hamilton A; some are listed among the A1 sub-clustering and some are among the A2 sub-clustering. The A1 subcluster tends to group near the bottom of the tree, although some appear mixed among the A2 group. While the AR group is scattered, you can see a grouping of 6 or 7 of them among the A1 subcluster at the bottom of the tree.
Now, what about the time relationships? We now look at the junction points on the tree. Those junction points show where mutations have caused evolutionary branching from the progenitors down to today's testees.
The B group shows little, if any, sub-clustering. But there appear to be groups of B that are probably related by pedigree because they are within an RCC of 5-10. There are about 4-5 of these groups in B that probably tie together with pedigrees. The most recent common ancestor (MRCA) of most of the Bs is at RCC ~ 8, but then other MRCAs show up at RCC ~ 12 (the lower half of the B are tied with the middle B at that point). The MRCA of all the B group is at RCC ~ 22 (an estimated 950 years ago). Then the MRCA of the B group AND the A group is estimated to be at RCC ~ 66 (2850 years ago, or about 2850-1945=900 BC).
Similarly, the MRCA of the A1 and A2 groups is located at about RCC ~ 10 (430 years ago) with the CA of the A2 group at RCC ~ 18-23 and the CA of the A1 group at RCC ~ 10.
In the papers I have written in which pedigrees are compared with the clusters on the phylogenetic tree, there is virtually a one-to-one correspondence between each cluster and the pedigrees of their cluster members. Note, however, that mutations still cause uncertainties in the placements on the tree, particularly when single pairs are compared. But the overall form of the tree should match reality pretty well. Individual uncertainties amount to a standard deviation of RCC=3 or less. Statistically, out of 100 placements one might expect a couple of testee pairings to be off by an RCC of about 9.
I invite the testees and Gordon Hamilton to comment on these clusters and pedigree groupings. 

- Bye from Bill Howard (Hamilton B line, with Tom Hamilton, Kit No. 111729, my 2d cousin, once removed, as my tie to this group.
----------------------------------------------------------
Gordon Hamilton is the Hamilton surname administrator. You can view his Hamilton website at the following URL:
http://www.personal.psu.edu/faculty/g/a/gah4/HamDNA/H1.html
This is one of the very best web sites I have seen that deals with this topic. It investigates various Hamilton pedigree lines and haplogroups analyzing the differences in marker values in detail. My investigation of the Hamilton A and B lines treats only those lines. This web site extends the analysis to additional lines in different haplogroups. I commend this site to you. It's an excellent tutorial. Gordon Hamilton responded to my note in the Hamilton Clan chat room. Here is his commentary of my analysis and the Hamilton A and B phylogenetic tree.
----------------------------------------------------------
Bill:


Your analysis of results for Groups A and B certainly indicates that they separated some time back as expected from the differences in the STR values. Your time to a most recent common ancestor for the two groups of about 3000 years is similar to what others have estimated as well.
Turning specifically to the Group A results first, the two outliers at the beginning (kits 46116 and 9248) are almost certainly due to RecLOH** events in each of their lines. Participant H-123 (46116) is known to be closely related to H-046 (15116), and participant H-014 (9248) is known to be closely related to H-054 (19325). You will note that 15116 and 19325 are far removed from their close relatives in your phylogenetic tree as one would expect if a RecLOH event occurred in the two lines. What this is really telling us is that the results for the two outliers (46116 an 9248) should be ignored. This then gives a tree for Group A which looks reasonable with the most recent common ancestor for this group living about 17 RCC or about 730 years ago. Since we believe that those in Group A are derived from Walter Fitzgilbert who was born about 1270, this number is almost too good to be true. However, it is certainly consistent with our earlier conclusions.
As indicated on our web site, the separation of Group A into two tables, A1 and A2, is fairly arbitrary; attempts were made to cluster those with similar STR results close to one another. Your finding that the A1 and A2 results separate to some extent is therefore consistent with that.
Turning to the Group B results, the first three results (14095, 21774, and 18060) are clearly outliers but for these I do not have a good explanation for why this should be the case. I note that in two of these cases (14095 and 21774) the value for one of the STR sites (CDYb) is off by two (35) from the modal (37). Possibly your program does not allow for the possibility that this difference may be due to only one mutation event. The other outlier (18060) is known to be closely related to H-053) which has two less mutations so maybe something unusual happened in the case of 18060. In any event I would tend to ignore the three outliers, in which case the rest of the tree looks reasonable with a most recent common ancestor of about 12 RCC or about 520 years. Again this is not too far off from what is expected if all of Group B, as we suspect, is derived from one man (James1) who lived about 1400.
As you imply, one should not put too much emphasis on the exact position of each person in your tree but overall the trees look reasonable with the foregoing caveats.
-- Gordon (H-003, Group B)
----------------------------------------------------------
** A good description of what is meant by the term RecLOH can be found at:
http://www.dna-fingerprint.com/modules.php?op=modload&name=Sections&file=index&req=viewarticle&artid=9
----------------------------------------------------------
I would appreciate any comments that our chat room may have on this work and these exchanges. – Bye from Bill Howard