Thursday, November 27, 2008

Journal of Genetic Genealogy

Fall Issue of the Journal of Genetic Genealogy


A few good articles in this season's edition of the Journal of Genetic Genealogy.

Those of you who are familiar with the DNA testing might recognize Whit Athey's name, he was the one to create the "Haplotype Predictor" (link found in the HAM Country DNA Tools area). Whit is the main editor of this "Journal of Genetic Genealogy."

Mentioned this month in JoGG is an interview with John Butler. You folks may not recognize him, but I had written him when I was first developing my program "ft2dna." John Butler is with NIST, the National Institute of Standards and Technology.

NIST keeps a catalog of Y-STR standards on their web site. I was converting FTDNA numbers into "ATGC" format a few years back, and many of the Y-STR markers were not yet posted to the internet. I wrote John Butler about it, and he was able to post the standards for all of the first 37 Y-STR markers tested from FTDNA. So, thanks to John Butler, I was able to complete the "ft2dna" program. (It is found in the "Tools" area of HAM Country).

Which, of course I used in the Lamarc mutation rate study for HAM DNA Group #2. (The bottom link on the main DNA Project page at HAM Country).

Funny thing, this past week I have been working on improvements to my "ft2dna" program, so that I can automate some of the work involved in running Lamarc (or PHYLIP) against our DNA groups. I have automated the "ft2dna" program sufficiently to generate a Genetic Distance chart of our entire project, as well as generate ATGC format for the entire HAM DNA Project these days. However, I have a number of bug fixes yet to complete, and I want to have the "ft2dna" program generate the results in the Lamarc file format (xml) for me. That could save me a considerable amount of time.

I have modified the "ft2dna" program to generate a "Dean McGee web page style" of a Genetic Distance chart, using the data that I use as input to Dean McGee's utility anyways. If you have downloaded the older version of the "ft2dna" program, the documentation has some links to NIST that I used as a reference to generate the "ATGC" format. Pretty grueling stuff to try to figure out on your own. For example, Sorenson uses DNA complements, which can be confusing if you are not aware of what they are doing. With a number of Y-DNA testing companies analyzing Y-STR values with different techniques, it becomes important to have a standard to apply for DNA Project administrators.

Butler has a PDF file in this issue of JoGG that shows the ATGC structure for Y-STR's that I was attempting to convert with the "ft2dna" program. A good reference if you are interested in how that conversion is done.

Ann Turner is on the Editorial Board at JOGG, and she helped me to figure out "how to" do the BLAST searches for the Y-STR values. I did those BLAST searches in order to verify that I was writing the "ft2na" program against reality. Ann Turner has also written a "Mutation Rate Calculator" also found in the DNA Tools area at HAM Country. She is also an expert at mtDNA, and has helped a number of Genetic Genealogy Project Administrators with their mtDNA analysis.

Anyways, it is good to see a standard from these Y-DNA testing companies. John Butler is interviewed in this season's issue of JOGG.





see: http://www.jogg.info/42/index.html








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Sunday, November 9, 2008

HAM Surname Counties of Origin in Virginia





I have uploaded a You Tube video of the Counties of Origin of the HAM Surname in Virginia prior to 1800. From the book "A Short History of the HAM Surname in Virginia & NC." A 3.5 minute video, about 5 MB in size.


Not all counties are included here. For example, counties are not included that were once in Virginia but now are in present day West Virginia. But, it does give a quick overview of the migration pattern for the HAM surname in Virginia prior to 1800. Lists names of first inhabitants with the surname HAM(/M/ES) by County.


In a few cases, I had to make a judgment call on which person to list. For example, Joseph HAM arrived in 1621 in Elizabeth City County, but died in York County. Or, for example, John HAM died in Stafford County in 1739, but Elizabeth HAM is the first to appear in Stafford County in the book (1716), so Elizabeth was listed in the video. Another example would be Jerome HAM, who first held land in Charles City County, but lived in York County.


Therefore, a few adjustments were made in order for the video
to make better sense.


The HAM Surname Counties of Origin in Virginia

You Tube video





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Friday, November 7, 2008

HAM County Origins in England

Last month's HAM Country Blog Poll indicated that folks don't know much about how the surname began. There is already a short description of how the name was derived at HAM Country, so I presume that doesn't do the trick on it's own. Therefore, HAM Surname County Origins in England has been posted to You Tube. A 3 minute video (about 4 MB in size).

Trying a different idea, it shows the Counties of Origin for the HAM surname in England. The locations are Counties in England, and have been taken from the book "A Short History of the HAM Surname in Virginia & NC."
It runs through the earliest HAM on record in volume #1. Then, it runs through the Counties graphically in alphabetical order. Set to music by Ilya Gordon.





There are actually more Counties in the book than the video mentions, such as Middlesex or Warwick.



The book has no graphs, so those of you who own a copy of volume #1 (Origins & Migration) will be better able to picture the Counties mentioned. For the rest of the folks, this is just a graphical overview.









(click on image to enlarge)



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Monday, November 3, 2008

Poll Results: Areas of Interest


Poll Results: Areas of Interest




In the blog
Poll for October, the questions were geared toward finding out the interests of those currently reading the blog. The blog saw 147 unique visitors in the month of October. Up to 16 votes were cast in the Poll.

One of the items (that people voted on) indicated that they did not know "How To" read a phylogenetic chart. Which resulted in a blog post and You Tube video on the subject. The poll was to help me set a priority on some things I should be setting a priority to work on.

Here were the results of the October poll:








64 % said they could identify 5 famous HAM(M)'s.
35 % said they could NOT name 5 famous HAM(M)'s












76 % of those who voted said they did NOT know how the HAM(M/N/E) surname began.

23 %
said they DID know how the HAM(M/N/E) surname began.













85 % said they did NOT know who Odon IV
was.

14 % said that they did know.












57 % of those who voted said they did NOT know if they descend from an immigrant ancestor who arrived in America prior to 1700.

42 % said they DO know
if they descend from an immigrant ancestor who arrived in America prior to 1700.










92 % said they did NOT know "H
ow To" interpret HAM DNA phylograms.

7 % said they did.











50 % said they DID NOT KNOW if their HAM(M?N?E) line is participating in the HAM DNA Project.

42 % said that their line was participating in the HAM DNA Project.

7 % said
that their line was NOT participating in the HAM DNA Project.







50 % said they have the most interest in Virginia
31 % said they have the most int
erest in South Carolina
18 % said they have the most interest in the states of:

Georgia
Illinois

Kansas
Missouri
North Carolina
12 % said they have the most interest in the states of:
Alabama
Indiana

Kentucky

Ohio
and 6 % said they have the most in the states of:

New York
Pennsylvania
Tennessee or "other" state

( * You could vote on more than one state for this question.)





46 % voted that they have an interest in England
40 % said Germany

26 % said United States
(presumably, could apply to Native Americans)

13 % said they have an interest in:
France
Ireland

- or "other" Country
6 % said they had an interest in:

Netherlands
Scotland


( * You could vote on more than one state for this question.)


I would also presume that African Americans are not yet voting in the Poll.










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Sunday, October 26, 2008

Glastonbury Ties?

Glastonbury Ties?

Tying shoestrings together in Glastonbury


County Somerset



Have you looked at a map of England for Butleigh?

I find it is a healthy exercise to try to paint a picture of a time line and locations of HAM families from our book, "A Short History of the HAM Surname in Virginia & NC." It's an exercise that might be of interest to folks who want to know more about origins or immigrants.

I started splitting out the entries for Somerset, and found the HAM name spilled over into County Devon in the area of Taunton. There is a corridor in this area that our book paints for us. Basically, it paints a swath of land going north from Tiverton to Taunton to Bridgewater, extending east from Honiton, Crewkerne, to Glastonbury. I was taking note of the towns, dates, and HAM names in our book.

Then I noticed something.

While looking up towns and making notes, I looked up the to
wn of Butleigh in vol #1 our book for the dates. There are HAM ties to the GIBBS surname in Butleigh.

In vol #2, we have Richard HAM in 1736 marrying Diana GIBBS in Middlesex County, VA.
In vol #3, we have the will of Richard HAM, who mentions his wife Dina.

What bugs me is that these entries are all inferences to the direct line of the folks from Franklin County, NC. The names that point directly to the line are not specifically mentioned. However, if you add in the facts for the GIBBS surname in Butleigh, County Somerset, then it gets interesting.

That's because Tony tested out his DNA (kit #N54540), which provides a match for Group #1 in County Somerset, England.
And, the Y-Search on our HAM DNA Group tested out for ties to the area of Crewkerne.
(Tony's ancestral land is just south of Weston-Super-Mare and north of Wedmore). Putting together the DNA, the maps, and the information from our book shows that our HAM DNA Group #1 has ties to the area in Somerset surrounding Glastonbury. And, again, not too far from Crewkerne.

You might notice (on this map) the towns of Wedmore and Curry Rivel from the 1861 Census of England.

And finally, not to forget, Ham Hill is also not far from Crewkerne. Glastonbury puts our Viking line within spitting distance from Ham Hill and Montacute, which contains an old Norman motte and bailey, and was owned by Robert, Count of Mortain.

I think that the GIBBS name points to possible ties for HAM DNA Group #1 to the general area of Crewkerne. This would support the DNA evidence thus far.

It will be good when we get additional DNA participants in the HAM DNA Project from England.
Due to the proximity to our HAM DNA Group #2 (Y-Search points to Worcestershire), I should expect to have the need to sort out the "I" and "R1b" haplotypes between the current residents named "HAM" in the area of Somerset today.

Below is a portion of the map that contains the areas covered in our book, with a number of the towns found in our book, dating from 1200 to 1800:





















References:


My notes from "A Short History of the HAM Surname in Virginia & NC":
(Notice the GIBBES name in Butleigh, County Somerset in 1594.)

vol #1, pgs 51-52:

1589 John HAMME buys 6 acres located in Baltonsborough (Wooton in Budleigh), Somerset.
1594 William HAM and John HAM are mentioned in the will of Julyan GIBBES of Butleigh, County Somerset, England.

Also tied in with the HAM lines of Middlesex County, Virginia in 1736 when Richard HAM marries Diana GIBBS.
vol #2, pgs 46-48:

1711 Richard GIBBS marries at Christ Church, Middlesex County, Virginia.
1712 Eliza GIBBS is born at Christ Church, Middlesex County, Virginia.
1714 Diana GIBBS is baptized at Christ Church, Middlesex County, Virginia.

1736 Richard HAM marries Diana GIBBS at Christ Church, Middlesex County, Virginia.

Current research suggests this Richard HAM migrated to Franklin County, North Carolina.
vol #3, pg 53, 54:

1794 Richard HAM files will in Franklin County, NC.
Mentions wife Dina HAM, oldest son Elisha HAM and daughters Agnes & Sarah HAM.

The HAM DNA Project suggests Franklin County, NC descendants are related to ancestors near Crewkerne, England.


For reference to Tony's ancestral land (kit #N54540), it should be here:

http://www.genuki.org.uk/big/eng/SOM/parishes.html
or
http://www.genuki.org.uk/big/eng/SOM/SouthBrent/index.html

Here's the description for the South Brent/East Brent in Somerset:
-----------
"SOUTH BRENT, a parish in the hundred of Brent-cum-Wrington, in the county of Somerset, 6 miles to the S.W. of Axbridge. Weston-super-Mare is its post town. It lies near the coast of the Bristol Channel, on the Bristol and Exeter railway, and contains the hamlet of Week, or Wick. Brent Knoll [see East Brent] rises to the N. of the village. The manor was formerly held by the Abbot of Glastonbury...."

From The National Gazetteer of Great Britain and Ireland (1868) Transcribed by Colin Hinson © 2003


Maps are available from map sites, such as Mapquest, Yellow Pages, or Google Earth.

Inferences are both from the HAM DNA Project and from our book, "A Short History of the HAM Surname in Virginia & NC."

Wikipedia's link on the Abbot of Glastonbury

A Brief history of Glastonbury Abbey

More on Glastonbury Abbey You might want to view the History or Photo Gallery.

History of the Norman Conquest by Freeman (1876) - 30 MB PDF file
It would appear (page 389) that AEthelnoth of Glastonbury was William the Conqueror's companion on his first voyage to Normandy circa 1078. This account says that Thurston was appointed Abbot in 1082 (see also the footnote in Latin at the bottom of page 390. Here, Oderic would have been a viking). Thurston's dastardly deeds are described on page 391.












Wednesday, October 8, 2008

How To Read HAM DNA Phylograms


How To Read
HAM DNA Phylograms
Oct 7, 2008




The HAM Country Poll for October has so far returned (from 100 % of the people voting) that they do not know "How To" interpret the HAM DNA Project phylogenetic charts. That was a surprise to me.
I have been posting these charts to HAM Country for years now, trying to keep them up to date with the new data as it arrives. I have received almost no requests to explain how to interpret these charts. I thought most of the folks would know how to read these charts.

Let me take the opportunity to try to remedy that. I have posted a 7 minute video to You Tube in order to explain "How To" read the HAM DNA Phylograms. And, I will go over the basics here.

Once you are familiar with phylograms, it should be easy to read. The charts are intended to tell you what the Y-DNA data tells you, pretty much at a glance.


I can remember some years back when I asked Dean McGee to add his TMRCA data in PHYLIP format. He has graciously provided that.
I'd hate to think that HAM genealogists still do not know how to use the data that he has so generously provided for us.

The main points to remember about a phylogenetic chart are:

- The software is only solely on the DNA data. The only input to the chart is the DNA data.
- The software will automatically try to organize the data into "groups."
- The chart is created from the TMRCA
data, which means a mutation rate has been applied. That means we have a timeline.
- In order to get an idea of how related two individuals may be, simply follow the
timeline back to the vertical line that connects the two.
- The software should automatically sort by Haplotype Group.

The graphs in use at HAM Country are always created with a few basic tools:

1) Dean McGee's Y-DNA Comparison Utility.
2) The PHYLIP software program called "kitsch."
3) and MEGA tree viewing software

There are other software packages that could be used to create charts, but the results may vary. I have selected these programs for their ease of use, ease of interpretation, and best of all, they are free for use by the general public. I have seen and used software that is much more difficult to use, and also software that is much more difficult to interpret. And the results from these particular packages are reasonably accurate when used properly.

Geneticists have used similar charts many time in the past in order to describe their data at a glance. The term "Phylo" means "name," and the basic concept is to create a chart based upon the kit number or name of the individual and also based upon some time driven mechanism.

The objective of the charts is to create a time driven chart, based upon the kit number (or name of the individual), using only the DNA data as input.

The first thing to remember is that since the graphs are based upon the Time to Most Recent Common Ancestor (or TMRCA),

In order to get an idea of how related two individuals may be, simply follow the timeline back to the vertical line that connects the two.

Here's an example of how related Conrad (kit # 112972) is to the other participants:







Following the line traced in purple back to the vertical line (that he has in common with the others) tells you that in order to connect to Conrad, the kits need to go back in time some 16,825 years.








The graph will also try to group similar kits into "Groups." The following picture shows HAM DNA Group #2 hi-lited in cyan:







Because the connecting (vertical) lines are not far from the present, the chart indicates that you do not have to go very far back in time to connect. So, you should find the HAM DNA Groups next to each other on the chart.








And finally, you should notice that the Haplotype Group is automatically sorted such that those in the same Haplotype Group will be next to each other on the chart.


That's about all there is to reading the HAM DNA Phylogenetic charts. The charts try to display all of the data for the HAM DNA Project together on on a picture that should be easy to understand.

Feel free to rate or comment on the
You Tube video that I have posted to explain "How To" read the HAM DNA Phylograms.

see also:

Instructions for creating a Phylogenetic Chart
Dean McGee's Y-DNA Comparison Utility
PHYLIP software package
MEGA tree viewing software
HAM DNA Project Phylogenetic charts







Saturday, October 4, 2008

John HAM, 1821 Grayson County Land Grant


John HAM
1821 Grayson County Land Grant



When doing research for our book, you could find Lands Grants for Virginia on an index card at the Archives, then look up the land grant on microfilm. And not all land grants were listed on the index card, nor were other names indexed (that would have been mentioned in the land grant).

I made an entry in our volume #2 for every index card they had at the time, but it was not a complete list at the time of my research.

Thanks to the internet, things are easier today. You can search the Library of Virginia for grants by name ( http://www.lva.virginia.gov/ ).
From the main menu, select "Search Catalogs."

For example, in our Volume #2, there is a land grant listed for John HAM of Grayson County on Sep 1, 1821. (Volumes #2, Virginia, page 206) It is listed as it was on that index card at the Archives. The Library of Virginia has an image of it on line at:

http://ajax.lva.lib.va.us/F/TJGSGP6NXST1J617FEYT63KTSD8PFGPXUP42PUU9F885PE79CA-24547?func=file&file_name=find-b-lva01&local_base=LVA01


Select:


- "Words Anywhere"
- then type in "John HAM Grayson County"
- then click "search"

An entry in the catalog should come up that looks like this:

#
Author Title Year Format Location/Items
(owned/checked out)
1

Ham, John. 1821 Archives


Then, just check the box, and click on "GO."

It is interesting to read, because of the details mentioned. It is also interesting because it happens at the time just before the HAM lines migrated to Ashe County, NC in 1826.

The details:

John HAM Land Grant for 300 acres in Grayson County, Virginia dated Sep 1, 1821.

(The last line mentions the date.) It also mentions a Survey done on Feb 11, 1816. Finally, it mentions the date of the Land Office Treasury Warrant #9100, issued Nov 22, 1781(?).

I have the year of the Treasury Warrant with a question mark here because it is hard to read, due to the overlapping letters and ink smear. It could be 1791, but the “9" listed elsewhere on the page does not have a “loop” at the bottom. The Treasury Warrant number (#9100) has no loop at the bottom of the “9,” so I don’t think the year would be 1791.







The year of the Warrant could be 1787, but upon magnification, I think not.

In any event, John HAM of Grayson County was born in 1780, so he should have been less than 10 years old when the Treasury Warrant was issued. When the survey was done in 1816, John would have been 36 years old. When the Land Grant was obtained in 1821, John would have been 41 years old. That tells us that the 1781(?) Treasury Warrant was probably first issued to William HAM, Sr. (John was the oldest son that we know of.).

At any rate, the Land Grant was for 300 acres, bounded by the lines of Paul BUNCH and Patience PERRY. The PERRY surname ties in with Geneva’s Ashe County HAM lines, and the BUNCH surname in Grayson County is mentioned in our book (vol #2 Virginia on page 205). David BUNCH and John BUNCH were witness to the purchase of 100 acres by William HAM (Junior) in 1820, on Brush Creek in Grayson County.

Geneva is very familiar with the area, and she has taken me to Brush Creek, among other places. She knows that part of the mountain country well, has surveyed cemeteries there, interviewed residents, and has taken me to several cemeteries of interest in the area.

In 1820, William HAM, Sr. No longer appears on the Grayson County Census records or Tax Lists, so we know that he is gone by that time. It is John HAM and William HAM who appear in the 1820 Census records for Grayson County, VA. It is son Thomas HAM who is first to migrate to Ashe County, North Carolina, and William HAM, Jr. sells this 100 acres on Brush Creek to Joseph LYNCH (or LINCH) in 1826 in order to follow Thomas HAM to Ashe County.


Further information regarding this item could be found by looking up the Survey, or Treasury Warrant.

More information about other Land Grants, deeds, and Court records, and so on are listed in our book "A Short History of the HAM Surname in Virginia & NC."


A transcript follows below.



John HAM
300 acres
Grayson

Thomas M. Randolph Esqr. Govenor of the Commonwealth of Virginia. To all to whom these
presents shall come greeting:
Know ye that in Conformity with a Survey made on the Eleventh day of February 1816,
by virtue of a Land Office treasury warrant Number 9100 iSsued the 22nd November 1781;
there is granted by the said Commonwealth, unto John HAM A Certain tract or parcel of
Land, Containing Three hundred Acres Situate in the County of Grayson on the waters of
New River and bounded as followeth to wit: Beginning at three white Oaks, thence North
twelve degrees East sixty poles to a Chestnut tree and two hickories East eighty two
poles to a red Oak and white Oak in Paul BUNCH's line, North thirty five degrees
East sixty poles to a red Oak sapling by a path North seventy seven degrees East
ninety eight poles CroSsing a branch to a double white Oak, South sixty degrees
East sixty eight poles to a red Oak, South fifty five degrees West forty four poles to a
white Oak near a branch, South thirty degrees West sixteen poles CroSsing a branch
to two white Oaks, Corner to Patience PERRY's line, and with her line South seventy degrees
West One hundred and forty poles to a white Oak and leaving her line, South fifteen
degrees East one hundred and twenty four poles CroSsing a branch to a white Oak near a
large rock, South twenty five degrees West seventy four poles to a white Oak
and buckeye on the bank of a branch, West One hundred and Six poles CroSsing a branch
to a white Oak on a ridge. North fifty five degrees West One hundred poles CroSsing a
branch to a Stake and thence North twenty Six degrees East One hundred and thirty poles
to the Beginning. To have and to hold the said tract or parcel of Land with its
Appurtenances, to the said John HAM and his heirs forever. In witneSs whereof
teh said Thomas M. Randolph Esqr. Governor of the Commonwealth of Virginia hath hereunto
set his hand, and Caused the leSser(?) Seal of the said Commonwealth to be
affixed at Richmond, on the first day of September in the year of Our Lord
One thousand eight hundred and twenty One and of the Commonwealth the forty sixth.

Thos. M. Randolph



citation: pg 347 Virginia State Land Office. Grants Reel 136. Sep 1, 1821 Other Format Available on microfilm. Virginia State Land Office. Grants A-Z, 1-124, reels 42-190; Virginia State Land Office. Grants 125- , reels 369-. link:

http://ajax.lva.lib.va.us/F/TJGSGP6NXST1J617FEYT63KTSD8PFGPXUP42PUU9F885PE79CA-24547?func=file&file_name=find-b-lva01&local_base=LVA01









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POLL: Areas of Interest



I have a few items on my "ToDo" list, but I usually want to work on the items that I thought are among the most interesting discoveries from our book or from the HAM DNA Project.



For example, during our book presentation in Ashe County, Geneva made a joke about the origins of the name. A couple of people chuckled, but it was quickly apparent that many in the audience did not know anything about the origins of the HAM surname. I have posted a quick page to HAM Country on it, but I've thought it would be a good topic for a video as well. Maybe a good topic for the Blog Poll, I don't know. However, it is obvious that among the folks who are not on the internet, many still do not know the story behind the name.


I am currently working on video scripts for topics like the origins of the HAM surname, first HAM immigrants to America, "How To" read a phylogenetic chart, as well as how the myth of Jerome HAM got started and evolved over time. It is clear to me that the Jerome HAM myth story would take a DVD length video in order to explain that problem completely, which means it may be hard to put together for a You Tube video.




So, this month I will take a Poll on the topics of interest. The Poll may not address the needs of folks overseas, but at least I can try to get an idea of the interests of the current HAM Country visitors.


I am about out of the space that Earthlink allocates to personal web pages, so I won't be asking about additions to the HAM Country web pages.


This month, I will post Poll questions related to the topics that you might want to see on the Blog, Poll or on video.







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Moved to Ohio

I have been on a short hiatus in order to move to Ohio.



Never thought it would take so long just to move back to my home state, but one event followed another. First, I had a health problem to deal with, then my car's transmission went out the day before the move, then my car's window fell into the car door the day of the move. Leaving the window wide open (no protection from the rain). Just after the move, there was the remnants of Hurricane Ike to deal with here in Ohio. One tree fell on the power lines to the house, and another tree fell on the high voltage lines, then caught fire. No electric for nearly a week.



Also, there were the bureaucratic items to tend to, like state license plates, state driver's license, insurance, etc.



Some distractions there, and I'm not done with the paperwork for the state to state move.



I have a few video scripts in progress, but none are ready to post to You Tube. I'd like to continue working on the videos, it's fun. Perhaps I can get some shorter videos up first.
(Dial up access to the internet really puts a cramp on the longer videos, so I have to consider making videos for DVD access only.)



Not to mention that the order forms for our book "A Short History of the HAM Surname in Virginia & NC" had to be changed on the HAM Country web page to reflect the move.




Anyways, I hope to get back to the HAM DNA Project and put up more posts to the HAM Country Blog.






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Thursday, August 7, 2008

The Ham Stone

The Ham Stone


County Somerset


I have received many letters over the years about HAM Surname origins.
The letter below turned out to be an interesting one.


----------------------------------------------------------------------------------

Subject: HAM
From: "Jenny Board"
Date: Thu, 31 Jul 2008 19:04:11

To: odoniv

Hi

I don't know if it's a red herring but I'm investigating my husband's family tree in Somerset and there are masses of Ham, presumably named after the ham stone prevalent thereabouts.


Jenny

----------------------------------------------------------------------------------


I have heard a lot of ideas about the origins of the name, but this was a new one.
The meaning of the name is still not known for many people. Lost in time somewhere.


Many people still think that because they spell the name with two "M's" that the name "Ham" does not apply to them, simply because they spell their name with two "M's" (that is, as in "Hamm"). Fortunately, I was able to do some research on the origins of the name for our book "A Short History of the HAM Surname in Virginia & NC" (co-authored with Geneva S. Greer and Susan Bullock). You can find my quick reference to Ham Hill and quarry on page 26 of Volume 1, "Origins & Migration" in about the year 1215.


The "ham stone" has an interesting history. It's known by it's honey color as it has a yellow-gold hue, a limestone mined from the vicinity of Ham Hill in County Somerset, UK.
Ham Hill is located near Crewkerne, you can find information and link to a map (south-east of Stoke Sub Hamdon or north-east of Norton Sub Hamdon or west of Montacute) at the GENUKI web site.

























Ham Hill is probably the largest Iron Age hill forts in Britain, and has a defensive perimeter that streches out for about 3 miles.
You can get a panoramic view of the megalithic stone circle at the BBC web site.


It was captured by Vespasian in 45 AD, known to the Romans for some time. And the stone was quarried in Roman times for coffins. (A Roman coffin can be seen in the Dorchester museum.) The Romans built a road nearby (Fosse Way), but eventually abandoned it as a fort, preferring forts closer to Wales.


Mottes and baileys were introduced to Britain in Norman times. A motte was a mound of earth, topped by a tower. A bailey was the surrounding area for buildings. A ditch could surround either.


Robert, Count of Mortain was known to be responsible for building the
motte and bailey castle at nearby Montacute (built in 1086). By 1519, the stone was being removed from this structure. Mortain is a small town in the Department of Manche, France. It was reserved for the reigning house of Normandy. It is said that Robert, Count of Mortain was the half brother of William the Conqueror.

In about 1600, the ham stone was quarried to build the Montacute House in the town of Montacute, County Somerset.


So, we can find the ham stone being used in the Iron Age, Roman times, at the time of the Norman Conquest, and up to the present day.

Thanks Jenny, for mentioning the ham stone.


See also:

Ham Hill megalithic stones panoramic view at the BBC Somerset web site

Ham Hill panoramic view at the BBC Somerset web site

Ham Hill Herald (PDF file) from the Ham Hill Country Park, South Somerset District Council.

Roman armour find from the Somerset Historic Environment Record




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Saturday, June 28, 2008

Y-DNA Mutation Rates - A Case Study

Y-DNA Mutation Rates

A case study of computational models for Genetic Genealogists


June 28, 2008


The wonderful side effect of using Y-DNA to study Genetic Genealogy is that the DNA begins to crack open long standing problems. One of the most significant problems is calculating the Time to Most Recent Common Ancestor (TMRCA). For the purposes of genetic genealogy, this concept was first devised or proposed in 2001 by Bruce Walsh of the University of Arizona. It has been vexing DNA Project Administrators ever since.

Why is this TMRCA a vexing problem?


Well, the theory proposed by Bruce Walsh dives head first into a perplexing trail of complicated mathematical equations, molecular genetic theory, infinite alleles models, Poisson distributions, Bayesian posterior distributions, Bessel functions, differential mutation rates, and the like. For most Y-DNA administrators, this is a little difficult to apply to their family project(s). Bruce Walsh
describes the calculations as an "upper boundary" (page 898) on the time back to a common ancestor shared by two individuals. That is, it was not to be taken as an exact calculation.

The Holy Grail of Genetic Genealogy:
Why would people want to know the Time to Most Recent Common Ancestor?


When you begin to use DNA for genealogy, the first thing you are able to determine is which family lines you relate to, and which family lines you do not relate to. That puts a whole new perspective on genealogy research. You begin to understand which family researchers you should be communicating with, and this also leads to which geographical areas should be of interest in your family line. That's because using genetics for TMRCA holds the promise of discovering migration paths going back thousands of years. That is, tracing your own line back several hundred years no longer seems like s
uch a huge problem.

Knowing "How To" calculate the Time to Most Recent Common Ancestor suddenly becomes an interesting problem for genealogists to solve. This calculation should tell you how long it has been since your own line split from another line. Information that genealogists may not have had before. This becomes very interesting as you share resources with other genealogists around the globe.

How TMRCA calculations work

For geneticists, this usually means breaking down probability distributions into a computer program that can be applied to the data. For genealogists, this usually means breaking down those complicated equations into something easy to calculate. For most folks, that means applying a mutation rate. This should be a simple calculation. But, most people find that the "simple" calculation soon breaks down into some type of quagmire when it comes to applying it their own line. The calculations quickly turn into an endless stream of details.

The idea is to apply the mutation rate to the Genetic Distance between your project participants.

The problem becomes which mutation rate should I apply? Which probability distribution is the correct one? What's the correct mutation model (stepwise, infinite alleles, etc.)? Should I apply individual marker mutation rates to my study? Or, for that matter, how do I figure out the marker mutation rates, and how is that calculated for TMRCA? And even perhaps, how do I know that I have calculated the correct Genetic Distance?

Far too many questions there. Why can't we just point and click on some computer program? I suppose the main reason is that no satisfactory "easy to use" computer program has been written for a genealogist to use in their DNA studies. At this point in time, there is one software program that has attempted something along these lines. That would be Dean McGee's Y-DNA Utility. It at least generates some TMRCA data for you. Dean McGee has made his program available for public use.

One of my favorites, I use the output from Dean McGee's Utility and pass it through the PHYLIP software package to produce a phylogenetic graph of the HAM DNA project. This is all obtained only by the use of the DNA data that we have collected for the project.

Discussion

While I enjoy the output from Dean McGee's Utility, there is a minor problem that I find when applying it to my data. I am observing that individuals with genetic distances of 0, 1, and 2 all descend from a common ancestor who is estimated to have been born in 1755 (or, TMRCA ~= 255 years ago). For these individuals (kits 40777, 68140, 58559, and 70450), Dean McGee's Utility calculates the TMRCA out (for the HAM DNA Project) as 150, 325, and 400 years ago. That is, for each of the differing genetic distances, there are corresponding differing TMRCA's. However, the results should show the same TMRCA.

The calculations are close to the genealogy information, but not quite exact. How do I resolve that? Can I obtain a TMRCA that actually corresponds better to the actual data? Does this have anything to do with Walsh's "upper boundary" theory? Is there something that Dean McGee's Utility should be doing differently? Are there calculations that I could do on my own data to improve the figure? Or, is it simply due to the number of markers tested? Page 909 of Walsh's paper suggests that per generation data will become accurate when about 580 markers have been tested between two individuals. To my knowledge, only about 417 Y-DNA markers have been discovered, and most testing companies only offer packages of 100 markers or less. Therefore, is the lack of accuracy due to the lack of the number of markers tested?

As for individuals making their own calculations, Bruce Walsh mentions how to modify the TMRCA equations for an individual haplotype (page 910 of his paper).

If I recall correctly, I believe one of Walsh's papers mentioned that Family Tree DNA has at least once considered generating this for their individual projects. But to date, FTDNA has only published information obtained from their data in very general terms, as it applies to the data as a whole.

Therefore, the question follows that if we are able to generate the same type of information from our own project (or haplotype), then will that data result in a more accurate estimation of TMRCA as it applies to our area of interest?

As of this writing, there are at least two individuals that have published thoughts along those lines (at least, to my knowledge). One is Charles Kerchner, who is tracking data across a multitude of projects. Charles is studying mutation rates for individual projects.

The other individual is David Roper, who shows how he has applied calculations for his own project on a very small scale. Mr. Roper has included some discussion of how to apply probabilities to genetic distance for an individual project , and he has posted the results of a simple example of "How To" calculate this out.


Comparison of Calculations:


I reviewed a case study of the calculations when applied to a special case in the HAM DNA Project. Comparisons of several of the more convenient models available on the internet, namely L. David Roper's probability model, Dean McGee's Y-DNA Utility, and the Lamarc software program.

For a review of the computations and results, see the PDF file posted to:

Y_DNA_Computational_Models.pdf


Observations

Many of the genetic genealogists are looking for specific results as they apply to their own project or group. They are not always content with generalized information, and the question of TMRCA is a topic of great interest especially if they can apply an equation to their own project(s).

It should be noted that a significant percentage of mutations have been reported for father son pairs. I have not examined the effect of a baseline to the case of father son pairs (mainly because I do not have that data at hand).

I should also note that there are any number of genetic software programs available, usually requiring input in the form of ATGC format. Nearly all of the genetic programs do not report output that the family genealogist can easily use to compute a reasonable TMRCA. That is, most programs do not take the input data as we have it from FTDNA, nor do most programs report TMRCA output expressed in terms such as generations or years. (See
Bill Jackson's MRCA Probability calculator for a given number of markers and generations, or Ann Turner's Mutation calculator.)

It should also be noted that other quantized methods could be employed to calculate meaningful results (even without the use of a mutation rate). However to date, I have not yet examined other quantized computational models that could be employed by geneticists for TMRCA.

Nor have I derived the appropriate equations (for a small population) from Bruce Walsh's paper. (The mathematics appear to be beyond my abilities.)

Finally, it should be remembered that this study is based upon a special (and rather unusual) case of 37 marker computations. That means, due to the low number of markers examined, probabilities are a large factor in the results. Last I checked, there have been about 417 Y-DNA markers discovered, bringing to mind Hammer's comment to Walsh (in Walsh's paper) that about 580 Y-DNA markers would be required to resolve time frames down to each generation. When we finally have good analysis on a large number of markers, then this type of discussion will probably become a non issue.

Conclusions

Since most participants have not gone through the process of detailed calculations for per marker mutation rates (for individual projects), it has yet to be determined if all of the work is useful. It is interesting that Roper has detailed the probability calculations for individual markers, which differed slightly from the "standard" calculations using a "standard" mutation rate. This type of research could be useful for individual projects.

How were the models checked independently for the HAM DNA Project?

An attempt was made to calculate TMRCA from various independent computational models. First off, I am presuming that my methodology and math is reasonably correct. There are a number of opportunities to introduce errors in any of the above computations. For example, using the Lamarc program could introduce errors when the data from FTDNA is translated into ATGC format. Or, more simply, my math in this report may not have been applied appropriately.

I had enough data for a Lamarc run on my project for two groups, Group #1 and Group #2. Lamarc calculates out "Theta" values for the Group as a whole, and also Theta values per individual marker. This appears to generate slightly more accurate TMRCA estimates than Dean McGee's Y-DNA Utility. (Roughly, a 13 % improvement in TMRCA estimates.) However, the Lamarc program can run for several days, and takes a great deal more effort than does Dean McGee's Utility.

Finally, it was found that adding a baseline value for no mutations doubles the accuracy of the Lamarc data. Of course, a baseline could also be applied to Dean McGee's utility, or to Roper's model as well. Therefore, one can only wonder how accurate Bruce Walsh's equations might be if a simple baseline were added to his equations.

At the moment, Dean McGee's Y-DNA Utility appears to provide the best calculations with considerably less effort. Also, the Y-DNA Utility can be adjusted for model (infinite alleles or hybrid), for probability, and mutation rate. I would have to conclude that Dean McGee's Utility is the best program available for ease of use, parameters offered, and of course, price.


See Also:

Time to Most Recent Common Ancestor (TMRCA) a PDF file by Bruce Walsh (2001) of the University of Arizona.
Dienke's Anthropology blog regarding Y-DNA mutation rates of father-son pairs (posted in 2006).
Dean McGee's Y-DNA Utility
David Roper's
discussion of how to apply probabilities to genetic distance for an individual project , and his posted results
PHYLIP software package
Mutation Rate calculations by Rosche and Foster (2006)
Lamarc - Likelihood Analysis with Metropolis Algorithm using Random Coalescence
Y-DNA Computational Models - my review of convenient computational models used to determine TMRCA from the Y-DNA data.

An arguable example has been posted here:

HAM DNA Group #02 Lamarc compute model TMRCA contrast to Dean McGee's Y-DNA Comparison Utility (July, 2008).







Sunday, June 1, 2008

POLL Results: HAM Revolutionary War Veterans

HAM Revolutionary War Poll Results

May, 2008


In May, we had a Free HAM Book Giveaway Contest at the HAM Country blog based on the Revolutionary War Poll questions. The Contest was to win a free three volume set of our book "A Short History of the HAM Surname in Virginia & NC." There were no entries in the contest.


This contest was held for the month of May, and over the Memorial Day weekend.
The largest number of votes on any one question was 4.
Pretty poor results. During the month of May, the HAM Country Blog saw 193 pageloads from 95 unique visitors. So, very few of the visitors actually voted in the Poll.

I had one complaint of a person who was not able to vote, as it did not appear to function correctly for him. We did have a lively discussion off line at the end of May regarding how the contest might be structured to enable more people to win a free set of books in this contest.

There were ten questions in that Poll. The questions were:

- What HAM's fought at the Battle of Guilford Courthouse?

- Which HAM was a Lieutenant in the Navy during the Revolutionary War?

- What was the name of the ship commanded by a HAM during the siege of Yorktown?


- Which HAM was an Indian Spy during the Revolutionary War?

- Which HAM Received a severe head wound during a skirmish with the Tories during the Revolutionary War?


- When was Mordecai HAM finally discharged from the service?


- Who was most likely to be Drury HAM's father, based upon the County land survey?


- Who served under Captain Daniel Sparks?


- Who was denied a pension (due to lack of records) after serving under General Sumpter?


- Who served as a surgeon during the Revolutionary War?


The contest closed May 31st, 2008 at 11:59 PM.

For the May's Contest, which included the Memorial Day holiday, the HAM Country Blog had 193 page loads, 95 unique visitors, and only 4 actually voted in the Poll (about 4 %) on any one question. The You Tube video got about 30 views. There were no video responses posted to the You Tube video.

For the ten polling questions, 28 answers were given in total. Of the 28 answers given, we had 8 that were actually the correct answers. That is, about 29 % (8 out of 28) of the votes were the correct answers. (One of those votes was mine, as a test for functionality.)


Here are the results from the Poll:



What HAM's fought at the Battle of Guilford Courthouse?


25 % said Drury HAM
25 % said Samuel HAM
25 % said Stephen HAM
25 % said William HAM



Of the four votes, nobody got this one right.









Which HAM was a Lieutenant in the Navy during the Revolutionary War?



50 % said John HAM
25 % said Mordecai HAM
25 % said William HAM










What was the name of the ship commanded by a HAM during the siege of Yorktown?





66 % said the Warwick
33 % said the Nicholson










Which HAM was an Indian Spy during the Revolutionary War?



66 % said Drury HAM
33 % said George HAM











Which HAM Received a severe head wound during a skirmish with the Tories during the Revolutionary War?


Only 2 votes on this one:

50 % said Mordecai HAM
50 % said Samuel HAM



Nobody got this one correct either.








When was Mordecai HAM finally discharged from the service?


Of 2 votes, 100 % said in 1781.



That was the correct answer.





Who was most likely to be Drury HAM's father, based upon the County land survey?

Three votes.

33 % said George HAM
33 % said Joseph HAM
33 % said Samuel HAM

Looks like all three were guessing here, nobody got this one correct. This was actually one of the toughest questions on this Poll.









Who served under Captain Daniel Sparks?



Only two votes.

50 % said John HAM
50 % said Mordecai HAM











Who was denied a pension (due to lack of records) after serving under General Sumpter?


Once again, only 2 votes.

50 % said Samuel HAM
50 % said William HAM



One person got this one correct.








Who served as a surgeon during the Revolutionary War?

66 % said George HAM
33 % said John HAM



Nobody got the right answer on this one either.