Thursday, May 7, 2009

KallOut - New Search Tool



Now here's a nifty little tool I just installed on my FireFox web browser - KallOut.


http://kallout.com/ff/welcome.html


Genealogists are always trying to find good reference material on the web, be it a primary source document, a news article, or even a You Tube video. A Google search doesn't always return everything that is available on the internet.


You can now search any of your favorite web sites in seconds, and no typing required. (Sweet!)


If you find an article on a web page that doesn't have an associated link, now you can just hi-lite a word on the page, then select the type of search you want from a menu of options.


I'd say this has to be an improvement over a plain vanilla Google search.
Currently, it can search Google, Yahoo, Ebay, flickr, Twitter, IMDb, FaceBook, etc.

(For example, I can hi-lite Tyler Ham, and select a search on IMDb... interesting!)

It should help with genealogy work, I should think.

- Enjoy




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Thursday, April 23, 2009

ft2phy: Y-DNA STR to ATGC conversion

ft2phy

Y-DNA Short Tandem Repeats to ATGC conversion




The software program "ft2phy" has been posted to the HAM Country Tools area. If you've ever thought it daunting using "ft2dna" to run LAMARC, or draw trees with DNAPARS or PHYML, or if you'd like to see the "alpha" or transversion ratios for your Group, then "ft2phy" can make life a bit easier for you.



"ft2phy" can read several lines of STR data from Family Tree DNA, and use the same input format that Dean McGee's Utility does. So, if you have saved your Dean McGee Utility data into a file, then "ft2phy" can read your data file in order to produce the ATGC conversion.


ft2phy can read multiple lines of data (up to 600 lines), and it sends the output to separate data files for each marker. These files can be used in genetics programs that are compatible with the Phylip format. This version can handle up to 37 markers.




http://ham-country.com/HamCountry/HAM_DNA_Project/Tools/FT2PHY.html





- Enjoy



Thursday, April 16, 2009

Y-DNA Project Grouping with Genetic Distance

"How To" create Y-DNA Project Groups
by using Genetic Distance
Or, How To Group Y-DNA by Genetic Distance using Dean McGee's Y-DNA Comparison Utility

There has been some discussion about "How To" create Y-DNA Project Groups, which does not appear to be a standard yet for Project Administrators. Nor is there any existing software that will do this for you automatically.


Family Tree DNA has an option to permit the Project Administrator to sort their Project into "Groups," but provides little or no guidance on "How To" do this, nor do they offer software to do this for you.



The PHYLIP package "Kitsch" program will sort the kits for you, but it would be up to you to the Project Administrator to do the "Grouping" by hand.



Grouping your DNA Project properly can add value to the DNA evidence by showing who is more closely related, and who is not. And, you can base this upon the DNA information. A valuable concept because sorting into groups can become more of a scientific procedure, as well as enhancing the analysis of that data.


DNA Grouping enables the use of DNA evidence as a tool which is independent of the usual
genealogy methods. What that delivers is either a clear joining or clear separation of families that are either related or not related genetically.


That means that you should be able to use Genetic Distance to verify whether or not lines are
related when normal genealogy records have been destroyed, or are otherwise not yet discovered.


You may have noticed that some Project Administrators don't appear to know what to do with Genetic Distance. That is usually obvious if they post a Genetic Distance table which looks "jumbled." Here's an example of a poorly structured Genetic Distance table, using a few selected kits from the HAM DNA Project:





Jumbled Genetic Distance Table
[ click on image to enlarge ]


Notice that the colored cells are jumbled all over the
place. You can look up your own ID and match it with other kits, but it makes little to no sense for the entire Project. A table that looks like this does not tell you how the DNA Project should be sorted into groups. In fact, it doesn't resemble anything like grouping at all.


There's a simple way to remedy this, which should give an overview of the entire Project at a glance. The remedy would be to sort the Genetic Distance table. Once you know how to sort the Genetic Distance table, an overview of the table starts to make sense.




Grouped Genetic Distance Table



Here's an example of the same kits that were used above, but this time they are sorted:



[ click on image to enlarge ]


Notice that the colors are now grouped together. Similar groups are now be found along the diagonal. The table is more symmetrical, and the "colored" cells now follow a recognizable pattern.


Then, the question becomes, what is the easiest way to sort the Genetic Distance table?



The answer is, that there are several ways to do sort
by Genetic Distance, but the simplest method is to sort on one of the Genetic Distance columns, then sort on the sums.


The easiest way to do that is by using Dean McGee's Y-DNA Utility to create the table, then sort on the first column.


Notice that column #1 of the "jumbled" Genetic Distance table is given in no particular order:




[ click on image to enlarge ]






The Genetic Distance values vary widely, and distances that are similar are certainly not on the table next to each other.











Here's column #1 of the "sorted" Genetic Distance table:








[ click on image to enlarge]



Notice that the Genetic Distance shows a similar increase, and the kits that are similar are next to each other on the table. You can check your work by creating a new Genetic Distance table with Dean McGee's Utility, and taking a second look at the grouping.











You
might have noticed the flaw by doing this simple sort (from the "sorted" Genetic Distance table above). That would be the grouping of kits #44176 and 47412. It doesn't sort correctly because they tested with a different number of markers. A simple "spot check" of the sort can usually show which kits did not sort correctly.


So, sorting your DNA Project by Genetic Distance (on one column) may leave a few unresolved groupings. That's because this example is a rough example only. You can get a better grouping by sorting a second time on sums for each row on either side of the diagonal. (It is possible to do some basic math in order to compensate for the varying number of markers tested.)



The trickiest part of using diagonal sums is that these sums could change with each re-arrangement. So, it may take a few iterations to get a better sorted table.



Or, if you are familiar with using the PHYLIP software package, a tree created with the "Kitsch" program will do the sorting for you. You can then use the MEGA software program to "Arrange Data for Balanced Shape." Arrange your data in the order suggested by the phylogram, and use that sorted data in your next run of Dean McGee's Utility.



The next run of Dean McGee's Utility should deliver a Genetic Distance table which shows the grouping for the DNA Project with colored cells along the diagonal.



Dean McGee's Y-DNA Comparison Utility can be found at:


http://www.mymcgee.com


If you are interested in the mathematics behind the Fitch-Margoliash method, a good starting point would be Professor Felsenstein's documentation on the software program "Kitsch" regarding the Fitch-Margoliash method with Evolutionary Clock:


http://evolution.genetics.washington.edu/phylip.html


The Genetic Distance table for the HAM DNA Project can be found with the output from Dean McGee's Utility at:

http://ham-country.com/HamCountry/HAM_DNA_Project/HAM_DNA_McGee_output.html

  
  




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Monday, April 6, 2009

Keeping Y-Search Up to Date


To the HAM DNA Project Participants:

I had been looking at mapped locations of (existing) towns called "Ham" in England tonight, and noticed that there are some possibilities of matching the FTDNA numbers with the locations of these towns. (There are more than two dozen towns in Britain called "Ham," about six "Ham Hill" locations, about seven "Ham Green" locations, etc.)

The best way to match DNA locations is with Y-Search.

Now, FTDNA hopes for a push in Britain in the upcoming year, so it is becoming more important to keep our Y-Search information up to date.

  
  UPDATE:  The Y-Search page was shut down in 2018, and is no longer available.
I say that because there is one town called "Ham" about 10 miles from Crewkerne (near Illminster), and another town called "Ham" near London. As you may recall from the 2007 DNA video, our Group #1 roughly matches these two areas in Y-Search. Our Franklin County line may have some parallels to the town called "Ham" near Frome (or Wells), if you recall the blog article about Glastonbury ties, for example. Tony, of course, has ancestors that come from a town called "Ham" near Brent Knoll (not too far from Wedmore).

Other possible examples could be the town of Ham near Plymouth, which the HAM lines from Maine are researching. (It would help if the HAM lines from Maine were participating in the DNA Project.)

Or possibility, since our Group #2 is matching Worchestershire, that puts them closest to the town called "Ham" (north of Bristol). Or, if our Group #4 is matching County Kent, there is a small town in County Kent called "Ham" near Sandwich (no pun intended).

You can check these maps out at Streetmap: http://www.streetmap.co.uk/


When we start getting participants in Britain, we should be getting some interesting information.

So, it is important to keep your Y-Search information up to date so that we have accurate information about our matches. Please enter your information on your oldest known ancestor correctly. In my case, that would be William HAM from Virginia, since any further ancestor has not yet been positively identified to date.
It was in May, 2008 that FTDNA changed the Haplotype Groupings:

This affected the following existing groups:


R1b1c became R1b1b2

I1a became I1

I1b became I

I1c became I2b

E3b1a became E1b1b1

Back then, I understood that FTDNA would be changing the Y-Search haplotype groups for us. But when I checked my Y-Search ID tonight, my haplotype group had been changed from "I1a" to "Unknown."

I had to manually set my haplotype group at the Y-Search database. So, I would guess everybody will need to check their haplotype group out there. This should help us to identify matches from other vendors as well.

UPDATE: The Y-Search site is no longer available.

- You can no longer edit or view your previous data.

and the "Haplogroup" is just below the area with the DYS values, under your "Last name"

If you have not yet submitted your information to Y-Search, then you can do that by visiting your personal web page at FTDNA.




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Wednesday, April 1, 2009

2009 April Free DVD Special


Book Order Special - Free DVD
with any order in April


For the month of April, 2009 we will be running a DVD special. Anybody that buys a book will also receive a free DVD of
the "HAM Counties of Origin" videos.


A graphical overview of HAM
surname counties of origin in England, Virginia, and North Carolina. Hi-lites the name and date of the first person with the HAM surname to appear in each county. These are DVD versions of the videos posted to You Tube on HAM Surname County Origins in England, Virginia, and North Carolina (with the exception that the video on Virginia has been updated).

The DVD version of the Virginia origins video now also includes
HAM surname origins in an additional 9 counties in Virginia (but are not included in the You Tube version). These are counties mentioned in the book "A Short History of the HAM Surname in Virginia & NC."




VA Counties on DVD that are not in the You Tube version:


Albemarle County
Elizabeth City County
Frederick County

Fluvanna County
Isle of Wight County
King & Queen County

Pittsylvania County

Rockingham County

Shenandoah County





Which brings to total video coverage of HAM surname origins to about 35 counties in Virginia, based upon
information from our book, "A Short History of the HAM Surname in Virginia & NC."


This DVD also includes and "Extras" area, which includes the video on "How To Read HAM DNA Phylograms" as
well as the "HAM Book Trailer" video.


So, order a book during the month of April and receive a free DVD.






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Monday, March 23, 2009

Tree Building for Y-DNA Surname Projects

Tree Building for Y-DNA Surname Projects

A brief comparison of a few genetic genealogy tree creation software programs

If you can't see the forest for the trees, then you're probably close enough





One item genealogists check for is accuracy. They check their sources, double check, and try to verify inconsistent data all of the time.
They cite their sources in order to know what each document tells them, as well as to know where to find the document.


Genealogists do this because incorrect data can affect your interpretation of who descends from whom. Without proper source information, you can draw the wrong conclusions about lineage. In genealogy, errors happen all the time, and is sometimes very annoying or frustrating to fix the errors created by the confusion of bad data or wrong information. The way in which phylogenetic trees are evaluated can affect your perception of who is closely related.


I spent a good part of March looking at trees. Creating phylogenetic trees is another item that can get confusing. If you have never
created your own Genetic Genealogy phylogram, then I suppose ignorance is bliss. If you have not converted your DNA data into ATGC format, then you may be wondering if there is a better way to analyze your data. At the moment, there are no genealogy courses, or even genetic genealogy books to explain this. So, short of taking a lot of time studying genetics courses at your local University, I thought a brief review of the subject might be helpful.

There are alternatives to building phylograms. Geneticists build trees all the time. The fact is, there are about 300 tree building programs. Which, of course makes you wonder how many Genetic Genealogists are building trees. I suspect few are building trees for their Projects at this time. There is no software that I know of that attempts to do this (other than "ft2dna" that I wrote).

I have heard via the FTDNA conference in 2009 that Family Tree DNA will be providing a new tree widget for folks, so there is hope for an easier way in the event that you don't have the time to build trees on your own. I understand that FTDNA is using the term "alpha," so I will be trying to gear this article along those lines.


In this article, I'd like to do a brief comparison of the Phylip software
packages. I will compare the use of ATGC frequency data with my standard method of using Dean McGee's Utility (using Dean McGee's Genetic Distance as evaluated with the Kitsch program). By default, Dean McGee's Y-DNA Utility builds the TMRCA charts using the infinite alleles method. This article should be somewhat of a comparison of an infinite alleles model vs. an ATGC frequencies approach to creating phylogenetic trees.


Hopefully, you will get an idea of the differences between DNAPARS, DNAML, DNAMLK, PHYML, and TreePuzzle.

PHYML and TreePuzzle are separate packages, and are not part of the Phylip package.
DNAPARS is a DNA Parsimony Program

DNAML is a DNA Maximum Likelihood Program
DNAMLK is a DNA Maximum Likelihood Program with a molecular clock


For this example, I will use the data from the HAM DNA Group #1, plus an individual from Group #5 (kit 27814) as an outgroup anchor. So, the data is composed of Y-DNA output for 9 individuals, using 37 marker data. ( Kit # 21554 not evaluated because this kit does not contain 37 markers, and most of these tree programs do not function well will data missing from a large number of markers.)


Genetic Distance and resulting trees are of interest to Group01 participants because most participants in this group have not yet identified their immigrant ancestor (through normal genealogical documentation). In fact, this immigration documentation may not even exist due to the destruction of records in Virginia. Kit #N54540 is a more recent immigrant, and has traced his line back to County Somerset, England. Kit #27814 has traced their line back to Elseheim, Germany (and is actually in HAM DNA Group #4, but is included here for the purpose of illustration). The remaining participants has not yet identified their immigrant ancestor. Therefore, understanding the Time to Most Recent Common Ancestor is significant for this group.


Putting it together:


The "control group" chart is from the standard method that is used from Dean McGee's Y-DNA Comparison Utility. It should be noted that this utility uses the infinite alleles model to create PHYLIP compatible Genetic Distance input. The Genetic Distance input is then used with
the Kitsch program to generate a phylogenetic tree.

The program "ft2dna" was used to convert into
ATGC format. At this time, I know of no other software program that will convert Y-DNA Project data (DYS repeat counts) into ATGC format. So, "ft2dna" was used for this purpose. I have tried to check the routines in "ft2dna" for accuracy, but the CAVEAT here is that if I have not done the conversion correctly, then it will affect the outcome of tree creation. Family Tree DNA has a funny way to calculate the Genetic Distance for DYS389i, DYS389ii, YCAIIa, and YCAIIb, and conversion to ATGC values is not published by FTDNA. Tree errors could easily be introduced at the time of conversion into ATGC format, so it is important to note that.


Next, this ATGC information was run through the PHYLIP program "DNADIST" in order to capture Genetic Distance in the form of ATGC frequencies.
That is, an effort was made to derive Genetic Distance independently from Dean McGee's Y-DNA Comparison Utility.


However, as Professor Felsenstein notes in his PHYLIP documentation on distance (distance.html), using frequency data may not be expected to be an independent evaluation (if the distance is computed from the original data by a method which does not correct for reversals and parallelisms in evolution). The example he gives is for (pure) genetic
drift, where the program CONTML may be more appropriate. Felsenstein says that Fitch, Kitsch, and Neighbor may be appropriate for use with frequency data if additivity holds, a neutral mutation model can be assumed, and Nei's genetic distance is used.

So, if you are a Genetic Genealogist, you should be aware that different software programs may deliver different tree results due to the underlying assumptions behind the software. If you are going to use these, then I would suggest that you use a kit with a greater Genetic Distance as an outgroup. The DNADIST program was used with ATGC data for input, and delivered output in the form of frequencies. The frequency output from DNADIST was evaluated using the programs Kitsch, Fitch, and Neighbor. The resulting trees were rooted on the outgroup kit, 27814 usually by selecting option "O" from within each program. Kitsch does not have an "outgroup" option, so the resulting tree was rooted on the outgroup (kit 27814) by the use of the MEGA software program.

The MEGA program was used to compute the "consensus" trees when a consensus was required, and was also used to set the "outgroup root" of the trees when required.


Only 37 markers were used in this study. Here's the normal Genetic Distance and TMRCA for
Group01 using Dean McGee's Utility:






And here's the tree generated by the PHYLIP package "Kitsch":














(click on image to enlarge)







You might notice that Robert is being depicted as having descent from the William HAM of Grayson County, VA, when in fact Robert's ancestors were in England at the time to most recent ancestor. Which should be telling us that 37 markers are not enough to discern a precise date for TMRCA. But, this graph has been close enough for use.


For the remaining comparisons, I converted the data from FTDNA's repeat values into ATGC format. Then, I used the ATGC format as input to the PHYLIP program DNADIST, which produced an output table in the form of frequencies.

The output would look something like this (repeated for each DYS value):

9


40777_WmVA 0.000000 0.000000 0.124014 0.000000 0.000000 0.101782 0.101782 0.101782 0.124014
68140_WmVA 0.000000 0.000000 0.124014 0.000000 0.000000 0.101782 0.101782 0.101782 0.124014
N54540_Rob 0.124014 0.124014 0.000000 0.124014 0.124014 0.103402 0.103402 0.103402 0.000000
58559_WmVA 0.000000 0.000000 0.124014 0.000000 0.000000 0.101782 0.101782 0.101782 0.124014

70450_WmVA 0.000000 0.000000 0.124014 0.000000 0.000000 0.101782 0.101782 0.101782 0.124014

42370_WmNC 0.101782 0.101782 0.103402 0.101782 0.101782 0.000000 0.000000 0.000000 0.103402
55330_WmNC 0.101782 0.101782 0.103402 0.101782 0.101782 0.000000 0.000000 0.000000 0.103402

46246_Geor 0.101782 0.101782 0.103402 0.101782 0.101782 0.000000 0.000000 0.000000
0.103402
27814_Valn 0.124014 0.124014 0.000000 0.124014 0.124014 0.103402 0.103402 0.103402 0.000000
... etc.

Next, these frequency values were used as input into the various options for Fitch and Kistch (F84, Jukes, Kimura, LogDet) programs. (The Fitch and Kistch output on frequency data are not shown here.) The remaining programs used the regular "ATGC" type format as input data.

DNAPARS then produced the following graph for this ATGC data:














(click on image to enlarge)




Which clearly is not correctly rooted. We know this because Valentine has the greatest Genetic Distance for this data. (The numbers there are frequency statistics, and not branch lengths). So, the DNAPARS tree was re-rooted to select Valentine (kit #27814) as the outgroup, which delivered this graph:















(click on image to enlarge)




Which makes better sense, as kit 27814 has the greatest Genetic Distance for this data.
Note that DNAPARS is a parsimony program, and has re-arranged Robert (kit N54540) between the kits that descend from the William HAM of Grayson County, Virginia. This corresponds to the Genetic Distance (above) and has similarities to Dean McGee's Utility output. But, Robert doesn't really belong there, as it is known that Robert does not descend from this particular William HAM. And, DNAPARS does not clearly separate out the paths between WmVA and WmNC. So, there is a slightly noticeable error with the use of DNAPARS.

Before we get to DNAML, let me run through the tree produced by the software program "TreePuzzle." FTDNA has indicated they may be basing new TMRCA estimates upon "alpha," and TreePuzzle was used to obtain "alpha" for HAM DNA Group #1.


Options used from TreePuzzle in order to obtain "alpha:"

"o" to select your outgroup (the one with the greatest Genetic Distance in this data is kit #27814)

"w" (model of heterogeneity) - this returns the number of Gamma rate categories, and it will automatically calculate "alpha"


TreePuzzle delivered the following values:

--------------------------------------------------------------------------------------------
Expected transition/transversion ratio: 2.18

Expected pyrimidine transition/purine transition ratio: 0.02


RATE HETEROGENEITY


Model of rate heterogeneity: Gamma distributed rates

Gamma distribution parameter alpha (estimated from data set): 0.03 (S.E. 0.02)

Number of Gamma rate categories: 8


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

This is the tree obtained from TreePuzzle:










(click on image to enlarge)






Which, of course, needs to be re-rooted about the kit with the greatest Genetic Distance, kit #27814 and this is probably not a fair depiction of where Robert should land on the tree. (The re-root is not shown here.)


At any rate, having obtained a values for "alpha" and "transition/transversion ratio" I am now able to run DNAML with these parameters.


Using alpha = 0.03 and "T" = 2.18, DNAML delivered this tree:















(click on image to enlarge)




DNAML has managed to retain a resemblance of the grouping for the separate William HAM's of VA and NC, the George should be depicted with a greater genetic distance than is indicated here.


The last package evaluated here from PHYLIP is the DNAMLK program, which delivered this tree:














(click on image to enlarge)




Which is to say, after rooting the tree about kit 27814, DNAMLK retains the separation of the NC and VA William
HAM's (two different individuals), but George is probably not best placed on this tree. George has a greater Genetic Distance than the two William's, and is not known to be a descendant of the William HAM of Franklin County, NC. So, there is a slight problem using the options chosen (alpha = 0.03 and "T" = 2.18) with DNAMLK.


Finally, I wanted to include a quick look at PHYML for this article. Here's the tree that I obtained from PHYML:













(click on image to enlarge)




Which is a fairly decent tree (after rooting on 27814), but Robert is mis-placed again here, as N54540 is located within the descendants of the William HAM of Grayson County, VA. Robert is not known to descend from this William (documentation shows his ancestors were in England at the time). But, in all fairness, the Genetic Distance for Robert (according to FTDNA counting methods), does not depict his descent quite correctly either.



In summary, it should be said that I have to work hard to get as good a tree as obtained via Dean McGee's Y-DNA Utility, as run through the Kistch program. To date, these DNA programs require much more effort and much more knowledge of the various options available to each individual program.

I will look forward to seeing the new tree widget from Family Tree DNA, as it will be some relief to see an easier method of generating trees.


If you have a favorite tree building software program not reviewed here, feel free to comment on this Blog.













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Wednesday, March 18, 2009

2009 Family Tree DNA Conference

2009 Family Tree DNA Conference

Two day conference for FTDNA Project Admins
March 14th & 15th, 2009
News items from the conference in Houston


This conference is usually held for FTDNA Project Administrators (such as myself). I didn't attend for a couple of reasons, nor have I ever attended previous conferences.

However, there were some interesting items in Vincent's Twitter area. The ones that caught my eye were the presentations from Michael Hammer on phylogenetic tree models, and the NIST material. The NIST material suggests that I need to check my "ft2dna" program for changes to the model on several DYS values.) Also,
two items that caught my eye are a new phylogenetic tree widget and National Genographic should end by 2011. (I am curious to see if this new tree widget is for individual Project use.)

Naturally, I have an interest in building phylogenetic trees (so that HAM genealogists can understand TMRCA better). That's because when records have been destroyed, TMRCA is a great tool for estimating when and where you should be looking for the more traditional genealogy evidence.

Just this past week, it had been suggested to me that I learn more about "alpha" with regard to my work on building phylogenetic trees.

"Alpha" is a term used along with another term, "Gamma." That term "alpha" was mentioned in Vincent's Twitter area along with Michael Hammer's presentation on phylogenetic trees. Hammer was talking about obtaining a more accurate TMRCA. To me, that's exciting news.

I suspect I will be learning more about alpha. I have run the "TreePuzzle" program for HAM DNA Group #1, and using the defaults, it tells me that HAM DNA Group #1 has a "transition/transversion" ratio of 2.18 and an "alpha" of 0.03. I can use that information in DNAML in order to obtain another tree view for HAM DNA Group #1.

The problem for most DNA Project Administrators is that many of these programs requires data in ATGC format. (FTDNA gives the data in numbers, or a count of the repeats of letters.)

However, I suspect that Hammer is more concerned with the traditional phylogenetic tree that FTDNA produces, a phylogenetic tree of all haplotype groups in the numerous FTDNA Projects. But, Hammer does have a call out for help from Project Administrators who have tested a large number of related families in their Project.

The PHYLIP package has several models to choose from such as neighbor, F84, Kimura, Jukes, LogDet, within his programs. You probably already know that I currently use his "Kitsch" program. That PHYLIP package also contains the maximum likelihood programs "DNAML" and "DNAMLK." There is also the parsimony program "DNAPARS." It stands to reason that maximum likelihood programs should deliver better phylogenetic charts than the parsimony programs due to the nature of how they work.

Anyways, great set of tools for Genetic Genealogists, if you're inclined toward the technical side.


I suspect that I will also be looking out for a program that can help me with Watkin's Gemetric model. There are many Geneticists named Watkins, and no note from ISOGG on which Watkins Vincent is referring to. Without further info, I would guess that Vincent might be referring to Norman E. Watkins.

It looks like the conference mostly followed the same agenda that FTDNA has posted on their web site (I found it through news from October, 2008 - I believe it was delayed due to hurricane Ike.):

http://www.familytreedna.com/news/2008-conference.aspx

Their press release is in PDF form at their web site:

http://www.familytreedna.com/documents/2008-conference-press-release.pdf

(The title of the press release has the 2009 date.)

Twitter is fairly cryptic when you are limited to 140 characters, so I would guess there are a number of folks who may not understand everything that Vincent posted there.

Vincent kept notes on items of interest from the conference in Houston, which occurred March 14th and 15th, 2009.
Vincent's Twitter area is located at:

http://twitter.com/vineviz

Other notes of interest:

Coming soon - a phylogenetic tree widget

FTDNA also announced that they will be returning to Who Do You Think You Are? (WDYTYA) next year in 2010.
FTDNA will have a booth at "The Gathering" in Scotland in July, 2009!

Roberta Estes and Terry Barton gave terrific ISOGG workshop presentations!













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Sunday, February 8, 2009

Researching in England



Researching in England





On occasion, I get a query about doing research in England.



As with any research trip, you get more out of traveling if you are well prepared before your trip. To get the most out of a research trip, you should know what you are looking for, and know where to find it.


If you are researching in the UK, there is a web site that can help you plan your trip:


Ancestor-search.info


In addition to tips on working from home, they include information on "How To" get organized, where you can find local and National Centers, Record Offices, Family History Societies, Parish Registers, Census Returns, Wills, scheduled talks, Calendar of Events, addresses, and local hotels.


For example, if you wanted to research Bristol, go to the section on "Record Centres" select "Record Offices," then "Gloucestershire." Scroll down and you will find the Bristol Record Office, with street address, opening hours, Bristol Record Office Online Catalogue, information about copying materials, web site for the office, the nearby University (library), and where to find bed & breakfast accommodations.


Very nice.


Some of the categories that you can find at this site:


"Organize yourself"


- Courses

- Family History Fairs

- Genealogy talks

- Planning for Archive visits

- Document Photography



"Local Centres"


- Record Offices

- local study centres

- LDS centres

- family history societies

- local history societies



"Sources of information"


- General Register of Births, Marriages, and Deaths

- Census returns

- International Genealogical Index (IGI)

- National Burial index

- Parish Registers

- Wills and Other Probate Documents



"Researching from Home"


- Internet Sources

- Subscription sites

- CD Publications

- Microfilm & Microfiche

- Books

- Copy Documents



Plus information about National and International Centers of information.


If you want to plan a trip for research in the UK, this is a web site that could be helpful.









Saturday, February 7, 2009

HAM Counties of Origin in North Carolina video



I have posted a You Tube video of the
Counties of origin of the HAM surname in North Carolina prior to 1830. From the book "A Short History of the HAM Surname in Virginia & NC."




It gives a quick overview of the migration pattern for the HAM surname in North Carolina prior to 1830. Lists names of first inhabitants with the surname HAM(M) by County.


As with the video on Virginia
origins, I had to make a judgment call on which person to list and a few adjustments were made in order for the video to make better sense. Sometimes only the last name is mentioned, or the full name is mentioned in a document without any indication if the person actually lived there. In one case, a person is named, but the next year, three people were named as living in the County. Judgment call to include all three (1790 Franklin County). Richard HAM and wife Diana are mentioned in Granville, Bute, and Warren Counties. Should help to distinguish from the Richard HAM of Wayne County. As with (Old) Rhappahannock County in Virginia, Bute and Dobbs Counties were abolished.


A judgment call was made to to include them for this video.
So, unlike the Virginia video, I attempted to include the now extinct counties of Bute and Dobbs.



The timeline on these extinct counties looks something like this:


------->1764-------> 1779

Granville -->> Bute County -->> Warren & Franklin Counties




------->1779------->1791------->1799


Dobbs -->> Dobbs & Wayne -->> Wayne, Glasgow & Lenoir -->> Wayne, Greene & Lenoir




Counties_of_Origin_North_Carolina.flv



http://www.youtube.com/watch?v=0vc--suf01A


3.5 minutes, 5 MB



Music by Ilya Gordon, "The GetAway" & "Winterfell"



http://music.download.com/ilyagordon


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Thursday, February 5, 2009

Parish Registers on line


Parish Registers on line

from the Internet Archive web site


Here's a genealogy related internet web site that is a thrill to see:



Internet Archive



They have an ongoing project to reproduce parish registers that have been long out of print.
Some of these can be purchased on CDROM from Broderbund, some can be found in our book, "A Short History of the HAM Surname in Virginia & NC."



They offer a small collection of Parish Registers, and is by no means complete.
But, if you'd like to have a copy of the Register in PDF format, or if you'd just like to search it in full text on line, you can do it at this site. (Nice!)



A short list of some of the titles:



Cornwall Parish Registers - (England) full text from the Phillimore Book, first published in 1905

Kent - Parish Register of St. Mary Chislet in England




Lancashire Parish Register #1 - from the Lancashire Parish Register Society

Middlesex - Parish Register of St. George, Hanover Square by John Henry Chapman, 1886

Middlesex - Parish Register of St. James Clarkenwell (part 1) by Robert Hovenden, Harleian Society, 1891

Middlesex - Parish Register of St. James Clarkenwell (part 2) by Robert Hovenden, Harleian Society, 1891

Register of St. Philip's Parish Charles Town, South Carolina, 1720-1758 by Alexander Samuel Salley (1904)




There are a number of parish registers located at this site. The list includes England, Ireland, Scotland, South Carolina, and Virginia. You can do a search for "parish register" among "All Media Types" to find a more complete list.



The only complaint that I could possibly have is that you have to contend with the typographical errors. The typing is usually pretty good, but at times it can throw you off.



Having many of these in our book, it is nice to have a personal PDF copy of these registers on my PC.






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Monday, February 2, 2009

HAM African American Origins in Virginia


HAM(M) Surname
African American Origins in Virginia



James Ham of Ashe County once told me that he once heard of African Americans carrying the name "Ham."

He looked at me as if he was surprised, as if he never heard of that. Well, yes, Jim they do exist. African American HAM's are out there somewhere. I suspect many of them now live near the larger cities in northern US.

I have to admit, when I started research on my ancestors, I was disillusioned by the Television series "Roots."
I thought I'd ve sure to find my plantation owning ancestor being cruel to their slaves. After all, I was researching my line in the south.

The reality is, I found plantation owners were few and far between, and certainly not in my direct line. I was not finding those slaves. No Kunte Kinte, no cracker jack slave master. No drama. The main thing I found in my line was mountain men, and a Church. The Church seemed to have some importance to them.

What was I doing wrong?

Nothing. Turns out that our research showed most HAM folks could not afford slaves. I was certainly not seeing many slaves among mountain men. But, we did find those slaves among other HAM lines. And yes, there was cruelty. As you will see below, a negro named Jack had an severe experience in the public Court of Amelia County.

I have seen a transcript that reported my William HAM owned a female slave in 1860.
I thought perhaps owned for less than 10 years to take care of an elderly couple. However, the actual image of the 1860 Census shows no slaves for the couple. The Census indicated by a mark in one column that his wife could not read. So, perhaps there could have been an error in transcription.

In my search for my own ancestors, I was hearing those (supposedly shameful) reports that some of my ancestors most likely deserted during the Civil War. Well, O.K., I can understand deserting when one lone deaf and dumb male is left out of the war to handle the farming for five other families whose males were off fighting for the cause. But, if you don't own slaves to start with, and when you get news that your first cousin dies, your step brother is maimed, and your father has passed away, then sure, I suppose I'd want to leave and tend to my father's funeral as well. But, that's another story.

African American ancestry is not something I concentrated on in the book. There were just not that many slaves to be found, in comparison with the rest of the material. But, you can glean some evidence for African American origins from a review of our volume on Virginia. For example, Geneva had researched Amelia County, and found an interesting story there.

Upon gaining their freedom, slaves would usually take on the last name of their owners. I suppose that was simply because they needed a last name. (While they were slaves, they only had first names in almost all cases.)

With the advent of President Obama, I am hoping that we might begin to see more African American participants in the HAM DNA Project.

Anyways, I tooks a quick survey of a timeline on African Americans in Virginia. We have detailed records from over 22 Virginia Counties in volume #2, and only about 9 of these Counties report African slaves in those early years. (Sorry, at the moment I don't recall exactly how many Counties we researched in Virginia and have in our book.)

More details on these entries that can be found in volume 2 of "A Short History of the HAM Surname in Virginia & NC."

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African Americans associated with the HAM surname:

First slaves to appear

1751 Estate of John LUCAS includes 3 slaves in Orange County, VA. Attending are Samuel HAM and William HAM
1760 Thomas HAMM estate divdes up his slaves in Caroline County, VA
1765 William DULANY to William HUME transaction of 2 slaves in Culpeper County, VA
1766 Thomas HAM witness to the will of Richard JONES, mentions negro woman Nancy in Amelia County, VA
1775 George HAM gives one negro boy named Lott to Dudley JOLLY in Amelia County, VA
1782 George HAM owns 2 blacks on the Enumerations in Amelia County, VA
1782 Mary HAM owns 4 blacks on the Enumerations in Amelia County, VA
1782 William HAM owns 5 blacks on the Enumerations in Amelia County, VA
1783 Stephen HAMM owns 3 blacks on the Enumerations for Amherst County, VA
1787 Mary HAM 6 blacks on the Enumerations in Amelia County, VA
1787 William HAM 4 blacks on the Enumerations in Amelia County, VA
1787 Stephen HAMM owns 6 blacks on the Enumerations for Amherst County, VA
1787 William HAM 1 black on the Enumerations in Madison County, VA
1790 George HAM and David ALLIN report stolen property in Amelia County, VA.
Missing include sheets, one tablecloth, shirts, and overalls.
A negro named Jack (property of William EGGLESTON) pleads not guilty, but is found guilty and burnt in the hand as he stands
at the bar.
1796 Samuel HAM has 1 negro on the Tax Lists for Greenbrier County, VA (now WV)
1800 John HAMM has one slave in Amelia County, VA
1800 William HAMM has one slave in Amelia County, VA
1800 William HAMM has one slave in Amherst County, VA
1804 William HAM will frees his slaves in Amelia County, VA. These freed slaves become successful landowners and slave owners themselves.
1810 Elijah HAM owns 5 slaves on the census for Albemarle County, VA
1810 James HAMM owns 1 slave on the census for Amelia County, VA
1810 Stephen HAM names slaves in his will in Amherst County, VA
1810 John HAM owns 3 slaves on the census for Amelia County, VA
1810 Stephen HAMM owns 16 slaves on the census for Amelia County, VA
1819 Joseph HAM names negro woman Leah in his will in Orange Co., VA
1833 Negro Ham is on the List of "Free Negroes" in King and Queen County, VA
King and Queen County 1833 lists "Free Negroes" Patty HAM, Henry HAM, Penelope HAM, Agnes HAM, Shadrack HAM, Roberta HAM, Randal HAM, Dandridge HAM, and Davy HAM
1835 Samuel HAM estate lists 12 slaves in Orange County, VA
1856 Stuther HAM loans slaves to his mother in Albemarle County, VA
1860 Betsy HAM is a free woman of color in Amelia County, VA

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Counties listed above, from volume #2:

01 Orange County beginning in 1751.
02 Caroline County beginning in 1760.
03 Culpeper County, this is for the HUME surname, beginning in 1765.
04 Amelia County beginning in 1766 with the JONES family.
05 Amherst County beginning in 1783.
06 Madison County beginning in 1787.
07 Greenbrier County (now WV) beginning in 1796
08 Albemarle County beginning in 1810.
09 King and Queen County beginning in 1833.

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Sunday, February 1, 2009

1637 John HAM of Bristol

1637 John HAM of Bristol


Bristol ties? HAM genealogists have been asking this question for the last 40 years.

The problem started in 1969 with the popular genealogy book "Historical Southern Families" by Mrs. John Bennett Boddie (Genealogical Publishing Company, Baltimore). She miss-identifies the wife of Jerome HAM of Virginia, and makes mention of Jerome HAM of Bristol. HAM Genealogists consistently tie the two together as one man since then.

"Historical Southern Families" has been a very popular book, selling thousands of copies. So, the miss-information has now spread widely and amateur genealogists stubbornly resist the facts. And, I have tried to lay out the facts in "A Short History of the HAM Surname in Virginia & NC."

The confusion is only heightened when Beverly Fleet's "Virginia Colonial Abstracts" mentions "Hierome" HAM in Charles City County in 1655. And the list of errors goes on and on....

If you look at the genealogy trees on Ancestry.com, you'd think 97% of genealogists have figured it out by now. Unfortunately, now hundreds of HAM family trees are based upon miss-information.

For those who are following the saga, let me add a document indexed at the Library of Virginia, which is not in any HAM genealogy book to date. This document relates to the sale of tobacco in Virginia by a John HAM of Bristol, England (published 1641).










---------------------------------------------------------
To see the record, follow these instructions:


Search the Colonial Records Project at:

http://www.lva.virginia.gov/
or
http://ajax.lva.lib.va.us/F/?func=file&file_name=find-b-clas27&local_base=CLAS27

Basic search:
Words to search: HAM Bristol

Fields to search:
Words Anywhere

Words Adjacent? No


(if you have Pop-Up Stopper software installed, you will need to disable it to enable this search.)


- Click on the number "1" to view the transcript record.
---------------------------------------------------------
Va. Colonial Records Survey Report No. SR 10962


Microfilm Reel No. Not Filmed, but there is a typed abstract on file with the Virginia Colonial Records Project
A copy of the original can probably be obtained from the Bristol Public Record Office.

Author/Depository: Public Record Office Class: E 134 17 Charles I, Mich 29.


Title LinkExchequer King’s Remembrancer. Depositions taken by Commission
Publication 1641 Gen. note Exchequer King’s Remembrancer. Depositions taken by Commission. vol. II, p. 517

Ham, John -- testimony by -- 1641, SR 10962, p. 2.
-------------------------------------------
dated Sep 27, 1641

Depositions taken at Bristol, Sep 27, 1641

Sep 27, 1641


John HAM testimony: Some tobacco was landed Legally, having a warrant from the Lord Treasurer, but some was not.


Deposition, n.d.:


John HAM testimony: Tobacco was put in warehouses.

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

note: - It appears that the Lord Treasurer issued Treasury Warrants in about 1637 for the importation of tobacco into Bristol ports on board some ships
such as the Lilley and the James. However, no warrant was issued for the ships Welcomb and Prudence. So, in 1641 (about three years later), a Commission was formed to investigate and impose custom rates and duties upon the tobacco that was imported without a warrant from the customs house. These ships were sailing from Virginia and the West Indies.

-------------------------------------------
The question is interesting is because there are several HAM's in both the areas of Bristol and Virginia at the time.


Jerome HAM of Bristol was Merchant and Town Clerk of Bristol from 1581 to 1621. That would be a 40 year career. As Town Clerk, his signature is
on numerous records, and his name is sometimes written as "Hierome HAM."


He marries the widow of John OLIVER in 1598/99. His wife Elizabeth HAM dies in 1619. No children bearing the HAM surname are mentioned in her will. Jerome HAM probably died some years prior to 1638. To my knowledge, his will has not yet been located.

Joseph HAM immigrates to Virginia in about 1621 at the age of 16. Indentured servant to Lt. Albiano Lupo. Settles on the New Posquoson.


In 1635, William HAM of Maine and New Hampshire arrives at the Richmond Isles on the ship named Speedwell. He is originally contracted to fish.


Joseph HAM of the New Posquoson dies in York County, Virginia on March 3, 1638. He had immigrated to Virginia in about 1621 at the age of 16,
and left no known children bearing the HAM surname.

From 1637 to 1641, this deposition at Bristol indicates that a John HAM of Bristol was importing tobacco from Virginia to Bristol from about 1637 to 1641.

In 1653, John HAM gentleman of Bristol files will. He mentions a son John HAM and three daughters, Penelope, Mary, and Anna. He dies in about 1654.

Jerome HAM of York County has not been found in records from Virginia until 1652. And, "Hierome HAM" is mentioned in Charles City County
records in 1655. It would appear that both the Jerome HAM of Bristol and the Jerome HAM of Virginia both went by the name of "Hierome HAM."

Very curious. The York County Jerome HAM is mentioned in Lower Norfolk County, Virginia as "Jeremy HAM," to note the difference in
pronunciation. He dies in 1659, leaving one son, Jerome HAM, Jr.

John HAM immigrates to Virginia in 1658. We may never know if he participated in the estate settlement on Jerome HAM because Jamestown
records were destroyed by fire in 1699.
George HAM immigrates to Maryland in 1660.

Rosse HAMM, apprenticed in Bristol, England is bound for 4 years as an indentured servant to John BEARE in Virginia in 1662.

John HAM of New Hampshire arrives in Dover, New Hampshire in 1665.

Thomas HAMMS, apprenticed in Bristol, England is bound for 4 years as an indentured servant to Edward POORE in Virginia in 1667.

Elijah HAM, of Albemarle County, VA purchases 132 acres of land from James HARTFORD of Bristol, Kingdom of Great Britain in 1810.


It has not yet been determined if these early immigrants are related in any way. The John HAM importing tobacco to Bristol in 1637 could be either the John HAM who dies in Bristol in 1653, or his son John HAM.

There are two items that we have been trying to address in order to help straighten out the miss-information. One is we give the details regarding the correct information in our book, "A Short History of the HAM Surname in Virginia & NC." The second is we are seeking participants in the HAM DNA Project which is helping to resolve this Bristol question, among other things.

At last count, over 700 family trees have bad information about Jerome HAM.
Let's hope that we don't have to wait another 40 years to clean this up.


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