Showing posts with label Journal of Genetic Genealogy. Show all posts
Showing posts with label Journal of Genetic Genealogy. Show all posts

Tuesday, November 24, 2009

Journal of Genetic Genealogy - Fall, 2009

The Journal of Genetic Genealogy (JoGG)
Fall Issue, 2009



The Fall issue of the Journal of Genetic Genealogy (JoGG) has just been released. The largest issue in their five year history, packed with a lot of material of interest to Genetic Genealogists. With over 220 pages, you should find about 10 articles and three reports in this issue.


Among the items of interest include an announcement from Whit Athey that he will retire as editor, being replaced by Blaine Bettinger. Many of you should recognize Whit as the creator of the Haplotype Predictor utility. Whit mentions that he has observed genetic genealogists move from dependence upon the scientific community for information, to the use of DNA now being led by "amateurs."


One article is from Roberta Estes, regarding the use of DNA with Native American dispersal and the Lost Colony of Roanoke. "Where Have All the Indians Gone? Native American Eastern Seaboard Dispersal, Genealogy and DNA in Relation to Sir Walter Raleigh's Lost Colony of Roanoke"


Another article is from Chris Pomery, "The Advantages of a Dual DNA/Documentary Approach to Reconstruct the Famiiy Trees of a Surname." Chris outlines a method for combining Y-DNA results with documentary evidence in order to reveal the origins of a surname.



There is also a "Special Section" here, regarding "Cluster Analysis and the TMRCA Problem." This includes about seven articles on:



Introduction by Whit Athey


An overview of the pitfalls and cutting edge views on topics related to calculating Time to Most Recent Common Ancestor (TMRCA). Whit looks at the use of mutation rates, transmissions, over-counting, rho, "genealogical structure factor," an "effective mutation rate" procedure, and more. Nice overview, if you want to take a deep dive into the following articles.


Y-STR Mountains in Haplospace, Part I: Methods
by Peter Gwozdz



Y-STR Mountains in Haplospace, Part II: Application to Common Polish Clades
by Peter Gwozdz


DNA Genealogy, Mutation Rates, and Some Historical Evidence Written in Y-Chromosome, Part I: Basic Principles and the Method
by Anatole A. Klyosov

DNA Genealogy, Mutation Rates, and Some Historical Evidence Written in Y-Chromosome, Part II: Walking the Map
by Anatole A. Klyosov

The Use of Correlation Techniques for the Analysis of Pairs of Y-Chromosome DNA Haplotypes, Part I: Rationale, Methodology and Genealogy Time Scale
by William E. Howard


The Use of Correlation Techniques for the Analysis of Pairs of Y-Chromosome DNA Haplotypes, Part II: Application to Surname and Other Haplotype Clusters
by William E. Howard

You will find the fall isuue of JoGG at:

http://www.jogg.info/
















Thursday, June 4, 2009

Journal of Genetic Genealogy - Spring, 2009



Journal Of Genetic Genealogy (JOGG)

Spring Issue now available




The spring issue of the Journal of Genetic Genealogy is now available. There may be a few items of interest to those who are keeping track of the DNA Project:




1) A commentary about the DAR vs. the use of DNA by Whit Athey.
The DAR is avoiding the use of DNA as evidence of descent from a Revolutionary War Veteran.


2) An article regarding Y-DNA traits of lines originating in Ireland.
Pointing to R1b types, there are certain DYS values that help determine Irish Origins.
Here, Dennis Wright expands on some work originally discovered by Ken Nordtvedt.


3) There are also three mtDNA articles.


You should find the Journal of Genetic Genealogy at:


http://www.jogg.info/





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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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