How to do a Y-DNA study: including Next Generation Sequencing Which can contain atDNA, STR Y-DNA and SNP Y-DNA Paperback – June 22, 2017

https://www.amazon.com/dp/1548313629/ref=sr_1_1?ie=UTF8&qid=1499667841&sr=8-1&keywords=how+to+do+a+Y+DNA+study  

by James Lee Rader

Some of the topics in the Index

 

One Name Study Published in Journal of One-Name Studies, 2012

You should use DNA like any other type of record to prove your research!

What do you want to prove?

Which type of DNA will help?

That includes Y-STR, Y-SNP testing,

Autosomal DNA testing (atDNA)

Mitochondrial DNA (mtDNA) testing where appropriate

How accurate are these tests?

What has Studying Y-DNA taught us

The Casper Rader Y-DNA study

The original test concluded in 2006

you should not take a DNA test!  Do a  Y- STR study

FTDNA finishes the testing, and we have unique SNPs

What does testing more STR locations in Y-DNA give you?

Family Tree DNA Y- STR Results

The original FTDNA Rader Y-DNA Surname study

Y111-STR results differences table

Y-Full Report  STRS 491

YFull’s report on STR matches from the Big-Y test

See Appendix for full list of STRs

What do other analysts have to say?

Y-Tree is producing a tree of matches

A progress report on using big Y results.

Big-Y results, do I understand this correctly?

Compare novel variants all 4

Why do you want to know the rest of your SNP errors?

Will you know where these people lived when the SNPs happened?

Big-Y Introduction

Goal of Big Y test

Detailed look at SNPs

How does YFull determine “formed” age and “TMRCA,”

What is YFull’s age estimation methodology?

clarifYDNA

A progress report on using big Y results.

ClarifyDNA results with just two BigY report

FTDNA reports for Big-Y

Family Finder reports – Rader relatives

YFull reports

We’ll solve your Y-Chromosome Puzzle!

NextGen Sequence Interpretation  $49

Yfull results based on YFull YTree v5.03 at 09 April 2017

Other information from Big-Y

110 to 170 years  between new SNPs

Age with 1 Big-Y test

Age with 3 Big-Y tests

Age with 4 Big-Y tests

Accuracy of Big-Y test according to YFull

Yfull finishes, and we no longer have unique SNPs

How to place your terminal SNP in time and place

Genetic Genealogy

New Genetics and Society

bell beaker behemoth coming out soon

Eurogenes Blog: The Bell Beaker Behemoth (Olalde et al. 2017 preprint)

Eurogenes Blog: Latest on Bell Beaker and Corded Ware

Population genetics: A map of human wanderlust

Wiley: An Introduction to Molecular Anthropology – Mark Stoneking

atDNA results

Summary of the Autosomal testing

Compared all STRS table

Jim’s YFull full SNP list and report

How closely are they related

The first test was processed by FTDNA with their relative finder. This test is like the one that’s offered by ancestry.com and called there everything test. This test is an autosomal test. It looks at samples of your DNA from all chromosomes except for the Y chromosome.

Our four candidates Alton Earl Jim and Harry are fourth cousins twice removed. The relationship between Harry and Jim are second cousin once removed but they also have fourth cousin removed relationships on two other lines. We know these relationships through standard genealogical research which is well-documented.

Using the GEDmatch 3D Chromosome Browser we get a nice chart showing the relationship between our four candidates. Earl and James share no DNA the rest of the relationships include one segment of the DNA. Harry and Jim share five segments because of their closer relationship.

Segments in common:

Kit Name T579239 T055537 T829743 T918718 Tot. Segments Largest cM
T579239 Earl Rader 0 2 2 4 31.8
T055537 James Lee Rader 0 5 1 6 22.1
T829743 Harry Rader 2 5 1 8 22.1
T918718 Alton Rader 2 1 1 4 31.8

Autosomal DNA shared between pairs of relatives at the fourth cousin level normally share 13 cM but the fourth cousins once removed would only share 6 cM. So in our circumstance with the twice removed we would expect 3 cM.

The expected level between Harry and Jim are that of second cousins once removed which on average 106 centiMorgans The expected level between Harry and Jim are that of second cousins once removed which on average 106 centiMorgans. Using this table you can see the share five segments.

 

Total Shared cM (Chr 1-22):

Kit Name T579239 T055537 T829743 T918718
T579239 Earl Rader None 19.7 48.3
T055537 James Lee Rader None 78.3 5.1
T829743 Harry Rader 19.7 78.3 11.4
T918718 Alton Rader 48.3 5.1 11.4

Summary by Chromosome:

Chr Tot. Matching Segments
for all individuals.
B36 Graphic Posn Range Largest
segment
From To
1 0 72017 247185615 None
2 0 8674 242697433 None
3 1 36495 199322659 20.2
4 1 49009 191200760 31.8
5 0 78452 180630744 None
6 0 100815 170761395 None
7 0 139250 158812247 None
8 2 154984 146264218 11.4
9 2 36587 140208462 16.5
10 0 84172 135358259 None
11 0 188510 134445626 None
12 0 61880 132288869 None
13 0 17956717 114121631 None
14 2 18325726 106358708 21.6
15 1 18294933 100278685 9.2
16 0 28165 88690776 None
17 1 8547 78653169 5.1
18 0 3034 76116152 None
19 0 211912 63788972 None
20 0 9098 62382907 None
21 0 9849404 46924583 None
22 1 14494244 49558258 22.1
23 0 2321 154889941 None

Segment Details:

Kit1 Kit2 Chr Build 36 cM
Kit Nbr. Name Kit Nbr. Name From To
T055537 James Lee Rader T829743 Harry Rader 3 10215159 25460760 20.2
T579239 Earl Rader T918718 Alton Rader 4 121202707 157186835 31.8
T055537 James Lee Rader T829743 Harry Rader 8 140535029 143182478 5.2
T829743 Harry Rader T918718 Alton Rader 8 135910061 141152797 11.4
T579239 Earl Rader T918718 Alton Rader 9 129350655 136524980 16.5
T579239 Earl Rader T829743 Harry Rader 9 136263069 140147760 13.6
T055537 James Lee Rader T829743 Harry Rader 14 88480306 97899028 21.6
T579239 Earl Rader T829743 Harry Rader 14 30421536 32553908 6.1
T055537 James Lee Rader T829743 Harry Rader 15 88047217 91532308 9.2
T055537 James Lee Rader T918718 Alton Rader 17 27056533 29380126 5.1
T055537 James Lee Rader T829743 Harry Rader 22 43130670 49528625 22.1

These results are based on the 5.0 cM / 500 SNP threshold that you specified on the preceeding page. Because of that,
these results may be somewhat different than those obtained in the one-to-one and one-to-many utilities, which
use the site default values. Default values vary depending on the testing company that provided the kit.

Top of Form

 

cM color coding < 3 cM 3 – 5 cM 5 – 10 cM 10 – 20 cM 20 – 50 cM 50 – 100 cM Over 100 cM

Bottom of Form
Software Version: Apr 12 2016 20:55:43

Big-Y results, do I understand this correctly?

These are the people involved in the 2016 Big-Y study

What can NGS testing prove?
I have a group of four men all who descended from the same person who was born in 1732. I have the big Y results for all four men. These four men match on Y-111 stir testing at least 110 out of 111 STRs.

My Genealogy research shows me that I am related to the 3 men who I am testing as follows:
1. Earl is a 4th cousin twice removed on my Rader line
2. Alton is a 4th cousin twice removed on my Rader line
3. Harry is a 2nd cousin once removed on my Rader line
And a 4th cousin twice removed on my Bauer line
And a 4th cousin twice removed on my Andes line
The genealogy research on these four men is quite thorough. It is been researched by multiple researchers who publish results over the last 50 years. Has been confirmed by extensive land of probate research.
The table below entitled “compare novel variants all 4 28Jan17” displays a lot of details obtained from that study.
The left column entitled Yseq with values highlighted in yellow are the locations which I had tested with Sanger test methods to verify that the results from the big Y were accurate.
The second column is the name that these particular locations are known by, at some companies.
The next section which is highlighted in green are the results from my big Y tests. The numbers are the physical location being tested.
The section which is not highlighted his Harry’s test results followed by the blue highlighted section with Earl’s test results and the final section in the right hand side is Alton’s results
I aligned them so that the places where there are blank spaces are locations where we do not match! You will see that we do not match an equal amount or in the same places. Jim has 23 unique variants, Harry has 16 variants, Earl has 28, and Alton 22.

I assume that any snip that they all have would be a snip the original man had. What I don’t know is when three out of four of them have a snip how could that happen? Harry’s test is lacking many matches that the other three have. If the original man Casper had them and Jim who is downline from harry has them then Harry must also have them!

One guess is that there is a mistake in testing and test missed that particular snip. Another guess would be that when his father created his spirm he made an error at that same location which caused the SNP to flip back to the original value. The problem with that is that 7 positions do not flip in 120 years (the time between Henry 1829 and Jim 1942)

This report is on the Y-111 part of those tests

January 16, 2017 Report on test results from

 the Descendants of Casper Rader Y-DNA study


This report is on the Y-111 part of those tests

There are three major groups of tests included in this study

SO WHAT’S YOUR STORY?

  1. With a simple cheek swab, discover your roots, connect the dots and unlock your family history. Our signature DNA test provides powerful tools to find your DNA matches, trace your lineage through time and validate family connections.
  2. Our Y-DNA tests check for specific markers on the Y chromosome. 37 markers is a good place to start and can confirm close relationships. Increase your marker count to 67 or 111 for even greater confidence!  Connect to matches

Free access to group projects & experts on your lineage. Automated updates to your results. Free webinars with a professional genetic genealogist. Personalized customer support. Uncover up to 340,000 years

  1. The Big Y product is a Y-chromosome direct paternal lineage test. We have designed it to explore deep ancestral links on our common paternal tree. Big Y tests thousands of known branch markers as well as millions of places where there may be new branch markers. It is intended for expert users with an interest in advancing science.

It may also be of great interest to genealogy researchers of a specific lineage. It is not, however, a test for matching you to one or more men with the same surname in the way of our Y-DNA37 and other tests.

What is a Y-Chromosome DNA (Y-DNA) STR test? What will I learn?

From www.ftdna.com

A Y-DNA test looks at male inherited Y-Chromosome DNA. As the Y-Chromosome is passed on from a father to his sons, it is only found in males. Y-DNA testing can then be used to trace clearly a direct paternal line.

When testing the Y-Chromosome, there are two types of tests, short tandem repeat (STR) and single nucleotide polymorphism (SNP). STR tests are best for recent ancestry while SNP tests tell about more ancient ancestry. Our standard Y-DNA panels use STRs and are useful in verifying common ancestry between two males and finding genetic cousins on the paternal line.

However, each of our Y-DNA STR tests comes with a haplogroup prediction that is backed by our SNP Assurance policy. Our Y-DNA STR tests can also then be used for determining geographic origins of the direct paternal line as well as the deep ancestral origins.

If two men share a surname, how should the genetic distance at 111 Y-chromosome STR markers be interpreted?

In cultures where surnames are passed from father to son, there is additional evidence beyond a DNA match that two men who share a surname are related. Y-chromosome DNA (Y-DNA) test results should be interpreted based on both this information and the actual results.

 

Confidence

50%    90%    95%    99%

0          Very Tightly Related           A 111/111 match indicates a very close or immediate relationship. Most exact matches are 3rd cousins or closer, and over half are related within two generations (1st cousins).

2          4          5          6

1          Tightly Related         A 110/111 match indicates a close relationship. Most one-off matches are 5th or more recent cousins, and over half are 2nd cousins or closer.

3          6          7          9

2          Tightly Related         A 109/111 match indicates a close relationship. Most matches are 7th cousins or closer, and over half are 4th or more recent cousins.

5          8          9          11

3          Related          A 108/111 match indicates a genealogical relationship. Most matches at this level are related as 9th cousins or closer, and over half will be 5th or more recent cousins. This is well within the range of traditional genealogy.

6          10       11       14

Source https://www.familytreedna.com/learn/y-dna-testing/y-str/two-men-share-surname-genetic-distance-111-y-chromosome-str-markers-interpreted/

Y-DNA111 will Confidently, affirm a family group match between two or more men, and rule out (disprove) genealogical connections. Distinguish with the highest certainty possible the difference between recent and distant genealogical matches.

Y-DNA111: The Y-DNA111 test includes a balanced panel of sixty-seven Y-DNA STR markers, those from the Y-DNA67 plus forty-four more. The additional markers refine the predicted time period in which two individuals are related. They completely eliminate unrelated matches. A close match at 111 markers indicates a common ancestor in recent generations, and an exact match indicates a close or immediate relationship.

Y-DNA111    results as displayed on individual page

Alton Rader

111 MARKERS – 3 MATCHES

GD         Name           DNA Haplogroup              Terminal SNP     Match Date

1            James Lee Rader             R-Y15646              Y15646           1/15/2017

1            Harry Wayne Rader        R-Y15784              Y15784            1/15/2017

2            Earl Francis Rader         R-Y15783              Y15783             1/15/2017

Harry Wayne Rader

GD         Name       Y-DNA Haplogroup              Terminal SNP     Match Date

0            James Lee Rader         R-Y15646              Y15646              12/11/2016

1            Alton Rader                 R-M269                                            1/15/2017

1            Earl Francis Rader      R-Y15783              Y15783               12/21/2016

Earl Francis Rader

GD         Name       Y-DNA Haplogroup              Terminal SNP     Match Date

1            James Lee Rader        R-Y15646              Y15646               12/21/2016

1            Harry Wayne Rader    R-Y15784              Y15784               12/21/2016

2            Alton Rader               R-M269                                             1/15/2017

James Lee Rader

GD         Name       Y-DNA Haplogroup              Terminal SNP     Match Date

0            Harry Wayne        R-Y15784              Y15784               12/11/2016

1            Alton Rader           R-M269                                            1/15/2017

1            Earl Francis Rader   R-Y15783              Y15783               12/21/2016

GD = Genetic Distance

So what does this prove, we are Tightly Related.  But Harry and Jim are Very Tightly Related.

Out of 111 places tested we all match on 110.  Earl has a different value at location DYS533 and Alton has a different match at location DYS712

How I started studying Rader/Roeder/Rotter families in the 80s

My study of the Rader or should I say my Rader ancestry began with a question from one of my nieces. Where do we come from? And I naïvely said I should be able to figure that out. It’s now been 30 years and I still don’t know where Casper Rader came from!

So where did I actually start and what did I do to get to the current point. I first started asking relatives family members and others where did my family come from.? After talking to my father’s sister multiple times she said “oh you don’t know that we came from Greenville Tennessee”. And furthermore there is a living cousin back there who is studying the family.

With that I contacted Margaret Rader from Greenville Tennessee. She liked to tell the story of her father’s calling her whenever a stranger came into town asking about Rader’s. He would say “sister go get your book” her book was a three-ring binder about 3 inches in size with what we call family group sheets and it. After she provided me a copy of her family group sheets I then started looking for a computer program to manage this data with.

In the early 1988 Roots III was the first database program I used followed by many others over the years. As I started entering the data I received from Margaret it became obvious that the names of the people were not unique. There are many John’s and Henry’s and Williams and many of them born the same time period. And it became very difficult to separate them and keep straight which one was on which tree. And the data wasn’t real complete so we weren’t sure how many trees there were.

Over the years that followed I attempted to create a complete database of all people who used the name Rader in the world. When they 1880 US Census became available on CD I extracted all of the Rader families in that Census and entered them in my database. I also harvested many databases from the roots web website and added them to my database. And by using the duplicates tool on the software I was able to merge people who I had found in more than one place. But I was still unable to tell whether I had the Raders from before the Civil War in Greene County Tennessee.

So at this point I started looking at land records and probate records try to figure out which John Rader was belonged to which family. In 2003 I hired a local researcher from Greene County Tennessee to map all of the deeds on quad maps so we could figure out where they were in Greene County. That also helped separate them and collect them properly.

In an attempt to get more people involved I started publishing the material I had collected. That effort culminated with the publishing in 1995 of my multi-volume work- “Second Attempt to collect ALL of the Roder, Reader, Raeder, ROder, Roeder, Ritter families in America”. I also loaded most of this genealogy on most of the on line databases. Over the years since then I’ve added to the database and corrected many things that were duplicates and errors in the database. Also use tools like ancestry.com to add siblings and other family members. I included my other great great great grandparents and also included all of their descendants of that effort to find living cousin’s. A database today has over 100,000 people in it.

In the year 2002 I took my first DNA test. And as I attempted to understand the use of the DNA as a tool for genealogy I took many more tests. I have been taking DNA tests for 14 years now and over 25 different test with many different companies.