Part 7 – Raw DNA From 5 Siblings and a Mother – DNA From Mom

I’ve spent my last 6 Blogs on this topic finding out which alleles came from my dad. In this Blog, I would like to work on finding my siblings’ and my alleles that come from mom.

The Ironic Step of Phasing – Mom Alleles from Dad Alleles

I call this ironic step in that it was my mom that was tested for DNA. Based on her results we found out a lot of the alleles that her children got from our dad who passed away quite a while ago. Now, we use those alleles we got from dad to figure out which alleles we got from mom. From the Whit Athey Paper referenced at the ISOGG Web Page on Phasing:

If a child is heterozygous at a particular SNP, and if it is possible to determine which parent contributed one of the bases, then the other parent necessarily contributed the other (or alternate) base.

 

First I copy my FillinOne Table to a MomfromDadOne Table. Then I’ll do a query on that.

This says where I am heterozygous, and I have an allele from dad, I want to see where I’m missing one from mom.

I have over 50,000 of these which will be easy to update. I will want to put Joelallele2 in the blank where JoelfromDad = Joelallele1. Then I will want Joelallele1 in the JoelfromMom space when my allele from Dad is Joelallele2.

I ran this query twice for each sibling, so 10 times. This updated 50-60,000 alleles per sibling, so about a quarter of a million alleles altogether.

Finding Mom Patterns

Now that I have filled in more alleles from Mom, it should be easier to find Mom Patterns. Here is a Query to find Min and Max for the AAAAB Pattern:

Results in:

This saves a lot of time and gives me the start and stop positions of all the AAAAB Mom Patterns. In my previous look which I now see as premature, I only found 2 AAAAB Patterns. Now thanks to my MomfromDad update above, I have at least 17 AAAAB Patterns. The only drawback is that if there is more than one AAAAB Pattern within a Chromosome, it will not show that. However, if I run all the Mom Patterns, and find overlapping Patterns, that can be reconciled later. In fact, I see an overlap already:

The first AAAAB Pattern I found was 162-233M which I did see as large. I already had found an AAABA Pattern from 192-249M. This could mean that AAAAB goes from 162-192 and that the 233M AAAAB pattern was just an outlying singleton.

I also recall that I want ID’s, so I’ll add that to my query:

Because I have so much new information, I’ll put this into a new spreadsheet:

AAABA Mom Pattern

I just have to change the Query slightly to get the AAABA Mom Pattern:

The results of this Query go into the new spreadsheet. This spreadsheet will be sorted by Chromosome later.

I added a column for IDEnd minus IDStart:

Where this is zero, it would indicate a single Pattern.

I went through all the Mom Patterns and got a spreadsheet of 194 rows that need to be reconciled. Here are Chromosomes 1 and 2 sorted:

Reconciling Chromosome 1

I have added in a column for possible assignment of a crossover to a sibling. Note that up to about 20M everything looks OK. There are discrete Patterns. ABBBA to AABBA is a change in the second position which belongs to Sharon. The change from AABBA to AABBB goes to Lori. Then the AABBB is the same as BBAAA which goes to ABAAA. That would be my crossover [Joel].

I did a Query showing where all the alleles were filled in for the Mom Patterns:

This shows where my Crossover is at ID # 8984. I have added a few more columns to my Mom Pattern Spreadsheet to add the more refined cut points:

Next I’ll look at 77M.

As best I can tell, there are two single AABAB’s in the middle of an AABBB Pattern. Next I will want to find the start of that AABBB Pattern. To find that I do a query to look for the AABBB Pattern in Chromosome 1. That Query results in more AABBB Patterns.

A Problem

I have a problem in that it appears that the Mom Patterns of AABBB and AABAB appear to overlap each other on Chromosome 1. I assume that means that I did something wrong.

refilling the dad patterns

That means that I should go back and fill the Dad Pattern back in:

First I recreate a Fill-in Table using the old Three Principles Table. Then I do update queries on that. Hopefully these numbers will work:

Back to Mom Patterns From Dad Patterns

Just so I’m not going backwards, I’ll redo this step. I copied my revised fill-in Table to a revised Mom from Dad Table. This time I’ll keep track of the alleles for fun:

So in retrospect, I don’t know if I made a mistake with the Dad fill-in’s or in the Mom fill-in from the Dad Pattern. Hopefully, there were no mistakes this time.

 

Beth’s Hartley DNA

In this Blog, I will be looking at Beth’s autosomal DNA. That is the DNA that she got from both her parents. However, I am more interested in Beth’s father’s mother’s DNA as she was a Hartley and the DNA that we share would be Hartley DNA.

Hartley Tree of DNA Testers

Here are those closer relatives that have had their DNA tested and uploaded to Gedmatch.com:

Here Hartley is shown as green and Snells are shown as yellow. The DNA testers are in gold. Any DNA that the four DNA testers have in common will belong to James Hartley and Annie Snell. However, it will be difficult to tell which. Any DNA that Patricia and Beth share could also belong to Charles Nute which Jim and my family will not share. Here is an example of that on Chromosome 1.

Here is a photo believed to be Mary Hartley with her sister Nellie:

Hartley and Nute DNA On Chromosome 1

This is a Chromosome browser from Gedmatch.com showing where Beth shares DNA with Heidi (1), Joel (2), Sharon (3), Jim (4) and her first cousin Patricia (5). Is the DNA that Beth and Patricia share Hartley DNA or Nute DNA? To find that out we can look at Patricia’s DNA browser. If she shares DNA in this same area with Heidi and Jim, then it will be Hartley DNA.

The above Browser shows Patricia matching Beth (1), Jim (2) and Joel (3). This means that the DNA that first cousins Beth and Patricia share in Chromosome 1 is Nute DNA. If I were to map Patricia’s maternal Chromosome 1, it would probably look like this:

This shows that Patricia got her green DNA (matching Jim and me) from her Hartley maternal grandmother and her pink DNA (matching Beth) from her Nute maternal grandfather.

First Cousins Vs. Second Cousins

First cousins share two grandparent as their most recent common ancestor. Second cousins share two great grandparents and get their shared DNA from one of them. The first cousin DNA matches will be larger in general. The second cousin matches will tend to be smaller.

First cousins

As shown above, first cousins will share the DNA from two of their grandparents. In the case of Patricia and Beth, those two grandparents will be maternal grandparents. The catch is, that when two first cousins match each other, they won’t know which grandparent they match on. They just know that it will be one or the other. In the example above, we did know which grandparent matched because of other second cousin matches.

second cousins – Two common Great grandparents

Second cousins have as their most recent common ancestors two of their great grandparents. But again they won’t know which great grandparent they are matching on.

The best way to identify which great grandparent the gold people match on would be to have a third cousin that is only related on the Hartley side OR the Snell side. I don’t know of anyone in this category right now, so I’m a bit stuck. I would like to figure out which DNA is which. The main reason is that I’m stuck on the Hartley genealogy. I know that Greenwood’s father was Robert, but before that, I’m not sure. If we could find another Hartley relative going back then it might break down the Hartley brick wall.

Any Other Way To Separate Hartley DNA From Snell DNA?

There is one main difference from James Hartley and Annie Snell above as it relates to their DNA. James was born in Bacup, Lancashire, England and Annie was born in Rochester, Massachusetts. All of James ancestors would also have been born in Lancashire. On the other hand, all of Annie’s ancestors that would produce matches go back to Colonial Southeastern New England. That means that if we find a match that is from England and has no ancestors in the United States, there would be a good chance that that DNA match was through the James Hartley side.

Beth’s X Chromosome

First, let’s look at my family. There is  no Hartley X Chromosome sharing with this group because the X-DNA does not travel from father to son.

Second, look at Beth compared to Jim:

Beth got one of her X Chromosomes from her dad. This was the same X that he got from his mother Mary. Jim got an X Chromosome from his mother. She got it from James Hartley b. 1862 and Annie Snell. So Beth and Jim have James Hartley and Annie Snell in common.

These pieces of blue where Beth and Jim match represent DNA that they share from James Hartley and/or Annie Snell.

How do Patricia and Beth compare by X-DNA?

Next we will look at Patricia and Beth. They will share X-DNA with their grandmother Mary Hartley. Beth’s dad got no X-DNA from his Nute dad, so Beth and Patricia will only match on Mary Hartley.

Note here that Beth and Patricia share some X-DNA from their grandmother that isn’t shared between Jim and Beth on the left side. They also share a longer segment at the right hand side than Beth and Jim shared. However, Jim and Beth shared a segment from 123 to 138M that wasn’t shared between Patricia and Beth.

Let’s See How Patricia Compares With Jim

The only comparison left is between Patricia and Jim.

I compared the three comparisons and came up with a bit of an X Chromosome map. In the first match between Beth and Patricia, I have that match in red. On the very right there are three matches, so I have that as great grandparent 1. We don’t know which great grandparent it is – just that it is the same one. On Jim’s map, it is his grandparent 1. Going from right to left on Jim’s map, he changes from getting his X-DNA from grandparent 1 to grandparent 2. However, Patricia and Beth continue to match on great grandparent 1. In the middle there are no matches, so we can’t tell what is going on. Also the two reds and one blue on the left may actually be two blues and a red as we don’t know how they match with the segments on the right.

Beth’s Hartley (and Snell) Chromosome Map

If we look at all the matches Beth has with Jim, my siblings and me, we will have a map of her known Hartley (and Snell) DNA:

I didn’t use the DNA shared between Patricia and Beth as they are first cousins. As such, they will share Nute and Hartley DNA and it will not be as easy to tell which is which. So second cousins are good for these maps. The red is in the bottom part of each chromosome. That represents the paternal chromosome. We have not mapped any of Beth’s maternal chromosome. If Beth were to look for Hartley or Snell matches, it looks like her best bet would be on Chromosome 12.

For comparison, here is my Chromosome Map.

On my map, the blue corresponds to Beth’s red Hartley DNA. We seem to share a stretch of Hartley DNA on Chromosome 1. But where Beth has a long stretch of Hartley DNA on Chromosome 12, I have none.

 

More Hartley DNA – Patricia’s DNA

This blog is a follow-up on my last Blog: My Hartley Autosomal DNA. I was inspired to write that blog following this year’s Hartley reunion in Rochester, Massachusetts. I intended to send around a little poster I made up about Hartley DNA and get a DNA sample from my father’s cousin Martha, but didn’t get a chance to. Instead I wrote a blog. I did talk to Patricia though. She is my second cousin and the sister of my childhood best friend, Warren. She had taken an AncestryDNA test. I think her daughter bought it for her. I asked if she could upload her DNA to gedmatch.com and she said that her daughter would be good at doing that.

Here are Patricia’s 2 brothers and Patricia. The one in the middle was my best friend in my first 6 years of school. I remember seeing home movies of Curtis, Warren’s older brother. He came to one of my older siblings’ birthday party when he was about this age.

Patricia and family

In my last blog, I wrote about the Hartley DNA matches my father’s first cousin Jim had with me and my 2 sisters. I was surprised to find out that every match that we had represented one of my four 2nd Great Grandparents. They were all born around the 1830’s. It turns out that Patricia’s matches with cousin Jim represent the same four 2nd great grandparents. In addition Patricia’s DNA matches with my 2 sisters and me represent the same four old timers.

Here is what my DNA match to Patricia looks like at AncestryDNA:

Patricia Ancestry

Here, AncestryDNA has it right that we are 2nd cousins. They show we match for a total of 206 cM (centimorgans) across 14 DNA segments. That is about all you can get out of ancestry. They won’t tell you which chromosomes we match on or how much we match on each chromosome. That is why people upload their results to gedmatch.com. Ancestry does show other people that match DNA to both Patricia and me. These are my 2 sisters and 5 others. All these people also descend from the same Rochester Hartley ancestors, but none of them have uploaded their results to gedmatch.com, so we don’t know their detailed DNA matching information.

Here is the same match between Patricia and me at Gedmatch:

Pat Joel Gedmatch

Ancestry has 14 segments vs. the 8 at Gedmatch. But at Gedmatch we know on which chromosome we match, how much on each chromosome and the exact start and stop location on the Chromosome. However, even with Ancestry’s 14 segments, their total is a bit smaller. Here is how I match Patricia on Chromosome 15 in the Gedmatch Chromosome Browser:

Joel Pat Chr 15

The blue areas represent the two DNA matches Patricia and I have on Chromosome 15.

Patricia on the Hartley Family Tree

Growing up, Patricia’s grandmother was my great aunt and also one of my neighbors, my Aunt Mary.

Patricia's Tree

The bottom box in each row are the people that have tested their DNA and uploaded to gedmatch.com. I now show 3 of the 13 children of James Hartley and Annie Louisa Snell (James, Mary and Annie). I now can check how my sisters and I match Patricia’s DNA as well as how Patricia matches Jim’s DNA.

Here are my great grandparents and three of their older children.

James and Annie Hartley

It is in interesting photo. Two of the children are looking away. I think that one is my grandfather James. The mother, Annie, is looking at something in her hands. The older son Dan is looking at a book and the father James doesn’t look comfortable being dressed up.

Patricia’s DNA at Gedmatch

One of the basic functions at gedmatch is called ‘One to Many’. In this case, I took Patricia’s DNA and compared them to everyone else that has ever uploaded their DNA results to gedmatch. Here are her 1st 4 matches:

Patricia's 1st 4 matches

Not surprisingly, her top matches are her 1st cousin, once removed, Jim, me and my sister’s Sharon and Heidi. The Gen column lists how far away gedmatch thinks Patricia’s matches are to a common ancestor. Patricia and I are 3 generations to James Hartley and Annie Snell, so that is right. Patricia shows 2.6 generations to a common ancestor with her match to Jim. A first cousin once removed would typically be 2.5 generations, so she shares a little less DNA than average here with Jim. Patricia also shares 19.3 cM of the X Chromosome with cousin Jim which I find interesting.

The Hartley X Chromosome

I’m taking the X Chromosome out of order because I find it interesting. There is one most important thing to know about the X Chromosome. If you are a male, you get one from your mother. If you are a female, you get one from your mother and one from your father. My father only got an X chromosome from his Frazer mother, so he doesn’t match anyone further up on the Hartley line by the X Chromosome. However Patricia and Jim both have maternal matches that carry up the line.

Here is how Jim got his X Chromosome from his mother and her ancestors:

Jim's X Inheritance

Jim only inherited his X Chromosome from those ancestors in pink or blue. So, for example, he got no X Chromosome from any Bradford before Harvey Bradford.

We need to compare Jim’s chart with Patricia’s X Inheritance Chart:

Patricia's X Inheritance

Here I didn’t show the X Chromosome that Patricia got from her father as this won’t match Jim. Then of what I show, only the bottom half will match Jim. This means that going back 4 generations from Patricia, she could match Jim by the X Chromosome on the Emmet, Snell or Bradford Line. One other difference between Jim and Patricia is that Jim got 100% of his total X Chromosome from his mother and Patricia only got 50%. However, that is a confusing way to put it because Patricia did get 2 X Chromosomes. So her one 50% must be similar to Jim’s 100% if that makes sense.

Here is what the X Chromosome match looks like between Patricia and Jim at gedmatch.com on their browser:

Jim Patricia X Match

The yellow part with the blue under it is where they match at the end of the X Chromosome. That is enough on my X diversion for now.

Back to the Hartley DNA Matches on the Other 22 Chromsomes

At gedmatch, I go to the Jim’s ‘One to Many’ matches to see how he matches my family and Patricia. Here are Jim’s top 4 matches. You may have already guessed who they are:

Jim's top 4 matches

Above, I said that Patricia matched Jim a little less than expected. My sister Heidi at the top of the list matches him a little more than average.

Here are Jim’s DNA matches on Chromosome 1

Pat Chr 1

  1. Me
  2. Heidi
  3. Sharon
  4. Patricia

Here Patricia has identified a new piece of DNA in green that is a Hartley ancestor that we didn’t know about before. Again, this “Hartley” ancestor may be Hartley, Emmet, Snell or Bradford.

Here is another new Hartley segment on Chromosome 2:

Pat Chr 2

Patricia matched Jim on Chromosome 2. My sisters and I had no match with Jim on that Chromosome.

It looks like Patricia got a double segment of Hartley DNA on Chromosome 5:

Patricia Chr 5

Patricia is #1 above. Where the color changes from orange to yellow likely represents a change from Greenwood Hartley to Ann Emmet DNA or Isaiah Snell to Hannah Bradford DNA.

Patricia Helping Me Map My Chromosome 7

I’ve tried to map all my chromosomes as well as my 2 sisters’ to my 4 grandparents. I got a little stuck on Chromosome 7:

Chr 7 Map Pat

My chromosome 7 depiction is the one with the J to the left of it. On my paternal side (which is the blue (FRAZER) and red bar), I have the DNA I got from my dad’s mother in blue and my dad’s Hartley dad in red. Above that is the gedmatch depiction of how I match my 2 sisters by DNA and how they match each other. The bright green bar is called the Fully Identical Region or FIR. This means wherever that occurs a sibling matches the other sibling by getting the same DNA from the same 2 grandparents (one maternal and the other paternal). So in comparing Sharon to Heidi, they have that FIR from 0 to 25. It turns out that their 2 grandparents were their mother’s mother (Lentz) and their father’s father (Hartley). In the tiny section between 0 and 4, I have what is called a Half Identical Region or HIR. That means that I shared one grandparent’s DNA  with my sisters and the other grandparent I didn’t get any of their DNA. In this case I had to share either the Lentz or Hartley grandparent with my 2 sisters, but I didn’t know which.

That is where Patricia’s results came in handy. Here is how she matches Sharon, Heidi and me:

Patricia Chromosome 7

Patricia has 3 good matches with Sharon and Heidi and one tiny one with me (#3 on the Chromosome Browser). However, the tiny one is the one I need. The pink match shows that my Chromosome 7 from 0-4 (in millions) is where I got my DNA from my Hartley grandfather and not my Frazer grandmother.

Here is my completed Chromosome 7 thanks to Patricia. I extended the Rathfelder on my Chromosome 7 all the way to the left or beginning and added a small chunk of red Hartley from my grandfather.

Chr 7 complete

Another Type of Chromosome Mapping

There’s is another type of Chromosome Mapping developed by Kitty Munson. The way the Munson Mapping is generally used is to map out your relatives’ common ancestors. In the case of Patricia and Jim our common ancestors are James Hartley and Annie Louisa Snell. Here is what my new Chromosome Map looks like with the addition of Patricia’s DNA matches with me shown in blue.

New Kitty Map for Joel based on Pat

Well, that’s about enough for Patricia’s DNA for now.

Summary and Conclusions

  • Patricia shared the first Hartley X Chromosome match that I’ve seen.
  • The X tends to shy away from the male line, so Patricia and Jim’s match is more likely down somewhere in the Massachusetts colonial line rather than the English Line.
  • I would like to use Hartley DNA to break through the Hartley genealogical brick wall. Right now I’m stuck in the early 1800’s in Trawden, England. There were too many Hartleys there with the same first name to figure out who was who. Patricia’s DNA may help in finding matches to other Hartleys
  • Patricia’s DNA helped me in mapping my chromosomes in 2 different ways.