DNA Discovery: Phasing the X Chromosome

In the last blog post, I wrote about red-green color blindness, a recessive trait linked to genes on the X Chromosome.^[1]See it here.  Let’s move on to talk about the X Chromosome as a whole and how mine compares to my siblings.

Yes, I’ve restarted my visual phasing project.  It began over two years ago but stopped after a point because I was struggling with the recombination points on several chromosomes.  Buying the lake cabin affected my ability to devote time as well.  I’ve learned that once I delve into genetic genealogy, I need to put everything else aside.  It’s complicated!

My genome-analysis goals are:

1. Identifying what percentage of my genome and the genomes of my siblings can be attributed to each grandparent
2. Identifying which ancestors have contributed DNA to me and which have not (i.e., fill out my genetic family tree)

Visual phasing is the process of comparing the chromosomes of siblings, determining the recombination points, and assigning the identified segments to each of the four grandparents (without the benefit of the DNA of their parents).

The key to assigning segments is cousin matching.  Second or third cousins work well because they share a lot of DNA with you and the DNA they share is linked to only one grandparent or great-grandparent.  First cousins help to identify maternal v. paternal segments, but cannot directly help identify which specific grandparent is involved.  First cousins once removed are actually the best for phasing if it is someone who is one generation older than you.  I have, for example, a match who is a first cousin to my mother, nicknamed Bifrost.  Anytime I find a segment that Bifrost and I share, I know it is a segment that came from my maternal grandfather.

I still have not phased all 23 chromosomes, mostly because of a lack of good cousin matches on various chromosomes, particularly on the paternal side.^[2]Actually, everyone has a pair of 23 chromosomes, one each from the mother and father, so there are 46 total.

Nonetheless, I have completed phasing the X Chromosomes for myself, one brother, and two sisters, as named below:

• Steven
• Boyboy
• Bizzy
• JazzMa 

The surnames of our four grandparents are:

• Jonnes (paternal-paternal)
• Lukemire (paternal-maternal)
• Bonn (maternal-paternal)
• Vermilyea (maternal-maternal)

First, let’s review our X Chromosome family tree to view potential lines of descent.^[3]As noted in the previous post, X-DNA inheritance is limited to certain lines.  The names of known ancestors are filled in.

The left side of the chart only pertains to the possible inheritance patterns for sisters Bizzy and JazzMa, based on the X Chromosome they received from our father Nelson Jonnes (1926-2011).  The right side of the chart shows the potential lines of X descent for all four of us, including Boyboy and I.

Our paternal grandmother, Barbara Lukemire (1899-1974), inherited her X Chromosomes from two ancestral lines – 2GG Kate Homan (1845-1912) and 1GG Centrilla Blalock (1868-1921).  Centrilla’s X-inheritance branches further into Wesley Blalock‘s mother (name unknown) and 2GG Harriet Kennelly (1835-1906).  Future cousin matching hopefully will reveal which of Barbara’s ancestors contributed X-DNA to her, and thus to Bizzy and JazzMa.

The inheritance pattern featured at the top of the post further illustrates how daughters potentially receive their X-DNA.

The results from phasing the X-chromosomes of the Jonnes siblings are shown below.  The diagram was created using Steven Fox’s popular spreadsheet tool.^[4]The Steven Fox tool is featured in the Visual Phasing Working Group administered by Blaine Bettinger on Facebook.

The top part of the diagram shows how the X Chromosomes of each pair of siblings compare to each other.  The bottom section combines those comparisons into a segment-by-segment display.  The vertical lines represent the identified recombination points, or crossovers.^[5]Recombination is the process by which DNA strands are broken and recombined during meiosis, thereby ensuring that offspring are genetically diverse from their parents.  A recombination point is the … Continue reading  Each recombination point is owned by one sibling.

Two colored horizontal bars accompany each sibling in the bottom section.  The top bar (orange and blue) represents the paternal X Chromosome and the bottom bar (purple and green) the maternal.  For Boyboy and I, the reference to Jonnes is a misnomer in that we obviously did not receive an X Chromosome from our father.  I’ve left the Jonnes name there simply to indicate our Y-chromosome inheritance.

The paternal half for my sisters is just as simple.  The X Chromosome that females receive from their fathers is always an unrecombinated chromosome from their paternal grandmother.  Visual phasing is not required to understand this.  Thus, the top-bar X Chromosome for both JazzMa and Bizzy is 100% from Barbara Lukemire (1899-1974), our paternal grandmother.  (As referenced above, the makeup of that chromosome could be from one or more of the Homan, Blalock, or Kennelly lines.)

The main purpose, in other words, for visually phasing X chromosomes is to reveal the ancestry of the maternal X Chromosome.

It turns out that all four siblings have recombination points on their maternal X Chromosomes.  JazzMa and I have one recombination point, which produces two segments each.  Bizzy has 2 crossovers and 3 segments.  Boyboy has 3 crossovers and 4 segments.

Through cousin matching, I have been able to identify which segments are derived from which maternal grandparent, Bonn or Vermilyea, as follows.  You can compare the percentages to the visual display above, where purple represents Bonn and green represents Vermilyea.

Hypothetically, each of us could have received anywhere from 100% Bonn to 100% Vermilyea, but instead each of us has at least one Bonn and one Vermilyea segment.  Clearly, Bizzy and I received more Bonn DNA,  Boyboy is about 50-50, while JazzMa inherited the least Bonn and the most Vermilyea.

Remember that any X Chromosome segments that arise from the maternal grandfather must originate with his mother.  Our maternal grandfather is Bertram Bonn (1902-1964).  His mother, as can be seen in the inheritance tree, is  Bertha Aaberge (1865-1937).^[6]Mrs. Bertha Bonn was born Berthe Petersdatter Aaberge in Sogndal, Norway on Christmas Day, 1865.  All Bonn segments in this phasing project were inherited from our Aaberge ancestry in Sogndal, Norway.

The Vermilyea segments, on the other hand, come from a wider list of possible sources.  The two immediate sources are:

1. 2GG Alice Jane Whitney (1855-1928), David M. Vermilyea’s mother
2. 1GG Mabel Alicia King (1885-1938)

Mabel, in turn, derived her X Chromosome segments from these two sources:

1. 3GG Rose Ann Green (1827-1869), Fred A. King’s mother
2. 2GG Caroline “Lena” Miller (1860-1932)

Bizzy fortunately has one good cousin match on her maternal X Chromosome whom I’ll call Sammy.  Sammy and Bizzy’s matching segment is from 114 to 132 megabase pairs (Mgb).^[7]The megabase numbers are approximate, given the fuzziness that occurs in visual phasing.  Sammy is a known 4C1R to us, sharing the common ancestors 4GGs Benjamin Green (1786-1853) and Elizabeth Ellsworth (1797-1861).  Therefore, this segment was inherited from 3GG Rose Ann Green (1831-1869), Fred A. King’s mother.

As a result, Bizzy is the one sibling who can identify the deeper origin of most of her maternal X Chromosome segments:

• Segment 1, Bonn (0-114 Mgb) = Bertha Aaberge
• Segment 2, Vermilyea (114-132 Mgb) = Rose Ann Green
• Segment 3, Bonn (144-154 Mgb) = Bertha Aaberge

Note that a short piece of the second segment (132 to 144 Mgb) is missing.  That portion of the Vermilyea segment may also be from Rose Ann Green but could be from Caroline “Lena” Miller (1860-1932).