Using a Multidisciplinary Approach to DNA Analysis, Part 1

 

Note: This post was updated on 30 July 2022 with new information. 

Recently, I suggested to a person on one of the many genetic genealogy forums that you may be able to use Y-DNA, mtDNA, and X-DNA to narrow down a particular line of descent for an individual autosomal match. I was immediately rebuffed by someone who basically said the following, “Y-DNA, mtDNA, and X-DNA have no place in an autosomal DNA study.” 

I responded, “While the inheritance patterns of other types of DNA are different, they still can be used (in some cases) to determine possible lines of relationship.” The responder was not convinced and was agitated that I would even suggest such tactics. However, a multidisciplinary approach to DNA may aid in eliminating certain lineages from consideration when determining the origin of a match.  

I thought most folks who have dipped their toes into the genetic genealogical pool would have known this; however, after being involved in several discussions on this topic, I felt the need to author several posts in this regard.

The Larger Study

In the past, I have used autosomal and Y-DNA to determine relationships, but up until recently, I have not had the opportunity to use mtDNA and X-DNA to do the same. The examples found in this discourse are part of an ongoing study that uses autosomal DNA, X-DNA, and mtDNA from nearly 30 participants who are related to our ancestral couple: Ancestral Father (AF) and Ancestral Mother (AM).  

In trying to determine a particular genealogical problem of whether a person was the natural or adopted child of one of AF and AM’s children, I used autosomal and mtDNA to test a null hypothesis. The null hypothesis (names changed) was similar to the following: H_0: Mary Smith was not the natural daughter of Jane Doe. By comparing the autosomal DNA from descendants of AF and AM and matching mtDNA transmitted from AM, the null hypothesis was rejected. Descent in this case was verified.

While this study is ongoing and we are still amassing evidence in hopes of submitting the finished product for publication, the surname of the family and all additional specific information concerning these lineages (including references and location) have been omitted to protect the original study. 

This has been done so that my work is not co-opted by another individual who has been known to plunder my research on this family and publish it online. I began this study during 2014 when I first became aware of several issues related to this lineage. This project involves a surreptitious narrative that is far more involved than the DNA analysis.

This isn't an analysis of this particular study per se; it is an exercise to show that using other DNA types can aid an autosomal study. So while the names, locations, and documentation of sources are absent, the techniques are present and that's what is important to this post.

The Current Problem

While working on the DNA analysis, we have identified two unknown individuals genetically related to this family: U1 – an adopted individual and U2 – who cannot be placed as of yet. It is believed that U2 descends from one of the Ancestral Mother’s siblings. Until more information is available, it is uncertain how U2 is connected to the family. 

This tangential part of the study was conducted to aid U1 in identifying her birth mother. Therefore, our task is to narrow the possible lines of descent for U1’s birth mother that may possibly lead to her identity.

Background of the Family 

While AF and AM had 11 children, three failed to attain the age of majority and their names are currently unknown. These additional children were listed in the number of children born to the mother in both the 1900 and 1910 censuses. Seven of 11 children were listed as living in the 1900 census and six of 11 were numbered as living in the 1910. E-Prime (E0) died before 1900 and her sister A-Prime (A0) expired prior to 1910.

Of the eight children who attained majority, one son never married nor had any known issue. Descendants of six of the remaining seven children have tested. We are still attempting to attract descendants of the youngest child S-Prime (S0) to test. While S0 had two sons and two daughters, neither of her daughters produced issue. Twenty of AF and AM's 35 grandchildren produced issue; descendants of 14 grandchildren are current participants. We are still soliciting participants to strengthen our original study's results.

The known children of the ancestral parents are as follows:

• E-Prime (E0) – daughter, born 1856; 8 participants
• K-Prime (K0) – daughter, born 1858; 2 participants
• J-Prime (J0) – son, born 1862; 9 participants
  
• Son, born 1864 (no issue)
• A-Prime (A0) – daughter, born 1867; 3 participants
• W-Prime (W0) – son, born 1869; 3 participants
• F-Prime (F0) – son, born 1871; 2 participants
• S-Prime (S0) – daughter, born 1875; no known tested descendants

Additionally, there are several others in this project

• Six descendants from AF’s surname lineage: X1-X6, with four descended from AF’s siblings.  
• Two likely descendants of J0 (not in the data presented). These two share sizeable amounts of autosomal DNA with J0’s descendants as well as to descendants of J0’s wife’s sisters.  
• Two unknowns: U1 and U2.

It is also noted that all the descendants of E0 and K0 share double relationships. Additionally, the grandchildren (E1, E2, & E3) of one of E0’s sons share double relationships with all the descendants of J0. Finally, the descendants of the oldest daughter of W0 share double relationships with the descendants of the oldest granddaughter of A0. None of these double relationships impact the results of this present analysis.

With U1, it is possible narrow down her birth relationship to two possible lines, but we are still soliciting family members to test to determine her mother’s exact identity. In this discourse, I’ll show how we are using autosomal, X-DNA, and mtDNA in an attempt to narrow the possibilities.

Autosomal DNA

In looking at the triangulated segments between U1 and others represented in this project, it is obvious that U1 is related to, if not descended from, AF and AM. The triangulated segments are listed below. 

We have also separated the triangulated segments between U1 and only those descended from A0. We’ll elaborate on this in the next paragraph. I have also separated out a triangulated segment between U1 and two descendants of a sister of AF. This is somewhat inconclusive, as the relationship could come through one of U1’s other lineages. 

The amount of DNA U1 matches with various tested individuals narrows to one child of AF & AM who is the likely ancestor of U1. In the chart below, except for the matches with J1 (at 50.6 cM) and E2 (48.6 cM), the larger matches are found among the descendants of A0. 

J1 is three generations from AF and AM. Her father was the last born grandchild of AF and AM and places her a generation or more above all other participants; therefore, she would likely share more than others at a further distance. As far as E2 (a brother of E1 and E3), he generally shares higher amounts of autosomal DNA from this ancestral couple than others descended from his great-grandmother with the exception of a second cousin (E6).

U1’s two largest autosomal DNA shares are with A1 and A3. Both individuals share 103.7 cM autosomal DNA and a little over 20 cM on the X-Chromosome. Using the Shared cM Project, the most likely predicted relationship for both A1 and A3 with U1 is that of second cousins, once removed. A2 is predicted as a third cousin, once removed. While other relationships are possible, these better fit the scenario in question. Therefore, it is likely that U1 descends from A0 – the fifth known child of the ancestral parents.

X-DNA

While the data from our analysis of 17 X-DNA matching segments among the participants is currently inconclusive, there are some possible theories that could be further tested. The chart below shows the X-DNA inheritance of 12 tested known descendants of AF and AM. F0’s living descendants are not present due to a double male lineage that negates the transmission of X-DNA in the living descendants of F0. It is possible that some of the untested descendants of one of S0's sons will have additional X-DNA matches. This remains to be seen. 

In the above chart, the circles represent females and squares represent males. The pink circles and squares represent X-DNA only coming from AM. The purple represents X-DNA possibly inherited through both AF and AM. The half purple and gray represent X-DNA inheritance that comes from AF, AM, and/or a shared paternal relative in the descendants of E0 and K0. This is not germane to this analysis, but it is to the original research project.

The 17 segments are depicted below. Pay particular attention to the eight matching segments with A1 and the three matching segments with U1. 

Note: The matches represented are inter-prime families and not intra-prime family. For example, the matches are shown for E5 and E6 with J5; however, the 11.6 cM match between E5 and E6 is not shown. 

The matches in black between the descendants of E0 and K0 are probably from a relationship outside of AF and AM’s family. E0’s children are first cousins to both K0’s daughter and her husband (the son of E0’s sister-in-law).

Any matches with J0’s and W0’s descendants are from AM and could come from her mother, father, or a combination of both, but not through AF. The matches between E0’s descendants an A0’s descendants could come from AF’s mother, AM’s parents, or any combination thereof.

The longest X-DNA match (in red) is between E5 and A1 at 41.9 cM. However, A1’s match to E5 has overlapping matches with J3 and J4 (in light blue) at the beginning of the segment and overlapping matches with W1 and W2 (in dark green) at the end of the segment. The overlaps would come from one or both of AM’s parents. It is noteworthy that A1’s matches with this family cover most of the X-chromosome – only 35-40 cM is not represented by one of her X-chromosomes. 

E5’s match with U1 does not correspond with A1’s match with W1 and W2. This signifies that at least part of E5’s match with U1 comes from either the other parent of AM or from AF’s mother. This may be the case with part or all A1’s match with U1. At this juncture, it is impossible to tell, but we are continuing to look for other possible X-DNA participants. 

Since A3's match with U1 is not triangulated with anyone else, this segment could have been inherited through a spouse of one of A0’s descendants and not directly from AF or AM.  

At this point, the X-DNA analysis is inconclusive; however, additional X-DNA matches may shed additional light on the connection. What we can conclude is that U1 matches E5, A1, and A3 on the X-chromosome through lines that share the unique transmission of X-DNA.

mtDNA

As mitochondrial DNA is passed from mother to child, we are fortunate to have three participants that share the same mtDNA haplogroup (K1a4a1) with their ancestral mother AM. They are E8, K1, and A3. These three individuals have an unbroken female descent from AM. 

Fortunately for this exercise, U1 also shares the K1a4a1 haplogroup. Before we proceed, there is a caveat. Just because there is a matching haplogroup, this is not conclusive by itself as coming directly from AM. It could have been passed through an unrelated ancestor or someone with deeper ancestry to AM’s family.

While this haplogroup could be shared from descendants of AM’s sisters, we can partially eliminate this possibility. AM had two sisters reach maturity. One could not be located after 1850. Additionally, her name is not listed in her mother’s 1879 will. Unfortunately, we cannot rule out that she lived beyond 1850 and produced issue. This will always be a possibility until her death without issue is confirmed.

The other sister had four daughters and a son. We can rule out the son, as he could not pass his mtDNA to his children. Of the four daughters, it does not appear that shared mtDNA was passed to present descendants through any of these children.  

• Daughter One – had one daughter who produced one son.
• Daughter Two – only had one son.
• Daughter Three – had one daughter who produced no issue.
• Daughter Four – had a son and an adopted daughter.

This, along with the larger match with A0’s descendants, mtDNA strengthens the theory that U1 is a female line descendant of A0.

Conclusion

The amount of shared DNA between U1’s and AF & AM's descendants indicates that U1 is descended from this couple. There is also matching mtDNA that is consistent with AM’s mtDNA.

Other considerations include the following inconclusive results:  

• U1’s matching to two descendants of AF’s sister (which may or may not come from other lineages),
  
• The possibility of inheriting X-DNA from AF’s mother, and 
• The lack of likely mtDNA matches among the known descendants of AM’s traceable sister. 

As the amount of autosomal DNA shared with A1, A2, and A3 indicates descent from A0, let’s look at the possibilities in A0’s family. 

A0 and her husband produced six children – four sons and two daughters. Three sons died as children. The remaining son (A0b) is the ancestor of A1 and A2. He can be eliminated, as he could not pass on his mitochondrial DNA. Additionally, A0b produced 11 children who all lived to the age of majority.

The eldest daughter (A0a)  had two sons. These sons could not pass their mtDNA to anyone.

This leaves the third child (A0c) – a daughter who was the great-grandmother of A3. 

A0c had nine children – all attained the age of majority. Five sons can be eliminated.

That leaves four daughters: A0c3, A0c6, A0c7, and A0c8. 

A0c6 is A3’s grandmother who had one daughter – A3’s mother. Any relationship through this lineage would produce a larger amount of shared autosomal DNA. This line can be eliminated.

A0c3 left the family home prior to 1940 and moved to New York City. She and her husband produced no children.   

A0c7 had one daughter who remained in the local area at least through 1999 and may be living there presently. She would have been 27 at the time of U1’s birth.

A0c8 also had one daughter – she would have been 21 at the time of U1’s birth. She remained in the same county where U1 was born and where the adoption occurred. She only moved to a neighboring county as a senior citizen.  

In the above possibilities, the relationship of U1 being born to a daughter of A0c7 or A0c8 would make her a second cousin to A3; a second cousin, once removed to A1; and a third cousin to A2.    

While a share of 103.7 cM is low for second cousins, the range for relationship according to the Shared cM Project is 41-592 cM. The average share for this relationship is 229 cM; therefore, 103.7 cM is consistent with other second cousin relationships.

This exercise allows us to narrow down possible individuals to test. Although this project did not set out to find the birth family of an adopted child, it has provided us this opportunity. The narrowing down the approximate ancestry of U1 required us to use genealogical records and a multidisciplinary DNA approach.

With autosomal DNA pointing to descent from A0 and without the use of mtDNA, the exercise would have required us to consider numerous lines in A0’s family. By using mtDNA, we narrowed the possibilities to only two lines instead of a possible 22 (2 children from A0a, 11 from A0b and 9 from A0c). 

I hope this has shown that, by using other forms of DNA in tandem with autosomal DNA, a multidisciplinary approach may be able to narrow your search to a smaller number of possible connections. 

Phasing the X-Chromosome

Understanding the transmission of most human DNA is fairly straightforward. Y-DNA is transmitted from father to son and follows a patrilineal descent equated with a man’s surname lineage. Only males have Y-DNA and they can only pass it on to their sons. Mitochondrial (mtDNA) is the exact opposite and is passed from mother to child. It follows a matrilineal descent – great-grandmother to grandmother to mother to child. While men receive mtDNA, they cannot pass it to their children. Only women can pass mtDNA.

A third type of DNA is autosomal DNA. It is passed from the 22 pairs of autosomes that we as humans have. For each pair, one chromosome comes from our mother and one from our father. The chromosomes we receive from our parents are also combinations of the chromosomes passed from our grandparents. All of our ancestors, to a point, contribute to our autosomal DNA.

Finally, there is X-chromosomal DNA. Contrary to popular belief that it was named after its X shape when two X-chromosomes appear together, the 22 autosomes also appear roughly “X” shaped during mitosis and therefore there was nothing unique about its appearance. Hermann Henking named the chromosome the X element because of its unique properties. The “X” designation has been applied to other items with unique or unknown properties such as X in algebra, X-rays, and Planet X (Pluto).

X Inheritance Patterns

The X-chromosome, however, has a bit of mystery to its transmission. While it is not difficult to understand, it takes time to explain the unique ancestry that contributes to an X-chromosome. Additionally, the X ancestry for women is different than for men adding to its mystique.

Men only receive one X-chromosome as they receive a Y-chromosome from their father which in turn determines their gender as a male. Men inherit their X-chromosome from their mother. It is possible that a man may inherit his X as one of his mother’s two X-chromosomes completely intact; however, it is more likely he will receive a recombined X that includes segments from each of his mother’s two Xs.

Since women receive two X-chromosomes, they inherit these from each parent. The one received from a woman’s mother is transmitted the same way as a man receives his X-chromosome. The other X-chromosome transmitted intact from a woman’s father. This comes from his mother and may be an intact chromosome or a recombined X transmitted to him from his mother.

To get a clearer picture on the overall inheritance patterns of the X-chromosome for men and women, I recommend two blog posts by Dr. Blaine T. Bettinger: Unlocking the Genealogical Secrets of the X Chromosome and More X-Chromosome Charts.

My Specific X-Chromosome Issues

My interest in the X-chromosome transmission is based on the lack of matching X segments I have with my two brothers. In fact, the amount of 14.7cM on one segment on the X that I share with my oldest brother is rather insignificant by comparison to others in my family. My other brother and I share 45.9cM over two segments. My two brothers share quite a bit with each other on the X with 142.2cM across three segments.

To add to this disparity, I share more with my two first cousins than I do with my oldest brother on the X: 44.7cM over two segments with one and 102.9cM across two segments with the other. Even larger than these shares, my family has two second cousins who share 122cM on one segment. The grandmothers of these two second cousins were sisters.

Others’ Experiences

I was curious about this inequality and I asked individuals to post on 23andMe’s Community Forum their total matches on the X-chromosome with known relatives; however, some exceptions needed to occur as parent/children relationships will share 100% on an X-chromosome, a paternal grandmother and granddaughters will share 100% on an X-chromosome, and sisters and paternal half-sisters will share an exact copy of their father’s X-chromosome. Obviously, these numbers would skew the results somewhat and do not represent an unknown quantity.

While I won’t list all of the results here, I will list relationships where at least five matches were documented. The lower and higher ranges, as well as the central tendencies of mean and median, are represented in centimorgans (cM).

Relationship	Number	Low	High	Mean	Median
Sibling*	34	14.7	182.8	98.9	97.9
Grandparent	14	38.1	170.0	91.1	77.5
Avuncular	53	10.0	201.0	92.1	83.6
Great Avuncular	9	11.0	178.0	41.5	26.1
First Cousin	23	16.0	135.2	66.4	61.4
First Cousin, Once Removed	21	11.1	196.0	63.9	56.3
Second Cousin	6	17.0	122.0	50.7	43.4
First Cousin, Twice Removed	9	7.1	83.8	18.0	31.9
Second Cousin, Once Removed	6	15.9	47.3	24.9	17.2

*full brothers, full brother/sister, maternal half-brothers, and maternal half sisters.

The numbers are probably skewing higher, as I discounted all non-matches. This was done because I could not verify if the given relationship fell within X-chromosome inheritance patterns. For example, a male subject may have listed a second cousin relationship as 0cM without realizing that a male’s paternal second cousins do not share genetic material on the X.

This exercise revealed that it is difficult to ascertain a relationship on the amount shared via the X-chromosome, as the numbers were across the board. Part of the inequality may be attributed to daughters receiving an intact X from their fathers. Without recombination during these transmissions, larger segments of X-DNA will be inherited across generations.

In my family, a sibling match of 14.7cM was the lowest of the observed sibling pairs; as mentioned earlier, this was between me and my oldest brother. The aforementioned second cousin match in our family at 122.0cM is the highest reported for that relationship.

Phasing My X-Chromosome

Since spring 2010 when my results and those of my siblings were returned, I have been immensely curious on why I share so little on the X-chromosome with either of my brothers. In addition, Ancestry Finder lists my oldest brother (Chuck) as having three matches on the X. Two of those matches exceed the amount we share (20.6cM and 26.6cM). My brother John also has three matches – two of those match Chuck’s shares and one is unique. Unfortunately, I have no X matches in Ancestry Finder.

As I ruminated on the results, I began to realize that recombination of my mother’s two X-chromosomes dealt Chuck and me X-DNA from divergent maternal grandparents. The question was who inherited from whom?  My mother's parents and siblings, which would help in determining this issue, had died decades ago.  While I have five living first cousins on my mother’s side, three were adopted.

Of the two remaining blood first cousins, I tested Joan first in 2011 – she is the daughter of my mother’s sister Louise. Unfortunately, she could have received her X-DNA from either or both of our grandparents and there was no way to determine the origin of her matching segments.

Jane, my other blood first cousin, tested in 2012 and she and I had two matching segments totaling 102.9cM. This large match was significant in that she is the daughter of my mother’s oldest brother. Because of this relationship, I could use her results and partially phase our X-chromosome segments to specific grandparents.

Since she received one X from her father and one X from her mother, the matching segments she had with me, my brothers, and Joan would come only from our maternal grandmother. The X-chromosome that passed from Jane’s dad came solely through our grandmother. This is unlike my mother and my aunt who received an X-chromosome from their mother and an X-chromosome from their father.

In addition, those areas where Jane matched me but not my brothers indicated that my siblings received their corresponding segments from our maternal grandfather. While I could not satisfactorily phase all of my X-chromosome, over half of it was attributed to my mother’s mother.

Those areas where we did not match Jane do not indicate that those segments came from my grandfather. If fact when comparing Jane with my mother, they only match on the same segments that Jane matches with me. This indicates that my mother and her brother received different X-DNA from their mother due to X recombination.

As far as further testing is concerned, there are some second cousins and second cousins, once removed that are descended from my grandmother’s sisters that may shed additional light on the propagation of the X in our family. Finding these individuals and convincing them to test may prove difficult.

While my grandfather was his mother's only child, his mother had siblings whose descendents should have some matching DNA segments to our family. Shared genetic material with these individuals may further confirm from whence my brothers’ and cousins’ X-DNA originated. In certain cases, tying our X-chromosome segments to a specific great-grandparent may also be possible.  

Some Theories

Since I can only confirm the originating grandparent of 51% my X-DNA, I tend to believe (but cannot confirm at the present) that my X-chromosome may be an exact copy of my mother’s inherited X from her mother. If this is the case, I would not have inherited any X-DNA from my grandfather. This would also indicate that my brother Chuck’s X-DNA is 97% from our grandfather and only 3% from our grandmother. My brother John would then have 77% of his X-DNA from our grandfather and 23% from our grandmother.

If my hypothesis is correct, it may suggest why I have no matches on the X-chromosome. With exception of one line which originated in Southern France, my grandmother’s ancestry was German. If one follows her X-chromosome inheritance to its natural genetic conclusion, her X-chromosomes were 100% Germanic in origin. The earliest date for her ancestors immigrating to the US was 1848.

While my grandfather had a significant German element to his ancestry, his X-inheritance contains Swiss, Scots-Irish, German, and probably English antecedents. To the best of my knowledge, my grandfather’s family appears to have been in America from at least the time of the Revolutionary War.

Since becoming a 23andMe customer in 2010, I have noticed a dearth of matches to my German lines. Since my mother is roughly 70% German and 12% Swiss, I find that most of her 23andMe matches appear to be related to her English and Scots-Irish ancestries rather than to her German and Swiss roots.

While I do not have facts and figures for 23andMe’s customer base, it appears that Germans are not among the best represented groups. While Ancestry Finder is not a perfect indicator of ancestral matches, it does allow for some additional conclusions to be drawn. For my mother, Germany ranks third behind the United Kingdom and Netherlands for her matches whose grandparents were born in these countries. I would have assumed that her German matches would have ranked first; however, this was not the case.

Conclusions

Despite my theories which remain unconfirmed, I was able to phase a large portion of our family's X-chromosomes to a particular grandparent by comparing our results with a first cousin who was the daughter of a maternal uncle. In the absence of a tested grandparent, a greater number of tested relationships of maternal uncles and female first cousins descended from maternal uncles would aid anyone in phasing his or her maternal X-DNA.