DNA Revisited

OK, so this is obviously not a post about John Ackley and his family, which was supposed to be the next post. There's been a pretty big gap since the last post, mainly because I got sidetracked on other things and just haven't gotten back to old John (I will get to it, I promise). One of the things that sidetracked me was DNA, so I thought I'd write a post about what I've learned.

Y-DNA

Recall that in the original post about DNA I mentioned Y-DNA briefly and also mentioned the existence of an Ackley surname project on Family Tree DNA (FTDNA). Surname projects are designed primarily for people who have done Y-DNA tests, but those who have done autosomal tests can also join if they have the Ackley surname and just want to look specifically for Ackley matches.


When I wrote that original DNA post I had just been made administrator of the Ackley surname project, and I was trying to learn what I could about DNA. Since that time, the project has grown from eight to 20 members. The members can be divided into three distinct groups: 

(1) People (both women and men) who have done autosomal DNA testing (called Family Finder on FTDNA) who have Ackleys somewhere in their tree and want to find Ackley matches within the group. Some of the men in this group have also done Y-DNA tests, but these tests are irrelevant for the purposes of an Ackley surname study since the testers do not have the Ackley surname. 

(2) Men with surnames that are close to Ackley (such as Ackerly and Akeley) who have done Y-DNA tests and would like to determine if their surname is a variation of Ackley. If their tests result in matches with men who have the Ackley surname, a case could be made that their surnames and Ackley are just variations of one another. So far, the results indicate that Ackley, Ackerly, and Akeley are not variations of the same surname and are in fact separate families; i.e., there are no Y-DNA matches between men with Ackley, Ackerley, and Akeley surnames. An important side note here: Recall that in the post on Nicholas Ackley's ancestors there was a lot of discussion about the Hackley surname, and the theory is that Nicholas Ackley and John Hackley were brothers whose father was also named John Hackley. Y-DNA testing could help us answer that question, and I have been successful in finding a descendant of John Hackley (who has the surname Hackley) who was willing to do a Y-DNA test. He has submitted his sample to FTDNA and is now waiting for the results. I will report on what is found when his results are available.

(3)  Men with the Ackley surname who have done Y-DNA testing and want to compare with other Ackley men to see if they are related. This could be useful, for example, for Ackley men who want to determine if they are descendants of Nicholas Ackley, or are from a different, possibly more distantly related or even unrelated Ackley line. There are just three men with the Ackley surname in the project, and the next section will discuss them in more detail.

Y-DNA Testing of Ackley Men in the Ackley Surname Project

Before discussing the actual results, I would like to spend a little time talking in detail about how Y-DNA testing works. I'll try not to get too technical (I probably don't know enough to get really technical anyway), but I think a little bit of technical talk is needed to appreciate the results. I can't do complete justice to the topic in just a paragraph or two, so if you want to read more, see this excellent blog post on Y-DNA by Roberta Estes at DNAeXplained [1]. You can find lots of articles about Y-DNA testing, but Roberta is my go-to blogger on DNA topics because she has a way of explaining things that just makes it more understandable.

Recall that only men have Y-DNA, and that Y-DNA does not recombine with anything from the mother, so each man's Y-DNA is received virtually unchanged from his father, who got it from his father, and so on. So, if I had my dad tested and compared it to my results, we would expect to see exactly the same values at every marker, and my brother should also match both my dad and me exactly, unless a mutation has occurred (more about that in a minute).

So what is a marker? Chromosomes contain sequences of repeating nucleotides, which are the basic building blocks of DNA (the A, T, C, and G patterns of your DNA). Simply stated, a Y-DNA marker is a segment of DNA at a known location on the Y chromosome where the number of Short Tandem Repeats (STRs) of these nucleotides are counted. STRs are short sequences of DNA that are repeated numerous times in a head-tail manner. There are hundreds of markers available to be tested, but there are some standard sets of markers that are used for genealogy purposes. FTDNA offers 37, 67, and 111 marker tests. If two men match each other on enough of these markers, it can be concluded with some level of confidence that they are related within some number of generations. The more markers tested, the more confidence there is in the conclusions drawn about family relationships (and the more the test costs).

Let's look at the three Ackley men who have tested at FTDNA and joined the Ackley surname project (I am one of those three men); we'll call them Ackley1, Ackley2, and Ackley3 (me). Two of us have done a 37 marker test and the other one did a 67 marker test, so the best we can do is compare the 37 markers we all had tested.

Here is a table of the 37 marker results for the three Ackley men. A quick look reveals that for most of the markers, the values are identical for all three.

To see if these men are related to each other, we need to compare their results to each other one-by-one. For example, if we compare Ackley1 and Ackley2 to each other, we can see that they match each other exactly on all the markers in green in the table below, and they differ from each other by 1 at marker DYS392 (Ackley1 has a value of 12 and Ackley2 has a value of 13) and also by one at DYS464 (all shown in red below).

Each difference contributes a value of 1 to a measure called genetic distance; the total genetic distance between these two men is 2. We'll discuss genetic distance in more detail shortly. Here is the comparison between Ackley1 and Ackley3:

You can see that there are a few more red cells, giving a total genetic distance of 5 in this case. Finally, here is the comparison of Ackley2 and Ackley3:

These two men have a total genetic distance of 3. The differences at the markers represent mutations; if there are "too many" mutations it is unlikely that two men would be related in the genealogical time frame. So how many mutations is "too many"? The answer is related to statistical probabilities based on mutation rates, and FTDNA provides a nice table that summarizes the possibilities [2]:

From the information in this table we can conclude that Ackley1 and Ackley2 are "Related" (genetic distance of 2), Ackley1 and Ackley3 are "Possibly Related" (genetic distance of 5), and Ackley2 and Ackley3 are "Related" (genetic distance of 3). 

So this is good, these three men all seem to be related to each other, although the relationship between Ackley1 and Ackley3 might be a little shaky -- they are only "Possibly Related". In fact, FTDNA would not report these two men as a match; the threshold on genetic distance is 4 at 37 markers; anything greater than that is not reported. For a genetic distance of 5, the "Interpretation" column in the table says "they may be related within the genealogical time frame, but additional evidence is needed to confirm the relationship." Additional testing is suggested, but in this case we can use other evidence to help us. It turns out that all three men have documented genealogies that show they are descended from Nicholas Ackley; in fact, all three are descended from his son James. Additional testing of other individuals who are also known descendants of James, preferably through different sons of James, could be done to try to determine where some of the mutations occurred.

Deep Ancestry Testing with Y-DNA

You may have noticed a column in the tables above labeled "Haplogroup" that has not been explained yet. According to the International Society of Genetic Genealogy (ISOGG) website, "A haplogroup is a genetic population group of people who share a common ancestor on the patrilineal or matrilineal line. Haplogroups are assigned letters of the alphabet, and refinements consist of additional number and letter combinations." [3] 

The definition implies that we are talking about deeper ancestry here, in fact FTDNA says "Haplogroups are associated with early human migrations." So, you probably won't learn much about who your 8th great grandfather is by knowing something about your paternal haplogroup, but it will tell you about where your people came from -- what "clan" you belong to. Men can learn something about their paternal haplogroup by doing a Y-DNA test, while both men and women can learn something about their maternal haplogroup by doing a mitochondrial DNA test. We'll stick to the paternal haplogroups in our discussion.

You'll notice that Ackley1 and Ackley2 both have R-M269 (these are the letters and numbers referred to above) listed in the haplogroup column, while Ackley3 has R-S1051, which is a subgroup of R-M269. R-M343, also called R1b, is the most frequently occurring haplogroup in Western Europe, and R-M269, also known as R1b1a2, is the most dominant branch of R-M343 in Western Europe. Men who take a Y-DNA test at FTDNA are given a predicted haplogroup based on a subset of 14 of the STR markers discussed above that are compared to a confirmed database of haplogroups; Ackley1 and Ackley2 were given a prediction of R-M269 based on their Y-DNA results.

To get confirmation of a haplogroup, along with further refinement deeper on the haplotree, additional Y-DNA tests can be performed. These additional tests look for a different type of mutation than STR tests; they are looking for single-nucleotide polymorphisms (SNPs), which are variations of a single nucleotide (remember the DNA building blocks mentioned above) at a specific location on the Y chromosome. The presence of SNPs in a test subject confirms their ancestors were members of a particular subgroup underneath the more general haplogroups. In the example we have been discussing, Ackley3 has done additional SNP testing, and his haplogroup has been confirmed as R-S1051, which is several levels deep in the R-M343 haplotree.

This is where things start to get very interesting. Besides the surname projects on FTDNA mentioned earlier, there are also haplogroup projects that attempt to discover the geographic origins of a given haplogroup. The project administrators of these projects are really bright people that have an incredible amount of knowledge about Y-DNA, SNPs, etc. It turns out that it is possible to estimate the age of the SNPs that define this branch of the haplotree; i.e., when the mutations occurred that distinguish members of this subgroup from other subgroups of the R-M343 branch. The administrator for the R-S1051 group (George Chandler) has some really good information on this somewhat unique group. George estimates that the defining SNPs for this group are between 3,200 and 4,500 years old, and that these people were part of the Bell Beaker culture (you can read more about them here [4]), and their geographic origin is what is now modern Scotland. He also states that this group is relatively small compared to other haplogroups of a similar age; he believes that a population bottleneck may have occurred that greatly reduced the number of males at some point (see here for a discussion of population bottlenecks [5]). George also believes that this group was part of the Pictish culture that inhabited eastern and northern Scotland during the late Iron Age and early Medieval periods [6]. The Picts were known for their intricate art carved in stones, such as the Hilton of Cadboll Stone shown below (this is a replica -- the original is in the Museum of Scotland). For more on the Picts, see the Wikipedia page here [7].

The Hilton of Cadboll Stone; picture is from http://www.pictishstone.freeuk.com/Framesbase.htm

So what does this mean for Ackleys in general? The assumption is that other Ackley men (at least those who are descendants of Nicholas Ackley) who choose to do Y-DNA SNP testing would have the same results; i.e., their tests should show that their haplogroup is R-S1051. Remember, SNP testing reveals deep ancestry -- the ancient origins of a group of people. All of the male descendants in the paternal line of a particular individual should be members of the same haplogroup. So although we believe we are English due to the fact that Nicholas likely came from England, Y-DNA testing would suggest that our ancient origins are in Scotland.

Next Generation Sequencing (NGS)

A recent development in Y-DNA testing is something called Next Generation Sequencing. NGS tests involve technology that allows high-throughput sequencing of DNA so that millions of base pairs can be analyzed in a fairly short amount of time. There are several companies that offer NGS testing, including the Big Y test at FTDNA and Y Elite 2.1 test by Full Genomes. I am most familiar with the Big Y, so I will concentrate on that. Although the Big Y test gets its name from the number of SNPs tested (over 10 million base pairs), I like to think it is called Big Y because it costs "big bucks" to take the test (currently $575 -- I know what I'm going to ask Santa for Christmas).

NGS tests like Big Y can be used to find your location deep in the haplotree because they look at a large number of known SNPs (about 25,000). These tests will also discover SNPs that are unique to you; i.e., SNPs that have not been discovered yet that could eventually lead to new branches on the haplotree if enough other test subjects also have the same SNPs. In short, NGS testing can uncover your deep ancestry as well as help the genetic genealogy community grow the haplotree.

If you are interested in learning more about SNP testing and NGS testing, I highly recommend the following set of YouTube videos by John Cleary at the 2016 "Who Do You Think You Are - Live" conference in Birmingham, England. I found them to be very informative and easy to understand.

Part 1 - https://www.youtube.com/watch?v=hlxvdayxZiI

Part 2 - https://www.youtube.com/watch?v=6l5QARvhb38#t=38.455813

Part 3 - https://www.youtube.com/watch?v=pxexkvfus6w#t=2.455583

Here Comes the Begging

This is going to sound like begging, and I admit I am begging. One of the ways we can learn more about our Ackley ancestors is to have more men with the Ackley surname take a Y-DNA test with FTDNA and join the Ackley surname project. If you are an Ackley male and you don't know if you are descended from Nicholas Ackley, the Y-DNA test can help answer that question. If you are an Ackley male and you are a descendant of Nicholas, taking the test will add to the database and can help establish the lines of descent below Nicholas that will be useful to future testers. Y-DNA testing could also help connect American Ackleys with Ackleys in England if an English Ackley took a Y-DNA test. It would also be interesting if other Ackley males would do the SNP testing to confirm our deep ancestry as mentioned above. So if you have considered taking a Y-DNA test, I encourage you to please take the plunge and add your results to the Ackley surname project. 

Link of the Day

This is the link to the R-S1051 Haplogroup Project on FTDNA. It gets a little technical, but there is some good information on this web site. Make sure to visit all of the tabs at the top (Overview, Background, Goals, News, Results)


https://www.familytreedna.com/groups/r-s1051/about

Quote of the Day

"Always do right--this will gratify some and astonish the rest."   

--Mark Twain

Sources

1. Estes, Roberta, "Concepts – Y DNA Matching and Connecting with your Paternal Ancestor", https://dna-explained.com/2016/04/14/concepts-y-dna-matching-and-connecting-with-your-paternal-ancestor/

2. Family Tree DNA Learning Center, https://www.familytreedna.com/learn/y-dna-testing/y-str/two-men-share-surname-genetic-distance-37-y-chromosome-str-markers-interpreted/

3. International Society of Genetic Genealogists, http://isogg.org/wiki/Haplogroup

4. Wikipedia contributors, "Beaker culture," Wikipedia, The Free Encyclopedia, https://en.wikipedia.org/w/index.php?title=Beaker_culture&oldid=721517090 (accessed June 2, 2016).

5. Wikipedia contributors, "Population bottleneck," Wikipedia, The Free Encyclopedia, https://en.wikipedia.org/w/index.php?title=Population_bottleneck&oldid=722697228 (accessed June 2, 2016).

6. Family Tree DNA, R-S1051 Haplogroup Project Page, https://www.familytreedna.com/groups/r-s1051/activity-feed

7. Wikipedia contributors, "Picts," Wikipedia, The Free Encyclopedia, https://en.wikipedia.org/w/index.php?title=Picts&oldid=722944060 (accessed June 2, 2016).