Y-DNA and mtDNA Primer

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A brief primer on DNA testing for the MayflowerDNA.org wiki ©2020 Raymond T. Wing email: wing.genealogist@gmail.com

DNA testing has been getting more publicity in the news and television recently. However, most of the attention (especially on television ads) is with autosomal DNA testing and ethnicity. This is NOT the type of testing which the MayflowerDNA.org wiki works with.

The MayflowerDNA.org wiki examines the Y sex chromosome and mitochondrial DNA. This is due to the fact these pass from parent to child without mixing, and for the most part, are relatively unchanged from generation to generation. Mutations do crop up from time to time, and they are random events. Most of the mutations happen in areas called “junk DNA” and as such, they have no known effect on the individual. The important part about these mutations is the fact they can be treated like the proverbial “bread crumb” trail of Hansel & Gretel and trace your personal genetic history back to the dawn of humanity.

Both Y-DNA and mitochondrial DNA are inherited through just one parent. Only males have a Y-Chromosome and men inherit it from their father, who inherited from his father, etc. Thus, the Y-DNA traces the straight paternal line (the father’s, father’s, father’s etc. father). Everyone has mtDNA, but we only inherit it from our mother who inherited it from her mother, etc. Thus, the mtDNA traces the straight maternal line (sometimes called the umbilical line) through the mother’s, mother’s, mother’s etc. mother.

The vast majority of people tracing their Mayflower ancestry did not inherit either their Y-DNA or their mtDNA from a Mayflower passenger. It is believed everyone alive today is at least ten generations removed from the dawn of the Seventeenth Century (1600). We have the potential for 1,024 ancestors of the eleventh generation, but we only inherited our mtDNA from one of them, and men only inherit Y-DNA from one of them.

Those lucky few individuals who happen to inherit either their Y-DNA or mtDNA from a Mayflower passenger have pieces of this ancestral path inside every cell of their body, which can reveal much information. Much like we can trace our family tree and create a pedigree chart tracing our ancestry, we can trace through the occasional random mutations and discover how these ancestral lines connect with others in the past. As a side note, the main reason why I became interested in tracing Mayflower DNA is due to the fact my Y-DNA (Wing) happens to be a remarkably close match to the Howland family Y-DNA. The two families share a common Y-DNA ancestry sometime in the dark mist of time, almost certainly before the creation of surnames.

This paper discusses mtDNA testing first, then will discuss Y-DNA testing. A good definition of mitochondrial DNA can be found at: www.genome.gov/genetics-glossary/Mitochondrial-DNA For the purposes of this primer, all we need to know is mtDNA is only matrilineally inherited (only inherited from your mother) and it is actually quite small (containing only 16,569 base pairs). While this may seem like a large number, Y-DNA (which is the smallest of the nuclear DNA chromosomes) contains 58 million base pairs.

There are both positives and negatives to having a relatively small number of base pairs. On the positive side, every single base pair is revealed in a full mtDNA test, and the cost is typically less than the cost of Y-DNA testing. On the flip side because it is so small, mtDNA mutations are VERY rare. Typically, mutations are found to occur in mtDNA in the thousands of years’ time scale and I am not personally aware of any mtDNA mutations which have occurred since the time of the Mayflower (within a Mayflower descendant).

For this reason, mtDNA results in and of themselves cannot be used to prove an individual descends in a mtDNA/umbilical line from a Mayflower passenger (or spouse), but it can be used to disprove such a connection. In fact, mtDNA testing has recently been used to disprove the commonly held belief that the wife of Daniel Doane was Constance Snow, granddaughter of Stephen Hopkins. The mtDNA of umbilical descendants of Daniel Doane’s wife did not at all match the mtDNA of known umbilical descendants of Mary Kent, first wife of Stephen Hopkins’ and mother of Constance (Hopkins) Snow.

There are a small number of testing companies offering mtDNA testing. These includes [www.familytreedna.com Family Tree DNA] and YSEQ. This primer will explain later about another type of testing which includes mtDNA testing. The important item to note is that a full mtDNA test covers the whole mtDNA and the other tests (often called HVR or Control Region tests) only cover a part of the mtDNA. Another note is the mitochondria contains a number of genes, which may reveal personal information. For this reason, DNA testing companies do NOT publicly reveal all the mtDNA results (but does send to each tester the full results). The MayflowerDNA.org wiki also does not reveal this personal information.

I would strongly encourage anyone who takes a Y-DNA or mtDNA test to join the appropriate projects or groups offered by the company they test with. This allows them to connect with knowledgeable administrators (who can answer any questions they may have as well as give you guidance regarding other options). It also does provide a forum for SOME of your information to be made available to others. Again, this information does not include the personal information. This primer will discuss how to join these groups/projects later.

Because the Y-DNA is much larger than the mtDNA, Y-DNA testing tends to be a bit more complicated and expensive. There are different types of DNA mutations, but for our purposes we only look at certain types of mutations, and I will refer to them only as mutations. Unfortunately, the best-known type of Y-DNA mutations (STR mutations) are not what is directly used by the MayflowerDNA.org wiki.

In addition, there is a huge difference in costs depending on whether we already know the mutation we are looking to test, whether we have a break in our “paper trail” but we believe we descend in a Y-DNA line from a Mayflower passenger (or a close relative of a passenger), or whether we are interested in discovering mutations not yet found by previous tests. For those folks lucky enough to have had others discover the mutations for them, there may be an inexpensive process to test for the individual mutation. This cost can be as low as about $20-$40 for an individual mutation. In case of the Howland family, where there were multiple brothers who came over to Plymouth Colony during the Great Migration period, a panel of tests can be created to test for a number of mutations to determine which brother a man descends from for about $100 or so.

There is also the ability to basically “take a gamble” and order a large panel Y-DNA test which will show you which will place you from the dawn of humanity down as far to the present day as is currently known. In some cases, this can result in being traced to the last couple of centuries or so, but in other cases it may only trace your line forward to roughly a thousand years ago or even more. This test costs roughly a couple hundred of dollars (depending on where you happen to fall in the Y-DNA tree). Y-Seq.net is the company which specializes in this type of test, although FTDNA also offers something somewhat similar.

Of course, before a mutation can be made available for purchase, it must be first discovered. One reason why the MayflowerDNA.org wiki was created was so folks can easily find out which families already have discovered mutations, so they do not have to order a much more expensive test.

There are two types of tests currently on the market which can discover new mutations. They are classified as Next Generation Sequence and Whole Genome Sequence (NGS/WGS) tests. These tests start at about $400 or so (although sales may occur making the cost less) and can run into the thousands of dollars. Next Generation Sequence testing utilizes a process to capture more of the Y-Chromosome than traditional (Sanger Sequence) tests. Over time improvements have been made to this process, so folks who ordered these tests now may receive results not found in older tests. Companies offering a NGS test include FTDNA’s Big Y-700 test as well as Full Genomes Corp. Y-Elite test. Both of these tests cost roughly $400 or so.

Whole Genome Sequence tests the entire DNA of an individual. These tests include both the mtDNA, Y-DNA as well as all of the 23 chromosomes. There are different levels of testing (basically how many times they “read” the chromosome) and the cost is based on how many reads. While companies offer 1x reads for fairly low price (roughly a couple hundred dollars or so) you really need to have more reads (as each read can have false positives and negatives). For comparative purposes, the Big Y-700 and current Y-Elite tests by and large has over 30x reads (although some feel this may be considered an overkill, some locations on the Y-chromosome are difficult for even this technology to read and having a lot of reads means a better chance of it being covered). Various folks recommend various levels of testing, but I feel at a minimum a 4x read is needed, and more is better.

There are a variety of companies which offer WGS testing, including FTDNA, YSEQ, Full Genomes, as well as Dante Labs Nebula Genomics and probably others.

Unfortunately, the testing labs are very proprietary. By this, I mean they do not allow you to load the results from a different company to your DNA account with them. Thus, the DNA results tend to be scattered across various testing companies. In addition, with WGS testing, the cost of testing typically does not include any analysis of the mtDNA and Y-DNA, meaning you would either have to learn how to do it yourself, or find someone to help you. A large barrier to either analyzing yourself or find someone to help you is that the files are VERY large, and most folks would not have the ability to download them on their computers (and getting a thumb drive or other option shipped to you is not only an additional cost, but has been inconsistent between vendors.)

As mentioned before, it is strongly encouraged that everyone who does a Y-DNA or mtDNA test to join a group/project. These are associated with the testing company, but they allow for groups of similar results to be posted together and be viewed by others. To join a group at YSEQ log into your account, then under My Account Information Look for My Groups then click on Group Browser and search for “Mayflower” (or whatever group you are interested in) then click on the join link.

A similar process allows folks to join a project at FTDNA. First you log into your account, then on your left- hand side under “My Projects” click on “JOIN A PROJECT” It will come up with a list of projects. If you have Y-DNA tested, I recommend you join the appropriate Y-DNA project and if you have mtDNA tested I would suggest you join the appropriate mtDNA project. There is also a Mayflower DNA Project which folks should join.