Difference between revisions of "Y-DNA and mtDNA Primer"

mtDNA testing

A good description of mitochondrial DNA can be found at: https://www.genome.gov/genetics-glossary/Mitochondrial-DNA For the purposes of this primer, all we need to know is mtDNA is only matrilineally inherited (inherited from your mother's mother's mother's etc.) and it is actually quite small (containing only about 16,569 base pairs). While this may seem like a large number, Y-DNA (which is the smallest of the nuclear DNA chromosomes) contains well over 50 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 only aware of a couple of instances where mtDNA mutations have been found to occur in a Mayflower descendancy line.

For this reason, mtDNA results in and of themselves usually cannot be solely 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 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 (including the Coding Region which is where all the known genes are located) while the other tests (often called HVR or Control Region tests) only cover a small 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 Coding Region results or other personal information. This primer will discuss how to join these groups/projects later.

Y-DNA testing

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 is the company which specializes in this type of test, although Family Tree DNA (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 Family Tree DNA (FTDNA), Y-SEQ, 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.