Genealogical Ponderings

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  1. Demystifying DNA 3: mtDNA testing

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    This is the third in my series of posts attempting to Demystify DNA testing for family historians. If you would like an overview to the many types of DNA test, do see the Introduction post. In my last blog we looked at Y-DNA testing in detail: when to use Y-DNA, who can test, where to test and how to interpret the results.

    This month we move onto mitochondrial DNA, or mtDNA, testing.

     

    Uses of mtDNA

     

    Mitochondrial DNA is to maternal research what Y-DNA testing is to paternal research as illustrated by the following schematic:

     

    The ancestors that may be traced using Y-DNA (blue) versus mtDNA (pink)

     

    mtDNA is specific to the matrilineal line, looking at your mother, her mother, her mother’s mother and so on. It does not include ALL of your mother’s ancestors, just those highlighted above.

    Just like Y-DNA, mtDNA is passed largely unchanged from one generation to another, enabling its use for tracing maternal ancient origins. You can also, in theory, use mtDNA to support your genealogy research. However this is complicated by the fact that the surname changes at every generation, making traditional research more challenging, and the way in which mtDNA mutates.

    Every now and again a mutation or copying error occurs with mtDNA, moving from one generation to the next. When I use the term “mutation” here I simply mean a change in DNA, no implication of anything to do with health. The main difference between the inheritance of mtDNA compared to Y-DNA is that the mutation rate of mtDNA is slower. A mtDNA match could share a common ancestor with you in recent generations or hundreds or even thousands of years ago.

    mtDNA is therefore not as useful for testing speculatively to find matches, as it is less likely that a mtDNA match will share with you a common ancestor in a genealogically relevant timeframe. The beauty of a match on mtDNA is the fact that you will know what small section of your family tree the match is connected to. Where mtDNA is particularly useful is for confirming suspected relationships. It is a very powerful test for comparing your own data with a suspected match to see if you are indeed related to the same maternal ancestor. This approach can equally be applied to adoption cases as to the situation where you have two candidates for your maternal great grandmother.

     

    Who can take a test?

     

    Contrary to popular belief, mtDNA tests can actually be taken by both males and females.

    mtDNA passes from a mother to her children, the difference being that only the females then pass this mtDNA on.  This is illustrated more clearly by the following schematic:

     

    Schematic showing the path of descent of mtDNA

     

    A is the great granddaughter of B. The diagram shows all descendants of B, outlined in blue or pink, depending on gender. Spouses are shown in black for clarity. The filled pink shapes indicate the path of descent of mtDNA. Remember, mtDNA is passed from a mother to her children but only her daughters will pass it on to the next generation. B had three children, but only her two daughters passed her mtDNA to the next generation, and so on.

    If A is unable to take the mtDNA test herself, you can see she has a number of options, assuming that the above represents only a bloodline. Her brother, C, could take the mtDNA test, her first cousin D, or even her second cousins, E and F. All have an unbroken line of female descent from B and all have the same mtDNA. This is an important point to note if you are looking to identify close living relative matches, say in adoption cases: a match could equally be a mother, sibling, aunt, cousin or grandparent, all of whom are descended from the same maternal ancestor, B.

     

    Types of Test

     

    Mitochondrial DNA is a circle of DNA, consisting of 16,569 base pairs. See the first post in this series, the Introduction, for an explanation of the terminology. Mitochondrial DNA consists of the following regions:

     

    mitochondrial DNA

     

    The area shown in white represents the hyper variable control regions (HVR1 & HVR2). These are the areas of the mtDNA known to mutate more quickly. They are therefore more likely to differ from one individual to another, unless they are closely related. The coding region undergoes changes less frequently.

    The first mtDNA tests analysed DNA in the HVR1 and HVR2 control regions only. Later mtDNA tests included both the HVR1 & HVR2 regions and the coding region. Some companies use SNP testing. Remember from the piece on Y-DNA testing, a Single Nucleotide Polymorph, or SNP, is a point along the DNA molecule known to differ from one individual to another – a point at which a mutation has occurred at some point in time. SNP (pronounced “snip”) testing analyses which nucleotide is found at many individual locations or SNPs.

    Also available for mtDNA are sequence tests. Rather than look at individual SNPs all base pairs are analysed in the region of interest. Early tests just looked at the base pairs in the HVR1 or HVR1 and HVR2 regions. Now it is possible to obtain a  full sequence test, which analyses all 16,569 base pairs. In much the same way as a higher number of markers on a Y-DNA STR tests gives you better data for comparison with others, more accurate mtDNA data is found with a full sequence test.

    If we imagine the ring of DNA opened out flat then a visual representation of the difference is:

     

    Graphical representation of Sequence vs SNP testing

     

    The Data

     

    When we looked at the Y-DNA STR tests we looked directly at the number of repeats at STR markers or the identity of bases at particular locations. mtDNA data analysis is different. Here we compare how each individual differs from reference standards. The first produced was the Cambridge Reference Standard (CRS), now superseded by the corrected revised Cambridge Reference Standard (rCRS), based on a European who had haplogroup H. A second standard, the Reconstructed Sapiens Reference Sequence (RSRS), was produced more recently and was an attempt to to compare mtDNA against a reference with an older haplogroup, closer to Mitochondrial Eve (see below for more on haplogroups). The details of the two standards are not appropriate here, more information can be found at the ISOGG website. It is, however, important to know which standard has been used by your testing company of choice if you are to compare results with those obtained elsewhere.

    Family Tree DNA supplies results against both reference standards. The images below show the (truncated) results of my own mtDNA test against the rCRS at Family Tree DNA.

     

    mtDNA results against the rCRS standard

     

    The results are actually reported in two ways, just to confuse you! In this case there are no differences to the standard in the HVR1 region. In the HVR2 region five differences are shown. The traditional way of reporting these is to the give the position number, followed by the letter of the base that you have compared to the original. So at position 152 I have C instead of the base of the rCRS. The second set of data (the lower table labelled “Revised Cambridge Reference Standard”) actually shows this more simply. It shows you that there should be a T at position 152 but I have a C.

    The addition of a “.1” indicates an addition at this position. In fact I have two additional Cs at position 309. Again this is more clearly seen in the bottom set of table for the rCRS results: there are no bases at 309.1 but I have two Cs. If a base is missing at a particular position it would be marked e.g. 309-, known as a deletion.

    Now let’s turn our attention to the RSRS results, again my own (truncated) data:

     

    mtDNA results against the RSRS standard

     

    There are some differences against the reference standard in the HVR1 region here. This is to be expected: The reference for the rCRS was in haplogroup H, as am I, whereas the reference for RSRS is based on older haplogroups. Here differences are marked:

    <reference base> POSITION NUMBER <your result>

    so you can readily compare the base in the reference standard with your own. For the RSRS results there are also extra mutations and missing mutations. These refer to differences from what is expected for my haplogroup compared to the RSRS.

    My current matches on mtDNA are show below:

     

    mtDNA matches at Family Tree DNA

     

    As you can see, I don’t yet have any matches at genetic distance of zero. A genetic difference of 1 means that there is a difference in my data compared to the other test taker’s data at one position, whether it be a different base, an addition or a missing mutation compared to their results.

    With Y-DNA we could calculate a reasonable estimate of the time to Most Recent Common Ancestor (MRCA) as Y-DNA mutations happen at a regular rate and there is some level of confidence in predictability. As I said earlier, with mtDNA the mutation rates are much slower and there is much greater range. The following table is taken from the Family Tree DNA website. Even if I had a match with a genetic distance of zero there’s only a 50% likelihood that person and I share an ancestor within 5 generations. It’s more likely that the common ancestor is somewhere within the last 5-22 generations.

     

    MRCA estimates for mtDNA (Family Tree DNA)

     

    mtDNA haplogroup

     

    What I find interesting is knowledge of my mtDNA haplogroup. Just as there is a haplogroup tree for Y-DNA, there is an equivalent mtDNA haplogroup tree, as all females are descended from mitochondrial Eve. An individual’s mtDNA haplogroup is their location in the human mtDNA haplogroup tree. Everyone fits on this tree, some branches dating far further back in time than those derived from more recent mutations. A simple graphic is shown below but there are many branches, or subclades, within each haplogroup.

     

    mtDNA haplotree (Wikipedia)

     

    Each haplogroup is connected to  particular time and place and more information on where the haplogroups originated can be found here: mtDNA haplogroups. My own haplogroup is H. This is a predominantly European haplogroup as I would expect and does not reveal anything exciting about my own family history. However, for those with a family story that 3x great grandmother was a local Indian girl that 3 x great grandfather met while he worked in British India, discovering the haplogroup can be very important.

     

    The Testing Companies

     

    Family Tree DNA:

    I’m only considering the main five DNA testing companies in this series of blogs, to keep things simple. Of these, only Family Tree DNA currently offers separate mtDNA tests. Both HVR1 / HVR2 (mtDNA Plus) and full sequence (mtFull Sequence) tests are available.

    Whilst the other DNA companies in “the big five” do not offer a separate mtDNA tests, some do provide the mtDNA haplogroup a part of their single combined DNA test:

    Living DNA:

    Living DNAs test results for includes measurement of roughly ~4700 positions on the mtDNA genome to define the haplogroup*.

    23 and Me:

    The 23 and Me DNA test results for include measurement of 2737 mtDNA single nucleotide polymorphisms (SNPs) to define the haplogroup*.

    * Data source: ISOGG wiki, MtDNA testing comparison chart.

    Remember

     

    Be careful with haplogroups – Y-DNA and mtDNA lettering conventions do not relate to one another. The Y-DNA haplogroup is an indication of paternal ancient origins, the mtDNA haplogroup an indication of maternal ancient origins. A man has both, a woman has only a mtDNA haplogroup.

    As with all DNA tests, the number of matches you get with mtDNA testing will depend on who else has tested. If you have no matches to start with: be patient.

    With any type of DNA test, the results obtained form only part of the analysis. DNA testing does not answer questions alone: it must always be assessed along with other information and documentary evidence.

    Next Up

     

    The next post will focus on the most popular type of DNA testing now: autosomal DNA, the type of test offered by Ancestry, My Heritage and Family Tree DNA (the Family Finder test) to find matches to close living relatives.

     

     

     

  2. Demystifying DNA 2: Y-DNA tests

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    In my last blog we looked at the science behind DNA testing and the different types of test available.

    Here we start to look at each type of DNA testing in more detail.

     

    Uses of Y-DNA

    Y-DNA is passed from father to son unchanged for many generations and this makes it a powerful tool for assessing your paternal line: a match on a Y-DNA test can only lead you up one part of your family tree.

    Y-DNA is often used by those running surname studies as, in principle, the descent of the male line is the same as the descent of the surname. Y-DNA can therefore be used to assess the likelihood of all bearers of a particular surname arising from the same single individual, no matter how far back in time this individual lived. There are single surname DNA projects through the commercial testing sites and a number of One-Name Studies (ONS) also operate DNA projects.

    However, human nature results in a number of scenarios where this hypothesis falls down. The most common issue is the bearer of a surname being found to be illegitimate: Mr Postlethwaite was actually a plain old Mr Brown. In DNA circles this is referred to as a “non-paternity event” or NPE. There are a number of other reasons a surname may be assumed: unofficial adoption, taking on a stepfather’s surname and so on.

    Y-DNA can also be used to identify an unknown father. The caveat here is that the results may point to a particular male line but not necessarily an individual within that line. Just using Y-DNA testing could point to Mr A being the father, but equally his brother, his paternal cousin or his uncle. Just as we said last time, the DNA test is one source of information that can be used to aid genealogical research. It needs to be used in the context of known information and documentary research, in this case, who was in the right place at the right time?

     

    Who can take a test?

    Y-DNA tests can only be taken by males. However, the power of the Y-DNA chromosome is that it is unchanged over many generations. If you have no brothers you can ask a cousin to test, or an uncle, or even a second or third cousin, So long as they are from an unbroken line of males from your common ancestor.

    Schematic showing the path of descent of Y-DNA

    The schematic above (click the image for a larger version) shows all descendants of a single couple, marked in blue or pink, depending on gender. Spouses are shown in black for clarity. Solid blue boxes indicate the path of descent of Y-DNA. Our test taker is shown at the bottom right in solid pink, a female family historian interested in her maternal grandfather’s line. Unfortunately, her grandfather died some years ago. At first it seems there is no way that she can find a male to test for Y-DNA. Her mother is one of two sisters and her grandfather also had no brothers. The beauty of Y-DNA is that we can keep moving backwards. A generation further back and our family historian’s great grandfather had one sister and one brother. If we look at the brother’s line was can see that he had two sons. One died without children but the other had a son and he also had a son. Assuming one of these individuals is still alive we have found a test candidate for the Y-DNA equivalent to that of our family historian’s grandfather. This approach does assume that all are the blood line of the uppermost male. A non-paternity event is a possibility and you should always test more than one candidate from more than one line if you can.

     

    The Data

    There are two different methods of analysing and comparing Y-DNA: STR or Short Tandem Repeat testing is useful for comparing the relationships between individuals in a genealogically relevant timeframe. What do we mean by genealogically relevant? Simply, the timeframe over which we are probably going to be able to support any findings with documentary evidence.  SNP or Single Nucleotide Polymorph testing is used to define a person’s haplogroup and investigate their ancient origins.

     

    STR Testing: haplotypes

    Short Tandem Repeats (STRs) are positions along the DNA molecule where the same sequence of nucleotides or bases is characteristically repeated a number of times, e.g. AGTCAGTCAGTCAGTCAGTC. Each STR marker is named, typically in the format DYS391 (where D = DNA, Y = Y chromosome and S = (unique) segment). The number of times the sequence is repeated at each marker is counted and the results of the Y-DNA test take the format shown below:

    This set of results is an individual’s haplotype. When purchasing a Y-DNA test you will see numbers Y-DNA37, Y-DNA67 and Y-DNA111. These are the number of STR markers tested or haplotype resolution. The example above tested at 12 markers only. Whilst early tests could only look at 12 markers, 37, 67 and 111 are now more common as the technology has developed, with some tests looking at even greater numbers of markers. You can still compare results with someone who tested with a different number of markers: a test at 37 markers looks at the same 12 markers as a 12 marker test, plus an additional 25, and so on.

    The results of the STR tests are compared with those of others on the commercial websites to see if they are matches. If all results match the genetic distance is zero. In the example above, if another set of results was compared and all were the same except the result for DYS391 was 9 instead of 10, this would be termed a genetic distance of one. If DYS391 was 9 and DYS426 was 13 this would be a genetic distance of 3, i.e. the difference of 1 at DYS391 plus the 2 on DYS426.

    Caution: If you have an exact match at 12 or 25 markers this does not necessarily mean you are closely related. A comparison of 67 markers is looking in more detail at the DNA and could reveal that there are actually large differences in the results. In the example below, there appear to be four exact matches when testing at 25 markers. However, the same four individuals also took Y-DNA67 tests. When these are considered it is seen that that is a genetic distance of anything between 4 and 6.

    STR matches at 25 markers, taken from Family Tree DNA website

    STR matches at 67 markers, taken from Family Tree DNA website

    But what does this mean in terms of how closely related you are to someone? Are these Cummings families all related if there are some differences in the STR results? Whilst Y-DNA largely passes down unchanged from one generation to the next, occasionally there is an error or mutation in the replication process and a difference will occur. As the changes tend to occur at regular intervals the knowledge of rate of mutation of STR markers can be used to predict the time to most recent common ancestor (MRCA). Not all STR markers mutate at the same rate; a genetic distance of, say, 4 will not always equate to the same time to MRCA.

    This sounds complicated but is simplified by the tools available to us online. The Family Tree DNA website allows you to get an idea how far back your common ancestor lived by clicking on the orange “TiP” (“Time Predictor”) icon. If we click on the “TiP” icon for  J Cummings in the 25 marker test example above we get the following:

    Likely relationships assessed on 25 marker match data

    This  indicates that J Cummings and the test subject have a 85% chance of sharing a common ancestor in the past 8 generations. However, when 67 markers are compared, this changes:

    Likely relationships assessed on 67 marker match data

    Now there is only a 51% chance they shared a common ancestor over the last 8 generations, but an 82% chance they shared an ancestor within 12 generations.

    A more generic way of assessing genetic distance, without bring in the difference in mutation rates, is as follows (click on the image for a larger version):

    Y-DNA genetic distances from FTDNA website

    So our J Cummings is likely to be related to the test taker within a genealogically relevant timeframe, but the other other individuals are probably connected further back in time. To get the best from a Y-DNA test, always test the highest number of markers you can sensibly afford to.

    The results of STR testing, in the format of number of repeats per STR marker, are called individual’s haplotype, as in the table above. However, the information regarding the known rate of mutation in the different STR markers can also be used to estimate an individual’s haplogroup.

    An individual’s haplogroup is their location in the human Y-DNA haplogroup tree. Everyone fits on this tree, some branches dating far further back in time than those derived from more recent mutations. A simple graphic is shown below but there are many branches, or subclades, within each haplogroup. Haplogroups are further defined with SNP testing, as described below.

    The Y-haplotree (Wikipedia)

     

    SNP testing: defining haplogroups

    A Single Nucleotide Polymorph (SNP) is a point along the DNA molecule known to differ from one individual to another – a point at which a mutation has occurred at some point in time. Rather than test areas of repeating nucleotide sequence like STR testing, this type of testing analyses which nucleotide is found at many individual locations or SNPs (pronounced “snips”).

    Graphical representation of STR vs SNP testing

    SNP testing is primarily used to improve upon the estimate from STR testing and define an individual’s haplogroup and can be used to assess ancient origins. As more SNP mutations occurred more branches formed in the haplotree (above), each defined by one or more SNPs. A more detailed version of the Y-DNA haplogroup tree can be found on the website of the ISOGG (International Society of Genetic Genealogy).

    If an individual has a mutation at a particular SNP he moves down to the relevant branch, if not he stays where he is on the tree. Y-DNA haplogroups used to be written in the form R1a1a1b2a2a1 but as more research is conducted more and more branches are discovered. Now the name of the haplogroup is shortened to the letter from the major haplogroup branch, follow by the final SNP at which a mutation was detected. Care needs to be taken with comparing haplogroups, as one tester may have conducted SNP testing to a deeper level than another (i.e. they may appear different but could actually be from the same higher branch).

    In the example above for Cummings Y-DNA all four individuals have had their haplogroups defined with extensive SNP testing, the “Big Y” test at Family Tree DNA. We can see that all individuals are within haplogroup R, but not the same branch. SNP testing can therefore be used to compliment the STR results: we would expect J Cummings and K R Cummings to be more closely related to one another than to the others tested (the test taker is also R-YP983).

    The haplogroup can also be used to assess the ancient origins of an individual. For example, the haplogroup R originated in Central Asia. More information on the origin of haplogroups can be found here.

     

    The Testing Companies

    STR testing:

    Only Family Tree DNA currently offers a separate Y-DNA test where STR results can be compared with other users. Your own STR data can also be downloaded for further analysis elsewhere.

    Haplogroup / SNP testing:

    Haplogroup and SNP testing is also available from Family Tree DNA.

    Whilst other DNA companies do not offer a separate Y-DNA test examining STRs, some do provide the Y-haplogroup a part of their single combined DNA test:

    Living DNA:

    Living DNAs test results for males includes measurement of roughly 20,000 SNPs on Y-DNA to define the haplogroup.

    23 and Me:

    The 23 and Me DNA test results for males include measurement of “hundreds of Y-chromosome single nucleotide polymorphisms (SNPs)” to define the haplogroup.

     

    Remember

    Using DNA testing to solve genealogical problems is dependent on the databases of test results. If no one else from your paternal line has yet tested, you won’t get any matches. In addition, all of the commercial companies databases currently contain more results of those from the US than anywhere else. This is changing as more and more test, from all over the world. The test results are powerful but you may have to be patient.

     

    A plea from me

    Do you have any COWLING ancestors from England? I have registered a Cowling One Name Study and am interested in expanding this to incorporate a DNA Project. If you are a male Cowling descended from Cowlings in England, particularly those from Cambridgeshire, Yorkshire and Cornwall and would be interested in taking part do please get in touch. Similarly if you have Cowling relatives and are just interested in the One Name Study, do get in touch too. I would love to hear from you.

     

    Next Up

    The next post will focus on mtDNA (mitochondrial DNA), the DNA we can use to assess ancient origins on the female line.

     

     

     

  3. Demystifying DNA 1: Introduction

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    DNA testing is becoming a more and more important part of genealogical research. It is estimated that 12 million people have now been tested, 7 million of those with AncestryDNA. Should you test and why? With so many tests available and so many companies to choose from it can be difficult to know where to start.

    This is the first in a series of articles that starts at the beginning, demystifying all that is DNA testing in genealogy.

     

    The Tests

    There is more than one type of DNA test and the test you choose will depend on what you are using DNA to look for:

    • Y-DNA testing
    • mtDNA (mitochondrial DNA) testing
    • autosomal DNA testing
    • X-DNA testing
    • deep ancestry or ethnicity tests

     

    The Testing Companies

    Some companies offer individual tests and some offer more than one type of data from a single test. The major testing companies are:

    • Ancestry DNA
    • Family Tree DNA
    • 23andme
    • Living DNA
    • My Heritage

     

    The Sciencey Bit

    Before we get into the detail of what each type of DNA testing looks at and why you should choose a particular test, let’s start with the “sciencey bit”, keeping things simple.

    DNA exists within almost every cell of the human body and contains long strings of nucleotides containing bases: adenine, cytosine, guanine and thymine, more commonly referred to as A, C, G and T. I am sure you are familiar with the double helix structure of DNA illustrated above. This is actually two DNA strands woven together, the interaction of the bases of one strand (blue circles) with the other (purple circles) forming the ladder like construction of base pairs, A always pairs with T and C always pairs with G.

    Most of the tests we are interested in are concerned with the DNA within the nucleus of each cell. This DNA is packaged into chromosomes and the chromosomes are grouped in chromosome pairs of two similar, but not identical chromosomes. This relationship is illustrated, thus:

    We have 22 pairs of chromosomes, known as autosomes, and a 23rd pair, the sex chromosomes. Females have two X chromosomes in this pair and males have one X chromosome and one Y chromosome. Chromosome pairs are shown below in an arrangement known as the human karyotype:

    Human karyotype

    So already you can start to see where the Y-DNA, X-DNA and autosomal DNA tests come in.

    The last type of DNA is a special case. Mitochondrial DNA is found within a different component of human cells: the mitochondria. It is not packaged into chromosomes but into a single ring of DNA.

    In each case our DNA makes us unique. It is the ways in which the DNA varies from one individual to another and the ways in which it is passed down the generations that enable us to use DNA for genealogy research.

    However, let’s not forget: human DNA is made up of around 3 billion base pairs and around 99.5% of those are the same in all of us – they are what makes us human. It’s only that 0.5% we are looking at when we talk about DNA testing in genealogy.

    We will talk about each type of testing in more detail in upcoming blog posts. In very general terms:

    • Y-DNA is passed from father to son and is unchanged for many generations.
    • mtDNA is passed from mother to her children (but is not passed on by her sons) and can be used to determine maternal ancestry, again unchanged for many generations.
    • X-DNA is passed from parent to child but a daughter will receive X-DNA from father and mother, a son will only receive X-DNA from his mother.
    • Autosomal DNA is passed from parent to child in varying combinations and can be used to assess close cousin relationships.

    It’s easy to see why there is so much confusion about which test to take. Before deciding which test to take it is important to be clear in your mind what you are looking for, what is the question you want answered?

     

    Next up

    Each type of DNA test will be discussed in detail in subsequent blog posts, looking at when to use each type of test, who can each test and what the results look like. Next up, Y-DNA.

     

    Remember

    With all types of DNA testing, the DNA test is one source of information that can be used to aid genealogical research. You would not base a family tree on a single census record and in much the same way, DNA needs to be used in the context of known information and documentary research.

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