Building a Mutation History Tree with STR data

In the previous blog post we explored Genetic Distance and how it can be used to group people together into the same Genetic Family (or Lineage). We also saw how a lot of your relevant non-matches only show up in surname projects because they are outside the FTDNA matching threshold. Lastly, we introduced the concept of the Mutation History Tree (MHT) and how traditional genealogies could be hung on its branches to give a combined tree that uses mutations when named individuals run out.

In this blog post, we will look at how to build a Mutation History Tree using STR data.

Building a simple Mutation History Tree

A huge thank you is due to project member Lisa Little who generated a lot of the data discussed below, and to Nigel McCarthy (Admin of the Munster Irish Project) who has offered invaluable advice.

It is clear from the Results Page of the Gleason DNA Project that each Lineage has a distinctive coloured pattern by virtue of the values for its STR markers. This distinctive coloured pattern reflects the unique marker values for each Lineage, and distinguishes one Lineage from another. The Modal Haplotype for each Lineage represents the "signature tune" for that particular Lineage.

The distinctive coloured patterns of Lineages I, II & III
(from the Results Page on the World Families.Net site)

Furthermore, within each Lineage, there are subtle differences among members. In other words, most people are not an exact match to the Modal Haplotype - everyone in the group sings the "signature tune" just ever so slightly differently. They're all in the same choir, but some hit a bum note! These differences between project members in their STR marker values allow us to construct a diagram that suggests how the various project members might be related to each other.

So, for example, if we take the first 12 markers in Lineage II we could construct a Mutation History Tree (MHT) that separates out the members of the group into different branches. Reading from left to right across the tree in the diagram below, the first 4 members (G22, G05, G57, and G64 in the diagram below) all match the Modal Haplotype at 12 markers (Branch 1). The fifth member (G42) has a single mutation (in red) at marker 385b which has mutated from the modal value of 14 to a new value of 15 (Branch 2). This may have happened in the previous generation or many many generations ago. The 6th member (G21) apparently has 2 mutations* from the modal (on markers 389i1 and 389i2), and the remaining members all have a mutation at marker 390 with 3 of them having an additional mutation on marker 392 (Branch 5).

12-marker MHT for Lineage II
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This diagram gives a pictorial representation of how the different members of Lineage II may be related. The branching pattern derived from the DNA mutations may very well correspond to the branching pattern that one might see in the traditional Family History Tree if we were able to trace it all the way back with documentary evidence to the MRCA (Most Recent Common Ancestor). Thus the Mutation History Tree can give us important clues regarding which individuals are likely to be on the same branch of the overall tree, and who is more closely related to whom. This in turn can help focus further documentary research. 

In the example above, the project members in the last branch on the right (Branch 5) are more closely related to each other than to anyone else in the project - they should get together and try to figure out how they are related. Their MRCA is a lot closer in time than the MRCA they share with (for example) the first group in the tree (on the far left, Branch 1). Similarly, because Branch 5 is in fact an off-shoot of Branch 4, the MRCA for these two groups is going to be closer in time than the MRCA either shares with any of the other groups. Thus, for example, Branch 5 members may share an MRCA born in 1750, Branches 4 & 5 share an MRCA born in 1610, Branches 4 & 3 share an MRCA born in 1390, and the MRCA for the entire group was born in 1125.

But this is the pattern based on the values of just 12 STR markers. What happens when we use 37 markers? or 67? or 111? The more markers that are used to generate the Mutation History Tree, the more accurate the picture is likely to become and the more likely we are to approximate the branching pattern in the actual Family History Tree.

However, not everyone in the group has tested to the same level of STR markers. Six people have tested to 111 markers, 3 people have tested to 67 markers, and 2 people have tested to 37 markers. And of the 4 people in "Possible Lineage II", one has tested to 25 markers and 3 have tested to only 12 markers. This obviously creates difficulties in accurately allocating people to the correct branch of the Mutation History Tree and such allocations are likely to change as these members upgrade their results and more data become available.

These are very important points that need to be born in mind and are worth repeating:

• Mutation History Trees are only as good as the data available 
• They are liable to change as more data becomes available
• The more data used to generate the tree, the more likely it is to approximate reality

Building a more complex Mutation History Tree

To generate a more advanced Mutation History Tree, using up to 111 markers, we can use programmes such as Fluxus to generate a phylogenetic tree / cladogram that produces a "best fit" model of the tree (i.e. with the fewest number of branches possible for the known mutations). This is often called a "maximum parsimony" approach and the principle is akin to that of Occam's razor which simply states that - all else being equal - the simplest hypothesis that explains the data should be the one that is selected. It may not be the correct one (there are usually other possible alternatives with varying degrees of plausibility), but it has the highest probability of being the correct one.

Using the Fluxus software is not easy - the process is multi-step and complicated, it is not user-friendly, and it takes time. Nevertheless, we will look at the output of this software in a separate blog post.

Below is a summary of the various STR mutations that occur within Lineage II (courtesy of Lisa Little). Mutations from the Modal Haplotype are highlighted in yellow and beige. The markers are divided into their various "Panels" by bold dark lines. Mutations among the first 12 markers are in the first 5 rows (Panel 1); the next 3 rows are mutations among markers 13-25 (Panel 2); and the following 4 rows have the mutations among markers 26 to 37 (Panel 3).

From these it is possible to build a more evolved Mutation History Tree than the one generated using only 12 marker data. As all 11 members have tested to 37 markers, let's construct a tree based on 37 markers and compare it to the one generated from the 12-marker data.

Lineage II's STR mutations (from Lisa Little)

37-marker Mutation History Tree
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The previous 12-marker Mutation History Tree (for comparison)
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In the new 37-maker Tree, additional branches and additional mutations are indicated in pink. The branches have doubled and are now numbered 1 through 10. Branch 3 is an exact match to the Modal Haplotype (but no members sit on this particular branch). There are several important points to note when comparing this new 37-marker Tree to the previous 12-marker Tree:

• The tree with more data (the 37-marker Tree) has more branches, more definition, more granularity, more fine detail
• The new branches allow us to revise our estimates for when the MRCA for the various branches may have been born. For example, what was Branch 5 has now split into two branches  (9 & 10), and the members in Branch 9 (G39, G51) share an MRCA who was possibly born several generations after the MRCA for Branch 9 & 10.
• There are several Parallel Mutations in the 37-marker Tree (i.e. identical mutations that occur in several different branches)
• 464b (16>17) occurs on 2 branches (Branches 4 & 8)
• 464c (17>16) occurs on 2 branches (Branches 1 & 10)
• CDYa (39>38) occurs on 5 branches (Branches 2, 4, 6, 7/8, & 10)
• CDYb (40>39) occurs on 2 branches (Branches 1 & 9)
• 456 (16>15) occurs on 3 branches (Branches 2, 6 & 7)
• The apparently large number of Parallel Mutations may be because this is not a "maximum parsimony" tree, and there may be another way of arranging the data that would produce a better "fit" with fewer branches. The Fluxus software could help clarify this. 
• Alternatively, this may be a very accurate reflection of the real Family History Tree (i.e. how people are actually related ancestrally) and the large number of Parallel Mutations are due to the rapid mutation rate of the STR markers in question. This is entirely plausible as several markers are known to mutate back and forth fairly frequently from one generation to the next (e.g. the CDYa and CDYb markers). FTDNA identifies such rapidly mutating markers by colouring them in dark red on the DNA Results page.
• Back Mutations may be present in the tree, but are hidden  ... and thus the tree may be wrong
• for illustrative purposes, in Branch 2, theoretically there may have been a mutation in one of the members ancestral lines such as CDYb (40>39) in (say) 1470, and a few generations after that a Back Mutation CDYb (39>40) in (say) 1610. This would place these members on 2 different branches rather than on the same branch where they currently sit. 
• And even though in reality, they share a Common Ancestor in 1470, the Back Mutation masks this, and makes them look much more closely related than they actually are, with a Common Ancestor that appears to be sometime in the 1700's perhaps, 300 years later than it actually is!
• This latter point is a common experience when working with any type of DNA - the Common Ancestor is further back than he/she looks.

Fast-mutating markers (in dark red) among the first 37 markers of FTDNA's Y-DNA test

Examples of Mutation History Trees generated using 37-marker results can be found in the Allen Patrilineage Project for their Patrilineage I and Patrilineage II.

When building a Mutation History Tree with larger numbers of markers (67 or 111), software programmes such as Fluxus become indispensable because doing it by hand is much more difficult. And as stated previously, the tree is likely to change as more data is used to generate the branching pattern. If we generated a tree based on 67 marker data it would become even more detailed, and more so too with a 111-marker based tree. Furthermore, adding more data is likely to change the branching pattern within the tree as a new "best fit" model is identified. 

And this essential point will be perfectly illustrated when we add SNP marker data into the mix - it throws our 37-marker "best fit" Mutation History Tree into a completely new configuration.

I don't know about you but I can hardly contain myself.

Maurice Gleeson

13 Aug 2015

* the 2 apparent mutations are in fact only 1. The marker DYS389 is a single STR marker that has four parts: m, n, p, and q. At FamilyTreeDNA they have two tests for DYS389. The first test looks at the first two parts of marker DYS389 (m and n). This is what they call DYS389I. The second test looks at all four parts of DYS389 (m, n, p, and q). This is what they call DYS389II. There are, by scientific convention, two ways to display the result of DYS389II.  The way FTDNA display the result is by showing the total for the entire DYS389 marker (m+n+p+q). This is described in their Learning Centre FAQ here. Member G-21 has a mutation in 389i - which is indicated by his value of 13 rather than the modal 14. For marker 389ii his value of 29 rather than 30 indicates that in the entire marker (parts m+n+p+q) he still only has a single mutation - that same single mutation which is reported as 389i. In reality, since 389ii includes all four parts of the marker, we should just drop 389i off our table. Any mutation in 389i will be included in 389ii. My thanks to Lisa Little for pointing this out.  

Genetic Distance, Genetic Families, & Mutation History Trees

In this blog post, we examine how people are grouped together into Lineages (sometimes called Genetic Families) and how the relationship between people within a Lineage can be mapped out and represented in a Mutation History Tree.

Grouping People Together

The members of each lineage within the project have been grouped together because their genetic signatures (aka haplotypes) are similar, suggesting a common ancestor some time in the past several hundred years. The degree of similarity between any two individuals can be assessed by the Genetic Distance between them, as discussed in a previous blog post and reproduced again below:

Who qualifies as a match to you? Anyone whose marker values are sufficiently similar that they meet the criteria set by FTDNA to be declared "a match". And here are those criteria:

• a Genetic Distance (GD) of 0 at 12 markers

• a GD of 2 at 25 markers

• a GD of 4 at 37 markers

• a GD of 7 at 67 markers

• and a GD of 10 at 111 markers

The ISOGG Wiki has a very nice summary of Genetic Distance and the criteria for matching.

However, Genetic Distance is not the only possible criteria for grouping people into the same "Genetic Family" or "Lineage". Other considerations include traditional genealogical indicators such as having the same surname (the main criterion for surname studies), or having an ancestor who came from the same location as the ancestors of other group members. Additional genetic criteria may include having the same rare marker values, or having the same terminal SNP. These considerations can also serve as indicators that Lineage members have been grouped correctly i.e. members may be grouped together on the basis of one criterion (e.g. Genetic Distance) and subsequently are found to share a second criterion (e.g. the same rare marker value, ancestors from the same location, or even the same MDKA). You can read more about some of the possible criteria for grouping people together into the same genetic family here.

Why do I match some Project Members but not others?

You will probably notice that not everyone in your Lineage turns up in your list of matches on your Matches Page. The reason for this is that they do not meet the FTDNA criteria for a "match" to you, but they do meet the criteria as a match either to the Modal Haplotype* for the Lineage or to other members of the project. This is one of the key benefits of joining a surname project (such as the Gleason/Gleeson DNA Project) - it can connect you to people within the FTDNA database who do not show up in your list of matches but to whom you are still likely to be related.

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For example, in Lineage II, my Dad (G21; N74958; yellow dot in the diagram above) is a match (at 37 markers) to only 5 of the other 10 members: G22, G57, G64, G55, and G66 (green dots). He does not match the members with red dots. In other words, his genetic distance to the green dot matches is 4/37 or less, whereas his GD to the red dot matches is 5/37 or greater (in fact, reading down, his GD to each of the red dot members is 5/37, 6/37, 5/37, 6/37, & 6/37 respectively).

But let's look at the member closest to the Modal Haplotype* for Lineage II. This is the person with the fewest number of mutations compared to the Modal Haplotype, or (in other words) the smallest Genetic Distance from the Modal Haplotype. There are no exact matches (i.e. 0/37) to the Modal Haplotype in Lineage II, but there are two members who are the closest (GD = 1/37) and these are members G57 and G64 (kits 60393 & 365763). They are uncle/nephew, both carry the surname Little, and they are believed to have a genetic Gleason ancestor somewhere in the last several hundred years. As Project Admin, I have access to their pages and I can look at their matches. This tells me that each of them matches 7 of the 10 other members in Lineage II. I can also see that their Genetic Distance to the remaining 3 members of Lineage II is only 5/37, just outside the FTDNA threshold for declaring them a match. Looking at these 3 latter members, one matches two other people within the project and the other two match 5 project members.

So everyone within the project is a match to at least one other person within the project, but the distance between any two project members can vary considerably - some are very close, others are very distant.

And this creates a wonderful possibility - by analysing the degree of Genetic Distance between members we can construct a diagram of the branching pattern within the group which shows how closely or how distantly each member may be related to each other member. Such a diagram is variously called a phylogenetic tree, a phylogram, a cladogram, or a Mutation History Tree. The same process is used to generate evolutionary diagrams showing where all living creatures sit on the Tree of Life.

Interactive version of the Tree of life 

Mutation History Trees

This concept has important potential implications for genealogy. Theoretically, it should be possible to take the known genealogies of each member within a Lineage and hang them onto the appropriate branch within the Mutation History Tree. In this way we will have a combined tree that starts off in modern times with named individuals, goes back along each ancestral line until the named individuals run out (at each branch's Brick Wall or MDKA, Most Distant Known Ancestor), and then the tree continues back in time using genetic marker mutations instead of people, culminating at the Modal Haplotype for that particular Lineage.

A combined Family History Tree & Mutation History Tree

In the combined tree above, named individuals appear in the blue boxes, starting with living individuals (born about 1960) and going back in time to the MDKA for each branch. Most branches have an MDKA born about 1810 to 1840 (which is typical for Irish research), and some have a Brick Wall at a later point (Branches 5, 6, & 7 have an MDKA about 1870). One lucky branch can trace their line back to 1690 which is highly unusual but something we all hope for. You never know when a new member will join your particular Lineage who happens to be in possession of the Family Bible! And because you are genetically related to him, his Family Bible pertains to your family too. In this way, all members within a particular Genetic Family can "piggyback" onto the pedigree of the member with the longest pedigree.

Where the named individuals end, DNA marker mutations take over. STR markers are in yellow, SNP markers are in pink, but this is just a crude representation of what the tree might look like. In reality it would be much more complicated than this.

The person sitting at the intersecting point of all the branches is the MRCA (Most Recent Common Ancestor) and he is likely to have the Modal Haplotype for that particular Lineage. And as we go back in time, we would identify NPEs (Non-Paternity Events), and we would identify other surnames to which we are directly related but with whom our common ancestor is prior to the time of surnames. And the tree would continue even further back than that, based on the SNP discoveries that are continuously being made in the ongoing Haplogroup Projects.

Eventually, by superimposing known genealogies on top of the Mutation History Tree, we could build a comprehensive evolutionary tree of all Mankind, that travels back in time to "Genetic Adam" and travels forward to culminate with each living person today.

Maurice Gleeson

7 August 2015

* Modal Haplotype - this is the haplotype (i.e. your genetic signature, your sequence of STR marker values) that is derived from the most frequent value for each of the STR markers in turn among members of the same Lineage. It is likely that the Modal Haplotype is identical or almost identical to the haplotype that the Common Ancestor of the Lineage would have had. In other words, he would have passed on the identical marker values to most descendants and only some of them would have developed the occasional mutation along the way.

Chromosomes, Markers & Evolutionary Trees

Let's recap on some of the basic science behind Y-DNA as this will help you understand what you are seeing when you look at your results, and how your results can be applied in practice.

Chromosomes - a closer look

We have 46 chromosomes, arranged in 23 pairs. Each pair has 2 copies, one of which you got from your mother, the other from your father. So for example, you have one paternal chromosome 14 and one maternal chromosome 14. Before you were conceived, your father made a copy of each of his 46 chromosomes but only passed on one copy from each pair to you. Similarly your mother made copies of all her 46 chromosomes but only passed on to you one copy from each pair. In this way the 23 chromosomes you got from your father combined with the 23 from your mother to bring your chromosome quotient back up to the usual 46.

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The 23rd pair is also known as the sex chromosomes. There are two types of sex chromosome - an X and a Y. At conception, if two X chromosomes combine, a female child is produced (XX). If an X and a Y chromosome combine, a male child is produced (XY). Women (XX) only have an X chromosome to pass on to their offspring, whereas men (XY) can pass on either an X or a Y to their offspring. Therefore the man's contribution decides the gender of the child. Women do not have a Y chromosome and so cannot do this particular DNA test.

Thus the Y chromosome is only passed on from Father to Son.  This is why it is perfect for tracing the father's father's father's line and is the main type of DNA used for surname studies. Be aware though that it only assesses this single ancestral line, and if you go back 10 generations, this represents only 1 of your 1024 ancestors (which is equivalent to about 0.1% of your ancestors at that particular level).

Each of our 46 chromosomes consists of a long double-stranded helix of DNA. If we unwrapped it, it would look like a long ladder extending into infinity, or a railway track running from New York to Los Angeles. It's huge. If you untwisted all 46 chromosomes from a single cell, it would stretch for 2-3 metres (6-10 feet). All the untwisted DNA from the human body would stretch to the moon and back several times.

All along the "ladder" are the nucleotide bases, like rungs in the ladder, binding each strand of the helix to the other strand of the helix. The bases are called A, T, C, and G, after the first letters in their respective names - Adenine, Thymine, Cytosine, & Guanine. A only ever binds with T, C only ever binds with G. You can remember this by thinking the straight-sided letters only bind to each other, and the curved letters bind only to each other. Each base pair effectively forms a rung in the ladder.

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Because A only ever binds with T, and C only ever binds with G, if we know the sequence of bases on one strand of the helix, we automatically can tell what bases are on the other strand. Therefore, the sequence of bases along the DNA is only ever written as a single line of letters (e.g. ATCCGAATTGG). The sequence is read from what is called the 5' (5 prime) end of the DNA molecule (and is read toward the 3' end, like reading from left to right).

In each pair of chromosomes, the two copies (maternal and paternal) are virtually identical to each other in terms of size, length, morphology, etc. The exception is the sex chromosome pair, X and Y ... the X chromosome is 3 times bigger than the Y chromosome.

Although each chromosome in a pair is virtually identical, there are subtle differences between the nucleotide bases that run along the entire length. These variations in the bases are called mutations and can be identified because they occur at specific locations along the chromosome. These locations where mutations occur are referred to as DNA "markers". Each marker can be identified because it occurs at a specific position along the chromosome and thus can be given a particular name (e.g. DYS390 or Z255). People who share the same mutation may have inherited it from a shared Common Ancestor, and this is why DNA can be so helpful for genealogy.

A note on terminology: Y-DNA refers to the Y chromosome. Autosomal DNA refers to all the chromosomes EXCEPT the last pair (Pair 23, the sex chromosomes, X and Y - all the other chromosomes are called autosomes, hence autosomal DNA). Mitochondrial DNA refers to the DNA found in mitochondria (the "batteries" that power each cell). For a more detailed introduction to the three types of DNA test and how they are applied in genealogy, watch this YouTube video here.

The different types of DNA marker

There are two types of DNA marker - STR markers and SNP markers.

STR stands for Short Tandem Repeat and the key word here is "repeat". An STR marker is a sequence of bases repeated many times (e.g. CATCATCATCAT). In this example, the sequence is CAT and the repeat value of the sequence is 4. When the DNA is being copied before being passed on to any offspring, there are occasional mistakes made in the copying process. So for example, a copying mistake in the CAT sequence above might result in 3 repeats instead of 4, and so the value of that marker may shift from 4 in the parent to 3 in the offspring. This may be the first mistake to be made in this particular marker for many generations, and so not only will the male child differ from his father, grandfather, and great grandfather, but also from all his male siblings and cousins, who will all have a value of 4 for this particular marker.

The second type of DNA marker is the SNP marker, which stands for Single Nucleotide Polymorphism. The key word here is "substitution" - a single base at a specific location changes from what it normally is to a different base (e.g. an A changes to a C or a T or a G). Whereas the STR markers involve several bases in a row, the SNP marker only involves the substitution of a single base.

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Kelly Wheaton has written some excellent blog posts about DNA markers on the Y chromosome. You can read them by clicking here - STR markers & SNP markers.

There are some very important characteristics of STR and SNP markers which are key to understanding how they are applied in surname studies:

• Mutations in STR markers are written as the value of the marker (e.g. 12) whereas mutations in SNP markers are given names (e.g. Z255) or are written as the location on the chromosome followed by the change that occurred in the bases there. For example, 17349992 (G>A) indicates that a G has been replaced by an A at position 17349992.
• The mutation rate of STR markers varies from marker to marker. Some mutate relatively quickly (e.g. 1 mutation every 5 generations) whilst others mutate very slowly (e.g. 1 mutation every 500 generations). Mutations in slow-mutating markers are very good for studying human migration, whereas mutations in fast-mutating markers can be very useful for genealogy research (in the last 500 years or so).
• A big problem with STR markers is that they can mutate back as well as forward. So for example an STR marker may have a value of 4 which changes to a 3 and then back to a 4. The first mutation (4 to 3) may have occurred 1000 years ago, and the second one (3 back to 4) may have occurred 300 years ago. The trouble is that the Back Mutation masks the fact that there was a significant mutation 1000 years ago and this may result in people with the 4 value being assigned to the wrong branch of the human evolutionary tree and hence the wrong family tree!
• Another problem with STR markers is the Parallel Mutation. This happens when two very separate branches of the same family experience the same mutation "in parallel", giving the impression that the two branches are more closely related than they actually are in reality.
• A further problem with STR markers is that it is very difficult to identify a Back Mutation, or a Parallel Mutation. And as a result we don't know how often they occur. We suspect that it happens fairly frequently, perhaps as often as a marker value mutates forward it also mutates back. We really don't know. But such "hidden" back mutations may seriously confound our interpretation of the data and may result in people being placed on the wrong branches of the human evolutionary tree.
• Convergence is the name given to the situation when Back Mutations and Parallel Mutations on STR markers result in people appearing to be more closely related to each other than they actually are. This is a big problem when comparing people at 12 markers, but less of a problem when comparing at higher numbers of markers (e.g. 37, 67, or 111). However, even at 67 markers significant Convergence has been detected.
• On the other hand, SNP markers mutate much more slowly. And because there are so many of them, Back Mutations and Parallel Mutations are extremely rare (and easily spotted). For this reason, when using DNA markers to place people on the human evolutionary tree, SNP markers trump STR markers i.e. more reliance is given to SNP markers than to STR markers.

Y-DNA, Population Migration, & the Human Evolutionary Tree

Because the Y chromosome is passed on virtually unchanged from father to son, and because mutations in the DNA markers along the Y chromosome happen relatively infrequently, it is also an extremely useful tool for studying the last great human migration out of the African Motherland (about 50,000 years ago) that ultimately led to the populating of the entire planet. There is an excellent interactive animation of human migration here, including the various ice ages and the catastrophic eruption of the Mount Toba volcano that almost destroyed Mankind.

Population geneticists have been studying the evolution of mutations on the human Y chromosome (and on mitochondrial DNA) for many years and have developed an evolutionary tree based on these mutations (called the Haplotree).  They refer to each of the major branches of the tree as Haplogroups and have named them after the letters of the alphabet (e.g. Haplogroup R, or its subgroup Haplogroup R1b). You can think of a Haplogroup as a group of people with a broadly similar genetic signature.

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As modern humans moved around Africa and then moved out of Africa and spread to different places around the world, the humans who moved to Europe developed a totally different set of mutations to those humans who moved to India or Australia (for example). Thus certain haplogroups are found more commonly in Europe (e.g. R1b, I2b) than in India (e.g. H, L) or Australia (e.g. C, T).

Furthermore, genetic genealogy is a very young science, and more markers are being discovered all the time (thanks to novel tests like the Big Y test from FTDNA). As a result, scientists are still discovering finer and finer sub-branches of the human evolutionary tree, and we are approaching the point where we will discover the finer branching patterns associated with individual surnames (such as those in the Gleason/Gleeson DNA Project).

The old nomenclature for the various branches of the tree used a long string of letters (e.g. R1b1a2a1a2c1e) but this has been superseded by a system that simply puts the main Haplogroup letter followed by the "terminal SNP" (e.g. R-Z255). You can still see both terminologies in use on the ISOGG tree.

The terminal SNP refers to the SNP marker that currently occurs at the end of a branch. The word "currently" is important because as new SNP markers are discovered the current terminal SNP marker is likely to be replaced with a new one, and we will continue to move further and further down the finer branches of the tree until we identify SNP markers that are specific for your own family branch and even single individuals.

This will eventually allow us to reconstruct family trees based on DNA marker mutations. These are sometimes called phylogenetic trees, sometimes cladograms or phylograms, but my favourite is Mutation History Trees because it sounds similar to Family History Trees. The difference between the two is that Family History Trees are constructed using named individuals, whereas Mutation History Trees use DNA markers. It should be possible to superimpose one upon the other and in this way we can look 'beyond the Brick Wall" of individual pedigrees and see where different family branches are likely to connect. This in turn will help focus further documentary research.

There are various groups working on the human evolutionary tree and they have produced their own version of the haplotree:

• The YCC Haplotree is produced by the Y-Chromosome Consortium. This is an academic effort and it is frequently out of date, being surpassed by the ISOGG tree which is updated much more frequently and harnesses the continuous output of genetic genealogists working on Haplogroup Projects (such as the R-Z255 & Subclades Project to which all members of Lineage II in the Gleason/Gleeson DNA Project belong). The most recent update of the YCC tree is from March 2015 but the tree itself is not user-friendly.
• The ISOGG tree is the result of the efforts of ISOGG (the International Society of Genetic Genealogy) who co-ordinates the analysis and interpretation of the findings from various Haplogroup Projects and as a result has developed a much larger tree than the YCC Tree. It too is quickly out-dated as the pace of new SNP marker discovery advances and further sub-branches are discovered. Lineage II members can click here and search (Cmd+F or Ctrl+F) for Z255 to see where this particular sub-branch sits on the main Haplogroup R branch.
• Several of the commercial companies have developed their own haplotrees which at times may be more advanced than the ISOGG tree, and at times less advanced:
• FTDNA tree - this can be accessed from the Haplotree & SNPs page of your personal FTDNA webpage
• YFULL Experimental Tree - YFULL is a company that offers SNP testing and will interpret the results of SNP testing carried out by other companies. This tree is relatively easy to navigate but again requires use of the Find function (Cmd+F or Ctrl+F).
• FGC tree - like YFULL, FGC (Full Genomes Corporation) also offer SNP testing and interpretation. The visual presentation of the tree is not easy to navigate.
• Haplogroup Project Administrators work at the coal face of scientific discovery in relation to the finer branches of their own particular haplogroup project. The R-Z255 & Subclades Haplogroup Project updates its draft tree periodically as new member results come in to the project. You have to sign up to the project to access these updates but here is the most recent update as of July 15th (for members only). It is important to appreciate the pivotal role that Haplogroup Project Administrators are playing in the ongoing discovery of the finer branches of the tree. Surname Project Admins will work closely with Haplogroup Project Admins to advise their project members regarding which tests to take next and why.
• Alex Williamson's "Big Tree" is a tree that specifically focuses on the Haplogroup R-P312 branch of the human evolutionary tree (of which Z255 is a subgroup). Alex has done incredible work placing newly discovered SNP markers in their best estimated position on the tree, and most importantly for us, creating a visual representation that is easy to navigate and makes the current state of the tree so much more understandable. The members of Lineage II feature here too, in the Z255 subsection. There are two interesting features to Alex's tree:
• if you click on the name of any individual, an analysis of their unique genetic signature comes up. Here is the analysis for member N74958 showing his position on the tree, his unique mutations, and his putative haplotype progression (i.e. the estimated progression of his mutations from previous ancestors).
• the Overlay STR Feature allows you to compare the results for all STR markers (one by one) across the whole group. Here it is for DYS439.
• Nigel McCarthy runs the McCarthy DNA Project and has pioneered the development of phylogenetic trees based on a combination of SNP and STR markers. Luckily for us in Lineage II, one particular area of his research is also focussed on the Z255 subclade to which we belong (Group E in his project). We'll be talking a lot about Nigel's work in due course as it is particularly relevant to the next steps in the DNA Project for Lineage II members.

The portion of Alex Williamson's "Big Tree" that deals specifically with members of Lineage II

You may have to read this several times before a lot of the information sinks in but stick with it - it's worth it! Knowing the basics behind the science of Y-DNA and how it can be applied will help you understand a lot of the discussion about SNP testing and Big Y results that will follow in subsequent posts.

Maurice Gleeson

30 July 2015

The Gleeson name in Surname Dictionaries

If you want to get some idea about the possible origin of a particular surname, a Surname Dictionary is a good place to start. There are several surname dictionaries that address the topic of Irish surnames, and perhaps the most well-respected are those of Woulfe and MacLysaght. But do they give us any clues as to the origins of the Irish version of the surname Gleason / Gleeson? Read on ... all will be revealed.

The Rev. Patrick Woulfe (1872-1933), or as he preferred to be known, An tAthair Pádraig de Bhulbh, was born in Cratloe to Seamus Woulfe, a farmer. He became a priest, worked in Limerick, and spent 25 years collecting names, communicating with native Irish speakers and studying the different forms of Gaelic to compile the Irish Names and Surnames dictionary. There are two versions of his book – a small version (138 pages) and a larger version (742 pages). The smaller version was originally published in 1906 and reprinted in 1922 – this is available online in its as original print form from Archive.org here. The larger version was printed in 1923 (reprinted in 1967) and consists of 696 pages, with 46 pages of preliminary text. A digital version of the book is available free of charge online from Library Ireland here. The search feature is very useful and allows you to find any mention of a particular name within the book. Woulfe’s work helped to popularise the use of Irish first-names during the last century and has been an important resource for genealogists. His work was subsequently superseded by that of other scholars, such as Edward MacLysaght.

Woulfe, Patrick. Sloinnte Gaedheal is Gall: Irish Names and Surnames, collected and edited with explanatory and historical notes (1923).

Edward MacLysaght was an interesting character. He lived to be 99 years old (1887-1986) and packed a lot into his lifetime. His father was from Cork, his mother from Lincolnshire, and he was born near Bristol. He went to school in Rugby and then Corpus Christi College, Oxford to study law. But a rugby injury changed his life - he went to Lahinch in Co. Clare and lived in a caravan for 6 months recovering. During this time he developed a love for genealogy, history, and the Irish language, in which he became fluent. He started a pioneer farm in Raheen and introduced electricity 40 years before his neighbours. He also set up local community projects and was deeply involved in the Irish Cultural Revival and the movement for Irish independence. His loyal support of Eamonn de Valera (then member of parliament, and later President of Ireland) resulted in his imprisonment. After independence (1922), he was elected to the Seanad Éireann (the Irish Senate). He later became an Inspector for the Irish Manuscripts Commission (1938), a member of the Royal Irish Academy (1942), Chief Herald of Ireland (1943-1954), Keeper of Manuscripts at the National Library of Ireland (1948-1954), and Chairman of the Irish Manuscripts Commission (1956-1973). It was during this latter period that he wrote his indispensible books on Irish surnames.

MacLysaght, Edward. The Surnames of Ireland. 1957 (sixth edition 1991)

This is a comprehensive list of over 4000 Irish surnames with a short description of each. It includes 1500 surnames not considered in the other books below, which only deal with about 20% of the surnames described in this present book (albeit in a lot more detail). 

MacLysaght, Edward. Irish Families. Their Names, Arms and Origins. 1957 (fourth edition 1985) 

MacLysaght, Edward. More Irish Families. 1970 (first paperback edition 1996, incorporating Supplement to Irish Families, 1964)

These latter two volumes (frequently abbreviated to IF and MIF) give a much more detailed account of many of the most common Irish surnames. Second hand copies can be bought online, usually for quite inflated prices.

Woulfe’s Surname Dictionary

Woulfe’s entry for Gleason / Gleeson as a surname can be found here: 

Ó GLASÁIN—I—O Glassane, O Glessaine, O Gleasan, Glessane, Glissane, Glissawn, Gleason, Gleeson; 'descendant of Glasán' (diminutive of glas, grey); a common surname in all the south of Ireland, especially in Cork, Limerick, Tipperary and Kilkenny; now generally pronounced Ó Gliasáin.

This does not provide us with a huge amount of information relating to the origins of the "clan" but MacLysaght has a lot more information.

MacLysaght’s Surname Dictionary

MacLysaght gives a brief account of the Gleeson surname in his Surnames of Ireland and a much more detailed account in his Irish Families. 

(O) Gleeson Ó Glasáin or O Gliasáin. The anglicized form of this name in Kerry is Glissane. The main sept was located in lower Ormond.

IF Map Tipperary.

(from Surnames of Ireland, p128)

The abbreviation IF refers to his book Irish Families, and Map Tipperary refers the reader to the map in that book on page 222 where the Gleeson name is located just below Lough Derg. The entry in Irish Families is much more informative: 

O'GLISSANE, GLEESON. In spite of its English appearance in it's anglicized form the name Gleeson, never found with the prefix O in English, is that of a genuine Gaelic Irish family. In modern Irish it is O Gliasáin, earlier Ó Glasáin and originally Ó Glesáin. They belong to the Aradh* and their original habitat was Mac Ui Bhriain Aradh's country, that is the country in Co. Tipperary between Nenagh and Lough Derg; but it should be emphasized that the Gleason's are not Dalcassians**; they are of the same stock as the O'Donegans, of the barony of Ara, Co. Tipperary, who were originally of Muskerry, Co. Cork. In the census of 1659 the name is very numerous in north Munster (Counties Tipperary, Clare and Limerick] being then given many spellings, e.g. Glisane, Glison, Glyssane, O'Gleasane, O'Glassane etc. They are still fairly numerous in their home county but are not found much outside Munster. Prior to 1641 the O'Glissanes were very extensive landowners in Co. Tipperary but as such they disappear in the Cromwellian settlement.

Persons of the name have not been prominent in Irish history or literature, but four Irish Gleesons are well known in America, viz. Father William Gleeson, called the "founder of the Church in California"; Edward Blakeney Gleeson, the Rochester millionaire; Frederick Grant Gleeson [1848–1903], the composer; and Mgr.^ Joseph M. Gleason [1869–1942], educator and historian.

(from Irish Families p95)

It's interesting that MacLysaght felt that the Gleesons were not prominent in Irish history - there are lots of examples. In fact, that could be the subject of a subsequent blog post. Submit your candidates now!

Other sources

A third surname resource, that is freely available online, is that of John O'Hart and entitled Irish pedigrees; or, The origin and stem of the Irish nation. However, O'Hart's research is not generally considered to be as good as that of Woulfe and MacLysaght. It was published originally in 1876 and is available in two volumes - click here for Volume 1 and Volume 2. The introduction to both volumes makes for interesting reading. There is a brief entry for Gleeson:

13. O'Breoghan (this name "Breoghan" is considered the root of Brown), O'Glaisin (Glashan, or Gleeson), O'Mictyre and O'Keely were chiefs of Hy-MacCaille, now the barony of "Imokilly," in the county Cork.

Next Steps

So MacLysaght asserts that the Gleeson sept is related to the O'Donegan's and originated in Muskerry, Co. Cork and later became prominent in Aradh, Co. Tipperary, whereas O'Hart asserts that they were chiefs in Imokilly, Co. Cork. Despite all the above, there are some people who disagree with the conclusions of these erudite scholars and would dispute some of the assertions made within the works. This is where DNA comes to the rescue.

Click to enlarge

Each of the areas indicated in the above map are associated with a preponderance of certain surnames. These are nicely illustrated in the maps included in MacLysaght's Irish Families (p222) . Surnames associated with the Aradh area include: O Kennedy, O Hogan, O Brien, O Reidy, O Donegan, O Lynch, O Meaghar, O Meara, O Mackey, and O Danagher.

Other online surname distribution map sources include the following:

• Surnames of Ireland map - 4,500 surnames are featured on this map and have been placed in the area where farmers with each surname cluster (based on the 1911 census). Hence each surname is positioned close to where it may have first appeared (assuming that land ownership remained relatively intact over the centuries despite any social mobility that took place). 
• "A geo-genealogy of Irish surnames" - a map showing surnames by county based on the 1890 census with an explanation of how the map was created here. The surnames are not necessarily placed near their ancient clan territories.

From A geo-genealogy of Irish surnames
Click to enlarge

We will explore this topic further in a subsequent post but it should be possible to identify the most likely Irish origins of the Gleeson septs of Lineages II and III within the DNA Project by examining the surnames of the closest matches to the members of these groups and through the additional SNP marker testing that is currently being carried out. This will help define on which branch of the human evolutionary tree these Gleeson septs sit, and furthermore, we will be able to determine which other surnames sit on adjacent branches. The surnames most closely related may represent the early neighbours of these particular Gleeson septs, some of whom will be directly related via a common ancestor prior to the advent of surnames, and others who may be associated with an ancient NPE (non-paternity event) where a Gleeson was the father. In this way we will be able to estimate the probability that each Gleeson sept was present in a particular area (i.e. Aradh, Muskerry, Imokilly) and we might even be able to give a rough timescale for their presence there.

Thus, with the advent of DNA testing, we will be in a very strong position to determine the various Irish origins of the Gleeson surname and thus confirm or refute the theories put forth in these surname dictionaries.

Maurice Gleeson

21st July 2015

---

* Aradh ... the territory east of the southern part of Lough Derg, now roughly corresponding with the Barony of Owney and Arra, which was previously ruled by the O'Donegans.
** Dalcassian ... people belonging to the sept of Dal gCais
^ Mgr. means Monsignor

A Brief Tour of the Project

The Gleason/Gleeson DNA Project has a number of different resources to help you trace your Gleason/Gleeson ancestry. If you are new to the Project, or even if you are an old hand, here is a useful summary of all the wonderful places you can visit and what each of them has to offer you.

But before we even get to the Project resources, the starting place for most people will be their own DNA results page on FamilyTreeDNA and here is my Dad's results page below as an example.

If you click on Matches under Y-DNA, that will show you what matches you have at different levels of comparison. The picture below shows that my Dad has 2 matches at 111 markers. But I could adjust the number of markers compared by clicking on the dropdown list beside the heading "Markers" (indicated by the red arrow) and choose 67 markers or 37 markers, etc. This will allow me to compare my Dad's results with other people within the FTDNA database who have tested to this particular marker level.

In the first column, the heading is Genetic Distance (GD), and my Dad has a GD of 6 and 9 for his two matches. As we are comparing at the 111 marker level, this can be written as 6/111 and 9/111. Genetic Distance refers to how close or how far away your marker values are when compared to another person. A Genetic Distance of zero means that the values for all of the markers are exactly the same - this is called an exact match.

Who qualifies as a match to you? Anyone whose marker values are sufficiently similar that they meet the criteria set by FTDNA to be declared "a match". And here are those criteria:

• a Genetic Distance (GD) of 0 at 12 markers
• a GD of 2 at 25 markers
• a GD of 4 at 37 markers
• a GD of 7 at 67 markers
• and a GD of 10 at 111 markers

The ISOGG Wiki has a very nice summary of Genetic Distance and the criteria for matching.

However, your own webpage only shows you your own matches - it does not show you other people's matches. And it does not show you matches that fall outside of FTDNA's matching criteria but which may still be relevant to you. For that, you need to visit the Gleason/Gleeson DNA Project website.

Click to enlarge

And the most useful page is probably the Results page because this is where you can compare your results to everyone else in the project. Above is a screenshot of the results page.

Explaining the Columns

Reading from left to right across the table ...

• the first column has the Identification Number assigned to each new member as they join the DNA project
• the second column lists their kit number
• the third column records the spelling of their surname (there are several common variants and a few probable NPE's - Non Paternity Events)
• the fourth column list the Earliest Known Ancestor (also known as the Most Distant Known Ancestor) for each member - this could be written as EKA aka MDKA ... don't you just love acronyms!
• the next column records the Haplogroup for each member using both the older "long-form" terminology along with the "terminal SNP" terminology (a Haplogroup is simply a collection of people with a broadly similar genetic signature)
• and thereafter are the values for each marker, one by one, going all the way up to 111 markers (although only the first 37 markers are shown here)

Explaining the Rows

• The first row contains the headers for the columns. Below that is the "Modal Haplotype" for Haplogroup R1b1 which is the Haplogroup to which all three R1b1 Lineages belong. The Modal Haplotype is simply the marker values that occur most frequently within that particular group.
• Below that, is the Modal Haplotype for the group Lineage I. You can see that it differs from the R1b1 Modal Haplotype on a number of markers, indicated by the coloured columns (i.e. orange for marker 391, purple for marker 458, orange again for 447, etc). This in turn differs from the Modal Haplotype for Lineage II, further down the table. The colouring of the differences from the R1b1 Modal Haplotype helps distinguish the unique patterns for each Lineage.
• Each of the subsequent rows contains the details for an individual member - it's as if the Y chromosomes for all of the members are stacked up on top of each other. This makes it easy to compare the values for each of the DNA markers to see if the members in a group match on a particular marker or have a different value. Any differences are again highlighted by coloured squares.

As Project Admins, Judy and I will allocate you to specific groups within the DNA project depending on who you match. So far there are four distinct groups or 'Lineages' within the project. Lineage I members are descended from Thomas Gleson of Cockfield, Suffolk, England (Judy's ancestor), whereas Lineages II & III are Irish groups with origins in Tipperary and Clare respectively. Lineage IV is a small group of people whose origins currently lie within the US. My own particular Gleeson branch belongs to Lineage II.

Click to enlarge

Another important page on the website is the Patriarchs Page. This is where we post the pedigree of each project member and as you can see in the screenshot above for Lineage I, it potentially helps in the reconstruction of the family tree of the Common Ancestor associated with each Lineage. All members are encouraged to submit their pedigrees for inclusion on this page. Have a look through it - you may discover your own ancestor there!

The other major resources associated with the Project include this blog and the Gleeson Genealogy Forum on Facebook. This currently boasts 178 members and is a great place for socialising with the other members of the project, sharing information, and making new friends.

And anyone who joins will get a brief "report" of their results courtesy of myself or Judy. This will include an analysis of haplogroup origins, interpretation of matches, what additional projects would be worth joining, and what further DNA testing might prove fruitful for their particular situation.

So do explore the website, this blog, and the Facebook group - there is lots to discover about your Gleason/Gleeson heritage. And come back to this blog often - it will be a repository of knowledge and a log of our ongoing discoveries.

Maurice Gleeson

16th July 2015

History of the Project

Welcome. My name is Judith Gleason Claassen, but all the project members just call me “Judy.” I serve as a co-administrator of the Family Tree DNA Gleason/Gleeson Project along with my counterpart across the Atlantic, Dr. Maurice Gleeson.

History of the Project

When I first became acquainted with the project in 2007, there were only five members, yet the World Families Network (WFN) already provided a hosted website full of information including a page for presentation of the test results. At the time, the concept of DNA testing as an aid to genealogy was a curiosity to me, and I was a bit skeptical as to what could be accomplished by this trendy new idea. 

Nevertheless I persuaded my brother, a second cousin and two fourth cousins to have the y-chromosome test. To my amazement, the four of them were a perfect match at 37 y-markers! That hooked me. Foreseeing the possibilities, I educated myself in the basics and volunteered for the job of administrator. The experts at WFN guided me until I was ready to take responsibility.

At first it took some work to get out the DNA message and find recruits, but soon members brought in other members and the project grew. It was great fun to get acquainted with curious prospective members and to help them get over that initial hesitancy that we all feel. After a few years our membership included Gleasons of all possible spellings from around the globe plus members with other surnames who had genetic ties through a female ancestor. 

When the membership rose to eighty in number, it became obvious that the job of administrator was more than one person could efficiently handle. The project needed new blood with innovative ideas and fresh enthusiasm. Fortunately Maurice accepted the job as co-administrator in 2014, and he has proved to be the perfect choice. He is abreast of the latest developments in DNA testing and has the skill to effectively demystify the science to others. His involvement in a number of Irish surname projects brings a needed dimension to the scope of the project.

Recent Discoveries for the Gleason Lineage I

The first male (y-chromosome) line that was identified among our membership is referred to as Lineage I. It represents the descendants of Thomas Gleason (Gleson) who immigrated to colonial New England mid-seventeenth century. Born in 1609 into a Puritan family of Cockfield, Suffolk, England, he married Susannah Page of nearby Hawstead, and they arrived with several young children.

A 16th Century house in Cockfield, Suffolk

Hawstead All Saints Church (pre-1300) where Susanna Page, wife of Thomas, was baptized

For years many amateur genealogists assumed their origin was Northamptonshire as suggested in the well-known Gleason genealogy by John Barber White. That assumption, as well as his theory that the immigrant patriarch’s name was actually Leeson, has been proven wrong. After years of searching for the true origin of my ancestor, I was thrilled at last to find his baptismal and marriage records in the church registers of St. Peter’s of Cockfield. Four of his children were also baptized there. The story of my search and of the discoveries made about this family was published in the January 2014 issue of The New England Historical and Genealogical Register.*

St Peter's Church, Cockfield, Suffolk

Y-DNA test results for the descendants of Thomas of Cockfield show interesting mutation patterns over the three hundred plus years of the Gleason surname in America. These mutations suggest the possibility of characterizing the DNA evolution of the individual family branches, given enough data samples. This characterization is one of our goals for Lineage I. New participants are enthusiastically solicited to help us achieve this goal. It’s a win-win situation. DNA testing expands your personal knowledge of your ancestral history while enriching the common pool of knowledge of genetic genealogy for all of those who follow.

The distinctive pattern of the Y-DNA-37 results for Lineage I

Judy Gleason Claassen

6 April 2015

* Claassen, Judith Gleason. The Origin of Thomas Gleason of Watertown and Cambridge, Massachusetts. New England Historical and Genealogical Register. (New England Historical & Genealogical Society, Jan 2014).