DNA Overlay Chart

Overview

DNA Overlay Charts are User Items that present DNA evidence in a traditional descendant chart format where lines of descent are arranged in rows and columns. The goal is to review and analyze DNA evidence within a tree structure supported by traditional genealogical evidence.^{Note 1} Boxes in the chart include the typical name and lifespan information, but the chart also includes a "DNA summary" box that displays DNA-derived or user-specified content and the chart also supports a popup "detail panel" to show DNA signatures and other information.

The DNA Overlay Chart currently supports Y-DNA processing only. mtDNA processing will be added in a future release.

You can see an example DNA Overlay Chart on the Second Site demonstration site.

The DNA Overlay Chart is quite different from "marker grids" that are often used to display DNA test results. Marker grids are very useful for analyzing sets of test results, but they do not meet the goal of presenting DNA evidence in the context of a lineage supported by traditional genealogical evidence. Second Site includes a DNA Grid User Item to create marker grids from test results; the DNA Overlay Chart and DNA User Item are complementary and together they make Second Site a very good platform for presenting DNA evidence.

The DNA Overlay Chart is similar to a descendant chart in that it starts with a progenitor and proceeds down through generations of descendants. Unlike a descendant chart, however, the user specifies one or more descendants in addition to the progenitor, and the chart is constrained to the lines of descent between the progenitor and those descendants. This makes the chart far more sparse than a typical descendant chart.

In the DNA Overlay Chart, the progenitor is called the MRCA, the most recent common ancestor.

Typically, the user will specify the ID numbers of descendants who have DNA test results in TMG's DNA Log. The user may choose to add other descendents when proposing a theory about the DNA of a descendant or demonstrating how having DNA from a specific branch of the tree would help the research project.

The DNA Overlay Chart includes an option to add DNA test results to the tree. Second Site summarizes the DNA evidence by constructing an abbreviated DNA signature that includes only the markers that vary between tests. That abbreviated signature is shown in the chart. The full DNA signature is available via a popup "detail panel".

The DNA Overlay Chart includes an option to derive DNA signatures for ancestors from the test results of their descendents. See the DNA Signatures section for more information.

Users may add content to the DNA Overlay Chart via "chart events", custom TMG events that are used to provide comments about the DNA evidence. See the Chart Events section for more information.

Detail Panels

The DNA Overlay Chart includes a Detail Panel that pops up to reveal more details than are shown in the chart proper. Click the [+] button to open the panel and click the [X] button to close the panel. The detail panel includes both contents specified by the user via Chart Events and the full and summarized DNA Signature of the given person.

DNA Signatures

As of version 8.03, Second Site's marker comparison logic is subject to a limitation that affects duplicated markers such as 464a/b/c/d. Second Site compares them as individual values whereas experts recommend reordering the values for maximum matching. This limitation will be removed in a future release.

The Y-DNA variation of the DNA Overlay Chart processes DNA signatures. Signatures include actual marker values from test results entered in the TMG DNA Log by the user as well as marker values derived by Second Site using logic described below. In the main chart, Second Site displays an abbreviated form of the signature which shows only marker values that vary among the tests included in the chart. The full signature is included in a detail panel.

Derived Signatures

The Y-DNA Overlay chart includes an option to compute a DNA signature for fathers in the chart. For the MRCA, a derived signature is often called a modal signature^{Note 3} and becomes the standard to which other test results are compared. The Y-DNA Overlay Chart analyzes DNA results within the context of the lines of descent to compute the DNA signature of fathers in the chart. The rules are designed to choose marker values that would produce the observed test results of descendants via the minimum number of mutations. The rules are as follows:^{Note 2}

1. A father with only one son (no branching) is assumed to have the same marker value as his son. If the son's marker value is (un)certain, then so is the father's.
2. A father at a branch point is assumed to have the value derived from the values of his sons that minimizes mutation probabilities. If this is (un)certain, then the father's value is (un)certain.

The result of employing those rules is shown in the example.

Using rule #1, Trevor's DNA test result is pushed up the tree to Bradford and becomes Bradford's DNA signature. That does not mean that Bradford actually had those marker values; we move the values up to the earliest branch in the tree where we have an opportunity to compare results of siblings. Some mutations may have occurred between Bradford and Trevor but without more test results, we can not tell where. Luckily, the exact location is not required.

Similarly, Michael's DNA test result is pushed up the tree to Aaron, and Peter's DNA test result is pushed up the tree to John.

The DNA signature for Thomas is based on rule #2 and the values of his sons Timothy and John.

The DNA signature for Timothy is a little more involved. Based solely on his son's DNA signatures, Timothy's DNA signature would be {kl}{op}{pq}ql, where the values in braces are possible values for a given marker. The DNA signature for his father Thomas is the result of combining {kl}{op}{pq}ql and lpqrm. If one son has {kl} ("k or l") for a marker, and the other son has a value l for that marker, then the father's likely value is l, the value that requires the least number of mutations. Thomas's DNA signature is therefore lpq{qr}{lm}. {qr} and {lm} remain uncertain because there is a tie: one son has ql and the other has rm.

After Thomas's signature is derived, Second Site reviews the DNA signatures for his descendants and at that point, the uncertainties in Timothy's DNA signature are resolved using values that minimize mutations. This is an extension of rule #2.

Second Site derives probable DNA signatures. It is possible for unlikely mutation sequences to occur, such as multiple mutations occurring in the same generation and thus obscuring the DNA signature of the father. All methods for deriving DNA signatures are subject to uncertainty, but the maximum parsimony method used by Second Site reduces the possibility that a bias in the test results (many people tested from one branch of the family) unduly influences the derived DNA signature of the MRCA.

Kit Numbers

Prior to version 7.04, TMG did not include a way to record the kit number associated with a test result. If you are using an older version of TMG, you can enter a kit number by adding the Kit directive to the Comment field of the test result. See the DNA Comment Field Directives page.

Person Names

By default, Second Site does not display the names associated with test results; it shows the kit number. When you want to show the name for a particular test, you can add the ShowName directive to the Comment field of the test result. See the DNA Comment Field Directives page.

Chart Events

Users have the option of using two special event types to add information to the chart. Both event types are custom tags that users must add to their TMG projects via the Master Tag Type List. If a person that appears in the chart has a primary event of the given type, Second Site will include information from that event in the chart, as explained below.

Y-DNA Summary Event

The M1 segment of the memo of a "Y-DNA Summary" event is displayed in a special "DNA summary" box that appears beneath the typical name/lifespan box. The DNA summary box is small and so the summary text should be short. If there is no "Y-DNA Summary" event for a given person, Second Site will display an abbreviated DNA signature in the DNA summary box.

Y-DNA Detail Event

The M1 segment of the memo of a "Y-DNA Detail" event is displayed in the detail panel explained above.

Chart Event Notes

The Y-DNA Summary and Y-DNA Detail events do not have to be selected in the Database.Tag List. Typically, it's best not to select them.

If either event includes a multi-part memo, the DNA Overlay Chart will only use the first memo segment, e.g., "[M1]".

Windows

Two windows are part of the user interface for the DNA Overlay Chart.

1. The Edit DNA Overlay Chart window is the main window users see when they edit a DNA Overlay Chart. It contains the properties that apply to the chart including the Most Recent Common Ancestor (MRCA) and a list of the descendants of interest.
2. The Edit DNA Member window is a sub-window of the Edit DNA Overlay Chart window. It is used to add descendants to the chart. People who are added to the chart usually have a DNA test result in the TMG DNA Log. If they do not, they will be added to the chart; that may be useful when proposing a theory about where someone fits in the tree or when explaining why having a test result from a particular line of descent would help reveal the DNA mutations.

Edit DNA Overlay Chart

The Edit DNA Overlay Chart window controls the properties of a DNA Overlay Chart.

Shared Properties

Second Site uses many of the same properties for all the different chart types. If you do not see a property explained here, look for it on the Chart Properties page.

Chart colors are determined by the Theme but can be changed by the user via the properties in the Stylesheets.Theme.Chart section. Other stylesheet options are controlled via the chart-related styles in the Stylesheet.System section.

MRCA ID

Enter the TMG ID number of the most recent common ancestor in the MRCA ID property.

Descendants

Use the Descendants list to manage the descendants included in the chart.

• Use the [Add...] button to add a descendant to the list.
• Use the [Edit...] button to edit an entry.
• Use the [Delete] button to delete an entry.
• Use the [Up Arrow] to move an entry up in the list.
• Use the [Down Arrow] to move an entry down in the list.

The sequence of the descendant entries influences the appearance of the chart. Second Site will attempt to honor the sequence of the descendants, with entries near the top of the list appearing above (top-to-bottom) or to the left (left-to-right) of entries near the bottom of the list. Second Site will re-sequence descendants on the chart to accommodate shared ancestors. So, for example, if the user specifies a set of descendents in the sequence 1-2-3, but descendants 1 and 3 share more common ancestors than descendants 1 and 2, the output sequence will be 1-3-2.

DNA Type

The DNA Type pull-down menu controls the type of DNA to process. At present, the DNA Overlay Chart only supports Y-DNA test results.

Test Name

The Test Name property lists all the DNA tests supported by Second Site. By choosing a Test Name, you are instructing Second Site to favor that particular test. If a person has more than one DNA test result in the DNA Log, Second Site will use the named test. If a person does not have a DNA test result for the chosen test, Second Site will convert the first test result it finds to the preferred test. Conversion results will vary; see the DNA Test Result Conversion page.

Marker Display

The Marker Display property controls whether the DNA Overlay Chart shows marker values using an alphabetic code or numeric values. The default is "Alphabetic".

Second Site expects that marker values in TMG's DNA Log will be numeric. By default, Second Site will display those values using an alphabetic code where a=1, b=2, ... z=26, A=27, B=28, etc. The alphabetic code is much more concise and lends itself well to both display and analysis. Users who want to use the more traditional—and more lengthy—numeric values should set the Marker Display property to "Numeric".

Direction

The Direction property controls whether generations increase by row or by column. The choices are "Top to Bottom", where generations increase by row, and "Left to Right", where generations increase by column. The default is "Top to Bottom".

Include Chart Events

The Include Chart Events property controls the processing of chart events. When checked, text from chart events will be added to the chart. When unchecked, chart events are ignored. See the Chart Events section.

Include Test Results

The Include Test Results checkbox controls the processing of DNA test results. When checked, the chart includes DNA test results. The default is checked. If unchecked, DNA test results are not included and the Derive Signatures option is disabled.

Derive Signatures

The Derive Signatures checkbox controls the processing of DNA test results. When checked, Second Site will compute derived signatures based on descendant test results. See the Derived Signatures section.

Optimize Space

The Optimize Space property controls whether or not all the generations are shown in a line of descent. If Optimize Space is set to "No optimization", all the generations are included. If Optimize Space is set to "Some optimization" or "More optimization" (which are treated the same for this chart), Second Site will remove people who can be ignored for the purposes of analyzing the DNA evidence. When optimizing:

• The MRCA is always retained, as are the descendants who were specifically identified by the user.
• Parents who have more than one child in the chart are always retained, as are all of those children.
• People who have one of the DNA "chart events" will always be retained.
• People who have DNA test results of the proper type (Y-DNA or mtDNA) will always be retained.

When generations are removed during optimization, Second Site displays the number of skipped generations in the chart.

Notes and Acknowledgements

Alvy Ray Smith and Robert Charles Anderson were instrumental in the design of the DNA Overlay Chart.

1. Robert Charles Anderson first described to me the basic form of a chart where DNA evidence was overlaid on a descendant-type chart.
2. Alvy Ray Smith described the DNA signature derivation algorithm in his article "The Probable Genetic Signature of Thomas1 Riggs, Immigrant to Gloucester, Massachusetts, by 1658", The New England Historical and Genealogical Register, volume 164, April, 2010. Mr. Smith described the two rules (described above) that Second Site subsequently adopted to push marker values up the tree from descendants to ancestors, including using maximum parsimony to choose a marker value when there are multiple candidate values.

   Second Site has also implemented two other practices recommended by Mr. Smith: (A) using alphabetic codes for marker values and (B) using "{" and "}" to indicate markers with multiple possible values.

3. The term modal signature is not accurate in this context because the DNA Overlay Chart does not derive DNA signatures using the statistical mode, i.e., it does not choose the values that occur the most frequently in the set of markers. It uses a maximum parsimony method described by Alvy Ray Smith.^{note 2}