Showing posts with label Advanced Techniques. Show all posts
Showing posts with label Advanced Techniques. Show all posts

Wednesday, June 3, 2026

First Look at Chromosome Analysis

One of the most common questions I hear from genealogists who have been using DNA for a few years is: “I’ve worked through my DNA matches and shared matches. What do I do next?”

For many researchers, the answer is chromosome analysis. 

The term can sound a little intimidating. It conjures up images of complicated charts, coloured segments and advanced genetics. In reality, chromosome analysis is simply another way of looking at the DNA evidence we already have.

It allows us to move beyond asking who we match and begin exploring how that DNA was inherited.




Looking Beyond the Match List

Most of us begin our DNA journey with match lists.  

We look at the amount of DNA shared with a match, examine shared matches and hopefully identify a common ancestor. These tools remain the foundation of genetic genealogy and are often all we need to solve a problem.  However, sometimes we reach a point where the match list no longer provides enough answers.

Perhaps we have identified a cluster of related matches but cannot determine which ancestral line they belong to. Maybe we share multiple possible common ancestors? Or perhaps we simply want greater confidence in our conclusions.

This is where chromosome analysis can help.


What Exactly Are We Looking At?

Each of us inherits 23 chromosomes from our mother and 23 chromosomes from our father.

As DNA is passed from generation to generation, those chromosomes are broken apart and recombined. The chromosomes we inherit today are therefore a patchwork of DNA segments contributed by many different ancestors.

Every segment has travelled through a chain of ancestors before reaching us.

Chromosome analysis allows us to examine those segments and ask questions such as:

  • Which ancestor contributed this piece of DNA?
  • Which matches inherited the same segment?
  • Can we identify the ancestral line responsible for that segment?
  • Does the segment support our documentary research?

These questions take us beyond simple matching and into the realm of DNA evidence.


Each chromosome contains millions of DNA markers inherited through generations of recombination.

 Understanding how chromosomes are structured is the first step towards chromosome analysis.



Chromosome Browsers

A chromosome browser is simply a tool that displays where DNA segments are shared between two or more people.

Instead of seeing only a total amount of shared DNA, we can see exactly where those shared segments occur on a chromosome.  Several testing companies and third-party tools provide chromosome browsers, including MyHeritage and GEDmatch.

For many researchers, the chromosome browser is their first introduction to segment analysis.  At first glance it may look like a collection of coloured bars. With practice, however, those coloured bars begin to tell stories about inheritance and ancestry.


A chromosome browser allows us to see exactly where DNA is shared between two or more individuals
 rather than simply reporting a total amount of shared DNA.


Why Segments Matter

Imagine two DNA matches who both descend from the same ancestral couple.

If they inherited the same segment of DNA from that ancestral line, we would expect them to share DNA with us in the same location on a chromosome.  Finding these shared segments provides another piece of evidence that supports the documented relationship.

The segment itself does not prove an ancestor.

Instead, it contributes to a growing body of evidence that can strengthen or weaken a hypothesis.

This distinction is important.

Chromosome analysis does not replace genealogy.  It enhances it.


Introducing Segment Triangulation

One of the most powerful concepts in chromosome analysis is segment triangulation.

In simple terms, segment triangulation occurs when three or more people:

  • Share the same segment of DNA.
  • Match each other on that segment.
  • Can trace their ancestry to a common ancestral line.

When these conditions are met, we can often be more confident that the segment was inherited from that ancestral line.

Triangulation helps move us from a collection of matches towards a clearer understanding of how DNA has been inherited.

For many genealogists, this is the point where chromosome analysis becomes truly useful.


Members of a triangulated group all share the same segment of DNA and match one another on that segment.
This can provide strong evidence that the segment came from a shared ancestral line.


Building a Chromosome Map

Over time, triangulated segments can be assigned to specific ancestral lines.

As more segments are identified, a chromosome map begins to emerge.

A chromosome map is simply a visual representation of which parts of our DNA were inherited from different ancestors.

Each newly identified segment adds another piece to the puzzle.

The process is gradual. Few people build a complete chromosome map overnight. Instead, it develops through ongoing research, collaboration and evidence gathering.


By combining documentary research, shared matches and triangulated groups, DNA segments can gradually be mapped to ancestral lines and usually to individual ancestors.


Validating Your Family Tree

One of the most valuable applications of chromosome analysis is tree validation.

Traditional records tell us who we believe our ancestors were.

DNA provides an independent source of evidence.

When documentary research, shared matches, triangulated groups and mapped segments all point towards the same conclusion, our confidence in that conclusion increases.

This is one of the reasons chromosome analysis has become an increasingly important tool for genetic genealogists.


Traditional records tell us who our ancestors were. DNA evidence helps test those conclusions. By combining documentary research with chromosome analysis, we can gradually build confidence in the relationships shown in our family tree.



Taking the Next Step

Chromosome analysis is not about replacing shared matches.

It is about building upon them.

Shared matches help us identify people who may be connected to us.

Segments help us understand how that connection was inherited.

Chromosome analysis becomes even more powerful when combining cluster analysis, triangulated groups and chromosome mapping.  The techniques can help us move beyond just identifying matches and to begin identifying ancestral lines—and the individual ancestors—responsible for the DNA we share today.

In many ways chromosome analysis is simply the next stage of genetic research process.  It allows us to move beyond asking who matches who and to explore and confirm exactly which ancestor handed down the DNA we share.  While the techniques may appear complex at first, the underlying principles are surprisingly straightforward - more like a logic puzzle, providing valuable insights into our family history.


REMEMBER

  • Shared matches and clusters help us identify people who may be related.
  • Chromosome analysis helps explain how the DNA was inherited.


Together, they provide a richer understanding of our family history.



Veronica Williams

First published 3 Jun 2026
Last updated 16 Jun 2026

Friday, August 4, 2023

Using chromosome analysis to find that elusive 2nd or 3rd great grandparent

If you are like me, you have a couple of distant ancestors that are brick walls or where the paper evidence is not being confirmed by your DNA analysis.  Is your paper evidence right, but there are just not enough descendants in the DNA mix?  Or, is there a problem with your genealogy and your ancestor is someone else entirely?

How can chromosome analysis help you with this problem?



This blogpost is aimed at documenting the process to follow in these types of cases.  It assumes that you have fully exhausted analysis techniques using total shared cMs and grouping processes at autosomal DNA sites such as AncestryDNA and need to go to the next step.


The plan and things to consider

  • Where does the ancestor sit in your tree?
  • What DNA test is most suitable, Y-DNA, mtDNA or autosomal DNA?
  • How many descendants have tested?
  • Have all these testers uploaded their data to a chromosome analysis site? 
  • Can you identify additional 'priority' testers that may assist in solving your problem?
  • Are you confident that your DNA analysis to date (using the totals shared cMs approach), has confirmed your pedigree back to 2nd great grandparents for all lines?  This ensures you have a solid pedigree base to start using chromosome analysis techniques.
  • Have each of the generations between you and the subject ancestor been DNA confirmed?
  • How many generations back on 'this line' do your confirmed DNA 'segments' go?
  • Can you identify segment data for each generation?
  • Review potential genetic networks from cluster analysis for more clues.

Then take the following actions
  • Identify triangulated groups in all of those segment areas;
  • Interrogate each of the groups, searching for common names, locations, ethnicities, look for patterns between matches in each triangulated group and genetic network clusters;
  • Build research trees, are there patterns or commonalities between triangulated groups?
  • Ensure all 'DNA confirmed' segments can be 'walked back' on each chromosome, for each triangulated group;
  • Continue to interrogate all triangulated groups with the aim to connecting them and revealing your shared ancestors;
  • Constantly review segment analysis and cluster analysis data for clues of common names and locations, use these for further traditional research.


Not all of their DNA got to you

We need to remember that due to the process of recombination, we don't all inherit DNA from our distant ancestors.  Every generation loses 50% of our ancestors DNA.  That's why it is so important to get as many of your relatives as possible to take a DNA test!  Our genealogical tree is not the same as our genetic tree - we can still be genealogically related to other cousins but share no DNA.  On average, you may have inherited about 3.1% of your 3rd great grandparents DNA - that is, if you got any at all!




How much DNA is available and who should I test?

DNA Painter has great tool called the Coverage Estimator, which can help to identify who is the best person to test to maximise the DNA for your 'target' ancestor.  The following examples show the amount of DNA my family has for my great grandmother Abigail Courtney and her father, my 2nd great grandfather Arthur George Courtney.



Walking back the segments

To start, you need a solid base of DNA confirmed matches that confirm your pedigree.  2nd cousins are ideal as they only share one grandparent with you, they need to have their results on a chromosome site such as GEDmatch, FamilyTreeDNA or My Heritage.  Your goal is to identify the segments inherited from the 'target' ancestor.  With matches at the 2nd cousin level you will be able to identify segments inherited from your shared great grandparents.  In my case they are Edward Roberts and Abigail Courtney.  

It is then a matter of separating the segments inherited from both ancestors to identify those that are on the 'target' ancestors line.  By interrogating all triangulated segments for my Roberts-Courtney line (the line shared with my 2nd cousins) I am seeking to separate out Roberts line matches from Courtney matches.  Then, we need to push each ancestors line back another generation so that we can isolate all triangulated segments belonging to the 'target' ancestor.   

In my case, once I have identified segments inherited from Abigail Courtney, I then need to continue to interrogate those triangulated groups to seperate out the segments she inherited from her mother.  By again separating these out, we should only be left with groups more likely to have been inherited from her father George Courtney (our target ancestor).

As you work through this process it is recommended to continually analyse both your triangulated groups and AncestryDNA clusters.  Finding a 'bridge' match in a triangulated group and also in an AncestryDNA cluster may help lead to other connected matches that may be relevant to your search.  Try to amass as many clues as possible to connect your triangulated group matches to find their common ancestor.  Look for common connections within each group and between groups, the names may not be known to you but they could be clues pointing to your 'target' ancestor.

The follow chart seeks to document my progress in identifying the parents of my 2nd great grandfather Arthur 'George' Courtney.   It can be a long term exercise to push segments back, but eventually you will find that the genetic clues will reveal common surnames, locations or ethnicities that may give clues to to help you progress your genealogical research.



Genetic research principles are very similar to traditional research, you start from yourself and move back one generation at a time.  Just as in traditional research we seek to obtain birth and death certificates for our ancestors, rather than just checking the index; so do we seek triangulated segment data as evidence of shared ancestors, rather than just having matches in common.  This becomes much more important for distant ancestors such as 2nd great grandparents and beyond, where shared cMs are more difficult in pinpointing a relationship given the plethora of possible relationships and the possibility of multiple shared ancestors.


Getting the segment data needed

Often the key matches that will help us solve our mystery are on AncestryDNA and there is no segment data available.  We need to be creative in our requests when asking these cousins to transfer their results to a chromosome site so we can analyse the segment matches between us. Offering to help them with the analysis of their own kits can be a good way to get them engaged.  Alternatively, think about setting up a group project at FamilyTreeDNA that might entice a broader range of testers that could assist in solving your mystery.


My Genetic Research

You can read more about my DNA analysis on my various blogs.  

* My biggest research challenge is my maternal 2GGF Arthur George Courtney.  He has a whole blog dedicated to him, read more on Finding George Courtney c1841.  The Research Summary provides an overview of my genealogical and genetic research.

* In researching George, I managed to identify another maternal 2GGF: read my post  - What is our family name?  Roberts, Baker or Dye?

* Our Irish ancestors are always a challenge due to missing records, but DNA can often piece it together.  My Britton family from Fermanagh are an example.  I have much more to document about this family but these two posts may give you some ideas about what's involved.  Meet Catherine 'Kitty' Britton, thanks to the X chromosome and Reuniting our Britton family, our unnamed Patriarch.


More information

For more information regarding chromosome analysis techniques, refer to the Table of Contents for this blog.


Veronica Williams

Originally published: 25 July 2023

Last updated: 9 October 2024

Tuesday, November 23, 2021

DNA Research Framework 4 - Use genetic research to prove and expand your pedigree

   There are five parts to the DNA Research Framework:

  1. Understand DNA Basics
  2. Know what you are working with
  3. Combine genetic and genealogical research
  4. Use genetic research to prove and expand your pedigree
  5. Continuous review

Within the framework we apply a DNA research methodology to ensure we systematically and methodically review our results, to improve our productivity and success rates.

The following blog posts provide more detailed information about the DNA Research framework, applying the DNA Research Methodology and building your DNA analysis skills:

This post contains reference material relevant to Module 4 
The ISOGG site also has a lot of useful material refer - ISOGG Beginners' guides to genetic genealogy.  You can find earlier material relevant to earlier modules here:

Use genetic research to prove and expand your pedigree - Total cMs approach
This module focusses on using your genetic research to prove and expand your pedigree.  It considers what relationships can be 'confirmed by DNA' (including when there is no paper trail) and the Genealogical Proof Standard.  


Use genetic research to prove and expand your pedigree - Chromosome analysis
To confirm your pedigree beyond 3rd cousins or where there is no documented paper trail  (with the exception of parent/child and sibling relationships) you need to undertake detailed chromosome analysis, using segment data. We use triangulated segment data to provide evidence regarding our hypotheses for cousin matching to confirm our shared ancestors.  Examining other matches in these groups can often help expand your pedigree back further generations and potentially break down brick walls.  

When using your DNA analysis to confirm relationships don't forget the requirements in the 'Genealogical Standards (GS)', there are five key elements to consider.

  • Reasonably exhaustive research
  • Complete and accurate source citations
  • Critical tests of relevant evidence through processes of analysis and correlation
  • Resolution of conflicting evidence
  • Soundly reasoned, coherently written conclusion

Most genealogical questions cannot meet the 'reasonably exhaustive research' test without the consideration of DNA evidence.  The GPS includes standards about each of the following aspects associated with DNA:

  • Planning DNA tests
  • Analysing DNA test results
  • Extent of DNA evidence
  • Sufficient verifiable data 
  • Integrating DNA and documentary evidence
  • Conclusions about genetic relationships
  • Respect for privacy rights

Remember, to confirm segments as belonging to a particular ancestor, you must ensure that three or more matches share an identical AND overlapping segment, i.e. a 'triangulated segment' that is 'identical by descent'.  There also needs to be sufficient genealogical distance between the matches in the group to demonstrate how the segment was passed down (i.e. not just close matches such as parent/child/siblings). 

When assessing likelihood of relationships it is important to:-
  • Assess the probable shared cMs for each individual match and their predicted relationship; 
  • Consider the relationship in the context of other matches who descend from the same common ancestors;
  • Use statistical analysis tools such as DNA Painter WATO (What Are The Odds) to assess probabilities for your hypotheses.  It should be noted that using total shared cMs alone will not be sufficient for distant matches as the WATO tool does not use matches below 40cMs in its underlying statistics;
  • Remember that WATO is a great visual tool to demonstrate relationships of matches beyond 3rd cousins, but it needs to be supported by additional evidence when matches are below 40cMs.  This should take the form of segment analysis including (ideally) multiple tests and triangulated groups, demonstrating that the chromosome segment has been 'walked back' through multiple generations;
  • When drawing conclusions, make sure you examine and review any conflicting evidence and document the reasons for your decision.
Mapping confirmed chromosome segment data can be a useful to assist in determining possible ancestral groups for new DNA matches and can demonstrate how confirmed segments have held up over multiple generations.   

Chromosome analysis techniques can be taken further with more advanced applications, such as phasing, inferred mapping and DNA reconstruction.  These techniques should not be attempted unless you fully understand the underlying DNA theory covered in Modules 1 and 2.





In closing

I hope you have enjoyed our chromosome analysis journey applying the DNA research methodology.  There is much to learn.  It can be challenging but equally rewarding.  It's an iterative process, requiring continuous review.  Go back over what you have learnt since module 1 and apply the methodology in practice, it will soon become second nature.

Some of our DNA mysteries may take decades to resolve, like my George Courtney - I've been at it so long I've dedicated a whole blog to him!  The key thing is to be systematic and methodical and eventually you should be able to solve your mystery.







REFERENCE MATERIAL

DNA Confirmations

Chromosome Mapping

You may also be interested in reading these blogposts relating to DNA research for my own family:

These and more can be found on 'The Genemonkey, my ancestors and DNA questions' blog @Wordpress.


Veronica Williams

Originally published: 23 November 2021
Last updated:  10 December 2023


Tuesday, June 29, 2021

Building your DNA competency

When you start working with DNA for your genealogy it may seem like there is too much to learn, but not so.  How deeply you want to expand your research using genetic genealogy will determine how you approach obtaining the skills required for analysis.  It is not the same for everyone.

There are generally 5 main reasons one might think about doing a DNA test.   

  1. I want to know my ethnicity
  2. I am interested in DNA for health reasons
  3. I am curious about what I will find out from knowing more about my DNA
  4. I am interested in using DNA to unravel a genealogical mystery
  5. I am interested in using DNA to validate my research tree

The competencies needed to be able to analyse your results for each of these are different, but they build on each other.  Points 1-3 require only a limited understanding DNA and its relevance for genealogy.  Whereas points 4-5 require a more detailed understanding of the DNA analysis process.  No matter what your goal, everyone needs to decide which DNA test is best for them.

This post seeks to outline the competencies you need to attain to build the DNA analysis skills you need for your research goal.  Not everyone needs to skill themselves in all of them.  Best practice suggests that you should start by looking at your results broadly, before diving into the detail of chromosome analysis.

Work through these lists systematically, tick off what you know!  Build your DNA analysis skills by understanding the basics before moving to the next level.


Before you test

If you are considering a DNA test, you need to understand which test is right for you depending on your DNA goal.  Make sure you consider the following points before testing.  Links in this section lead to blog articles that explain the points (adding links is an ongoing work in progress).  

  • I am aware of the limitations of DNA testing and its usefulness for genealogy
  • I have identified my DNA research goal/s
  • I am aware of the various companies offering DNA tests 
  • I am aware of the general principles of DNA inheritance to help me choose the right test
  • I am aware of the differences between the 3 DNA tests, yDNA, mtDNA and au/atDNA
  • I have a general understanding of how DNA testing companies identify ethnicities
  • I have a general understanding of how DNA testing companies provide health information

Starting to work with your DNA results - the basics (beginners-intermediate)
  • I have developed a pedigree for my known ancestry, to at least 16 x 2GGP's (if possible). 
  • I have developed a DNA Research Plan and documented my DNA research goals.
  • I understand the principles of DNA inheritance and how it is used in the analysis process.
  • I understand the differences between the 3 DNA tests, yDNA, mtDNA and au/atDNA and how to use them in the analysis process
  • I am aware that by working within a research framework and applying a DNA research methodology I will improve my success rate and productivity.
  • I understand the meaning of the key DNA terms and concepts - shared centimorgans (cMs), shared segments, shared matches, predicted relationships and cousinship.
  • I am able to use my testing company's system to identify and sort my autosomal DNA matches by shared cMs and identify shared matches.
  • I understand the limitations of 'shared matches' (called 'in common with' at FTDNA).
  • I understand how the shared cMs with my match can be used to predict possible relationships.
  • I am aware of how to use grouping and clustering techniques like the Leeds Method, to help classify my matches into potential grandparent groups.
  • I am aware of how to develop research trees using 'tree triangulation' to aid my genetic research.
  • I am aware of how to document and test relationship hypotheses using tools like 'What are the Odds @ DNA Painter' (WATO).
  • I am aware of the Genealogical Proof Standard, particularly as it applies to genetic genealogy.
  • I understand my responsibilities if I am administering a kit for someone else.
  • I am able to use my testing company's system to download my raw data.

Working with your DNA results - using chromosome analysis (intermediate-advanced)
  • I am competent in all aspects of 'the basics' when working with my DNA results (shown above). 
  • I understand there are 4 different types of DNA for research purposes, requiring different analysis techniques.
  • I have downloaded my raw data (autosomal only) from my testing site and uploaded it to other sites including GEDmatch, FTDNA, My Heritage and LivingDNA.
  • I understand the principles of DNA inheritance and how recombination impacts on chromosome analysis.
  • I understand the different inheritance factors for men and women for the X/23rd chromosome.
  • I understand the meaning of more involved DNA terms and concepts such as - recombination, Single Nucleotide Polymorphisms (SNP's pronounced snips), Fully Identical Regions (FIR), Half Identical Regions (HIR), Identical by Descent (IBD), Identical by chance/state (IBC/IBS), Identical by population (IBP).
  • I understand that there are two sides to each of the 23 chromosomes and how to allocate matches to either the paternal or maternal side.
  • I understand the difference between 'shared matches' and matches with 'shared segments on a chromosome’ for autosomal analysis.
  • I understand the differences between ‘in common with - on a segment (sometimes called overlapping segments)’ and 'segment triangulation'.
  • I understand the meaning of the terms 'triangulated segment' and 'triangulated group' and why they are important for autosomal analysis.
  • I have developed a method for organising, storing and searching my DNA matches by chromosome, shared cMs and potential ancestor groups (including clusters and triangulated groups).
  • I am aware of how to use 'triangulated groups' to identify potential shared ancestors by developing research trees to aid my genetic research.
  • I understand what constitutes 'tentative' and 'confirmed' DNA matches when identifying potential shared ancestors.
  • I am able to identify segments inherited from a specific ancestor or ancestral couple and apply them to a chromosome map, such as DNA Painter.
  • I am aware of the limitations of tools like WATO when testing relationship hypotheses and understand the need for 'segment triangulation' to confirm relationships beyond 3rd cousins or where no paper trail exists.
  • I have read and understand the Genealogical Proof Standard, particularly as it applies to genetic genealogy.


Doing more with your DNA results - advanced techniques 

Once you are competent in all aspects of 'the basics' and 'using chromosome analysis' you could consider more advanced DNA techniques.  Tackling these tools/techniques should only be attempted once you are competent in all the above.
  • Phasing techniques
  • Using Gedmatch tools including Evil Twin, Lazarus
  • Visual Phasing
  • Inverted Mapping
  • Inferred Mapping
  • Deductive Mapping (inferred inversions)
  • Developing chromosome maps for your ancestors
  • DNA Reconstruction techniques

Further Reading

Read more about the DNA Research Framework and Methodology here.

Christine Woodlands has developed an AncestryDNA course that addresses all the steps outlined in 'the basics' section, delivered since 2020 at the Society of Australian Genealogists (SAG).    Read more about the course on Mossie's Musings and check the SAG website for possible future delivery dates.

Veronica Williams has developed a complementary course for 'chromosome analysis' for more experienced DNA researchers.  It was trialled as webinar series in 2021 and the recordings are available in the SAG shop.  The subsequent course with 12 modules has been delivered in 2023 and 2024.  We anticipate it will be run again in 2025.  Check the SAG website for possible future delivery dates.

Join the International Society of Genetic Genealogy - it's free!  Please consult the ISOOG website and the ISOOG wiki for more information, including their helpful Genetics Glossary.



Veronica Williams
Originally published: 29 Jun 2021
Last updated:  September 2024