Tree Hygiene and DNA Algorithms: Why Structure Matters Before You Link DNA

A common problem appears as soon as people link their DNA test to a family tree.

Most genealogists start with solid documentary research. They build trees using census records, vital records, newspapers, and other sources. A person is assigned two parents. Those parents may have multiple marriages, stepchildren, or missing information. On paper, the tree looks reasonable.

Then DNA enters the picture.

DNA matches may suggest a different biological parent than the one documented in records. Now the individual has two recorded parents, complex family structures on both sides, and a possible biological parent supported by DNA evidence.

This is where many trees begin to struggle.

The issue is not whether DNA or records are “right.” They answer different questions. The real issue is structure. Ancestry’s DNA tools do not evaluate evidence. They interpret relationships as they are recorded in trees.

This is why tree hygiene matters.

Features like ThruLines and Common Ancestor hints rely entirely on how people are connected in your tree and in the trees of your DNA matches. They do not assess source quality or resolve conflicting evidence. If documented parents, step-parents, and possible biological parents are all attached without clear structure, the algorithms still attempt to build relationship paths through them.

The result is often confusing hints, incorrect shared ancestors, or ThruLines pointing to the wrong families.

Important: Ancestry’s DNA tools generate hypotheses, not conclusions. They propose relationship paths based on tree structure and shared DNA. They do not determine biological truth.

ThruLines does not identify a biological parent. It reflects how trees are currently connected.

Before DNA tools can work well, the tree must reflect what is known, what is uncertain, and what is unresolved. Tree hygiene is not about removing evidence or choosing sides. It is about structuring relationships clearly so the tools behave predictably.

Two Ways to Structure a Tree When DNA Is Involved

When DNA suggests a different biological parent than the one shown in records, there are two practical approaches.

Option 1. Separate trees for different purposes

One approach is to maintain two clearly labeled trees.

The first is a documented research tree. It reflects the historical and social relationships supported by records. It shows who raised whom and how the family appeared on paper.

The second is a DNA-focused tree. It reflects biological relationships suggested by DNA evidence, even when those differ from documentary conclusions.

This separation keeps analysis cleaner. It allows DNA hypotheses to be tested without constantly disrupting a well-researched documentary tree. It also reduces confusion in Ancestry’s algorithms when biological questions are unresolved.

It is also important context that most Ancestry trees were created before DNA testing was common and are copied repeatedly. When you introduce DNA-based relationships, you may be creating one of the few trees that reflects biological relationships suggested by DNA evidence for that line.

That does not mean other trees are careless. They were built for a different purpose.

Option 2. One tree with carefully defined relationships

The second approach is to keep everything in one tree and be very deliberate about relationship types.

An individual may have a biological father, a stepfather, and an adoptive father, each recorded correctly. The same may apply to mothers or other parental figures. When done carefully, this approach preserves all evidence in one place and reflects real family complexity.

The downside is scale. Trees become complex quickly. Branches multiply. Algorithms attempt to route DNA connections through every possible relationship path. Without careful control, this can produce misleading hints.

This approach requires regular maintenance and a clear understanding of how Ancestry interprets relationships.

Conclusion: Structure Comes Before Tools

DNA analysis does not start with matches or hints. It starts with structure.

How a tree is built determines how Ancestry’s DNA tools behave. When relationships are unclear or mixed without intention, the tools still generate results, but those results are harder to interpret.

There is no single correct way to structure a tree once DNA introduces new biological information. What matters is choosing an approach deliberately and understanding the tradeoffs. Clear structure gives DNA analysis a stable foundation.

In the next article, I will cover practical best practices for maintaining tree hygiene during DNA research, including privacy settings, research trees, and experimental work.

If you are working through a DNA case and want help interpreting matches, identifying biological parents, or restructuring a tree so Ancestry’s DNA tools work more effectively, I offer professional DNA match analysis services.

Learn more here:
https://www.technicalgenealogist.com/services/dna-matches