Understanding nodes with multiple parents

[madeline-chase]

Hello everyone,

I wanted to ask a question to try to understand conceptually what it means when a node in the ARG has multiple parents. I understand that a node with two parents can represent a recombination event, but what does it mean for a node to have more than two parents?

I have been using tsinfer+tsdate with a dataset of ~370 birds, and as we've been evaluating the tree sequences we've observed that many nodes have >2 parents (almost 1/3). I wanted to see if there can be a biological reason for this or if this indicates an issue with the inference.

Thank you!

[gregorgorjanc]

@madeline-chase this is because ARG encodes relationships between haplotypes of individuals and haplotypes of their ancestors - these ancestors can be immediate (as in sample(=child)-parent relationship where you would expect only 2 parental nodes in case of a recombination) or the ancestors can be much much older (as in sample-grandgrand…parent relationship where you would expect many parental nodes). The terminology is indeed confusing until you get used to it.

Maybe this pre-print can help you understanding these aspects of ARGs https://www.biorxiv.org/content/10.1101/2023.11.03.565466v2