Mastodawn

Álex Gil-Gómez🔬🧫🧬Nov 10, 2022

A question for my #PopulationGenetics #EvolutionaryGenetics friends. In a paper, the authors refer to this figure as a #HaplotypeNetwork. Wouldn't this be a #SplitsTree or #PhylogeneticNetwork? Do they represent different things?

#evolution #PopulationGenomics #bioinformatics #phylogenetics

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Carmelo Fruciano Nov 11, 2022

@alex_glgz I concur with @jby . I'd add that from the text in your screenshot, it sounds like the authors are referring to part B of the figure, which is based on mitochondrial DNA data and I think it's correctly characterised as a "haplotype network"...

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Álex Gil-Gómez🔬🧫🧬Nov 11, 2022

Thank you for the response @carmelofruciano @jby

So in this view, a phylogenetic network of haplotype data (using ML or another method) can also be called a "haplotype network", even if it is not a conventional haplotype network like in image 2.

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grimmiges

@alex_glgz @carmelofruciano @jby No. A haplotype network depicts ancestor-descendant relationships (if a root is defined) or mutation pathways (if unrooted) between sequence variants (in a strict sense, alleles of a haplome): when a root is known it's not only a phylogenetic network but an evolutionary network as it depicts actual ancestor-descendant relationships.
How to interpret a rooted haplotype network? https://phylonetworks.blogspot.com/2013/09/how-do-we-interpret-rooted-haplotype.html

How do we interpret a rooted haplotype network?

A splits graph is an unrooted phylogenetic network (see How to interpret splits graphs ). It can be produced by any of several algorithms, ...