Álex Gil-Gómez🔬🧫🧬

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

Nov 10, 2022 at 10:07pmWeb
Show threadCarmelo FrucianoNov 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"...
Show threadÁlex 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.

Show threadCarmelo FrucianoNov 11, 2022
@alex_glgz Sorry, my bad, I wasn't clear and sort of mixed the two figures. The one on S3B looks like a phylogenetic network based on haplotype data, the one in image two a haplotype network...lack of sleep doesn't help!😅
Show threadÁlex Gil-Gómez🔬🧫🧬Nov 11, 2022
@carmelofruciano I see, that makes sense. 😊
Show threadgrimmigesNov 20, 2022
@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, ...

Show threadgrimmigesNov 20, 2022
@alex_glgz Both Fig. S3A and B are "neighbour-net splits graphs", a neighbo[u]r-net is a planar (2-dim.) network that can serve as a phylogenetic network in a general sense, being a graph depicting (alternative) phylogenetic relationships. In that respect A is pointless: too noisy input data -> unrepresentative distance matrix = spider-web. B is not a haplotype network but a NNet based on a more meaningful distance matrix.
See also: How to interpret splits graphs: https://phylonetworks.blogspot.com/2012/08/how-to-interpret-splits-graphs.html
How to interpret splits graphs

Splits graphs are produced by distance-based network methods such as NeighborNet and Split Decomposition, by character-based methods such a...