Largest-ever comparison of chromosome-scale genomes

[u/jnpha]

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• University of Vienna press release:
  • Roadmap of animal biodiversity: largest-ever comparison of chromosome-scale genomes
• Paper:
  • Schultz, D. T., Blümel, A., Destanović, D., Sarigol, F., & Simakov, O. (2026). Topological mixing and irreversibility in animal chromosome evolution. Science Advances.
    https://www.science.org/doi/10.1126/sciadv.adz5561
    From which:

... Our approach shows that irreversible genomic changes, caused in particular by chromosomal consolidation, dissociation, and fusion-with-mixing, place clades in distinct regions of genome architecture space. Progressive accumulation of these mixed states across genomic scales contributes to the diverging paths of animal genome evolution and has a long-lasting impact on a broad range of genes, including key developmental loci.

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Related: Evolutionary History of Mammalian Ancestor Chromosomes (Damas et al 2022) : evolution

[u/ProfPathCambridge]

Interesting!

For what it’s worth, I’m not sure a UMAP is a great tool to display its data, since it doesn’t project long-distance relationships. All this plot says is that “beetles are similar to other beetles” etc.

[u/jnpha → u/ProfPathCambridge]

A snapshot in time. My initial thought was that - at least artistically for the press release - the time dimension, like here (https://commons.wikimedia.org/wiki/File:Phylogenetics.svg), would have been awesome.

[u/furiouscarp → u/ProfPathCambridge]

umap is so wonderful

[u/ProfPathCambridge → u/furiouscarp]

It serves a function

[u/ProfMooreiarty → u/ProfPathCambridge]

Looks more like eu_map.

[u/Nexen4]

Glancing at the image, I thought I was looking at a map of Europe for a moment

[u/itsatoe → u/Nexen4]

With the beetles over in the UK lolol.

Or is that more like Iceland? Hm. 🙃

[u/Heterodynist → u/itsatoe]

Well that would make Iberia all mollusks and jellyfish?! Ha!! I mean they do have those Portuguese Man-O-Wars!!

[u/furiouscarp]

what was the clustering algorithm used?

[u/jnpha → u/furiouscarp]

The paper is open access:

To address this, we implemented an EGT approach, which allows us to view genomes and FWM processes on chromosomes as topological operations (Supplementary Text). In this work, we quantify EGT by calculating pairwise distances between BCnS orthologs. More generally, this approach can be extended to any homologous features in genomes, such as genes, conserved noncoding elements, or repeat families and their insertions (see the “Evolutionary topology methods” section). This allows us to implement two topological approaches as a part of the EGT framework. The first approach ...

[u/HC-Sama-7511]

Is there a key to the colors?

[u/jnpha → u/HC-Sama-7511]

At least for the paper, not the press release image, see Fig. 4 (https://www.science.org/doi/10.1126/sciadv.adz5561#F4), where the coloring is by clade.

[u/Mountain_Dentist5074]

is this how much related animals to each other?

[u/Unfortunya333 → u/Mountain_Dentist5074]

No

[u/Mountain_Dentist5074 → u/Unfortunya333]

my native language not english and translator did translate akward can you explain like i am 5?

[u/Unfortunya333 → u/Mountain_Dentist5074]

I think it's a mapping of certain genomic architectures across a fixed sample of around 4000 different chromosome scale genomes and how they cluster, rather than a clean taxonomic relationship. It says more about biodiversity and how different clusters speciate rather than just phylogeny.

[u/bzbub2]

very cool to see the same method from this scaled up to all-the-animals https://www.nature.com/articles/s41586-023-05936-6 (they showed ctenophore as oldest branch on the animal tree of life)

[u/GloomyKnowledge7407]

Thanks, very helpful and interesting

[u/nihilism_squared]

"largest ever"

only animals